From signabdm at gmail.com  Mon Sep 12 06:58:59 2016
From: signabdm at gmail.com (Valeriy Signatulin)
Date: Mon, 12 Sep 2016 16:58:59 +0600
Subject: [Rtk-users] rotation of detector plane
Message-ID: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>

Hello RTK users.
Is it possible to specify rotation of detector plane in RTK ? (in
rtksimulategeom for example) If not, what is the best way to code this ?
By rotation of detector plane i mean twist, tilt, skew around the normal of
the detector as described in
http://www.ndt.net/article/v10n09/yisun/yisun.pdf page 6.
I'm trying to write the geometry calibration method described in this
article in RTK and i need to simulate these rotations to check the results.
Thanks.
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 12 08:40:31 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 12 Sep 2016 14:40:31 +0200
Subject: [Rtk-users] rotation of detector plane
In-Reply-To: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
References: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
Message-ID: <CAF0oig0C3zFcAaAhWHV9g+UY02i7cws7OU-7r2YadyAt3TH5GA@mail.gmail.com>

Hi,
You can do any rotation with RTK. The rotation is described 3 Euler angles,
see the geometry doc <http://www.openrtk.org/Doxygen/geometry.pdf>. From
the command line, that would be the --in_angle and out_angle that allow you
to modify the other angles than the standard angle for the position along
the circular rotation (GantryAngle). If you want to modify it per
projection, that's possible using C++ or Python code (AddProjection
<http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
method).
Good luck,
Simon

On Mon, Sep 12, 2016 at 12:58 PM, Valeriy Signatulin <signabdm at gmail.com>
wrote:

> Hello RTK users.
> Is it possible to specify rotation of detector plane in RTK ? (in
> rtksimulategeom for example) If not, what is the best way to code this ?
> By rotation of detector plane i mean twist, tilt, skew around the normal
> of the detector as described in http://www.ndt.net/article/
> v10n09/yisun/yisun.pdf page 6.
> I'm trying to write the geometry calibration method described in this
> article in RTK and i need to simulate these rotations to check the results.
> Thanks.
>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From andreasg at phys.au.dk  Tue Sep 13 13:06:46 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Tue, 13 Sep 2016 19:06:46 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
Message-ID: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>

Dear RTK experts,

I am reconstructing Varian ProBeam projections of the Xim image format. I
have written the reader myself - very similar to the Hnd one already
available with RTK.
Links to my fork: [XimReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkXimImageIO.cxx>,
XMLReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamXMLFileReader.cxx>,
GeometryReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamGeometryReader.cxx>
]

The reader apparently works (Images and angles displays as expected in UI),
however when reconstructing with a regular FDK* I get a reconstructed image
that is smeared out around the high and low density areas *[see attached
image]

I'm using half arc, full fan images with no bow-tie filter from Scripps
(~520 projections). Fixed detector and source (offset=0) with SID=2m,
SDD=3m.

*For the Hnd projections the reconstruction works perfectly (Same algorithm
<https://github.com/agravgaard/cbctrecon/blob/master/cbctrecon.cpp#L2726>).*
The reconstruction of the Xim projections performed on Varian software
works perfectly.

Without the Parker Short Scan Filter the first and last projections creates
streaks across the reconstruction as if they were way too bright.
If the first few projections are excluded, the following projection will
act the same way.

The projections are corrected for beam hardening and all the projections
have the expected attenuation.
No "smearing" filters (like median) is used, and iterative reconstruction
makes the same artifacts.

Setting the value of the first and last projection to zero has the same
effect as excluding. Changing the ramp filter only changes noise, not the
artifacts.

*Have any of you had a similar problem? *Am I missing something?
Any suggestions are welcome I'm running out of ideas.

Best regards
Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 13 16:18:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 13 Sep 2016 22:18:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
Message-ID: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>

Hi,
I have almost never worked with Varian data but it looks like a
geometry problem. Maybe the problem comes from a bad ordering of the
projections which results in assigning a bad geometry to each
projection. How did you name your projections? Maybe check that the
order matches that of the RTK geometry file. Otherwise, there might be
an issue in the creation of the geometry file itself.
All this sounds good, happy bug hunt and don't hesitate to share your
code when you feel it's ready.
Simon

On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
<andreasg at phys.au.dk> wrote:
> Dear RTK experts,
>
> I am reconstructing Varian ProBeam projections of the Xim image format. I
> have written the reader myself - very similar to the Hnd one already
> available with RTK.
> Links to my fork: [XimReader, XMLReader, GeometryReader]
>
> The reader apparently works (Images and angles displays as expected in UI),
> however when reconstructing with a regular FDK I get a reconstructed image
> that is smeared out around the high and low density areas [see attached
> image]
>
> I'm using half arc, full fan images with no bow-tie filter from Scripps
> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
> SDD=3m.
>
> For the Hnd projections the reconstruction works perfectly (Same algorithm).
> The reconstruction of the Xim projections performed on Varian software works
> perfectly.
>
> Without the Parker Short Scan Filter the first and last projections creates
> streaks across the reconstruction as if they were way too bright.
> If the first few projections are excluded, the following projection will act
> the same way.
>
> The projections are corrected for beam hardening and all the projections
> have the expected attenuation.
> No "smearing" filters (like median) is used, and iterative reconstruction
> makes the same artifacts.
>
> Setting the value of the first and last projection to zero has the same
> effect as excluding. Changing the ramp filter only changes noise, not the
> artifacts.
>
> Have any of you had a similar problem? Am I missing something?
> Any suggestions are welcome I'm running out of ideas.
>
> Best regards
> Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>

From cyril.mory at creatis.insa-lyon.fr  Wed Sep 14 03:10:42 2016
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 14 Sep 2016 09:10:42 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
Message-ID: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>

One suggestion since it works with the Hnd projections:
You can run rtkprojections twice (with the Hnd projections, then with 
Xim projections) and output two projection stack files and two geometry 
files, then compare the projection stack files by subtracting one to the 
other (with SimpleRTK or clitk) and the geometry files with diff. If 
they are identical, then I do not see any reason why the reconstructions 
should be different, so my guess is that you will find differences.

On 09/13/2016 10:18 PM, Simon Rit wrote:
> Hi,
> I have almost never worked with Varian data but it looks like a
> geometry problem. Maybe the problem comes from a bad ordering of the
> projections which results in assigning a bad geometry to each
> projection. How did you name your projections? Maybe check that the
> order matches that of the RTK geometry file. Otherwise, there might be
> an issue in the creation of the geometry file itself.
> All this sounds good, happy bug hunt and don't hesitate to share your
> code when you feel it's ready.
> Simon
>
> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
> <andreasg at phys.au.dk> wrote:
>> Dear RTK experts,
>>
>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>> have written the reader myself - very similar to the Hnd one already
>> available with RTK.
>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>
>> The reader apparently works (Images and angles displays as expected in UI),
>> however when reconstructing with a regular FDK I get a reconstructed image
>> that is smeared out around the high and low density areas [see attached
>> image]
>>
>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>> SDD=3m.
>>
>> For the Hnd projections the reconstruction works perfectly (Same algorithm).
>> The reconstruction of the Xim projections performed on Varian software works
>> perfectly.
>>
>> Without the Parker Short Scan Filter the first and last projections creates
>> streaks across the reconstruction as if they were way too bright.
>> If the first few projections are excluded, the following projection will act
>> the same way.
>>
>> The projections are corrected for beam hardening and all the projections
>> have the expected attenuation.
>> No "smearing" filters (like median) is used, and iterative reconstruction
>> makes the same artifacts.
>>
>> Setting the value of the first and last projection to zero has the same
>> effect as excluding. Changing the ramp filter only changes noise, not the
>> artifacts.
>>
>> Have any of you had a similar problem? Am I missing something?
>> Any suggestions are welcome I'm running out of ideas.
>>
>> Best regards
>> Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>


From andreasg at phys.au.dk  Fri Sep 16 08:56:34 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 14:56:34 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
Message-ID: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>

Thanks for the suggestions, Simon and Cyril!

I have been carefully looking though the geometry and from what I
understand of the transformations matrices, the geometry looks correct/(as
expected).

HOWEVER: I found out that the reason for the Hnd to behave differently were
because had used half-fan scans (full-arc).
When I used a full-fan (half-arc) scan of Hnd projections the same
artifacts occurs!

Are there other (built-in) means of improving half-arc scans, than the
parker short scan filter?

Parker short scan does a decent job, but the result is still far from the
quality of the Varian software reconstruction at least for the CatPhan.

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:

> One suggestion since it works with the Hnd projections:
> You can run rtkprojections twice (with the Hnd projections, then with Xim
> projections) and output two projection stack files and two geometry files,
> then compare the projection stack files by subtracting one to the other
> (with SimpleRTK or clitk) and the geometry files with diff. If they are
> identical, then I do not see any reason why the reconstructions should be
> different, so my guess is that you will find differences.
>
>
> On 09/13/2016 10:18 PM, Simon Rit wrote:
>
>> Hi,
>> I have almost never worked with Varian data but it looks like a
>> geometry problem. Maybe the problem comes from a bad ordering of the
>> projections which results in assigning a bad geometry to each
>> projection. How did you name your projections? Maybe check that the
>> order matches that of the RTK geometry file. Otherwise, there might be
>> an issue in the creation of the geometry file itself.
>> All this sounds good, happy bug hunt and don't hesitate to share your
>> code when you feel it's ready.
>> Simon
>>
>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>> <andreasg at phys.au.dk> wrote:
>>
>>> Dear RTK experts,
>>>
>>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>>> have written the reader myself - very similar to the Hnd one already
>>> available with RTK.
>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>
>>> The reader apparently works (Images and angles displays as expected in
>>> UI),
>>> however when reconstructing with a regular FDK I get a reconstructed
>>> image
>>> that is smeared out around the high and low density areas [see attached
>>> image]
>>>
>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>> SDD=3m.
>>>
>>> For the Hnd projections the reconstruction works perfectly (Same
>>> algorithm).
>>> The reconstruction of the Xim projections performed on Varian software
>>> works
>>> perfectly.
>>>
>>> Without the Parker Short Scan Filter the first and last projections
>>> creates
>>> streaks across the reconstruction as if they were way too bright.
>>> If the first few projections are excluded, the following projection will
>>> act
>>> the same way.
>>>
>>> The projections are corrected for beam hardening and all the projections
>>> have the expected attenuation.
>>> No "smearing" filters (like median) is used, and iterative reconstruction
>>> makes the same artifacts.
>>>
>>> Setting the value of the first and last projection to zero has the same
>>> effect as excluding. Changing the ramp filter only changes noise, not the
>>> artifacts.
>>>
>>> Have any of you had a similar problem? Am I missing something?
>>> Any suggestions are welcome I'm running out of ideas.
>>>
>>> Best regards
>>> Andreas
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Sep 16 10:13:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 16 Sep 2016 16:13:26 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
Message-ID: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>

Hi,
You can try any iterative reconstruction, they can also handle short scans.
Start with a few iterations of rtksart or rtkconjugategradient. However,
the nature of the artifacts indicate more a problem in the geometry in my
opinion. I have seen such errors when, for example, rotating in the wrong
direction. I can have a look if you share the dataset.
Cheers,
Simon

On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the suggestions, Simon and Cyril!
>
> I have been carefully looking though the geometry and from what I
> understand of the transformations matrices, the geometry looks correct/(as
> expected).
>
> HOWEVER: I found out that the reason for the Hnd to behave differently
> were because had used half-fan scans (full-arc).
> When I used a full-fan (half-arc) scan of Hnd projections the same
> artifacts occurs!
>
> Are there other (built-in) means of improving half-arc scans, than the
> parker short scan filter?
>
> Parker short scan does a decent job, but the result is still far from the
> quality of the Varian software reconstruction at least for the CatPhan.
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>
>> One suggestion since it works with the Hnd projections:
>> You can run rtkprojections twice (with the Hnd projections, then with Xim
>> projections) and output two projection stack files and two geometry files,
>> then compare the projection stack files by subtracting one to the other
>> (with SimpleRTK or clitk) and the geometry files with diff. If they are
>> identical, then I do not see any reason why the reconstructions should be
>> different, so my guess is that you will find differences.
>>
>>
>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>
>>> Hi,
>>> I have almost never worked with Varian data but it looks like a
>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>> projections which results in assigning a bad geometry to each
>>> projection. How did you name your projections? Maybe check that the
>>> order matches that of the RTK geometry file. Otherwise, there might be
>>> an issue in the creation of the geometry file itself.
>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>> code when you feel it's ready.
>>> Simon
>>>
>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>> <andreasg at phys.au.dk> wrote:
>>>
>>>> Dear RTK experts,
>>>>
>>>> I am reconstructing Varian ProBeam projections of the Xim image format.
>>>> I
>>>> have written the reader myself - very similar to the Hnd one already
>>>> available with RTK.
>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>
>>>> The reader apparently works (Images and angles displays as expected in
>>>> UI),
>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>> image
>>>> that is smeared out around the high and low density areas [see attached
>>>> image]
>>>>
>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>> SDD=3m.
>>>>
>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>> algorithm).
>>>> The reconstruction of the Xim projections performed on Varian software
>>>> works
>>>> perfectly.
>>>>
>>>> Without the Parker Short Scan Filter the first and last projections
>>>> creates
>>>> streaks across the reconstruction as if they were way too bright.
>>>> If the first few projections are excluded, the following projection
>>>> will act
>>>> the same way.
>>>>
>>>> The projections are corrected for beam hardening and all the projections
>>>> have the expected attenuation.
>>>> No "smearing" filters (like median) is used, and iterative
>>>> reconstruction
>>>> makes the same artifacts.
>>>>
>>>> Setting the value of the first and last projection to zero has the same
>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>> the
>>>> artifacts.
>>>>
>>>> Have any of you had a similar problem? Am I missing something?
>>>> Any suggestions are welcome I'm running out of ideas.
>>>>
>>>> Best regards
>>>> Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> N?rrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     andreasg at phys.au.dk
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From andreasg at phys.au.dk  Fri Sep 16 16:37:43 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 22:37:43 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
Message-ID: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>

Thanks for the fast response Simon!

I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
right all along!
I just didn't get why it makes a difference. I think I do now, as the
resulting image was flipped upside down and not left/right as I expected.
[attached]

The reconstruction is significantly better, I'll look into what should be
included in the reader and what I should keep in my program to keep
conformity with the other readers. Then I'll create a pull request.

Just for the purpose of others hitting the same or a similar bug, I also
attempted:
I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
back/forward projection, *but with no* significant improvement [attached]

And:
If you want you can download the data set from: [Dropbox link to 460MB zip
<https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep it
up as long as Dropbox allows me)] Only the Acquisitions/subfolder is used
along with the Scan.xml (Calibrations folder may be used in the future in
my program, but I'm not sure if you can rely on the existence of the
content).

A MatLab XimReader is available: link
<https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
available from Varian bitbucket along a with a python version and a
C#->matlab plugin
<https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). Otherwise
my fork with the RTK-style reader is available from the same repository (I
have also added Hnc support, thanks to the Geoff Hugo fork, so bzip2 is a
new dependancy).

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:

> Hi,
> You can try any iterative reconstruction, they can also handle short
> scans. Start with a few iterations of rtksart or rtkconjugategradient.
> However, the nature of the artifacts indicate more a problem in the
> geometry in my opinion. I have seen such errors when, for example, rotating
> in the wrong direction. I can have a look if you share the dataset.
> Cheers,
> Simon
>
> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
> andreasg at phys.au.dk> wrote:
>
>> Thanks for the suggestions, Simon and Cyril!
>>
>> I have been carefully looking though the geometry and from what I
>> understand of the transformations matrices, the geometry looks correct/(as
>> expected).
>>
>> HOWEVER: I found out that the reason for the Hnd to behave differently
>> were because had used half-fan scans (full-arc).
>> When I used a full-fan (half-arc) scan of Hnd projections the same
>> artifacts occurs!
>>
>> Are there other (built-in) means of improving half-arc scans, than the
>> parker short scan filter?
>>
>> Parker short scan does a decent job, but the result is still far from the
>> quality of the Varian software reconstruction at least for the CatPhan.
>>
>> Best regards
>> Andreas
>>
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>>
>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>
>>> One suggestion since it works with the Hnd projections:
>>> You can run rtkprojections twice (with the Hnd projections, then with
>>> Xim projections) and output two projection stack files and two geometry
>>> files, then compare the projection stack files by subtracting one to the
>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>> are identical, then I do not see any reason why the reconstructions should
>>> be different, so my guess is that you will find differences.
>>>
>>>
>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>
>>>> Hi,
>>>> I have almost never worked with Varian data but it looks like a
>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>> projections which results in assigning a bad geometry to each
>>>> projection. How did you name your projections? Maybe check that the
>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>> an issue in the creation of the geometry file itself.
>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>> code when you feel it's ready.
>>>> Simon
>>>>
>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>> <andreasg at phys.au.dk> wrote:
>>>>
>>>>> Dear RTK experts,
>>>>>
>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>> format. I
>>>>> have written the reader myself - very similar to the Hnd one already
>>>>> available with RTK.
>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>
>>>>> The reader apparently works (Images and angles displays as expected in
>>>>> UI),
>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>> image
>>>>> that is smeared out around the high and low density areas [see attached
>>>>> image]
>>>>>
>>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>> SDD=3m.
>>>>>
>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>> algorithm).
>>>>> The reconstruction of the Xim projections performed on Varian software
>>>>> works
>>>>> perfectly.
>>>>>
>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>> creates
>>>>> streaks across the reconstruction as if they were way too bright.
>>>>> If the first few projections are excluded, the following projection
>>>>> will act
>>>>> the same way.
>>>>>
>>>>> The projections are corrected for beam hardening and all the
>>>>> projections
>>>>> have the expected attenuation.
>>>>> No "smearing" filters (like median) is used, and iterative
>>>>> reconstruction
>>>>> makes the same artifacts.
>>>>>
>>>>> Setting the value of the first and last projection to zero has the same
>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>> the
>>>>> artifacts.
>>>>>
>>>>> Have any of you had a similar problem? Am I missing something?
>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>
>>>>> Best regards
>>>>> Andreas
>>>>>
>>>>> __________________________________
>>>>>
>>>>> Andreas Gravgaard Andersen
>>>>>
>>>>> Department of Oncology,
>>>>>
>>>>> Aarhus University Hospital
>>>>>
>>>>> N?rrebrogade 44,
>>>>>
>>>>> 8000, Aarhus C
>>>>>
>>>>> Mail:     andreasg at phys.au.dk
>>>>>
>>>>> Cell:      +45 3165 8140
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 03:26:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 09:26:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
 <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
Message-ID: <CAF0oig2TSmAsSn=o3aLo6LEFDOSaKRtfknjMer24rcDKJ-0Fqg@mail.gmail.com>

Hi,
Thanks for sharing. There still seems to be some streak artefacts, do you
see the same in the Varian reconstruction?
I'm looking forward to the pull-request, I think we should try to make the
bzip2 optional.
Simon

On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the fast response Simon!
>
> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
> right all along!
> I just didn't get why it makes a difference. I think I do now, as the
> resulting image was flipped upside down and not left/right as I expected.
> [attached]
>
> The reconstruction is significantly better, I'll look into what should be
> included in the reader and what I should keep in my program to keep
> conformity with the other readers. Then I'll create a pull request.
>
> Just for the purpose of others hitting the same or a similar bug, I also
> attempted:
> I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
> back/forward projection, *but with no* significant improvement [attached]
>
> And:
> If you want you can download the data set from: [Dropbox link to 460MB zip
> <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep
> it up as long as Dropbox allows me)] Only the Acquisitions/subfolder is
> used along with the Scan.xml (Calibrations folder may be used in the future
> in my program, but I'm not sure if you can rely on the existence of the
> content).
>
> A MatLab XimReader is available: link
> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
> available from Varian bitbucket along a with a python version and a
> C#->matlab plugin
> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>).
> Otherwise my fork with the RTK-style reader is available from the same
> repository (I have also added Hnc support, thanks to the Geoff Hugo fork,
> so bzip2 is a new dependancy).
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> Hi,
>> You can try any iterative reconstruction, they can also handle short
>> scans. Start with a few iterations of rtksart or rtkconjugategradient.
>> However, the nature of the artifacts indicate more a problem in the
>> geometry in my opinion. I have seen such errors when, for example, rotating
>> in the wrong direction. I can have a look if you share the dataset.
>> Cheers,
>> Simon
>>
>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
>> andreasg at phys.au.dk> wrote:
>>
>>> Thanks for the suggestions, Simon and Cyril!
>>>
>>> I have been carefully looking though the geometry and from what I
>>> understand of the transformations matrices, the geometry looks correct/(as
>>> expected).
>>>
>>> HOWEVER: I found out that the reason for the Hnd to behave differently
>>> were because had used half-fan scans (full-arc).
>>> When I used a full-fan (half-arc) scan of Hnd projections the same
>>> artifacts occurs!
>>>
>>> Are there other (built-in) means of improving half-arc scans, than the
>>> parker short scan filter?
>>>
>>> Parker short scan does a decent job, but the result is still far from
>>> the quality of the Varian software reconstruction at least for the CatPhan.
>>>
>>> Best regards
>>> Andreas
>>>
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>>
>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>>
>>>> One suggestion since it works with the Hnd projections:
>>>> You can run rtkprojections twice (with the Hnd projections, then with
>>>> Xim projections) and output two projection stack files and two geometry
>>>> files, then compare the projection stack files by subtracting one to the
>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>>> are identical, then I do not see any reason why the reconstructions should
>>>> be different, so my guess is that you will find differences.
>>>>
>>>>
>>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>>
>>>>> Hi,
>>>>> I have almost never worked with Varian data but it looks like a
>>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>>> projections which results in assigning a bad geometry to each
>>>>> projection. How did you name your projections? Maybe check that the
>>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>>> an issue in the creation of the geometry file itself.
>>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>>> code when you feel it's ready.
>>>>> Simon
>>>>>
>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>>> <andreasg at phys.au.dk> wrote:
>>>>>
>>>>>> Dear RTK experts,
>>>>>>
>>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>>> format. I
>>>>>> have written the reader myself - very similar to the Hnd one already
>>>>>> available with RTK.
>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>>
>>>>>> The reader apparently works (Images and angles displays as expected
>>>>>> in UI),
>>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>>> image
>>>>>> that is smeared out around the high and low density areas [see
>>>>>> attached
>>>>>> image]
>>>>>>
>>>>>> I'm using half arc, full fan images with no bow-tie filter from
>>>>>> Scripps
>>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>>> SDD=3m.
>>>>>>
>>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>>> algorithm).
>>>>>> The reconstruction of the Xim projections performed on Varian
>>>>>> software works
>>>>>> perfectly.
>>>>>>
>>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>>> creates
>>>>>> streaks across the reconstruction as if they were way too bright.
>>>>>> If the first few projections are excluded, the following projection
>>>>>> will act
>>>>>> the same way.
>>>>>>
>>>>>> The projections are corrected for beam hardening and all the
>>>>>> projections
>>>>>> have the expected attenuation.
>>>>>> No "smearing" filters (like median) is used, and iterative
>>>>>> reconstruction
>>>>>> makes the same artifacts.
>>>>>>
>>>>>> Setting the value of the first and last projection to zero has the
>>>>>> same
>>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>>> the
>>>>>> artifacts.
>>>>>>
>>>>>> Have any of you had a similar problem? Am I missing something?
>>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>>
>>>>>> Best regards
>>>>>> Andreas
>>>>>>
>>>>>> __________________________________
>>>>>>
>>>>>> Andreas Gravgaard Andersen
>>>>>>
>>>>>> Department of Oncology,
>>>>>>
>>>>>> Aarhus University Hospital
>>>>>>
>>>>>> N?rrebrogade 44,
>>>>>>
>>>>>> 8000, Aarhus C
>>>>>>
>>>>>> Mail:     andreasg at phys.au.dk
>>>>>>
>>>>>> Cell:      +45 3165 8140
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:05:24 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:05:24 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
Message-ID: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>

Dear RTK users,
I have quickly tested calling the SimpleRTK python lib from Matlab and it
seems to work well:
http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
Therefore, I don't think we have to work on Matlab wrappings but let us
know if you think otherwise.
Future works include a simple installation mechanism for pre-compiled
SimpleRTK libraries. We'll keep you posted!
Simon
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From bottiger at gmail.com  Mon Sep 19 05:14:03 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 11:14:03 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
Message-ID: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>

Dear Simon

This look very interesting! Which platform did you successfully execute
this on?
I will give it a try at once (on windows) and let you know if I run into
any problems.

best

Arvid

On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> I have quickly tested calling the SimpleRTK python lib from Matlab and it
> seems to work well:
> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
> Therefore, I don't think we have to work on Matlab wrappings but let us
> know if you think otherwise.
> Future works include a simple installation mechanism for pre-compiled
> SimpleRTK libraries. We'll keep you posted!
> Simon
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:19:28 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:19:28 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
Message-ID: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>

The latest MacOS. It's nice if you can test it on other platforms, I'll try
to run it on Linux but I have to upgrade matlab first (I think python calls
are available starting with Matlab 2014).
Simon

On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Dear Simon
>
> This look very interesting! Which platform did you successfully execute
> this on?
> I will give it a try at once (on windows) and let you know if I run into
> any problems.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> Dear RTK users,
>> I have quickly tested calling the SimpleRTK python lib from Matlab and it
>> seems to work well:
>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>> Therefore, I don't think we have to work on Matlab wrappings but let us
>> know if you think otherwise.
>> Future works include a simple installation mechanism for pre-compiled
>> SimpleRTK libraries. We'll keep you posted!
>> Simon
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From bottiger at gmail.com  Mon Sep 19 08:30:32 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 14:30:32 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
Message-ID: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>

Hi again.

I've been trying to get it working. However, I did run into some problems
compiling SimpleRTK. The main issue seems to be that it depends on
SimpleRTKCommon - which I do not have.

Here is the last few lines from VS2013

> 5>LINK : fatal error LNK1181: cannot open input file
'..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib' [C:\Users\aplb\Work\RTK\RTK1.2-
> bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> 5>
> 5>      0 Warning(s)
> 5>      2 Error(s)
> 5>
> 5>  Time Elapsed 00:00:25.26
> ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
==========

I'm not quite sure what is going on, because the only reference I can find
to SimpleRTKCommon is the CMakeLists.txt on github:
https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt

best

Arvid

On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> The latest MacOS. It's nice if you can test it on other platforms, I'll
> try to run it on Linux but I have to upgrade matlab first (I think python
> calls are available starting with Matlab 2014).
> Simon
>
> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Dear Simon
>>
>> This look very interesting! Which platform did you successfully execute
>> this on?
>> I will give it a try at once (on windows) and let you know if I run into
>> any problems.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Dear RTK users,
>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>> it seems to work well:
>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>> know if you think otherwise.
>>> Future works include a simple installation mechanism for pre-compiled
>>> SimpleRTK libraries. We'll keep you posted!
>>> Simon
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 12:50:33 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 18:50:33 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
Message-ID: <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>

 SimpleRTKCommon is a library generated when compiling. Don't you have
another error before that which explains why it did not compile?
Simon

On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I've been trying to get it working. However, I did run into some problems
> compiling SimpleRTK. The main issue seems to be that it depends on
> SimpleRTKCommon - which I do not have.
>
> Here is the last few lines from VS2013
>
> > 5>LINK : fatal error LNK1181: cannot open input file '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
> [C:\Users\aplb\Work\RTK\RTK1.2-
> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> > 5>
> > 5>      0 Warning(s)
> > 5>      2 Error(s)
> > 5>
> > 5>  Time Elapsed 00:00:25.26
> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
> ==========
>
> I'm not quite sure what is going on, because the only reference I can find
> to SimpleRTKCommon is the CMakeLists.txt on github:
> https://github.com/SimonRit/RTK/blob/master/utilities/
> SimpleRTK/CMakeLists.txt
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>> try to run it on Linux but I have to upgrade matlab first (I think python
>> calls are available starting with Matlab 2014).
>> Simon
>>
>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Dear Simon
>>>
>>> This look very interesting! Which platform did you successfully execute
>>> this on?
>>> I will give it a try at once (on windows) and let you know if I run into
>>> any problems.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Dear RTK users,
>>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>>> it seems to work well:
>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>>> know if you think otherwise.
>>>> Future works include a simple installation mechanism for pre-compiled
>>>> SimpleRTK libraries. We'll keep you posted!
>>>> Simon
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 01:33:46 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 07:33:46 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
Message-ID: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>

I'm not an msvc specialist but your first line suggests that you have 
pasted only part of the log:

20>  Done Building Project 
"C:\Users\aplb\Work\RTK\RTK1.2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" 
(default targets) -- FAILED.

What you need to find out is why this build failed. If the build fails, 
the linking cannot work.
Cheers,
Simon

On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
> I did a complete rebuild, and here is the end of the output: 
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that 
> I'm trying to compile the version I just pulled from git earlier 
> today, since the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     SimpleRTKCommon is a library generated when compiling. Don't you
>     have another error before that which explains why it did not compile?
>     Simon
>
>     On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger
>     <bottiger at gmail.com <mailto:bottiger at gmail.com>> wrote:
>
>         Hi again.
>
>         I've been trying to get it working. However, I did run into
>         some problems compiling SimpleRTK. The main issue seems to be
>         that it depends on SimpleRTKCommon - which I do not have.
>
>         Here is the last few lines from VS2013
>
>         > 5>LINK : fatal error LNK1181: cannot open input file
>         '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>         [C:\Users\aplb\Work\RTK\RTK1.2-
>         > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>         > 5>
>         > 5>      0 Warning(s)
>         > 5>      2 Error(s)
>         > 5>
>         > 5>  Time Elapsed 00:00:25.26
>         > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0
>         skipped ==========
>
>         I'm not quite sure what is going on, because the only
>         reference I can find to SimpleRTKCommon is the CMakeLists.txt
>         on github:
>         https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt
>         <https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt>
>
>         best
>
>         Arvid
>
>         On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit
>         <simon.rit at creatis.insa-lyon.fr
>         <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>             The latest MacOS. It's nice if you can test it on other
>             platforms, I'll try to run it on Linux but I have to
>             upgrade matlab first (I think python calls are available
>             starting with Matlab 2014).
>             Simon
>
>             On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen
>             B?ttiger <bottiger at gmail.com <mailto:bottiger at gmail.com>>
>             wrote:
>
>                 Dear Simon
>
>                 This look very interesting! Which platform did you
>                 successfully execute this on?
>                 I will give it a try at once (on windows) and let you
>                 know if I run into any problems.
>
>                 best
>
>                 Arvid
>
>                 On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit
>                 <simon.rit at creatis.insa-lyon.fr
>                 <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>                     Dear RTK users,
>                     I have quickly tested calling the SimpleRTK python
>                     lib from Matlab and it seems to work well:
>                     http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>                     <http://wiki.openrtk.org/index.php/SimpleRTK#Matlab>
>                     Therefore, I don't think we have to work on Matlab
>                     wrappings but let us know if you think otherwise.
>                     Future works include a simple installation
>                     mechanism for pre-compiled SimpleRTK libraries.
>                     We'll keep you posted!
>                     Simon
>
>                     _______________________________________________
>                     Rtk-users mailing list
>                     Rtk-users at public.kitware.com
>                     <mailto:Rtk-users at public.kitware.com>
>                     http://public.kitware.com/mailman/listinfo/rtk-users
>                     <http://public.kitware.com/mailman/listinfo/rtk-users>
>
>
>
>
>
>

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From bottiger at gmail.com  Tue Sep 20 08:17:35 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Tue, 20 Sep 2016 14:17:35 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
Message-ID: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>

Hi again.

I understand, but could you please help me get in contact with the person
who knows something about the windows build (if any), I think there is
something wrong.

I have been investigating the build problems I had and found that in the
sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
opened it up and found the projects which I had problems building:
"SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.

When I then tried to build SimpleRTKCommon manually it just compiled
without any problems. However, when I followed up by building
"SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
find "SimpleRTKCommon-0.9.lib" - which I just build.

After some more investigation I realized that the SimpleRTKCommon is set to
build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects it
to be a static linked library (LIB). After changing SimpleRTKCommon to be
build as a static library - and changing the output location - I could
build SimpleRTKBasicFilters0.

However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
to a LIB as well I could build SimpleRTKBasicFilters1, then
SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.

I'm unsure if the intention is to build them as static or dynamic
libraries, but in any case the current build configuration doesn't work -
on my setup at least.

However, I should note than for some reason the "lua5" project did build
successfully out of the box. Whatever it does differently works.

best

Arvid



On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> I'm not an msvc specialist but your first line suggests that you have
> pasted only part of the log:
>
> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.
> 2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
> What you need to find out is why this build failed. If the build fails,
> the linking cannot work.
> Cheers,
> Simon
>
>
> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>
> I did a complete rebuild, and here is the end of the output:
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that I'm
> trying to compile the version I just pulled from git earlier today, since
> the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> SimpleRTKCommon is a library generated when compiling. Don't you have
>> another error before that which explains why it did not compile?
>> Simon
>>
>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Hi again.
>>>
>>> I've been trying to get it working. However, I did run into some
>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>> SimpleRTKCommon - which I do not have.
>>>
>>> Here is the last few lines from VS2013
>>>
>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>> > 5>
>>> > 5>      0 Warning(s)
>>> > 5>      2 Error(s)
>>> > 5>
>>> > 5>  Time Elapsed 00:00:25.26
>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>> ==========
>>>
>>> I'm not quite sure what is going on, because the only reference I can
>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>> RTK/CMakeLists.txt
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>>>> try to run it on Linux but I have to upgrade matlab first (I think python
>>>> calls are available starting with Matlab 2014).
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Dear Simon
>>>>>
>>>>> This look very interesting! Which platform did you successfully
>>>>> execute this on?
>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>> into any problems.
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Dear RTK users,
>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>> and it seems to work well:
>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>> us know if you think otherwise.
>>>>>> Future works include a simple installation mechanism for pre-compiled
>>>>>> SimpleRTK libraries. We'll keep you posted!
>>>>>> Simon
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 10:19:20 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 16:19:20 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
Message-ID: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>

Hi,
Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
I can't solve your problem but Kitware is going to look into an upgrade of
SimpleRTK in the coming days, I'll ask them if they know what is the issue.
If you look here:
http://my.cdash.org/viewNotes.php?buildid=1052065
this is a nightly build of SimpleRTK on Windows and it seems to work. I
don't see why it wouldn't work for you.
Simon

On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I understand, but could you please help me get in contact with the person
> who knows something about the windows build (if any), I think there is
> something wrong.
>
> I have been investigating the build problems I had and found that in the
> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
> opened it up and found the projects which I had problems building:
> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>
> When I then tried to build SimpleRTKCommon manually it just compiled
> without any problems. However, when I followed up by building
> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
> find "SimpleRTKCommon-0.9.lib" - which I just build.
>
> After some more investigation I realized that the SimpleRTKCommon is set
> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
> it to be a static linked library (LIB). After changing SimpleRTKCommon to
> be build as a static library - and changing the output location - I could
> build SimpleRTKBasicFilters0.
>
> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
> to a LIB as well I could build SimpleRTKBasicFilters1, then
> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>
> I'm unsure if the intention is to build them as static or dynamic
> libraries, but in any case the current build configuration doesn't work -
> on my setup at least.
>
> However, I should note than for some reason the "lua5" project did build
> successfully out of the box. Whatever it does differently works.
>
> best
>
> Arvid
>
>
>
> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> I'm not an msvc specialist but your first line suggests that you have
>> pasted only part of the log:
>>
>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
>> What you need to find out is why this build failed. If the build fails,
>> the linking cannot work.
>> Cheers,
>> Simon
>>
>>
>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>
>> I did a complete rebuild, and here is the end of the output:
>> http://pastebin.com/hvQ33WWg
>>
>> I have to admit I'm not sure what to make of it. I should note that I'm
>> trying to compile the version I just pulled from git earlier today, since
>> the other version I normally work with is really old.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>> another error before that which explains why it did not compile?
>>> Simon
>>>
>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>> bottiger at gmail.com> wrote:
>>>
>>>> Hi again.
>>>>
>>>> I've been trying to get it working. However, I did run into some
>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>> SimpleRTKCommon - which I do not have.
>>>>
>>>> Here is the last few lines from VS2013
>>>>
>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>> > 5>
>>>> > 5>      0 Warning(s)
>>>> > 5>      2 Error(s)
>>>> > 5>
>>>> > 5>  Time Elapsed 00:00:25.26
>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>> ==========
>>>>
>>>> I'm not quite sure what is going on, because the only reference I can
>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>> RTK/CMakeLists.txt
>>>>
>>>> best
>>>>
>>>> Arvid
>>>>
>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>> python calls are available starting with Matlab 2014).
>>>>> Simon
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>> bottiger at gmail.com> wrote:
>>>>>
>>>>>> Dear Simon
>>>>>>
>>>>>> This look very interesting! Which platform did you successfully
>>>>>> execute this on?
>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>> into any problems.
>>>>>>
>>>>>> best
>>>>>>
>>>>>> Arvid
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>
>>>>>>> Dear RTK users,
>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>> and it seems to work well:
>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>>> us know if you think otherwise.
>>>>>>> Future works include a simple installation mechanism for
>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>> Simon
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 02:40:50 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 08:40:50 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
Message-ID: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>

Dear RTK users,
RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
been released, about 7 months after RTK v1.2.0.

Release notes :
- Style updated (follow more closely latest ITK guidelines).
- Started using Travis CI, github pull requests should now be used for code
submission.
- New pre-processing functionalities:
  * CUDA polynomial gain correction,
  * scatter glare correction,
  * lag correction,
  * idark option,
  * removed threshold to positive values after i0 LUT.
- Improved CUDA forward and backprojection speed using projection slabs.
- Added motion-compensated forward and back projection operators in CUDA,
in both 3D and 4D.
- Added the rtkregularizedconjugategradient application, which performs 3D
regularized reconstruction by conjugate gradient + optional regularizations
(Positivity, TV, Wavelets).
- Made the rtkfourdrooster, rtkmcrooster and rtkregularizedconjugategradient
fully modular. Each regularization step can be made active or inactive.
- Added a filter to minimize the L0 norm of the temporal gradient (one-D
only).

Many thanks to the contributors, in alphabetical order for this release: Cyril
Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien
Jomier, S?bastien
Brousmiche, Simon Rit

As usual, be aware that we don't focus on releases since we have a public
github repository <http://github.com/SimonRit/RTK> that we try to keep
stable. I still recommend the use of the master HEAD over releases to enjoy
the new RTK developments before their release. We still have a few on-going
projects for which we will use and enhance RTK.

Simon (for the RTK consortium)
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 04:48:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 10:48:26 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
In-Reply-To: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
References: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
Message-ID: <CAF0oig0=5_KPN198JzsGQXDd07Nvw_Ew+qSGhguk0m27s3U-3Q@mail.gmail.com>

Sorry, I had forgotten to change the release number in the source file.
It's been corrected, you will have to move your tag locally or update your
file if you had already downloaded it.
Simon

On Thu, Sep 22, 2016 at 8:40 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
> been released, about 7 months after RTK v1.2.0.
>
> Release notes :
> - Style updated (follow more closely latest ITK guidelines).
> - Started using Travis CI, github pull requests should now be used for
> code submission.
> - New pre-processing functionalities:
>   * CUDA polynomial gain correction,
>   * scatter glare correction,
>   * lag correction,
>   * idark option,
>   * removed threshold to positive values after i0 LUT.
> - Improved CUDA forward and backprojection speed using projection slabs.
> - Added motion-compensated forward and back projection operators in CUDA,
> in both 3D and 4D.
> - Added the rtkregularizedconjugategradient application, which performs
> 3D regularized reconstruction by conjugate gradient + optional
> regularizations (Positivity, TV, Wavelets).
> - Made the rtkfourdrooster, rtkmcrooster and
> rtkregularizedconjugategradient fully modular. Each regularization step
> can be made active or inactive.
> - Added a filter to minimize the L0 norm of the temporal gradient (one-D
> only).
>
> Many thanks to the contributors, in alphabetical order for this release: Cyril
> Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien Jomier, S?bastien
> Brousmiche, Simon Rit
>
> As usual, be aware that we don't focus on releases since we have a public
> github repository <http://github.com/SimonRit/RTK> that we try to keep
> stable. I still recommend the use of the master HEAD over releases to
> enjoy the new RTK developments before their release. We still have a few
> on-going projects for which we will use and enhance RTK.
>
> Simon (for the RTK consortium)
>
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From bottiger at gmail.com  Fri Sep 23 04:29:06 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Fri, 23 Sep 2016 10:29:06 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
 <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
Message-ID: <CANBwxwEvaUrvd1X=74g=V2JmDwtrQKFDtyUdAZJn5CRCBCkb8g@mail.gmail.com>

Hi again.

I've been spending some more time with this, and feel I learned a little
bit more. I have now tested this on several machines with several compiler
versions (more or less all of them) and serveral cmake versions - all with
Windows 7.

I can actually reproduce the successful build you linked to, but this can
only be done if you do not include any of the language wrappings, like in
the build you linked to. Enable any of them, and the build will break. (see
attachment)

I suspect it must have been working in the past, but since none of them are
included in your test there have been a breaking change, and none of them
work anymore.

I am still trying to tweak then projects manually to build SimpleRTK with
some sort of language support, but still without any luck.

best

Arvid

On Tue, Sep 20, 2016 at 4:19 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
> at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
> I can't solve your problem but Kitware is going to look into an upgrade of
> SimpleRTK in the coming days, I'll ask them if they know what is the issue.
> If you look here:
> http://my.cdash.org/viewNotes.php?buildid=1052065
> this is a nightly build of SimpleRTK on Windows and it seems to work. I
> don't see why it wouldn't work for you.
> Simon
>
> On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Hi again.
>>
>> I understand, but could you please help me get in contact with the person
>> who knows something about the windows build (if any), I think there is
>> something wrong.
>>
>> I have been investigating the build problems I had and found that in the
>> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
>> opened it up and found the projects which I had problems building:
>> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>>
>> When I then tried to build SimpleRTKCommon manually it just compiled
>> without any problems. However, when I followed up by building
>> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
>> find "SimpleRTKCommon-0.9.lib" - which I just build.
>>
>> After some more investigation I realized that the SimpleRTKCommon is set
>> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
>> it to be a static linked library (LIB). After changing SimpleRTKCommon to
>> be build as a static library - and changing the output location - I could
>> build SimpleRTKBasicFilters0.
>>
>> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing
>> that to a LIB as well I could build SimpleRTKBasicFilters1, then
>> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>>
>> I'm unsure if the intention is to build them as static or dynamic
>> libraries, but in any case the current build configuration doesn't work -
>> on my setup at least.
>>
>> However, I should note than for some reason the "lua5" project did build
>> successfully out of the box. Whatever it does differently works.
>>
>> best
>>
>> Arvid
>>
>>
>>
>> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> I'm not an msvc specialist but your first line suggests that you have
>>> pasted only part of the log:
>>>
>>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) --
>>> FAILED.
>>> What you need to find out is why this build failed. If the build fails,
>>> the linking cannot work.
>>> Cheers,
>>> Simon
>>>
>>>
>>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>>
>>> I did a complete rebuild, and here is the end of the output:
>>> http://pastebin.com/hvQ33WWg
>>>
>>> I have to admit I'm not sure what to make of it. I should note that I'm
>>> trying to compile the version I just pulled from git earlier today, since
>>> the other version I normally work with is really old.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>>> another error before that which explains why it did not compile?
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Hi again.
>>>>>
>>>>> I've been trying to get it working. However, I did run into some
>>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>>> SimpleRTKCommon - which I do not have.
>>>>>
>>>>> Here is the last few lines from VS2013
>>>>>
>>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>>> > 5>
>>>>> > 5>      0 Warning(s)
>>>>> > 5>      2 Error(s)
>>>>> > 5>
>>>>> > 5>  Time Elapsed 00:00:25.26
>>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>>> ==========
>>>>>
>>>>> I'm not quite sure what is going on, because the only reference I can
>>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>>> RTK/CMakeLists.txt
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>>> python calls are available starting with Matlab 2014).
>>>>>> Simon
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>>> bottiger at gmail.com> wrote:
>>>>>>
>>>>>>> Dear Simon
>>>>>>>
>>>>>>> This look very interesting! Which platform did you successfully
>>>>>>> execute this on?
>>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>>> into any problems.
>>>>>>>
>>>>>>> best
>>>>>>>
>>>>>>> Arvid
>>>>>>>
>>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Dear RTK users,
>>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>>> and it seems to work well:
>>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but
>>>>>>>> let us know if you think otherwise.
>>>>>>>> Future works include a simple installation mechanism for
>>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
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From ajbatkinson at gmail.com  Wed Sep 28 08:11:12 2016
From: ajbatkinson at gmail.com (Abby Bryce Atkinson)
Date: Wed, 28 Sep 2016 13:11:12 +0100
Subject: [Rtk-users] 4DROOSTERReconstruction Example
Message-ID: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>

Hi,

I am trying to work through the 4DROOSTER example using the POPI patient
images (
http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) but
I am getting stuck when extracting the respiratory signal using the
amsterdam shroud.

I receive this error:


C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
--path .\Projections\ ^
More?                    --regexp '.*.his' ^
More?                    --output shroud.mha ^
More?                    --unsharp 650
ExceptionObject caught with writer->Update() in file
C:\RTK\applications\rtkamst
erdamshroud\rtkamsterdamshroud.cxx line 91

itk::ExceptionObject (0030E9E0)
Location: "void __thiscall itk::ImageFileWriter<class itk::Image<double,2>
>::Wr
ite(void)"
File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
Line: 284
Description: itk::ERROR: ImageFileWriter(03670318): Largest possible region
does
 not fully contain requested paste IO regionPaste IO region: ImageIORegion
(0030
EDD4)
  Dimension: 2
  Index: 0 0
  Size: 0 0
Largest possible region: ImageRegion (0030EE70)
  Dimension: 2
  Index: [0, 0]
  Size: [0, 0]


Can anyone help with a solution/tell me what I am doing wrong please?

Thanks,

Abby
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From simon.rit at creatis.insa-lyon.fr  Wed Sep 28 12:49:32 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 28 Sep 2016 18:49:32 +0200
Subject: [Rtk-users] 4DROOSTERReconstruction Example
In-Reply-To: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
References: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
Message-ID: <e23fc5ec-f7b4-846c-e349-f07564e2da8a@creatis.insa-lyon.fr>

Hi,

My guess is that the software does not find the projections. I would add 
the --verbose option and check that you actually input some projections. 
If not, I guess there is an issue with the path or the regexp in your 
command line.

Simon

On 28/09/2016 14:11, Abby Bryce Atkinson wrote:
> Hi,
>
> I am trying to work through the 4DROOSTER example using the POPI 
> patient images 
> (http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) 
> but I am getting stuck when extracting the respiratory signal using 
> the amsterdam shroud.
>
> I receive this error:
>
>
> C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
> --path .\Projections\ ^
> More?                    --regexp '.*.his' ^
> More?                    --output shroud.mha ^
> More?                    --unsharp 650
> ExceptionObject caught with writer->Update() in file 
> C:\RTK\applications\rtkamst
> erdamshroud\rtkamsterdamshroud.cxx line 91
>
> itk::ExceptionObject (0030E9E0)
> Location: "void __thiscall itk::ImageFileWriter<class 
> itk::Image<double,2> >::Wr
> ite(void)"
> File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
> Line: 284
> Description: itk::ERROR: ImageFileWriter(03670318): Largest possible 
> region does
>  not fully contain requested paste IO regionPaste IO region: 
> ImageIORegion (0030
> EDD4)
>   Dimension: 2
>   Index: 0 0
>   Size: 0 0
> Largest possible region: ImageRegion (0030EE70)
>   Dimension: 2
>   Index: [0, 0]
>   Size: [0, 0]
>
>
> Can anyone help with a solution/tell me what I am doing wrong please?
>
> Thanks,
>
> Abby
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users

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From signabdm at gmail.com  Mon Sep 12 06:58:59 2016
From: signabdm at gmail.com (Valeriy Signatulin)
Date: Mon, 12 Sep 2016 16:58:59 +0600
Subject: [Rtk-users] rotation of detector plane
Message-ID: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>

Hello RTK users.
Is it possible to specify rotation of detector plane in RTK ? (in
rtksimulategeom for example) If not, what is the best way to code this ?
By rotation of detector plane i mean twist, tilt, skew around the normal of
the detector as described in
http://www.ndt.net/article/v10n09/yisun/yisun.pdf page 6.
I'm trying to write the geometry calibration method described in this
article in RTK and i need to simulate these rotations to check the results.
Thanks.
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 12 08:40:31 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 12 Sep 2016 14:40:31 +0200
Subject: [Rtk-users] rotation of detector plane
In-Reply-To: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
References: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
Message-ID: <CAF0oig0C3zFcAaAhWHV9g+UY02i7cws7OU-7r2YadyAt3TH5GA@mail.gmail.com>

Hi,
You can do any rotation with RTK. The rotation is described 3 Euler angles,
see the geometry doc <http://www.openrtk.org/Doxygen/geometry.pdf>. From
the command line, that would be the --in_angle and out_angle that allow you
to modify the other angles than the standard angle for the position along
the circular rotation (GantryAngle). If you want to modify it per
projection, that's possible using C++ or Python code (AddProjection
<http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
method).
Good luck,
Simon

On Mon, Sep 12, 2016 at 12:58 PM, Valeriy Signatulin <signabdm at gmail.com>
wrote:

> Hello RTK users.
> Is it possible to specify rotation of detector plane in RTK ? (in
> rtksimulategeom for example) If not, what is the best way to code this ?
> By rotation of detector plane i mean twist, tilt, skew around the normal
> of the detector as described in http://www.ndt.net/article/
> v10n09/yisun/yisun.pdf page 6.
> I'm trying to write the geometry calibration method described in this
> article in RTK and i need to simulate these rotations to check the results.
> Thanks.
>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From andreasg at phys.au.dk  Tue Sep 13 13:06:46 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Tue, 13 Sep 2016 19:06:46 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
Message-ID: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>

Dear RTK experts,

I am reconstructing Varian ProBeam projections of the Xim image format. I
have written the reader myself - very similar to the Hnd one already
available with RTK.
Links to my fork: [XimReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkXimImageIO.cxx>,
XMLReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamXMLFileReader.cxx>,
GeometryReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamGeometryReader.cxx>
]

The reader apparently works (Images and angles displays as expected in UI),
however when reconstructing with a regular FDK* I get a reconstructed image
that is smeared out around the high and low density areas *[see attached
image]

I'm using half arc, full fan images with no bow-tie filter from Scripps
(~520 projections). Fixed detector and source (offset=0) with SID=2m,
SDD=3m.

*For the Hnd projections the reconstruction works perfectly (Same algorithm
<https://github.com/agravgaard/cbctrecon/blob/master/cbctrecon.cpp#L2726>).*
The reconstruction of the Xim projections performed on Varian software
works perfectly.

Without the Parker Short Scan Filter the first and last projections creates
streaks across the reconstruction as if they were way too bright.
If the first few projections are excluded, the following projection will
act the same way.

The projections are corrected for beam hardening and all the projections
have the expected attenuation.
No "smearing" filters (like median) is used, and iterative reconstruction
makes the same artifacts.

Setting the value of the first and last projection to zero has the same
effect as excluding. Changing the ramp filter only changes noise, not the
artifacts.

*Have any of you had a similar problem? *Am I missing something?
Any suggestions are welcome I'm running out of ideas.

Best regards
Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 13 16:18:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 13 Sep 2016 22:18:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
Message-ID: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>

Hi,
I have almost never worked with Varian data but it looks like a
geometry problem. Maybe the problem comes from a bad ordering of the
projections which results in assigning a bad geometry to each
projection. How did you name your projections? Maybe check that the
order matches that of the RTK geometry file. Otherwise, there might be
an issue in the creation of the geometry file itself.
All this sounds good, happy bug hunt and don't hesitate to share your
code when you feel it's ready.
Simon

On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
<andreasg at phys.au.dk> wrote:
> Dear RTK experts,
>
> I am reconstructing Varian ProBeam projections of the Xim image format. I
> have written the reader myself - very similar to the Hnd one already
> available with RTK.
> Links to my fork: [XimReader, XMLReader, GeometryReader]
>
> The reader apparently works (Images and angles displays as expected in UI),
> however when reconstructing with a regular FDK I get a reconstructed image
> that is smeared out around the high and low density areas [see attached
> image]
>
> I'm using half arc, full fan images with no bow-tie filter from Scripps
> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
> SDD=3m.
>
> For the Hnd projections the reconstruction works perfectly (Same algorithm).
> The reconstruction of the Xim projections performed on Varian software works
> perfectly.
>
> Without the Parker Short Scan Filter the first and last projections creates
> streaks across the reconstruction as if they were way too bright.
> If the first few projections are excluded, the following projection will act
> the same way.
>
> The projections are corrected for beam hardening and all the projections
> have the expected attenuation.
> No "smearing" filters (like median) is used, and iterative reconstruction
> makes the same artifacts.
>
> Setting the value of the first and last projection to zero has the same
> effect as excluding. Changing the ramp filter only changes noise, not the
> artifacts.
>
> Have any of you had a similar problem? Am I missing something?
> Any suggestions are welcome I'm running out of ideas.
>
> Best regards
> Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>


From cyril.mory at creatis.insa-lyon.fr  Wed Sep 14 03:10:42 2016
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 14 Sep 2016 09:10:42 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
Message-ID: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>

One suggestion since it works with the Hnd projections:
You can run rtkprojections twice (with the Hnd projections, then with 
Xim projections) and output two projection stack files and two geometry 
files, then compare the projection stack files by subtracting one to the 
other (with SimpleRTK or clitk) and the geometry files with diff. If 
they are identical, then I do not see any reason why the reconstructions 
should be different, so my guess is that you will find differences.

On 09/13/2016 10:18 PM, Simon Rit wrote:
> Hi,
> I have almost never worked with Varian data but it looks like a
> geometry problem. Maybe the problem comes from a bad ordering of the
> projections which results in assigning a bad geometry to each
> projection. How did you name your projections? Maybe check that the
> order matches that of the RTK geometry file. Otherwise, there might be
> an issue in the creation of the geometry file itself.
> All this sounds good, happy bug hunt and don't hesitate to share your
> code when you feel it's ready.
> Simon
>
> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
> <andreasg at phys.au.dk> wrote:
>> Dear RTK experts,
>>
>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>> have written the reader myself - very similar to the Hnd one already
>> available with RTK.
>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>
>> The reader apparently works (Images and angles displays as expected in UI),
>> however when reconstructing with a regular FDK I get a reconstructed image
>> that is smeared out around the high and low density areas [see attached
>> image]
>>
>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>> SDD=3m.
>>
>> For the Hnd projections the reconstruction works perfectly (Same algorithm).
>> The reconstruction of the Xim projections performed on Varian software works
>> perfectly.
>>
>> Without the Parker Short Scan Filter the first and last projections creates
>> streaks across the reconstruction as if they were way too bright.
>> If the first few projections are excluded, the following projection will act
>> the same way.
>>
>> The projections are corrected for beam hardening and all the projections
>> have the expected attenuation.
>> No "smearing" filters (like median) is used, and iterative reconstruction
>> makes the same artifacts.
>>
>> Setting the value of the first and last projection to zero has the same
>> effect as excluding. Changing the ramp filter only changes noise, not the
>> artifacts.
>>
>> Have any of you had a similar problem? Am I missing something?
>> Any suggestions are welcome I'm running out of ideas.
>>
>> Best regards
>> Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>



From andreasg at phys.au.dk  Fri Sep 16 08:56:34 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 14:56:34 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
Message-ID: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>

Thanks for the suggestions, Simon and Cyril!

I have been carefully looking though the geometry and from what I
understand of the transformations matrices, the geometry looks correct/(as
expected).

HOWEVER: I found out that the reason for the Hnd to behave differently were
because had used half-fan scans (full-arc).
When I used a full-fan (half-arc) scan of Hnd projections the same
artifacts occurs!

Are there other (built-in) means of improving half-arc scans, than the
parker short scan filter?

Parker short scan does a decent job, but the result is still far from the
quality of the Varian software reconstruction at least for the CatPhan.

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:

> One suggestion since it works with the Hnd projections:
> You can run rtkprojections twice (with the Hnd projections, then with Xim
> projections) and output two projection stack files and two geometry files,
> then compare the projection stack files by subtracting one to the other
> (with SimpleRTK or clitk) and the geometry files with diff. If they are
> identical, then I do not see any reason why the reconstructions should be
> different, so my guess is that you will find differences.
>
>
> On 09/13/2016 10:18 PM, Simon Rit wrote:
>
>> Hi,
>> I have almost never worked with Varian data but it looks like a
>> geometry problem. Maybe the problem comes from a bad ordering of the
>> projections which results in assigning a bad geometry to each
>> projection. How did you name your projections? Maybe check that the
>> order matches that of the RTK geometry file. Otherwise, there might be
>> an issue in the creation of the geometry file itself.
>> All this sounds good, happy bug hunt and don't hesitate to share your
>> code when you feel it's ready.
>> Simon
>>
>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>> <andreasg at phys.au.dk> wrote:
>>
>>> Dear RTK experts,
>>>
>>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>>> have written the reader myself - very similar to the Hnd one already
>>> available with RTK.
>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>
>>> The reader apparently works (Images and angles displays as expected in
>>> UI),
>>> however when reconstructing with a regular FDK I get a reconstructed
>>> image
>>> that is smeared out around the high and low density areas [see attached
>>> image]
>>>
>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>> SDD=3m.
>>>
>>> For the Hnd projections the reconstruction works perfectly (Same
>>> algorithm).
>>> The reconstruction of the Xim projections performed on Varian software
>>> works
>>> perfectly.
>>>
>>> Without the Parker Short Scan Filter the first and last projections
>>> creates
>>> streaks across the reconstruction as if they were way too bright.
>>> If the first few projections are excluded, the following projection will
>>> act
>>> the same way.
>>>
>>> The projections are corrected for beam hardening and all the projections
>>> have the expected attenuation.
>>> No "smearing" filters (like median) is used, and iterative reconstruction
>>> makes the same artifacts.
>>>
>>> Setting the value of the first and last projection to zero has the same
>>> effect as excluding. Changing the ramp filter only changes noise, not the
>>> artifacts.
>>>
>>> Have any of you had a similar problem? Am I missing something?
>>> Any suggestions are welcome I'm running out of ideas.
>>>
>>> Best regards
>>> Andreas
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Sep 16 10:13:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 16 Sep 2016 16:13:26 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
Message-ID: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>

Hi,
You can try any iterative reconstruction, they can also handle short scans.
Start with a few iterations of rtksart or rtkconjugategradient. However,
the nature of the artifacts indicate more a problem in the geometry in my
opinion. I have seen such errors when, for example, rotating in the wrong
direction. I can have a look if you share the dataset.
Cheers,
Simon

On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the suggestions, Simon and Cyril!
>
> I have been carefully looking though the geometry and from what I
> understand of the transformations matrices, the geometry looks correct/(as
> expected).
>
> HOWEVER: I found out that the reason for the Hnd to behave differently
> were because had used half-fan scans (full-arc).
> When I used a full-fan (half-arc) scan of Hnd projections the same
> artifacts occurs!
>
> Are there other (built-in) means of improving half-arc scans, than the
> parker short scan filter?
>
> Parker short scan does a decent job, but the result is still far from the
> quality of the Varian software reconstruction at least for the CatPhan.
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>
>> One suggestion since it works with the Hnd projections:
>> You can run rtkprojections twice (with the Hnd projections, then with Xim
>> projections) and output two projection stack files and two geometry files,
>> then compare the projection stack files by subtracting one to the other
>> (with SimpleRTK or clitk) and the geometry files with diff. If they are
>> identical, then I do not see any reason why the reconstructions should be
>> different, so my guess is that you will find differences.
>>
>>
>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>
>>> Hi,
>>> I have almost never worked with Varian data but it looks like a
>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>> projections which results in assigning a bad geometry to each
>>> projection. How did you name your projections? Maybe check that the
>>> order matches that of the RTK geometry file. Otherwise, there might be
>>> an issue in the creation of the geometry file itself.
>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>> code when you feel it's ready.
>>> Simon
>>>
>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>> <andreasg at phys.au.dk> wrote:
>>>
>>>> Dear RTK experts,
>>>>
>>>> I am reconstructing Varian ProBeam projections of the Xim image format.
>>>> I
>>>> have written the reader myself - very similar to the Hnd one already
>>>> available with RTK.
>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>
>>>> The reader apparently works (Images and angles displays as expected in
>>>> UI),
>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>> image
>>>> that is smeared out around the high and low density areas [see attached
>>>> image]
>>>>
>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>> SDD=3m.
>>>>
>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>> algorithm).
>>>> The reconstruction of the Xim projections performed on Varian software
>>>> works
>>>> perfectly.
>>>>
>>>> Without the Parker Short Scan Filter the first and last projections
>>>> creates
>>>> streaks across the reconstruction as if they were way too bright.
>>>> If the first few projections are excluded, the following projection
>>>> will act
>>>> the same way.
>>>>
>>>> The projections are corrected for beam hardening and all the projections
>>>> have the expected attenuation.
>>>> No "smearing" filters (like median) is used, and iterative
>>>> reconstruction
>>>> makes the same artifacts.
>>>>
>>>> Setting the value of the first and last projection to zero has the same
>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>> the
>>>> artifacts.
>>>>
>>>> Have any of you had a similar problem? Am I missing something?
>>>> Any suggestions are welcome I'm running out of ideas.
>>>>
>>>> Best regards
>>>> Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> N?rrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     andreasg at phys.au.dk
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From andreasg at phys.au.dk  Fri Sep 16 16:37:43 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 22:37:43 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
Message-ID: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>

Thanks for the fast response Simon!

I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
right all along!
I just didn't get why it makes a difference. I think I do now, as the
resulting image was flipped upside down and not left/right as I expected.
[attached]

The reconstruction is significantly better, I'll look into what should be
included in the reader and what I should keep in my program to keep
conformity with the other readers. Then I'll create a pull request.

Just for the purpose of others hitting the same or a similar bug, I also
attempted:
I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
back/forward projection, *but with no* significant improvement [attached]

And:
If you want you can download the data set from: [Dropbox link to 460MB zip
<https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep it
up as long as Dropbox allows me)] Only the Acquisitions/subfolder is used
along with the Scan.xml (Calibrations folder may be used in the future in
my program, but I'm not sure if you can rely on the existence of the
content).

A MatLab XimReader is available: link
<https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
available from Varian bitbucket along a with a python version and a
C#->matlab plugin
<https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). Otherwise
my fork with the RTK-style reader is available from the same repository (I
have also added Hnc support, thanks to the Geoff Hugo fork, so bzip2 is a
new dependancy).

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:

> Hi,
> You can try any iterative reconstruction, they can also handle short
> scans. Start with a few iterations of rtksart or rtkconjugategradient.
> However, the nature of the artifacts indicate more a problem in the
> geometry in my opinion. I have seen such errors when, for example, rotating
> in the wrong direction. I can have a look if you share the dataset.
> Cheers,
> Simon
>
> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
> andreasg at phys.au.dk> wrote:
>
>> Thanks for the suggestions, Simon and Cyril!
>>
>> I have been carefully looking though the geometry and from what I
>> understand of the transformations matrices, the geometry looks correct/(as
>> expected).
>>
>> HOWEVER: I found out that the reason for the Hnd to behave differently
>> were because had used half-fan scans (full-arc).
>> When I used a full-fan (half-arc) scan of Hnd projections the same
>> artifacts occurs!
>>
>> Are there other (built-in) means of improving half-arc scans, than the
>> parker short scan filter?
>>
>> Parker short scan does a decent job, but the result is still far from the
>> quality of the Varian software reconstruction at least for the CatPhan.
>>
>> Best regards
>> Andreas
>>
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>>
>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>
>>> One suggestion since it works with the Hnd projections:
>>> You can run rtkprojections twice (with the Hnd projections, then with
>>> Xim projections) and output two projection stack files and two geometry
>>> files, then compare the projection stack files by subtracting one to the
>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>> are identical, then I do not see any reason why the reconstructions should
>>> be different, so my guess is that you will find differences.
>>>
>>>
>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>
>>>> Hi,
>>>> I have almost never worked with Varian data but it looks like a
>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>> projections which results in assigning a bad geometry to each
>>>> projection. How did you name your projections? Maybe check that the
>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>> an issue in the creation of the geometry file itself.
>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>> code when you feel it's ready.
>>>> Simon
>>>>
>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>> <andreasg at phys.au.dk> wrote:
>>>>
>>>>> Dear RTK experts,
>>>>>
>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>> format. I
>>>>> have written the reader myself - very similar to the Hnd one already
>>>>> available with RTK.
>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>
>>>>> The reader apparently works (Images and angles displays as expected in
>>>>> UI),
>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>> image
>>>>> that is smeared out around the high and low density areas [see attached
>>>>> image]
>>>>>
>>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>> SDD=3m.
>>>>>
>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>> algorithm).
>>>>> The reconstruction of the Xim projections performed on Varian software
>>>>> works
>>>>> perfectly.
>>>>>
>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>> creates
>>>>> streaks across the reconstruction as if they were way too bright.
>>>>> If the first few projections are excluded, the following projection
>>>>> will act
>>>>> the same way.
>>>>>
>>>>> The projections are corrected for beam hardening and all the
>>>>> projections
>>>>> have the expected attenuation.
>>>>> No "smearing" filters (like median) is used, and iterative
>>>>> reconstruction
>>>>> makes the same artifacts.
>>>>>
>>>>> Setting the value of the first and last projection to zero has the same
>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>> the
>>>>> artifacts.
>>>>>
>>>>> Have any of you had a similar problem? Am I missing something?
>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>
>>>>> Best regards
>>>>> Andreas
>>>>>
>>>>> __________________________________
>>>>>
>>>>> Andreas Gravgaard Andersen
>>>>>
>>>>> Department of Oncology,
>>>>>
>>>>> Aarhus University Hospital
>>>>>
>>>>> N?rrebrogade 44,
>>>>>
>>>>> 8000, Aarhus C
>>>>>
>>>>> Mail:     andreasg at phys.au.dk
>>>>>
>>>>> Cell:      +45 3165 8140
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 03:26:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 09:26:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
 <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
Message-ID: <CAF0oig2TSmAsSn=o3aLo6LEFDOSaKRtfknjMer24rcDKJ-0Fqg@mail.gmail.com>

Hi,
Thanks for sharing. There still seems to be some streak artefacts, do you
see the same in the Varian reconstruction?
I'm looking forward to the pull-request, I think we should try to make the
bzip2 optional.
Simon

On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the fast response Simon!
>
> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
> right all along!
> I just didn't get why it makes a difference. I think I do now, as the
> resulting image was flipped upside down and not left/right as I expected.
> [attached]
>
> The reconstruction is significantly better, I'll look into what should be
> included in the reader and what I should keep in my program to keep
> conformity with the other readers. Then I'll create a pull request.
>
> Just for the purpose of others hitting the same or a similar bug, I also
> attempted:
> I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
> back/forward projection, *but with no* significant improvement [attached]
>
> And:
> If you want you can download the data set from: [Dropbox link to 460MB zip
> <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep
> it up as long as Dropbox allows me)] Only the Acquisitions/subfolder is
> used along with the Scan.xml (Calibrations folder may be used in the future
> in my program, but I'm not sure if you can rely on the existence of the
> content).
>
> A MatLab XimReader is available: link
> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
> available from Varian bitbucket along a with a python version and a
> C#->matlab plugin
> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>).
> Otherwise my fork with the RTK-style reader is available from the same
> repository (I have also added Hnc support, thanks to the Geoff Hugo fork,
> so bzip2 is a new dependancy).
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> Hi,
>> You can try any iterative reconstruction, they can also handle short
>> scans. Start with a few iterations of rtksart or rtkconjugategradient.
>> However, the nature of the artifacts indicate more a problem in the
>> geometry in my opinion. I have seen such errors when, for example, rotating
>> in the wrong direction. I can have a look if you share the dataset.
>> Cheers,
>> Simon
>>
>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
>> andreasg at phys.au.dk> wrote:
>>
>>> Thanks for the suggestions, Simon and Cyril!
>>>
>>> I have been carefully looking though the geometry and from what I
>>> understand of the transformations matrices, the geometry looks correct/(as
>>> expected).
>>>
>>> HOWEVER: I found out that the reason for the Hnd to behave differently
>>> were because had used half-fan scans (full-arc).
>>> When I used a full-fan (half-arc) scan of Hnd projections the same
>>> artifacts occurs!
>>>
>>> Are there other (built-in) means of improving half-arc scans, than the
>>> parker short scan filter?
>>>
>>> Parker short scan does a decent job, but the result is still far from
>>> the quality of the Varian software reconstruction at least for the CatPhan.
>>>
>>> Best regards
>>> Andreas
>>>
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>>
>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>>
>>>> One suggestion since it works with the Hnd projections:
>>>> You can run rtkprojections twice (with the Hnd projections, then with
>>>> Xim projections) and output two projection stack files and two geometry
>>>> files, then compare the projection stack files by subtracting one to the
>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>>> are identical, then I do not see any reason why the reconstructions should
>>>> be different, so my guess is that you will find differences.
>>>>
>>>>
>>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>>
>>>>> Hi,
>>>>> I have almost never worked with Varian data but it looks like a
>>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>>> projections which results in assigning a bad geometry to each
>>>>> projection. How did you name your projections? Maybe check that the
>>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>>> an issue in the creation of the geometry file itself.
>>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>>> code when you feel it's ready.
>>>>> Simon
>>>>>
>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>>> <andreasg at phys.au.dk> wrote:
>>>>>
>>>>>> Dear RTK experts,
>>>>>>
>>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>>> format. I
>>>>>> have written the reader myself - very similar to the Hnd one already
>>>>>> available with RTK.
>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>>
>>>>>> The reader apparently works (Images and angles displays as expected
>>>>>> in UI),
>>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>>> image
>>>>>> that is smeared out around the high and low density areas [see
>>>>>> attached
>>>>>> image]
>>>>>>
>>>>>> I'm using half arc, full fan images with no bow-tie filter from
>>>>>> Scripps
>>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>>> SDD=3m.
>>>>>>
>>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>>> algorithm).
>>>>>> The reconstruction of the Xim projections performed on Varian
>>>>>> software works
>>>>>> perfectly.
>>>>>>
>>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>>> creates
>>>>>> streaks across the reconstruction as if they were way too bright.
>>>>>> If the first few projections are excluded, the following projection
>>>>>> will act
>>>>>> the same way.
>>>>>>
>>>>>> The projections are corrected for beam hardening and all the
>>>>>> projections
>>>>>> have the expected attenuation.
>>>>>> No "smearing" filters (like median) is used, and iterative
>>>>>> reconstruction
>>>>>> makes the same artifacts.
>>>>>>
>>>>>> Setting the value of the first and last projection to zero has the
>>>>>> same
>>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>>> the
>>>>>> artifacts.
>>>>>>
>>>>>> Have any of you had a similar problem? Am I missing something?
>>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>>
>>>>>> Best regards
>>>>>> Andreas
>>>>>>
>>>>>> __________________________________
>>>>>>
>>>>>> Andreas Gravgaard Andersen
>>>>>>
>>>>>> Department of Oncology,
>>>>>>
>>>>>> Aarhus University Hospital
>>>>>>
>>>>>> N?rrebrogade 44,
>>>>>>
>>>>>> 8000, Aarhus C
>>>>>>
>>>>>> Mail:     andreasg at phys.au.dk
>>>>>>
>>>>>> Cell:      +45 3165 8140
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:05:24 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:05:24 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
Message-ID: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>

Dear RTK users,
I have quickly tested calling the SimpleRTK python lib from Matlab and it
seems to work well:
http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
Therefore, I don't think we have to work on Matlab wrappings but let us
know if you think otherwise.
Future works include a simple installation mechanism for pre-compiled
SimpleRTK libraries. We'll keep you posted!
Simon
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From bottiger at gmail.com  Mon Sep 19 05:14:03 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 11:14:03 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
Message-ID: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>

Dear Simon

This look very interesting! Which platform did you successfully execute
this on?
I will give it a try at once (on windows) and let you know if I run into
any problems.

best

Arvid

On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> I have quickly tested calling the SimpleRTK python lib from Matlab and it
> seems to work well:
> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
> Therefore, I don't think we have to work on Matlab wrappings but let us
> know if you think otherwise.
> Future works include a simple installation mechanism for pre-compiled
> SimpleRTK libraries. We'll keep you posted!
> Simon
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:19:28 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:19:28 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
Message-ID: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>

The latest MacOS. It's nice if you can test it on other platforms, I'll try
to run it on Linux but I have to upgrade matlab first (I think python calls
are available starting with Matlab 2014).
Simon

On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Dear Simon
>
> This look very interesting! Which platform did you successfully execute
> this on?
> I will give it a try at once (on windows) and let you know if I run into
> any problems.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> Dear RTK users,
>> I have quickly tested calling the SimpleRTK python lib from Matlab and it
>> seems to work well:
>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>> Therefore, I don't think we have to work on Matlab wrappings but let us
>> know if you think otherwise.
>> Future works include a simple installation mechanism for pre-compiled
>> SimpleRTK libraries. We'll keep you posted!
>> Simon
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From bottiger at gmail.com  Mon Sep 19 08:30:32 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 14:30:32 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
Message-ID: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>

Hi again.

I've been trying to get it working. However, I did run into some problems
compiling SimpleRTK. The main issue seems to be that it depends on
SimpleRTKCommon - which I do not have.

Here is the last few lines from VS2013

> 5>LINK : fatal error LNK1181: cannot open input file
'..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib' [C:\Users\aplb\Work\RTK\RTK1.2-
> bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> 5>
> 5>      0 Warning(s)
> 5>      2 Error(s)
> 5>
> 5>  Time Elapsed 00:00:25.26
> ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
==========

I'm not quite sure what is going on, because the only reference I can find
to SimpleRTKCommon is the CMakeLists.txt on github:
https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt

best

Arvid

On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> The latest MacOS. It's nice if you can test it on other platforms, I'll
> try to run it on Linux but I have to upgrade matlab first (I think python
> calls are available starting with Matlab 2014).
> Simon
>
> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Dear Simon
>>
>> This look very interesting! Which platform did you successfully execute
>> this on?
>> I will give it a try at once (on windows) and let you know if I run into
>> any problems.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Dear RTK users,
>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>> it seems to work well:
>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>> know if you think otherwise.
>>> Future works include a simple installation mechanism for pre-compiled
>>> SimpleRTK libraries. We'll keep you posted!
>>> Simon
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 12:50:33 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 18:50:33 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
Message-ID: <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>

 SimpleRTKCommon is a library generated when compiling. Don't you have
another error before that which explains why it did not compile?
Simon

On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I've been trying to get it working. However, I did run into some problems
> compiling SimpleRTK. The main issue seems to be that it depends on
> SimpleRTKCommon - which I do not have.
>
> Here is the last few lines from VS2013
>
> > 5>LINK : fatal error LNK1181: cannot open input file '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
> [C:\Users\aplb\Work\RTK\RTK1.2-
> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> > 5>
> > 5>      0 Warning(s)
> > 5>      2 Error(s)
> > 5>
> > 5>  Time Elapsed 00:00:25.26
> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
> ==========
>
> I'm not quite sure what is going on, because the only reference I can find
> to SimpleRTKCommon is the CMakeLists.txt on github:
> https://github.com/SimonRit/RTK/blob/master/utilities/
> SimpleRTK/CMakeLists.txt
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>> try to run it on Linux but I have to upgrade matlab first (I think python
>> calls are available starting with Matlab 2014).
>> Simon
>>
>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Dear Simon
>>>
>>> This look very interesting! Which platform did you successfully execute
>>> this on?
>>> I will give it a try at once (on windows) and let you know if I run into
>>> any problems.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Dear RTK users,
>>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>>> it seems to work well:
>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>>> know if you think otherwise.
>>>> Future works include a simple installation mechanism for pre-compiled
>>>> SimpleRTK libraries. We'll keep you posted!
>>>> Simon
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 01:33:46 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 07:33:46 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
Message-ID: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>

I'm not an msvc specialist but your first line suggests that you have 
pasted only part of the log:

20>  Done Building Project 
"C:\Users\aplb\Work\RTK\RTK1.2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" 
(default targets) -- FAILED.

What you need to find out is why this build failed. If the build fails, 
the linking cannot work.
Cheers,
Simon

On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
> I did a complete rebuild, and here is the end of the output: 
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that 
> I'm trying to compile the version I just pulled from git earlier 
> today, since the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     SimpleRTKCommon is a library generated when compiling. Don't you
>     have another error before that which explains why it did not compile?
>     Simon
>
>     On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger
>     <bottiger at gmail.com <mailto:bottiger at gmail.com>> wrote:
>
>         Hi again.
>
>         I've been trying to get it working. However, I did run into
>         some problems compiling SimpleRTK. The main issue seems to be
>         that it depends on SimpleRTKCommon - which I do not have.
>
>         Here is the last few lines from VS2013
>
>         > 5>LINK : fatal error LNK1181: cannot open input file
>         '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>         [C:\Users\aplb\Work\RTK\RTK1.2-
>         > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>         > 5>
>         > 5>      0 Warning(s)
>         > 5>      2 Error(s)
>         > 5>
>         > 5>  Time Elapsed 00:00:25.26
>         > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0
>         skipped ==========
>
>         I'm not quite sure what is going on, because the only
>         reference I can find to SimpleRTKCommon is the CMakeLists.txt
>         on github:
>         https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt
>         <https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt>
>
>         best
>
>         Arvid
>
>         On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit
>         <simon.rit at creatis.insa-lyon.fr
>         <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>             The latest MacOS. It's nice if you can test it on other
>             platforms, I'll try to run it on Linux but I have to
>             upgrade matlab first (I think python calls are available
>             starting with Matlab 2014).
>             Simon
>
>             On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen
>             B?ttiger <bottiger at gmail.com <mailto:bottiger at gmail.com>>
>             wrote:
>
>                 Dear Simon
>
>                 This look very interesting! Which platform did you
>                 successfully execute this on?
>                 I will give it a try at once (on windows) and let you
>                 know if I run into any problems.
>
>                 best
>
>                 Arvid
>
>                 On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit
>                 <simon.rit at creatis.insa-lyon.fr
>                 <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>                     Dear RTK users,
>                     I have quickly tested calling the SimpleRTK python
>                     lib from Matlab and it seems to work well:
>                     http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>                     <http://wiki.openrtk.org/index.php/SimpleRTK#Matlab>
>                     Therefore, I don't think we have to work on Matlab
>                     wrappings but let us know if you think otherwise.
>                     Future works include a simple installation
>                     mechanism for pre-compiled SimpleRTK libraries.
>                     We'll keep you posted!
>                     Simon
>
>                     _______________________________________________
>                     Rtk-users mailing list
>                     Rtk-users at public.kitware.com
>                     <mailto:Rtk-users at public.kitware.com>
>                     http://public.kitware.com/mailman/listinfo/rtk-users
>                     <http://public.kitware.com/mailman/listinfo/rtk-users>
>
>
>
>
>
>

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From bottiger at gmail.com  Tue Sep 20 08:17:35 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Tue, 20 Sep 2016 14:17:35 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
Message-ID: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>

Hi again.

I understand, but could you please help me get in contact with the person
who knows something about the windows build (if any), I think there is
something wrong.

I have been investigating the build problems I had and found that in the
sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
opened it up and found the projects which I had problems building:
"SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.

When I then tried to build SimpleRTKCommon manually it just compiled
without any problems. However, when I followed up by building
"SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
find "SimpleRTKCommon-0.9.lib" - which I just build.

After some more investigation I realized that the SimpleRTKCommon is set to
build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects it
to be a static linked library (LIB). After changing SimpleRTKCommon to be
build as a static library - and changing the output location - I could
build SimpleRTKBasicFilters0.

However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
to a LIB as well I could build SimpleRTKBasicFilters1, then
SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.

I'm unsure if the intention is to build them as static or dynamic
libraries, but in any case the current build configuration doesn't work -
on my setup at least.

However, I should note than for some reason the "lua5" project did build
successfully out of the box. Whatever it does differently works.

best

Arvid



On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> I'm not an msvc specialist but your first line suggests that you have
> pasted only part of the log:
>
> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.
> 2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
> What you need to find out is why this build failed. If the build fails,
> the linking cannot work.
> Cheers,
> Simon
>
>
> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>
> I did a complete rebuild, and here is the end of the output:
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that I'm
> trying to compile the version I just pulled from git earlier today, since
> the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> SimpleRTKCommon is a library generated when compiling. Don't you have
>> another error before that which explains why it did not compile?
>> Simon
>>
>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Hi again.
>>>
>>> I've been trying to get it working. However, I did run into some
>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>> SimpleRTKCommon - which I do not have.
>>>
>>> Here is the last few lines from VS2013
>>>
>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>> > 5>
>>> > 5>      0 Warning(s)
>>> > 5>      2 Error(s)
>>> > 5>
>>> > 5>  Time Elapsed 00:00:25.26
>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>> ==========
>>>
>>> I'm not quite sure what is going on, because the only reference I can
>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>> RTK/CMakeLists.txt
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>>>> try to run it on Linux but I have to upgrade matlab first (I think python
>>>> calls are available starting with Matlab 2014).
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Dear Simon
>>>>>
>>>>> This look very interesting! Which platform did you successfully
>>>>> execute this on?
>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>> into any problems.
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Dear RTK users,
>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>> and it seems to work well:
>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>> us know if you think otherwise.
>>>>>> Future works include a simple installation mechanism for pre-compiled
>>>>>> SimpleRTK libraries. We'll keep you posted!
>>>>>> Simon
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 10:19:20 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 16:19:20 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
Message-ID: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>

Hi,
Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
I can't solve your problem but Kitware is going to look into an upgrade of
SimpleRTK in the coming days, I'll ask them if they know what is the issue.
If you look here:
http://my.cdash.org/viewNotes.php?buildid=1052065
this is a nightly build of SimpleRTK on Windows and it seems to work. I
don't see why it wouldn't work for you.
Simon

On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I understand, but could you please help me get in contact with the person
> who knows something about the windows build (if any), I think there is
> something wrong.
>
> I have been investigating the build problems I had and found that in the
> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
> opened it up and found the projects which I had problems building:
> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>
> When I then tried to build SimpleRTKCommon manually it just compiled
> without any problems. However, when I followed up by building
> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
> find "SimpleRTKCommon-0.9.lib" - which I just build.
>
> After some more investigation I realized that the SimpleRTKCommon is set
> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
> it to be a static linked library (LIB). After changing SimpleRTKCommon to
> be build as a static library - and changing the output location - I could
> build SimpleRTKBasicFilters0.
>
> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
> to a LIB as well I could build SimpleRTKBasicFilters1, then
> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>
> I'm unsure if the intention is to build them as static or dynamic
> libraries, but in any case the current build configuration doesn't work -
> on my setup at least.
>
> However, I should note than for some reason the "lua5" project did build
> successfully out of the box. Whatever it does differently works.
>
> best
>
> Arvid
>
>
>
> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> I'm not an msvc specialist but your first line suggests that you have
>> pasted only part of the log:
>>
>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
>> What you need to find out is why this build failed. If the build fails,
>> the linking cannot work.
>> Cheers,
>> Simon
>>
>>
>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>
>> I did a complete rebuild, and here is the end of the output:
>> http://pastebin.com/hvQ33WWg
>>
>> I have to admit I'm not sure what to make of it. I should note that I'm
>> trying to compile the version I just pulled from git earlier today, since
>> the other version I normally work with is really old.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>> another error before that which explains why it did not compile?
>>> Simon
>>>
>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>> bottiger at gmail.com> wrote:
>>>
>>>> Hi again.
>>>>
>>>> I've been trying to get it working. However, I did run into some
>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>> SimpleRTKCommon - which I do not have.
>>>>
>>>> Here is the last few lines from VS2013
>>>>
>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>> > 5>
>>>> > 5>      0 Warning(s)
>>>> > 5>      2 Error(s)
>>>> > 5>
>>>> > 5>  Time Elapsed 00:00:25.26
>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>> ==========
>>>>
>>>> I'm not quite sure what is going on, because the only reference I can
>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>> RTK/CMakeLists.txt
>>>>
>>>> best
>>>>
>>>> Arvid
>>>>
>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>> python calls are available starting with Matlab 2014).
>>>>> Simon
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>> bottiger at gmail.com> wrote:
>>>>>
>>>>>> Dear Simon
>>>>>>
>>>>>> This look very interesting! Which platform did you successfully
>>>>>> execute this on?
>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>> into any problems.
>>>>>>
>>>>>> best
>>>>>>
>>>>>> Arvid
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>
>>>>>>> Dear RTK users,
>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>> and it seems to work well:
>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>>> us know if you think otherwise.
>>>>>>> Future works include a simple installation mechanism for
>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>> Simon
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 02:40:50 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 08:40:50 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
Message-ID: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>

Dear RTK users,
RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
been released, about 7 months after RTK v1.2.0.

Release notes :
- Style updated (follow more closely latest ITK guidelines).
- Started using Travis CI, github pull requests should now be used for code
submission.
- New pre-processing functionalities:
  * CUDA polynomial gain correction,
  * scatter glare correction,
  * lag correction,
  * idark option,
  * removed threshold to positive values after i0 LUT.
- Improved CUDA forward and backprojection speed using projection slabs.
- Added motion-compensated forward and back projection operators in CUDA,
in both 3D and 4D.
- Added the rtkregularizedconjugategradient application, which performs 3D
regularized reconstruction by conjugate gradient + optional regularizations
(Positivity, TV, Wavelets).
- Made the rtkfourdrooster, rtkmcrooster and rtkregularizedconjugategradient
fully modular. Each regularization step can be made active or inactive.
- Added a filter to minimize the L0 norm of the temporal gradient (one-D
only).

Many thanks to the contributors, in alphabetical order for this release: Cyril
Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien
Jomier, S?bastien
Brousmiche, Simon Rit

As usual, be aware that we don't focus on releases since we have a public
github repository <http://github.com/SimonRit/RTK> that we try to keep
stable. I still recommend the use of the master HEAD over releases to enjoy
the new RTK developments before their release. We still have a few on-going
projects for which we will use and enhance RTK.

Simon (for the RTK consortium)
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 04:48:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 10:48:26 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
In-Reply-To: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
References: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
Message-ID: <CAF0oig0=5_KPN198JzsGQXDd07Nvw_Ew+qSGhguk0m27s3U-3Q@mail.gmail.com>

Sorry, I had forgotten to change the release number in the source file.
It's been corrected, you will have to move your tag locally or update your
file if you had already downloaded it.
Simon

On Thu, Sep 22, 2016 at 8:40 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
> been released, about 7 months after RTK v1.2.0.
>
> Release notes :
> - Style updated (follow more closely latest ITK guidelines).
> - Started using Travis CI, github pull requests should now be used for
> code submission.
> - New pre-processing functionalities:
>   * CUDA polynomial gain correction,
>   * scatter glare correction,
>   * lag correction,
>   * idark option,
>   * removed threshold to positive values after i0 LUT.
> - Improved CUDA forward and backprojection speed using projection slabs.
> - Added motion-compensated forward and back projection operators in CUDA,
> in both 3D and 4D.
> - Added the rtkregularizedconjugategradient application, which performs
> 3D regularized reconstruction by conjugate gradient + optional
> regularizations (Positivity, TV, Wavelets).
> - Made the rtkfourdrooster, rtkmcrooster and
> rtkregularizedconjugategradient fully modular. Each regularization step
> can be made active or inactive.
> - Added a filter to minimize the L0 norm of the temporal gradient (one-D
> only).
>
> Many thanks to the contributors, in alphabetical order for this release: Cyril
> Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien Jomier, S?bastien
> Brousmiche, Simon Rit
>
> As usual, be aware that we don't focus on releases since we have a public
> github repository <http://github.com/SimonRit/RTK> that we try to keep
> stable. I still recommend the use of the master HEAD over releases to
> enjoy the new RTK developments before their release. We still have a few
> on-going projects for which we will use and enhance RTK.
>
> Simon (for the RTK consortium)
>
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From bottiger at gmail.com  Fri Sep 23 04:29:06 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Fri, 23 Sep 2016 10:29:06 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
 <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
Message-ID: <CANBwxwEvaUrvd1X=74g=V2JmDwtrQKFDtyUdAZJn5CRCBCkb8g@mail.gmail.com>

Hi again.

I've been spending some more time with this, and feel I learned a little
bit more. I have now tested this on several machines with several compiler
versions (more or less all of them) and serveral cmake versions - all with
Windows 7.

I can actually reproduce the successful build you linked to, but this can
only be done if you do not include any of the language wrappings, like in
the build you linked to. Enable any of them, and the build will break. (see
attachment)

I suspect it must have been working in the past, but since none of them are
included in your test there have been a breaking change, and none of them
work anymore.

I am still trying to tweak then projects manually to build SimpleRTK with
some sort of language support, but still without any luck.

best

Arvid

On Tue, Sep 20, 2016 at 4:19 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
> at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
> I can't solve your problem but Kitware is going to look into an upgrade of
> SimpleRTK in the coming days, I'll ask them if they know what is the issue.
> If you look here:
> http://my.cdash.org/viewNotes.php?buildid=1052065
> this is a nightly build of SimpleRTK on Windows and it seems to work. I
> don't see why it wouldn't work for you.
> Simon
>
> On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Hi again.
>>
>> I understand, but could you please help me get in contact with the person
>> who knows something about the windows build (if any), I think there is
>> something wrong.
>>
>> I have been investigating the build problems I had and found that in the
>> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
>> opened it up and found the projects which I had problems building:
>> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>>
>> When I then tried to build SimpleRTKCommon manually it just compiled
>> without any problems. However, when I followed up by building
>> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
>> find "SimpleRTKCommon-0.9.lib" - which I just build.
>>
>> After some more investigation I realized that the SimpleRTKCommon is set
>> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
>> it to be a static linked library (LIB). After changing SimpleRTKCommon to
>> be build as a static library - and changing the output location - I could
>> build SimpleRTKBasicFilters0.
>>
>> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing
>> that to a LIB as well I could build SimpleRTKBasicFilters1, then
>> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>>
>> I'm unsure if the intention is to build them as static or dynamic
>> libraries, but in any case the current build configuration doesn't work -
>> on my setup at least.
>>
>> However, I should note than for some reason the "lua5" project did build
>> successfully out of the box. Whatever it does differently works.
>>
>> best
>>
>> Arvid
>>
>>
>>
>> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> I'm not an msvc specialist but your first line suggests that you have
>>> pasted only part of the log:
>>>
>>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) --
>>> FAILED.
>>> What you need to find out is why this build failed. If the build fails,
>>> the linking cannot work.
>>> Cheers,
>>> Simon
>>>
>>>
>>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>>
>>> I did a complete rebuild, and here is the end of the output:
>>> http://pastebin.com/hvQ33WWg
>>>
>>> I have to admit I'm not sure what to make of it. I should note that I'm
>>> trying to compile the version I just pulled from git earlier today, since
>>> the other version I normally work with is really old.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>>> another error before that which explains why it did not compile?
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Hi again.
>>>>>
>>>>> I've been trying to get it working. However, I did run into some
>>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>>> SimpleRTKCommon - which I do not have.
>>>>>
>>>>> Here is the last few lines from VS2013
>>>>>
>>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>>> > 5>
>>>>> > 5>      0 Warning(s)
>>>>> > 5>      2 Error(s)
>>>>> > 5>
>>>>> > 5>  Time Elapsed 00:00:25.26
>>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>>> ==========
>>>>>
>>>>> I'm not quite sure what is going on, because the only reference I can
>>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>>> RTK/CMakeLists.txt
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>>> python calls are available starting with Matlab 2014).
>>>>>> Simon
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>>> bottiger at gmail.com> wrote:
>>>>>>
>>>>>>> Dear Simon
>>>>>>>
>>>>>>> This look very interesting! Which platform did you successfully
>>>>>>> execute this on?
>>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>>> into any problems.
>>>>>>>
>>>>>>> best
>>>>>>>
>>>>>>> Arvid
>>>>>>>
>>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Dear RTK users,
>>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>>> and it seems to work well:
>>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but
>>>>>>>> let us know if you think otherwise.
>>>>>>>> Future works include a simple installation mechanism for
>>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
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From ajbatkinson at gmail.com  Wed Sep 28 08:11:12 2016
From: ajbatkinson at gmail.com (Abby Bryce Atkinson)
Date: Wed, 28 Sep 2016 13:11:12 +0100
Subject: [Rtk-users] 4DROOSTERReconstruction Example
Message-ID: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>

Hi,

I am trying to work through the 4DROOSTER example using the POPI patient
images (
http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) but
I am getting stuck when extracting the respiratory signal using the
amsterdam shroud.

I receive this error:


C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
--path .\Projections\ ^
More?                    --regexp '.*.his' ^
More?                    --output shroud.mha ^
More?                    --unsharp 650
ExceptionObject caught with writer->Update() in file
C:\RTK\applications\rtkamst
erdamshroud\rtkamsterdamshroud.cxx line 91

itk::ExceptionObject (0030E9E0)
Location: "void __thiscall itk::ImageFileWriter<class itk::Image<double,2>
>::Wr
ite(void)"
File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
Line: 284
Description: itk::ERROR: ImageFileWriter(03670318): Largest possible region
does
 not fully contain requested paste IO regionPaste IO region: ImageIORegion
(0030
EDD4)
  Dimension: 2
  Index: 0 0
  Size: 0 0
Largest possible region: ImageRegion (0030EE70)
  Dimension: 2
  Index: [0, 0]
  Size: [0, 0]


Can anyone help with a solution/tell me what I am doing wrong please?

Thanks,

Abby
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From simon.rit at creatis.insa-lyon.fr  Wed Sep 28 12:49:32 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 28 Sep 2016 18:49:32 +0200
Subject: [Rtk-users] 4DROOSTERReconstruction Example
In-Reply-To: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
References: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
Message-ID: <e23fc5ec-f7b4-846c-e349-f07564e2da8a@creatis.insa-lyon.fr>

Hi,

My guess is that the software does not find the projections. I would add 
the --verbose option and check that you actually input some projections. 
If not, I guess there is an issue with the path or the regexp in your 
command line.

Simon

On 28/09/2016 14:11, Abby Bryce Atkinson wrote:
> Hi,
>
> I am trying to work through the 4DROOSTER example using the POPI 
> patient images 
> (http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) 
> but I am getting stuck when extracting the respiratory signal using 
> the amsterdam shroud.
>
> I receive this error:
>
>
> C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
> --path .\Projections\ ^
> More?                    --regexp '.*.his' ^
> More?                    --output shroud.mha ^
> More?                    --unsharp 650
> ExceptionObject caught with writer->Update() in file 
> C:\RTK\applications\rtkamst
> erdamshroud\rtkamsterdamshroud.cxx line 91
>
> itk::ExceptionObject (0030E9E0)
> Location: "void __thiscall itk::ImageFileWriter<class 
> itk::Image<double,2> >::Wr
> ite(void)"
> File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
> Line: 284
> Description: itk::ERROR: ImageFileWriter(03670318): Largest possible 
> region does
>  not fully contain requested paste IO regionPaste IO region: 
> ImageIORegion (0030
> EDD4)
>   Dimension: 2
>   Index: 0 0
>   Size: 0 0
> Largest possible region: ImageRegion (0030EE70)
>   Dimension: 2
>   Index: [0, 0]
>   Size: [0, 0]
>
>
> Can anyone help with a solution/tell me what I am doing wrong please?
>
> Thanks,
>
> Abby
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users

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From signabdm at gmail.com  Mon Sep 12 06:58:59 2016
From: signabdm at gmail.com (Valeriy Signatulin)
Date: Mon, 12 Sep 2016 16:58:59 +0600
Subject: [Rtk-users] rotation of detector plane
Message-ID: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>

Hello RTK users.
Is it possible to specify rotation of detector plane in RTK ? (in
rtksimulategeom for example) If not, what is the best way to code this ?
By rotation of detector plane i mean twist, tilt, skew around the normal of
the detector as described in
http://www.ndt.net/article/v10n09/yisun/yisun.pdf page 6.
I'm trying to write the geometry calibration method described in this
article in RTK and i need to simulate these rotations to check the results.
Thanks.
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 12 08:40:31 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 12 Sep 2016 14:40:31 +0200
Subject: [Rtk-users] rotation of detector plane
In-Reply-To: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
References: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
Message-ID: <CAF0oig0C3zFcAaAhWHV9g+UY02i7cws7OU-7r2YadyAt3TH5GA@mail.gmail.com>

Hi,
You can do any rotation with RTK. The rotation is described 3 Euler angles,
see the geometry doc <http://www.openrtk.org/Doxygen/geometry.pdf>. From
the command line, that would be the --in_angle and out_angle that allow you
to modify the other angles than the standard angle for the position along
the circular rotation (GantryAngle). If you want to modify it per
projection, that's possible using C++ or Python code (AddProjection
<http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
method).
Good luck,
Simon

On Mon, Sep 12, 2016 at 12:58 PM, Valeriy Signatulin <signabdm at gmail.com>
wrote:

> Hello RTK users.
> Is it possible to specify rotation of detector plane in RTK ? (in
> rtksimulategeom for example) If not, what is the best way to code this ?
> By rotation of detector plane i mean twist, tilt, skew around the normal
> of the detector as described in http://www.ndt.net/article/
> v10n09/yisun/yisun.pdf page 6.
> I'm trying to write the geometry calibration method described in this
> article in RTK and i need to simulate these rotations to check the results.
> Thanks.
>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From andreasg at phys.au.dk  Tue Sep 13 13:06:46 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Tue, 13 Sep 2016 19:06:46 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
Message-ID: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>

Dear RTK experts,

I am reconstructing Varian ProBeam projections of the Xim image format. I
have written the reader myself - very similar to the Hnd one already
available with RTK.
Links to my fork: [XimReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkXimImageIO.cxx>,
XMLReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamXMLFileReader.cxx>,
GeometryReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamGeometryReader.cxx>
]

The reader apparently works (Images and angles displays as expected in UI),
however when reconstructing with a regular FDK* I get a reconstructed image
that is smeared out around the high and low density areas *[see attached
image]

I'm using half arc, full fan images with no bow-tie filter from Scripps
(~520 projections). Fixed detector and source (offset=0) with SID=2m,
SDD=3m.

*For the Hnd projections the reconstruction works perfectly (Same algorithm
<https://github.com/agravgaard/cbctrecon/blob/master/cbctrecon.cpp#L2726>).*
The reconstruction of the Xim projections performed on Varian software
works perfectly.

Without the Parker Short Scan Filter the first and last projections creates
streaks across the reconstruction as if they were way too bright.
If the first few projections are excluded, the following projection will
act the same way.

The projections are corrected for beam hardening and all the projections
have the expected attenuation.
No "smearing" filters (like median) is used, and iterative reconstruction
makes the same artifacts.

Setting the value of the first and last projection to zero has the same
effect as excluding. Changing the ramp filter only changes noise, not the
artifacts.

*Have any of you had a similar problem? *Am I missing something?
Any suggestions are welcome I'm running out of ideas.

Best regards
Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 13 16:18:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 13 Sep 2016 22:18:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
Message-ID: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>

Hi,
I have almost never worked with Varian data but it looks like a
geometry problem. Maybe the problem comes from a bad ordering of the
projections which results in assigning a bad geometry to each
projection. How did you name your projections? Maybe check that the
order matches that of the RTK geometry file. Otherwise, there might be
an issue in the creation of the geometry file itself.
All this sounds good, happy bug hunt and don't hesitate to share your
code when you feel it's ready.
Simon

On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
<andreasg at phys.au.dk> wrote:
> Dear RTK experts,
>
> I am reconstructing Varian ProBeam projections of the Xim image format. I
> have written the reader myself - very similar to the Hnd one already
> available with RTK.
> Links to my fork: [XimReader, XMLReader, GeometryReader]
>
> The reader apparently works (Images and angles displays as expected in UI),
> however when reconstructing with a regular FDK I get a reconstructed image
> that is smeared out around the high and low density areas [see attached
> image]
>
> I'm using half arc, full fan images with no bow-tie filter from Scripps
> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
> SDD=3m.
>
> For the Hnd projections the reconstruction works perfectly (Same algorithm).
> The reconstruction of the Xim projections performed on Varian software works
> perfectly.
>
> Without the Parker Short Scan Filter the first and last projections creates
> streaks across the reconstruction as if they were way too bright.
> If the first few projections are excluded, the following projection will act
> the same way.
>
> The projections are corrected for beam hardening and all the projections
> have the expected attenuation.
> No "smearing" filters (like median) is used, and iterative reconstruction
> makes the same artifacts.
>
> Setting the value of the first and last projection to zero has the same
> effect as excluding. Changing the ramp filter only changes noise, not the
> artifacts.
>
> Have any of you had a similar problem? Am I missing something?
> Any suggestions are welcome I'm running out of ideas.
>
> Best regards
> Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>


From cyril.mory at creatis.insa-lyon.fr  Wed Sep 14 03:10:42 2016
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 14 Sep 2016 09:10:42 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
Message-ID: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>

One suggestion since it works with the Hnd projections:
You can run rtkprojections twice (with the Hnd projections, then with 
Xim projections) and output two projection stack files and two geometry 
files, then compare the projection stack files by subtracting one to the 
other (with SimpleRTK or clitk) and the geometry files with diff. If 
they are identical, then I do not see any reason why the reconstructions 
should be different, so my guess is that you will find differences.

On 09/13/2016 10:18 PM, Simon Rit wrote:
> Hi,
> I have almost never worked with Varian data but it looks like a
> geometry problem. Maybe the problem comes from a bad ordering of the
> projections which results in assigning a bad geometry to each
> projection. How did you name your projections? Maybe check that the
> order matches that of the RTK geometry file. Otherwise, there might be
> an issue in the creation of the geometry file itself.
> All this sounds good, happy bug hunt and don't hesitate to share your
> code when you feel it's ready.
> Simon
>
> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
> <andreasg at phys.au.dk> wrote:
>> Dear RTK experts,
>>
>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>> have written the reader myself - very similar to the Hnd one already
>> available with RTK.
>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>
>> The reader apparently works (Images and angles displays as expected in UI),
>> however when reconstructing with a regular FDK I get a reconstructed image
>> that is smeared out around the high and low density areas [see attached
>> image]
>>
>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>> SDD=3m.
>>
>> For the Hnd projections the reconstruction works perfectly (Same algorithm).
>> The reconstruction of the Xim projections performed on Varian software works
>> perfectly.
>>
>> Without the Parker Short Scan Filter the first and last projections creates
>> streaks across the reconstruction as if they were way too bright.
>> If the first few projections are excluded, the following projection will act
>> the same way.
>>
>> The projections are corrected for beam hardening and all the projections
>> have the expected attenuation.
>> No "smearing" filters (like median) is used, and iterative reconstruction
>> makes the same artifacts.
>>
>> Setting the value of the first and last projection to zero has the same
>> effect as excluding. Changing the ramp filter only changes noise, not the
>> artifacts.
>>
>> Have any of you had a similar problem? Am I missing something?
>> Any suggestions are welcome I'm running out of ideas.
>>
>> Best regards
>> Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>



From andreasg at phys.au.dk  Fri Sep 16 08:56:34 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 14:56:34 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
Message-ID: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>

Thanks for the suggestions, Simon and Cyril!

I have been carefully looking though the geometry and from what I
understand of the transformations matrices, the geometry looks correct/(as
expected).

HOWEVER: I found out that the reason for the Hnd to behave differently were
because had used half-fan scans (full-arc).
When I used a full-fan (half-arc) scan of Hnd projections the same
artifacts occurs!

Are there other (built-in) means of improving half-arc scans, than the
parker short scan filter?

Parker short scan does a decent job, but the result is still far from the
quality of the Varian software reconstruction at least for the CatPhan.

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:

> One suggestion since it works with the Hnd projections:
> You can run rtkprojections twice (with the Hnd projections, then with Xim
> projections) and output two projection stack files and two geometry files,
> then compare the projection stack files by subtracting one to the other
> (with SimpleRTK or clitk) and the geometry files with diff. If they are
> identical, then I do not see any reason why the reconstructions should be
> different, so my guess is that you will find differences.
>
>
> On 09/13/2016 10:18 PM, Simon Rit wrote:
>
>> Hi,
>> I have almost never worked with Varian data but it looks like a
>> geometry problem. Maybe the problem comes from a bad ordering of the
>> projections which results in assigning a bad geometry to each
>> projection. How did you name your projections? Maybe check that the
>> order matches that of the RTK geometry file. Otherwise, there might be
>> an issue in the creation of the geometry file itself.
>> All this sounds good, happy bug hunt and don't hesitate to share your
>> code when you feel it's ready.
>> Simon
>>
>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>> <andreasg at phys.au.dk> wrote:
>>
>>> Dear RTK experts,
>>>
>>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>>> have written the reader myself - very similar to the Hnd one already
>>> available with RTK.
>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>
>>> The reader apparently works (Images and angles displays as expected in
>>> UI),
>>> however when reconstructing with a regular FDK I get a reconstructed
>>> image
>>> that is smeared out around the high and low density areas [see attached
>>> image]
>>>
>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>> SDD=3m.
>>>
>>> For the Hnd projections the reconstruction works perfectly (Same
>>> algorithm).
>>> The reconstruction of the Xim projections performed on Varian software
>>> works
>>> perfectly.
>>>
>>> Without the Parker Short Scan Filter the first and last projections
>>> creates
>>> streaks across the reconstruction as if they were way too bright.
>>> If the first few projections are excluded, the following projection will
>>> act
>>> the same way.
>>>
>>> The projections are corrected for beam hardening and all the projections
>>> have the expected attenuation.
>>> No "smearing" filters (like median) is used, and iterative reconstruction
>>> makes the same artifacts.
>>>
>>> Setting the value of the first and last projection to zero has the same
>>> effect as excluding. Changing the ramp filter only changes noise, not the
>>> artifacts.
>>>
>>> Have any of you had a similar problem? Am I missing something?
>>> Any suggestions are welcome I'm running out of ideas.
>>>
>>> Best regards
>>> Andreas
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Sep 16 10:13:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 16 Sep 2016 16:13:26 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
Message-ID: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>

Hi,
You can try any iterative reconstruction, they can also handle short scans.
Start with a few iterations of rtksart or rtkconjugategradient. However,
the nature of the artifacts indicate more a problem in the geometry in my
opinion. I have seen such errors when, for example, rotating in the wrong
direction. I can have a look if you share the dataset.
Cheers,
Simon

On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the suggestions, Simon and Cyril!
>
> I have been carefully looking though the geometry and from what I
> understand of the transformations matrices, the geometry looks correct/(as
> expected).
>
> HOWEVER: I found out that the reason for the Hnd to behave differently
> were because had used half-fan scans (full-arc).
> When I used a full-fan (half-arc) scan of Hnd projections the same
> artifacts occurs!
>
> Are there other (built-in) means of improving half-arc scans, than the
> parker short scan filter?
>
> Parker short scan does a decent job, but the result is still far from the
> quality of the Varian software reconstruction at least for the CatPhan.
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>
>> One suggestion since it works with the Hnd projections:
>> You can run rtkprojections twice (with the Hnd projections, then with Xim
>> projections) and output two projection stack files and two geometry files,
>> then compare the projection stack files by subtracting one to the other
>> (with SimpleRTK or clitk) and the geometry files with diff. If they are
>> identical, then I do not see any reason why the reconstructions should be
>> different, so my guess is that you will find differences.
>>
>>
>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>
>>> Hi,
>>> I have almost never worked with Varian data but it looks like a
>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>> projections which results in assigning a bad geometry to each
>>> projection. How did you name your projections? Maybe check that the
>>> order matches that of the RTK geometry file. Otherwise, there might be
>>> an issue in the creation of the geometry file itself.
>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>> code when you feel it's ready.
>>> Simon
>>>
>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>> <andreasg at phys.au.dk> wrote:
>>>
>>>> Dear RTK experts,
>>>>
>>>> I am reconstructing Varian ProBeam projections of the Xim image format.
>>>> I
>>>> have written the reader myself - very similar to the Hnd one already
>>>> available with RTK.
>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>
>>>> The reader apparently works (Images and angles displays as expected in
>>>> UI),
>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>> image
>>>> that is smeared out around the high and low density areas [see attached
>>>> image]
>>>>
>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>> SDD=3m.
>>>>
>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>> algorithm).
>>>> The reconstruction of the Xim projections performed on Varian software
>>>> works
>>>> perfectly.
>>>>
>>>> Without the Parker Short Scan Filter the first and last projections
>>>> creates
>>>> streaks across the reconstruction as if they were way too bright.
>>>> If the first few projections are excluded, the following projection
>>>> will act
>>>> the same way.
>>>>
>>>> The projections are corrected for beam hardening and all the projections
>>>> have the expected attenuation.
>>>> No "smearing" filters (like median) is used, and iterative
>>>> reconstruction
>>>> makes the same artifacts.
>>>>
>>>> Setting the value of the first and last projection to zero has the same
>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>> the
>>>> artifacts.
>>>>
>>>> Have any of you had a similar problem? Am I missing something?
>>>> Any suggestions are welcome I'm running out of ideas.
>>>>
>>>> Best regards
>>>> Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> N?rrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     andreasg at phys.au.dk
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From andreasg at phys.au.dk  Fri Sep 16 16:37:43 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 22:37:43 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
Message-ID: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>

Thanks for the fast response Simon!

I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
right all along!
I just didn't get why it makes a difference. I think I do now, as the
resulting image was flipped upside down and not left/right as I expected.
[attached]

The reconstruction is significantly better, I'll look into what should be
included in the reader and what I should keep in my program to keep
conformity with the other readers. Then I'll create a pull request.

Just for the purpose of others hitting the same or a similar bug, I also
attempted:
I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
back/forward projection, *but with no* significant improvement [attached]

And:
If you want you can download the data set from: [Dropbox link to 460MB zip
<https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep it
up as long as Dropbox allows me)] Only the Acquisitions/subfolder is used
along with the Scan.xml (Calibrations folder may be used in the future in
my program, but I'm not sure if you can rely on the existence of the
content).

A MatLab XimReader is available: link
<https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
available from Varian bitbucket along a with a python version and a
C#->matlab plugin
<https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). Otherwise
my fork with the RTK-style reader is available from the same repository (I
have also added Hnc support, thanks to the Geoff Hugo fork, so bzip2 is a
new dependancy).

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:

> Hi,
> You can try any iterative reconstruction, they can also handle short
> scans. Start with a few iterations of rtksart or rtkconjugategradient.
> However, the nature of the artifacts indicate more a problem in the
> geometry in my opinion. I have seen such errors when, for example, rotating
> in the wrong direction. I can have a look if you share the dataset.
> Cheers,
> Simon
>
> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
> andreasg at phys.au.dk> wrote:
>
>> Thanks for the suggestions, Simon and Cyril!
>>
>> I have been carefully looking though the geometry and from what I
>> understand of the transformations matrices, the geometry looks correct/(as
>> expected).
>>
>> HOWEVER: I found out that the reason for the Hnd to behave differently
>> were because had used half-fan scans (full-arc).
>> When I used a full-fan (half-arc) scan of Hnd projections the same
>> artifacts occurs!
>>
>> Are there other (built-in) means of improving half-arc scans, than the
>> parker short scan filter?
>>
>> Parker short scan does a decent job, but the result is still far from the
>> quality of the Varian software reconstruction at least for the CatPhan.
>>
>> Best regards
>> Andreas
>>
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>>
>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>
>>> One suggestion since it works with the Hnd projections:
>>> You can run rtkprojections twice (with the Hnd projections, then with
>>> Xim projections) and output two projection stack files and two geometry
>>> files, then compare the projection stack files by subtracting one to the
>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>> are identical, then I do not see any reason why the reconstructions should
>>> be different, so my guess is that you will find differences.
>>>
>>>
>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>
>>>> Hi,
>>>> I have almost never worked with Varian data but it looks like a
>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>> projections which results in assigning a bad geometry to each
>>>> projection. How did you name your projections? Maybe check that the
>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>> an issue in the creation of the geometry file itself.
>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>> code when you feel it's ready.
>>>> Simon
>>>>
>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>> <andreasg at phys.au.dk> wrote:
>>>>
>>>>> Dear RTK experts,
>>>>>
>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>> format. I
>>>>> have written the reader myself - very similar to the Hnd one already
>>>>> available with RTK.
>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>
>>>>> The reader apparently works (Images and angles displays as expected in
>>>>> UI),
>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>> image
>>>>> that is smeared out around the high and low density areas [see attached
>>>>> image]
>>>>>
>>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>> SDD=3m.
>>>>>
>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>> algorithm).
>>>>> The reconstruction of the Xim projections performed on Varian software
>>>>> works
>>>>> perfectly.
>>>>>
>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>> creates
>>>>> streaks across the reconstruction as if they were way too bright.
>>>>> If the first few projections are excluded, the following projection
>>>>> will act
>>>>> the same way.
>>>>>
>>>>> The projections are corrected for beam hardening and all the
>>>>> projections
>>>>> have the expected attenuation.
>>>>> No "smearing" filters (like median) is used, and iterative
>>>>> reconstruction
>>>>> makes the same artifacts.
>>>>>
>>>>> Setting the value of the first and last projection to zero has the same
>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>> the
>>>>> artifacts.
>>>>>
>>>>> Have any of you had a similar problem? Am I missing something?
>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>
>>>>> Best regards
>>>>> Andreas
>>>>>
>>>>> __________________________________
>>>>>
>>>>> Andreas Gravgaard Andersen
>>>>>
>>>>> Department of Oncology,
>>>>>
>>>>> Aarhus University Hospital
>>>>>
>>>>> N?rrebrogade 44,
>>>>>
>>>>> 8000, Aarhus C
>>>>>
>>>>> Mail:     andreasg at phys.au.dk
>>>>>
>>>>> Cell:      +45 3165 8140
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 03:26:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 09:26:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
 <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
Message-ID: <CAF0oig2TSmAsSn=o3aLo6LEFDOSaKRtfknjMer24rcDKJ-0Fqg@mail.gmail.com>

Hi,
Thanks for sharing. There still seems to be some streak artefacts, do you
see the same in the Varian reconstruction?
I'm looking forward to the pull-request, I think we should try to make the
bzip2 optional.
Simon

On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the fast response Simon!
>
> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
> right all along!
> I just didn't get why it makes a difference. I think I do now, as the
> resulting image was flipped upside down and not left/right as I expected.
> [attached]
>
> The reconstruction is significantly better, I'll look into what should be
> included in the reader and what I should keep in my program to keep
> conformity with the other readers. Then I'll create a pull request.
>
> Just for the purpose of others hitting the same or a similar bug, I also
> attempted:
> I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
> back/forward projection, *but with no* significant improvement [attached]
>
> And:
> If you want you can download the data set from: [Dropbox link to 460MB zip
> <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep
> it up as long as Dropbox allows me)] Only the Acquisitions/subfolder is
> used along with the Scan.xml (Calibrations folder may be used in the future
> in my program, but I'm not sure if you can rely on the existence of the
> content).
>
> A MatLab XimReader is available: link
> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
> available from Varian bitbucket along a with a python version and a
> C#->matlab plugin
> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>).
> Otherwise my fork with the RTK-style reader is available from the same
> repository (I have also added Hnc support, thanks to the Geoff Hugo fork,
> so bzip2 is a new dependancy).
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> Hi,
>> You can try any iterative reconstruction, they can also handle short
>> scans. Start with a few iterations of rtksart or rtkconjugategradient.
>> However, the nature of the artifacts indicate more a problem in the
>> geometry in my opinion. I have seen such errors when, for example, rotating
>> in the wrong direction. I can have a look if you share the dataset.
>> Cheers,
>> Simon
>>
>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
>> andreasg at phys.au.dk> wrote:
>>
>>> Thanks for the suggestions, Simon and Cyril!
>>>
>>> I have been carefully looking though the geometry and from what I
>>> understand of the transformations matrices, the geometry looks correct/(as
>>> expected).
>>>
>>> HOWEVER: I found out that the reason for the Hnd to behave differently
>>> were because had used half-fan scans (full-arc).
>>> When I used a full-fan (half-arc) scan of Hnd projections the same
>>> artifacts occurs!
>>>
>>> Are there other (built-in) means of improving half-arc scans, than the
>>> parker short scan filter?
>>>
>>> Parker short scan does a decent job, but the result is still far from
>>> the quality of the Varian software reconstruction at least for the CatPhan.
>>>
>>> Best regards
>>> Andreas
>>>
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>>
>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>>
>>>> One suggestion since it works with the Hnd projections:
>>>> You can run rtkprojections twice (with the Hnd projections, then with
>>>> Xim projections) and output two projection stack files and two geometry
>>>> files, then compare the projection stack files by subtracting one to the
>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>>> are identical, then I do not see any reason why the reconstructions should
>>>> be different, so my guess is that you will find differences.
>>>>
>>>>
>>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>>
>>>>> Hi,
>>>>> I have almost never worked with Varian data but it looks like a
>>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>>> projections which results in assigning a bad geometry to each
>>>>> projection. How did you name your projections? Maybe check that the
>>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>>> an issue in the creation of the geometry file itself.
>>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>>> code when you feel it's ready.
>>>>> Simon
>>>>>
>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>>> <andreasg at phys.au.dk> wrote:
>>>>>
>>>>>> Dear RTK experts,
>>>>>>
>>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>>> format. I
>>>>>> have written the reader myself - very similar to the Hnd one already
>>>>>> available with RTK.
>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>>
>>>>>> The reader apparently works (Images and angles displays as expected
>>>>>> in UI),
>>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>>> image
>>>>>> that is smeared out around the high and low density areas [see
>>>>>> attached
>>>>>> image]
>>>>>>
>>>>>> I'm using half arc, full fan images with no bow-tie filter from
>>>>>> Scripps
>>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>>> SDD=3m.
>>>>>>
>>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>>> algorithm).
>>>>>> The reconstruction of the Xim projections performed on Varian
>>>>>> software works
>>>>>> perfectly.
>>>>>>
>>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>>> creates
>>>>>> streaks across the reconstruction as if they were way too bright.
>>>>>> If the first few projections are excluded, the following projection
>>>>>> will act
>>>>>> the same way.
>>>>>>
>>>>>> The projections are corrected for beam hardening and all the
>>>>>> projections
>>>>>> have the expected attenuation.
>>>>>> No "smearing" filters (like median) is used, and iterative
>>>>>> reconstruction
>>>>>> makes the same artifacts.
>>>>>>
>>>>>> Setting the value of the first and last projection to zero has the
>>>>>> same
>>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>>> the
>>>>>> artifacts.
>>>>>>
>>>>>> Have any of you had a similar problem? Am I missing something?
>>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>>
>>>>>> Best regards
>>>>>> Andreas
>>>>>>
>>>>>> __________________________________
>>>>>>
>>>>>> Andreas Gravgaard Andersen
>>>>>>
>>>>>> Department of Oncology,
>>>>>>
>>>>>> Aarhus University Hospital
>>>>>>
>>>>>> N?rrebrogade 44,
>>>>>>
>>>>>> 8000, Aarhus C
>>>>>>
>>>>>> Mail:     andreasg at phys.au.dk
>>>>>>
>>>>>> Cell:      +45 3165 8140
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:05:24 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:05:24 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
Message-ID: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>

Dear RTK users,
I have quickly tested calling the SimpleRTK python lib from Matlab and it
seems to work well:
http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
Therefore, I don't think we have to work on Matlab wrappings but let us
know if you think otherwise.
Future works include a simple installation mechanism for pre-compiled
SimpleRTK libraries. We'll keep you posted!
Simon
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From bottiger at gmail.com  Mon Sep 19 05:14:03 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 11:14:03 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
Message-ID: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>

Dear Simon

This look very interesting! Which platform did you successfully execute
this on?
I will give it a try at once (on windows) and let you know if I run into
any problems.

best

Arvid

On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> I have quickly tested calling the SimpleRTK python lib from Matlab and it
> seems to work well:
> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
> Therefore, I don't think we have to work on Matlab wrappings but let us
> know if you think otherwise.
> Future works include a simple installation mechanism for pre-compiled
> SimpleRTK libraries. We'll keep you posted!
> Simon
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:19:28 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:19:28 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
Message-ID: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>

The latest MacOS. It's nice if you can test it on other platforms, I'll try
to run it on Linux but I have to upgrade matlab first (I think python calls
are available starting with Matlab 2014).
Simon

On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Dear Simon
>
> This look very interesting! Which platform did you successfully execute
> this on?
> I will give it a try at once (on windows) and let you know if I run into
> any problems.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> Dear RTK users,
>> I have quickly tested calling the SimpleRTK python lib from Matlab and it
>> seems to work well:
>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>> Therefore, I don't think we have to work on Matlab wrappings but let us
>> know if you think otherwise.
>> Future works include a simple installation mechanism for pre-compiled
>> SimpleRTK libraries. We'll keep you posted!
>> Simon
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From bottiger at gmail.com  Mon Sep 19 08:30:32 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 14:30:32 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
Message-ID: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>

Hi again.

I've been trying to get it working. However, I did run into some problems
compiling SimpleRTK. The main issue seems to be that it depends on
SimpleRTKCommon - which I do not have.

Here is the last few lines from VS2013

> 5>LINK : fatal error LNK1181: cannot open input file
'..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib' [C:\Users\aplb\Work\RTK\RTK1.2-
> bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> 5>
> 5>      0 Warning(s)
> 5>      2 Error(s)
> 5>
> 5>  Time Elapsed 00:00:25.26
> ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
==========

I'm not quite sure what is going on, because the only reference I can find
to SimpleRTKCommon is the CMakeLists.txt on github:
https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt

best

Arvid

On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> The latest MacOS. It's nice if you can test it on other platforms, I'll
> try to run it on Linux but I have to upgrade matlab first (I think python
> calls are available starting with Matlab 2014).
> Simon
>
> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Dear Simon
>>
>> This look very interesting! Which platform did you successfully execute
>> this on?
>> I will give it a try at once (on windows) and let you know if I run into
>> any problems.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Dear RTK users,
>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>> it seems to work well:
>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>> know if you think otherwise.
>>> Future works include a simple installation mechanism for pre-compiled
>>> SimpleRTK libraries. We'll keep you posted!
>>> Simon
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 12:50:33 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 18:50:33 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
Message-ID: <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>

 SimpleRTKCommon is a library generated when compiling. Don't you have
another error before that which explains why it did not compile?
Simon

On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I've been trying to get it working. However, I did run into some problems
> compiling SimpleRTK. The main issue seems to be that it depends on
> SimpleRTKCommon - which I do not have.
>
> Here is the last few lines from VS2013
>
> > 5>LINK : fatal error LNK1181: cannot open input file '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
> [C:\Users\aplb\Work\RTK\RTK1.2-
> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> > 5>
> > 5>      0 Warning(s)
> > 5>      2 Error(s)
> > 5>
> > 5>  Time Elapsed 00:00:25.26
> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
> ==========
>
> I'm not quite sure what is going on, because the only reference I can find
> to SimpleRTKCommon is the CMakeLists.txt on github:
> https://github.com/SimonRit/RTK/blob/master/utilities/
> SimpleRTK/CMakeLists.txt
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>> try to run it on Linux but I have to upgrade matlab first (I think python
>> calls are available starting with Matlab 2014).
>> Simon
>>
>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Dear Simon
>>>
>>> This look very interesting! Which platform did you successfully execute
>>> this on?
>>> I will give it a try at once (on windows) and let you know if I run into
>>> any problems.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Dear RTK users,
>>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>>> it seems to work well:
>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>>> know if you think otherwise.
>>>> Future works include a simple installation mechanism for pre-compiled
>>>> SimpleRTK libraries. We'll keep you posted!
>>>> Simon
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 01:33:46 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 07:33:46 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
Message-ID: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>

I'm not an msvc specialist but your first line suggests that you have 
pasted only part of the log:

20>  Done Building Project 
"C:\Users\aplb\Work\RTK\RTK1.2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" 
(default targets) -- FAILED.

What you need to find out is why this build failed. If the build fails, 
the linking cannot work.
Cheers,
Simon

On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
> I did a complete rebuild, and here is the end of the output: 
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that 
> I'm trying to compile the version I just pulled from git earlier 
> today, since the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     SimpleRTKCommon is a library generated when compiling. Don't you
>     have another error before that which explains why it did not compile?
>     Simon
>
>     On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger
>     <bottiger at gmail.com <mailto:bottiger at gmail.com>> wrote:
>
>         Hi again.
>
>         I've been trying to get it working. However, I did run into
>         some problems compiling SimpleRTK. The main issue seems to be
>         that it depends on SimpleRTKCommon - which I do not have.
>
>         Here is the last few lines from VS2013
>
>         > 5>LINK : fatal error LNK1181: cannot open input file
>         '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>         [C:\Users\aplb\Work\RTK\RTK1.2-
>         > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>         > 5>
>         > 5>      0 Warning(s)
>         > 5>      2 Error(s)
>         > 5>
>         > 5>  Time Elapsed 00:00:25.26
>         > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0
>         skipped ==========
>
>         I'm not quite sure what is going on, because the only
>         reference I can find to SimpleRTKCommon is the CMakeLists.txt
>         on github:
>         https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt
>         <https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt>
>
>         best
>
>         Arvid
>
>         On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit
>         <simon.rit at creatis.insa-lyon.fr
>         <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>             The latest MacOS. It's nice if you can test it on other
>             platforms, I'll try to run it on Linux but I have to
>             upgrade matlab first (I think python calls are available
>             starting with Matlab 2014).
>             Simon
>
>             On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen
>             B?ttiger <bottiger at gmail.com <mailto:bottiger at gmail.com>>
>             wrote:
>
>                 Dear Simon
>
>                 This look very interesting! Which platform did you
>                 successfully execute this on?
>                 I will give it a try at once (on windows) and let you
>                 know if I run into any problems.
>
>                 best
>
>                 Arvid
>
>                 On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit
>                 <simon.rit at creatis.insa-lyon.fr
>                 <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>                     Dear RTK users,
>                     I have quickly tested calling the SimpleRTK python
>                     lib from Matlab and it seems to work well:
>                     http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>                     <http://wiki.openrtk.org/index.php/SimpleRTK#Matlab>
>                     Therefore, I don't think we have to work on Matlab
>                     wrappings but let us know if you think otherwise.
>                     Future works include a simple installation
>                     mechanism for pre-compiled SimpleRTK libraries.
>                     We'll keep you posted!
>                     Simon
>
>                     _______________________________________________
>                     Rtk-users mailing list
>                     Rtk-users at public.kitware.com
>                     <mailto:Rtk-users at public.kitware.com>
>                     http://public.kitware.com/mailman/listinfo/rtk-users
>                     <http://public.kitware.com/mailman/listinfo/rtk-users>
>
>
>
>
>
>

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From bottiger at gmail.com  Tue Sep 20 08:17:35 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Tue, 20 Sep 2016 14:17:35 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
Message-ID: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>

Hi again.

I understand, but could you please help me get in contact with the person
who knows something about the windows build (if any), I think there is
something wrong.

I have been investigating the build problems I had and found that in the
sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
opened it up and found the projects which I had problems building:
"SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.

When I then tried to build SimpleRTKCommon manually it just compiled
without any problems. However, when I followed up by building
"SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
find "SimpleRTKCommon-0.9.lib" - which I just build.

After some more investigation I realized that the SimpleRTKCommon is set to
build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects it
to be a static linked library (LIB). After changing SimpleRTKCommon to be
build as a static library - and changing the output location - I could
build SimpleRTKBasicFilters0.

However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
to a LIB as well I could build SimpleRTKBasicFilters1, then
SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.

I'm unsure if the intention is to build them as static or dynamic
libraries, but in any case the current build configuration doesn't work -
on my setup at least.

However, I should note than for some reason the "lua5" project did build
successfully out of the box. Whatever it does differently works.

best

Arvid



On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> I'm not an msvc specialist but your first line suggests that you have
> pasted only part of the log:
>
> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.
> 2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
> What you need to find out is why this build failed. If the build fails,
> the linking cannot work.
> Cheers,
> Simon
>
>
> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>
> I did a complete rebuild, and here is the end of the output:
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that I'm
> trying to compile the version I just pulled from git earlier today, since
> the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> SimpleRTKCommon is a library generated when compiling. Don't you have
>> another error before that which explains why it did not compile?
>> Simon
>>
>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Hi again.
>>>
>>> I've been trying to get it working. However, I did run into some
>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>> SimpleRTKCommon - which I do not have.
>>>
>>> Here is the last few lines from VS2013
>>>
>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>> > 5>
>>> > 5>      0 Warning(s)
>>> > 5>      2 Error(s)
>>> > 5>
>>> > 5>  Time Elapsed 00:00:25.26
>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>> ==========
>>>
>>> I'm not quite sure what is going on, because the only reference I can
>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>> RTK/CMakeLists.txt
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>>>> try to run it on Linux but I have to upgrade matlab first (I think python
>>>> calls are available starting with Matlab 2014).
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Dear Simon
>>>>>
>>>>> This look very interesting! Which platform did you successfully
>>>>> execute this on?
>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>> into any problems.
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Dear RTK users,
>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>> and it seems to work well:
>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>> us know if you think otherwise.
>>>>>> Future works include a simple installation mechanism for pre-compiled
>>>>>> SimpleRTK libraries. We'll keep you posted!
>>>>>> Simon
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 10:19:20 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 16:19:20 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
Message-ID: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>

Hi,
Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
I can't solve your problem but Kitware is going to look into an upgrade of
SimpleRTK in the coming days, I'll ask them if they know what is the issue.
If you look here:
http://my.cdash.org/viewNotes.php?buildid=1052065
this is a nightly build of SimpleRTK on Windows and it seems to work. I
don't see why it wouldn't work for you.
Simon

On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I understand, but could you please help me get in contact with the person
> who knows something about the windows build (if any), I think there is
> something wrong.
>
> I have been investigating the build problems I had and found that in the
> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
> opened it up and found the projects which I had problems building:
> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>
> When I then tried to build SimpleRTKCommon manually it just compiled
> without any problems. However, when I followed up by building
> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
> find "SimpleRTKCommon-0.9.lib" - which I just build.
>
> After some more investigation I realized that the SimpleRTKCommon is set
> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
> it to be a static linked library (LIB). After changing SimpleRTKCommon to
> be build as a static library - and changing the output location - I could
> build SimpleRTKBasicFilters0.
>
> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
> to a LIB as well I could build SimpleRTKBasicFilters1, then
> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>
> I'm unsure if the intention is to build them as static or dynamic
> libraries, but in any case the current build configuration doesn't work -
> on my setup at least.
>
> However, I should note than for some reason the "lua5" project did build
> successfully out of the box. Whatever it does differently works.
>
> best
>
> Arvid
>
>
>
> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> I'm not an msvc specialist but your first line suggests that you have
>> pasted only part of the log:
>>
>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
>> What you need to find out is why this build failed. If the build fails,
>> the linking cannot work.
>> Cheers,
>> Simon
>>
>>
>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>
>> I did a complete rebuild, and here is the end of the output:
>> http://pastebin.com/hvQ33WWg
>>
>> I have to admit I'm not sure what to make of it. I should note that I'm
>> trying to compile the version I just pulled from git earlier today, since
>> the other version I normally work with is really old.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>> another error before that which explains why it did not compile?
>>> Simon
>>>
>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>> bottiger at gmail.com> wrote:
>>>
>>>> Hi again.
>>>>
>>>> I've been trying to get it working. However, I did run into some
>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>> SimpleRTKCommon - which I do not have.
>>>>
>>>> Here is the last few lines from VS2013
>>>>
>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>> > 5>
>>>> > 5>      0 Warning(s)
>>>> > 5>      2 Error(s)
>>>> > 5>
>>>> > 5>  Time Elapsed 00:00:25.26
>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>> ==========
>>>>
>>>> I'm not quite sure what is going on, because the only reference I can
>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>> RTK/CMakeLists.txt
>>>>
>>>> best
>>>>
>>>> Arvid
>>>>
>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>> python calls are available starting with Matlab 2014).
>>>>> Simon
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>> bottiger at gmail.com> wrote:
>>>>>
>>>>>> Dear Simon
>>>>>>
>>>>>> This look very interesting! Which platform did you successfully
>>>>>> execute this on?
>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>> into any problems.
>>>>>>
>>>>>> best
>>>>>>
>>>>>> Arvid
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>
>>>>>>> Dear RTK users,
>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>> and it seems to work well:
>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>>> us know if you think otherwise.
>>>>>>> Future works include a simple installation mechanism for
>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>> Simon
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 02:40:50 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 08:40:50 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
Message-ID: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>

Dear RTK users,
RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
been released, about 7 months after RTK v1.2.0.

Release notes :
- Style updated (follow more closely latest ITK guidelines).
- Started using Travis CI, github pull requests should now be used for code
submission.
- New pre-processing functionalities:
  * CUDA polynomial gain correction,
  * scatter glare correction,
  * lag correction,
  * idark option,
  * removed threshold to positive values after i0 LUT.
- Improved CUDA forward and backprojection speed using projection slabs.
- Added motion-compensated forward and back projection operators in CUDA,
in both 3D and 4D.
- Added the rtkregularizedconjugategradient application, which performs 3D
regularized reconstruction by conjugate gradient + optional regularizations
(Positivity, TV, Wavelets).
- Made the rtkfourdrooster, rtkmcrooster and rtkregularizedconjugategradient
fully modular. Each regularization step can be made active or inactive.
- Added a filter to minimize the L0 norm of the temporal gradient (one-D
only).

Many thanks to the contributors, in alphabetical order for this release: Cyril
Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien
Jomier, S?bastien
Brousmiche, Simon Rit

As usual, be aware that we don't focus on releases since we have a public
github repository <http://github.com/SimonRit/RTK> that we try to keep
stable. I still recommend the use of the master HEAD over releases to enjoy
the new RTK developments before their release. We still have a few on-going
projects for which we will use and enhance RTK.

Simon (for the RTK consortium)
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 04:48:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 10:48:26 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
In-Reply-To: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
References: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
Message-ID: <CAF0oig0=5_KPN198JzsGQXDd07Nvw_Ew+qSGhguk0m27s3U-3Q@mail.gmail.com>

Sorry, I had forgotten to change the release number in the source file.
It's been corrected, you will have to move your tag locally or update your
file if you had already downloaded it.
Simon

On Thu, Sep 22, 2016 at 8:40 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
> been released, about 7 months after RTK v1.2.0.
>
> Release notes :
> - Style updated (follow more closely latest ITK guidelines).
> - Started using Travis CI, github pull requests should now be used for
> code submission.
> - New pre-processing functionalities:
>   * CUDA polynomial gain correction,
>   * scatter glare correction,
>   * lag correction,
>   * idark option,
>   * removed threshold to positive values after i0 LUT.
> - Improved CUDA forward and backprojection speed using projection slabs.
> - Added motion-compensated forward and back projection operators in CUDA,
> in both 3D and 4D.
> - Added the rtkregularizedconjugategradient application, which performs
> 3D regularized reconstruction by conjugate gradient + optional
> regularizations (Positivity, TV, Wavelets).
> - Made the rtkfourdrooster, rtkmcrooster and
> rtkregularizedconjugategradient fully modular. Each regularization step
> can be made active or inactive.
> - Added a filter to minimize the L0 norm of the temporal gradient (one-D
> only).
>
> Many thanks to the contributors, in alphabetical order for this release: Cyril
> Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien Jomier, S?bastien
> Brousmiche, Simon Rit
>
> As usual, be aware that we don't focus on releases since we have a public
> github repository <http://github.com/SimonRit/RTK> that we try to keep
> stable. I still recommend the use of the master HEAD over releases to
> enjoy the new RTK developments before their release. We still have a few
> on-going projects for which we will use and enhance RTK.
>
> Simon (for the RTK consortium)
>
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From bottiger at gmail.com  Fri Sep 23 04:29:06 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Fri, 23 Sep 2016 10:29:06 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
 <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
Message-ID: <CANBwxwEvaUrvd1X=74g=V2JmDwtrQKFDtyUdAZJn5CRCBCkb8g@mail.gmail.com>

Hi again.

I've been spending some more time with this, and feel I learned a little
bit more. I have now tested this on several machines with several compiler
versions (more or less all of them) and serveral cmake versions - all with
Windows 7.

I can actually reproduce the successful build you linked to, but this can
only be done if you do not include any of the language wrappings, like in
the build you linked to. Enable any of them, and the build will break. (see
attachment)

I suspect it must have been working in the past, but since none of them are
included in your test there have been a breaking change, and none of them
work anymore.

I am still trying to tweak then projects manually to build SimpleRTK with
some sort of language support, but still without any luck.

best

Arvid

On Tue, Sep 20, 2016 at 4:19 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
> at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
> I can't solve your problem but Kitware is going to look into an upgrade of
> SimpleRTK in the coming days, I'll ask them if they know what is the issue.
> If you look here:
> http://my.cdash.org/viewNotes.php?buildid=1052065
> this is a nightly build of SimpleRTK on Windows and it seems to work. I
> don't see why it wouldn't work for you.
> Simon
>
> On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Hi again.
>>
>> I understand, but could you please help me get in contact with the person
>> who knows something about the windows build (if any), I think there is
>> something wrong.
>>
>> I have been investigating the build problems I had and found that in the
>> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
>> opened it up and found the projects which I had problems building:
>> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>>
>> When I then tried to build SimpleRTKCommon manually it just compiled
>> without any problems. However, when I followed up by building
>> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
>> find "SimpleRTKCommon-0.9.lib" - which I just build.
>>
>> After some more investigation I realized that the SimpleRTKCommon is set
>> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
>> it to be a static linked library (LIB). After changing SimpleRTKCommon to
>> be build as a static library - and changing the output location - I could
>> build SimpleRTKBasicFilters0.
>>
>> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing
>> that to a LIB as well I could build SimpleRTKBasicFilters1, then
>> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>>
>> I'm unsure if the intention is to build them as static or dynamic
>> libraries, but in any case the current build configuration doesn't work -
>> on my setup at least.
>>
>> However, I should note than for some reason the "lua5" project did build
>> successfully out of the box. Whatever it does differently works.
>>
>> best
>>
>> Arvid
>>
>>
>>
>> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> I'm not an msvc specialist but your first line suggests that you have
>>> pasted only part of the log:
>>>
>>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) --
>>> FAILED.
>>> What you need to find out is why this build failed. If the build fails,
>>> the linking cannot work.
>>> Cheers,
>>> Simon
>>>
>>>
>>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>>
>>> I did a complete rebuild, and here is the end of the output:
>>> http://pastebin.com/hvQ33WWg
>>>
>>> I have to admit I'm not sure what to make of it. I should note that I'm
>>> trying to compile the version I just pulled from git earlier today, since
>>> the other version I normally work with is really old.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>>> another error before that which explains why it did not compile?
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Hi again.
>>>>>
>>>>> I've been trying to get it working. However, I did run into some
>>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>>> SimpleRTKCommon - which I do not have.
>>>>>
>>>>> Here is the last few lines from VS2013
>>>>>
>>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>>> > 5>
>>>>> > 5>      0 Warning(s)
>>>>> > 5>      2 Error(s)
>>>>> > 5>
>>>>> > 5>  Time Elapsed 00:00:25.26
>>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>>> ==========
>>>>>
>>>>> I'm not quite sure what is going on, because the only reference I can
>>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>>> RTK/CMakeLists.txt
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>>> python calls are available starting with Matlab 2014).
>>>>>> Simon
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>>> bottiger at gmail.com> wrote:
>>>>>>
>>>>>>> Dear Simon
>>>>>>>
>>>>>>> This look very interesting! Which platform did you successfully
>>>>>>> execute this on?
>>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>>> into any problems.
>>>>>>>
>>>>>>> best
>>>>>>>
>>>>>>> Arvid
>>>>>>>
>>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Dear RTK users,
>>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>>> and it seems to work well:
>>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but
>>>>>>>> let us know if you think otherwise.
>>>>>>>> Future works include a simple installation mechanism for
>>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
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From ajbatkinson at gmail.com  Wed Sep 28 08:11:12 2016
From: ajbatkinson at gmail.com (Abby Bryce Atkinson)
Date: Wed, 28 Sep 2016 13:11:12 +0100
Subject: [Rtk-users] 4DROOSTERReconstruction Example
Message-ID: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>

Hi,

I am trying to work through the 4DROOSTER example using the POPI patient
images (
http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) but
I am getting stuck when extracting the respiratory signal using the
amsterdam shroud.

I receive this error:


C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
--path .\Projections\ ^
More?                    --regexp '.*.his' ^
More?                    --output shroud.mha ^
More?                    --unsharp 650
ExceptionObject caught with writer->Update() in file
C:\RTK\applications\rtkamst
erdamshroud\rtkamsterdamshroud.cxx line 91

itk::ExceptionObject (0030E9E0)
Location: "void __thiscall itk::ImageFileWriter<class itk::Image<double,2>
>::Wr
ite(void)"
File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
Line: 284
Description: itk::ERROR: ImageFileWriter(03670318): Largest possible region
does
 not fully contain requested paste IO regionPaste IO region: ImageIORegion
(0030
EDD4)
  Dimension: 2
  Index: 0 0
  Size: 0 0
Largest possible region: ImageRegion (0030EE70)
  Dimension: 2
  Index: [0, 0]
  Size: [0, 0]


Can anyone help with a solution/tell me what I am doing wrong please?

Thanks,

Abby
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From simon.rit at creatis.insa-lyon.fr  Wed Sep 28 12:49:32 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 28 Sep 2016 18:49:32 +0200
Subject: [Rtk-users] 4DROOSTERReconstruction Example
In-Reply-To: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
References: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
Message-ID: <e23fc5ec-f7b4-846c-e349-f07564e2da8a@creatis.insa-lyon.fr>

Hi,

My guess is that the software does not find the projections. I would add 
the --verbose option and check that you actually input some projections. 
If not, I guess there is an issue with the path or the regexp in your 
command line.

Simon

On 28/09/2016 14:11, Abby Bryce Atkinson wrote:
> Hi,
>
> I am trying to work through the 4DROOSTER example using the POPI 
> patient images 
> (http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) 
> but I am getting stuck when extracting the respiratory signal using 
> the amsterdam shroud.
>
> I receive this error:
>
>
> C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
> --path .\Projections\ ^
> More?                    --regexp '.*.his' ^
> More?                    --output shroud.mha ^
> More?                    --unsharp 650
> ExceptionObject caught with writer->Update() in file 
> C:\RTK\applications\rtkamst
> erdamshroud\rtkamsterdamshroud.cxx line 91
>
> itk::ExceptionObject (0030E9E0)
> Location: "void __thiscall itk::ImageFileWriter<class 
> itk::Image<double,2> >::Wr
> ite(void)"
> File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
> Line: 284
> Description: itk::ERROR: ImageFileWriter(03670318): Largest possible 
> region does
>  not fully contain requested paste IO regionPaste IO region: 
> ImageIORegion (0030
> EDD4)
>   Dimension: 2
>   Index: 0 0
>   Size: 0 0
> Largest possible region: ImageRegion (0030EE70)
>   Dimension: 2
>   Index: [0, 0]
>   Size: [0, 0]
>
>
> Can anyone help with a solution/tell me what I am doing wrong please?
>
> Thanks,
>
> Abby
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users

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From signabdm at gmail.com  Mon Sep 12 06:58:59 2016
From: signabdm at gmail.com (Valeriy Signatulin)
Date: Mon, 12 Sep 2016 16:58:59 +0600
Subject: [Rtk-users] rotation of detector plane
Message-ID: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>

Hello RTK users.
Is it possible to specify rotation of detector plane in RTK ? (in
rtksimulategeom for example) If not, what is the best way to code this ?
By rotation of detector plane i mean twist, tilt, skew around the normal of
the detector as described in
http://www.ndt.net/article/v10n09/yisun/yisun.pdf page 6.
I'm trying to write the geometry calibration method described in this
article in RTK and i need to simulate these rotations to check the results.
Thanks.
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 12 08:40:31 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 12 Sep 2016 14:40:31 +0200
Subject: [Rtk-users] rotation of detector plane
In-Reply-To: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
References: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
Message-ID: <CAF0oig0C3zFcAaAhWHV9g+UY02i7cws7OU-7r2YadyAt3TH5GA@mail.gmail.com>

Hi,
You can do any rotation with RTK. The rotation is described 3 Euler angles,
see the geometry doc <http://www.openrtk.org/Doxygen/geometry.pdf>. From
the command line, that would be the --in_angle and out_angle that allow you
to modify the other angles than the standard angle for the position along
the circular rotation (GantryAngle). If you want to modify it per
projection, that's possible using C++ or Python code (AddProjection
<http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
method).
Good luck,
Simon

On Mon, Sep 12, 2016 at 12:58 PM, Valeriy Signatulin <signabdm at gmail.com>
wrote:

> Hello RTK users.
> Is it possible to specify rotation of detector plane in RTK ? (in
> rtksimulategeom for example) If not, what is the best way to code this ?
> By rotation of detector plane i mean twist, tilt, skew around the normal
> of the detector as described in http://www.ndt.net/article/
> v10n09/yisun/yisun.pdf page 6.
> I'm trying to write the geometry calibration method described in this
> article in RTK and i need to simulate these rotations to check the results.
> Thanks.
>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From andreasg at phys.au.dk  Tue Sep 13 13:06:46 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Tue, 13 Sep 2016 19:06:46 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
Message-ID: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>

Dear RTK experts,

I am reconstructing Varian ProBeam projections of the Xim image format. I
have written the reader myself - very similar to the Hnd one already
available with RTK.
Links to my fork: [XimReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkXimImageIO.cxx>,
XMLReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamXMLFileReader.cxx>,
GeometryReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamGeometryReader.cxx>
]

The reader apparently works (Images and angles displays as expected in UI),
however when reconstructing with a regular FDK* I get a reconstructed image
that is smeared out around the high and low density areas *[see attached
image]

I'm using half arc, full fan images with no bow-tie filter from Scripps
(~520 projections). Fixed detector and source (offset=0) with SID=2m,
SDD=3m.

*For the Hnd projections the reconstruction works perfectly (Same algorithm
<https://github.com/agravgaard/cbctrecon/blob/master/cbctrecon.cpp#L2726>).*
The reconstruction of the Xim projections performed on Varian software
works perfectly.

Without the Parker Short Scan Filter the first and last projections creates
streaks across the reconstruction as if they were way too bright.
If the first few projections are excluded, the following projection will
act the same way.

The projections are corrected for beam hardening and all the projections
have the expected attenuation.
No "smearing" filters (like median) is used, and iterative reconstruction
makes the same artifacts.

Setting the value of the first and last projection to zero has the same
effect as excluding. Changing the ramp filter only changes noise, not the
artifacts.

*Have any of you had a similar problem? *Am I missing something?
Any suggestions are welcome I'm running out of ideas.

Best regards
Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 13 16:18:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 13 Sep 2016 22:18:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
Message-ID: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>

Hi,
I have almost never worked with Varian data but it looks like a
geometry problem. Maybe the problem comes from a bad ordering of the
projections which results in assigning a bad geometry to each
projection. How did you name your projections? Maybe check that the
order matches that of the RTK geometry file. Otherwise, there might be
an issue in the creation of the geometry file itself.
All this sounds good, happy bug hunt and don't hesitate to share your
code when you feel it's ready.
Simon

On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
<andreasg at phys.au.dk> wrote:
> Dear RTK experts,
>
> I am reconstructing Varian ProBeam projections of the Xim image format. I
> have written the reader myself - very similar to the Hnd one already
> available with RTK.
> Links to my fork: [XimReader, XMLReader, GeometryReader]
>
> The reader apparently works (Images and angles displays as expected in UI),
> however when reconstructing with a regular FDK I get a reconstructed image
> that is smeared out around the high and low density areas [see attached
> image]
>
> I'm using half arc, full fan images with no bow-tie filter from Scripps
> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
> SDD=3m.
>
> For the Hnd projections the reconstruction works perfectly (Same algorithm).
> The reconstruction of the Xim projections performed on Varian software works
> perfectly.
>
> Without the Parker Short Scan Filter the first and last projections creates
> streaks across the reconstruction as if they were way too bright.
> If the first few projections are excluded, the following projection will act
> the same way.
>
> The projections are corrected for beam hardening and all the projections
> have the expected attenuation.
> No "smearing" filters (like median) is used, and iterative reconstruction
> makes the same artifacts.
>
> Setting the value of the first and last projection to zero has the same
> effect as excluding. Changing the ramp filter only changes noise, not the
> artifacts.
>
> Have any of you had a similar problem? Am I missing something?
> Any suggestions are welcome I'm running out of ideas.
>
> Best regards
> Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>


From cyril.mory at creatis.insa-lyon.fr  Wed Sep 14 03:10:42 2016
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 14 Sep 2016 09:10:42 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
Message-ID: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>

One suggestion since it works with the Hnd projections:
You can run rtkprojections twice (with the Hnd projections, then with 
Xim projections) and output two projection stack files and two geometry 
files, then compare the projection stack files by subtracting one to the 
other (with SimpleRTK or clitk) and the geometry files with diff. If 
they are identical, then I do not see any reason why the reconstructions 
should be different, so my guess is that you will find differences.

On 09/13/2016 10:18 PM, Simon Rit wrote:
> Hi,
> I have almost never worked with Varian data but it looks like a
> geometry problem. Maybe the problem comes from a bad ordering of the
> projections which results in assigning a bad geometry to each
> projection. How did you name your projections? Maybe check that the
> order matches that of the RTK geometry file. Otherwise, there might be
> an issue in the creation of the geometry file itself.
> All this sounds good, happy bug hunt and don't hesitate to share your
> code when you feel it's ready.
> Simon
>
> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
> <andreasg at phys.au.dk> wrote:
>> Dear RTK experts,
>>
>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>> have written the reader myself - very similar to the Hnd one already
>> available with RTK.
>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>
>> The reader apparently works (Images and angles displays as expected in UI),
>> however when reconstructing with a regular FDK I get a reconstructed image
>> that is smeared out around the high and low density areas [see attached
>> image]
>>
>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>> SDD=3m.
>>
>> For the Hnd projections the reconstruction works perfectly (Same algorithm).
>> The reconstruction of the Xim projections performed on Varian software works
>> perfectly.
>>
>> Without the Parker Short Scan Filter the first and last projections creates
>> streaks across the reconstruction as if they were way too bright.
>> If the first few projections are excluded, the following projection will act
>> the same way.
>>
>> The projections are corrected for beam hardening and all the projections
>> have the expected attenuation.
>> No "smearing" filters (like median) is used, and iterative reconstruction
>> makes the same artifacts.
>>
>> Setting the value of the first and last projection to zero has the same
>> effect as excluding. Changing the ramp filter only changes noise, not the
>> artifacts.
>>
>> Have any of you had a similar problem? Am I missing something?
>> Any suggestions are welcome I'm running out of ideas.
>>
>> Best regards
>> Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>



From andreasg at phys.au.dk  Fri Sep 16 08:56:34 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 14:56:34 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
Message-ID: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>

Thanks for the suggestions, Simon and Cyril!

I have been carefully looking though the geometry and from what I
understand of the transformations matrices, the geometry looks correct/(as
expected).

HOWEVER: I found out that the reason for the Hnd to behave differently were
because had used half-fan scans (full-arc).
When I used a full-fan (half-arc) scan of Hnd projections the same
artifacts occurs!

Are there other (built-in) means of improving half-arc scans, than the
parker short scan filter?

Parker short scan does a decent job, but the result is still far from the
quality of the Varian software reconstruction at least for the CatPhan.

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:

> One suggestion since it works with the Hnd projections:
> You can run rtkprojections twice (with the Hnd projections, then with Xim
> projections) and output two projection stack files and two geometry files,
> then compare the projection stack files by subtracting one to the other
> (with SimpleRTK or clitk) and the geometry files with diff. If they are
> identical, then I do not see any reason why the reconstructions should be
> different, so my guess is that you will find differences.
>
>
> On 09/13/2016 10:18 PM, Simon Rit wrote:
>
>> Hi,
>> I have almost never worked with Varian data but it looks like a
>> geometry problem. Maybe the problem comes from a bad ordering of the
>> projections which results in assigning a bad geometry to each
>> projection. How did you name your projections? Maybe check that the
>> order matches that of the RTK geometry file. Otherwise, there might be
>> an issue in the creation of the geometry file itself.
>> All this sounds good, happy bug hunt and don't hesitate to share your
>> code when you feel it's ready.
>> Simon
>>
>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>> <andreasg at phys.au.dk> wrote:
>>
>>> Dear RTK experts,
>>>
>>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>>> have written the reader myself - very similar to the Hnd one already
>>> available with RTK.
>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>
>>> The reader apparently works (Images and angles displays as expected in
>>> UI),
>>> however when reconstructing with a regular FDK I get a reconstructed
>>> image
>>> that is smeared out around the high and low density areas [see attached
>>> image]
>>>
>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>> SDD=3m.
>>>
>>> For the Hnd projections the reconstruction works perfectly (Same
>>> algorithm).
>>> The reconstruction of the Xim projections performed on Varian software
>>> works
>>> perfectly.
>>>
>>> Without the Parker Short Scan Filter the first and last projections
>>> creates
>>> streaks across the reconstruction as if they were way too bright.
>>> If the first few projections are excluded, the following projection will
>>> act
>>> the same way.
>>>
>>> The projections are corrected for beam hardening and all the projections
>>> have the expected attenuation.
>>> No "smearing" filters (like median) is used, and iterative reconstruction
>>> makes the same artifacts.
>>>
>>> Setting the value of the first and last projection to zero has the same
>>> effect as excluding. Changing the ramp filter only changes noise, not the
>>> artifacts.
>>>
>>> Have any of you had a similar problem? Am I missing something?
>>> Any suggestions are welcome I'm running out of ideas.
>>>
>>> Best regards
>>> Andreas
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Sep 16 10:13:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 16 Sep 2016 16:13:26 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
Message-ID: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>

Hi,
You can try any iterative reconstruction, they can also handle short scans.
Start with a few iterations of rtksart or rtkconjugategradient. However,
the nature of the artifacts indicate more a problem in the geometry in my
opinion. I have seen such errors when, for example, rotating in the wrong
direction. I can have a look if you share the dataset.
Cheers,
Simon

On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the suggestions, Simon and Cyril!
>
> I have been carefully looking though the geometry and from what I
> understand of the transformations matrices, the geometry looks correct/(as
> expected).
>
> HOWEVER: I found out that the reason for the Hnd to behave differently
> were because had used half-fan scans (full-arc).
> When I used a full-fan (half-arc) scan of Hnd projections the same
> artifacts occurs!
>
> Are there other (built-in) means of improving half-arc scans, than the
> parker short scan filter?
>
> Parker short scan does a decent job, but the result is still far from the
> quality of the Varian software reconstruction at least for the CatPhan.
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>
>> One suggestion since it works with the Hnd projections:
>> You can run rtkprojections twice (with the Hnd projections, then with Xim
>> projections) and output two projection stack files and two geometry files,
>> then compare the projection stack files by subtracting one to the other
>> (with SimpleRTK or clitk) and the geometry files with diff. If they are
>> identical, then I do not see any reason why the reconstructions should be
>> different, so my guess is that you will find differences.
>>
>>
>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>
>>> Hi,
>>> I have almost never worked with Varian data but it looks like a
>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>> projections which results in assigning a bad geometry to each
>>> projection. How did you name your projections? Maybe check that the
>>> order matches that of the RTK geometry file. Otherwise, there might be
>>> an issue in the creation of the geometry file itself.
>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>> code when you feel it's ready.
>>> Simon
>>>
>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>> <andreasg at phys.au.dk> wrote:
>>>
>>>> Dear RTK experts,
>>>>
>>>> I am reconstructing Varian ProBeam projections of the Xim image format.
>>>> I
>>>> have written the reader myself - very similar to the Hnd one already
>>>> available with RTK.
>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>
>>>> The reader apparently works (Images and angles displays as expected in
>>>> UI),
>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>> image
>>>> that is smeared out around the high and low density areas [see attached
>>>> image]
>>>>
>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>> SDD=3m.
>>>>
>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>> algorithm).
>>>> The reconstruction of the Xim projections performed on Varian software
>>>> works
>>>> perfectly.
>>>>
>>>> Without the Parker Short Scan Filter the first and last projections
>>>> creates
>>>> streaks across the reconstruction as if they were way too bright.
>>>> If the first few projections are excluded, the following projection
>>>> will act
>>>> the same way.
>>>>
>>>> The projections are corrected for beam hardening and all the projections
>>>> have the expected attenuation.
>>>> No "smearing" filters (like median) is used, and iterative
>>>> reconstruction
>>>> makes the same artifacts.
>>>>
>>>> Setting the value of the first and last projection to zero has the same
>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>> the
>>>> artifacts.
>>>>
>>>> Have any of you had a similar problem? Am I missing something?
>>>> Any suggestions are welcome I'm running out of ideas.
>>>>
>>>> Best regards
>>>> Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> N?rrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     andreasg at phys.au.dk
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From andreasg at phys.au.dk  Fri Sep 16 16:37:43 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 22:37:43 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
Message-ID: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>

Thanks for the fast response Simon!

I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
right all along!
I just didn't get why it makes a difference. I think I do now, as the
resulting image was flipped upside down and not left/right as I expected.
[attached]

The reconstruction is significantly better, I'll look into what should be
included in the reader and what I should keep in my program to keep
conformity with the other readers. Then I'll create a pull request.

Just for the purpose of others hitting the same or a similar bug, I also
attempted:
I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
back/forward projection, *but with no* significant improvement [attached]

And:
If you want you can download the data set from: [Dropbox link to 460MB zip
<https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep it
up as long as Dropbox allows me)] Only the Acquisitions/subfolder is used
along with the Scan.xml (Calibrations folder may be used in the future in
my program, but I'm not sure if you can rely on the existence of the
content).

A MatLab XimReader is available: link
<https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
available from Varian bitbucket along a with a python version and a
C#->matlab plugin
<https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). Otherwise
my fork with the RTK-style reader is available from the same repository (I
have also added Hnc support, thanks to the Geoff Hugo fork, so bzip2 is a
new dependancy).

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:

> Hi,
> You can try any iterative reconstruction, they can also handle short
> scans. Start with a few iterations of rtksart or rtkconjugategradient.
> However, the nature of the artifacts indicate more a problem in the
> geometry in my opinion. I have seen such errors when, for example, rotating
> in the wrong direction. I can have a look if you share the dataset.
> Cheers,
> Simon
>
> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
> andreasg at phys.au.dk> wrote:
>
>> Thanks for the suggestions, Simon and Cyril!
>>
>> I have been carefully looking though the geometry and from what I
>> understand of the transformations matrices, the geometry looks correct/(as
>> expected).
>>
>> HOWEVER: I found out that the reason for the Hnd to behave differently
>> were because had used half-fan scans (full-arc).
>> When I used a full-fan (half-arc) scan of Hnd projections the same
>> artifacts occurs!
>>
>> Are there other (built-in) means of improving half-arc scans, than the
>> parker short scan filter?
>>
>> Parker short scan does a decent job, but the result is still far from the
>> quality of the Varian software reconstruction at least for the CatPhan.
>>
>> Best regards
>> Andreas
>>
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>>
>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>
>>> One suggestion since it works with the Hnd projections:
>>> You can run rtkprojections twice (with the Hnd projections, then with
>>> Xim projections) and output two projection stack files and two geometry
>>> files, then compare the projection stack files by subtracting one to the
>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>> are identical, then I do not see any reason why the reconstructions should
>>> be different, so my guess is that you will find differences.
>>>
>>>
>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>
>>>> Hi,
>>>> I have almost never worked with Varian data but it looks like a
>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>> projections which results in assigning a bad geometry to each
>>>> projection. How did you name your projections? Maybe check that the
>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>> an issue in the creation of the geometry file itself.
>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>> code when you feel it's ready.
>>>> Simon
>>>>
>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>> <andreasg at phys.au.dk> wrote:
>>>>
>>>>> Dear RTK experts,
>>>>>
>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>> format. I
>>>>> have written the reader myself - very similar to the Hnd one already
>>>>> available with RTK.
>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>
>>>>> The reader apparently works (Images and angles displays as expected in
>>>>> UI),
>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>> image
>>>>> that is smeared out around the high and low density areas [see attached
>>>>> image]
>>>>>
>>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>> SDD=3m.
>>>>>
>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>> algorithm).
>>>>> The reconstruction of the Xim projections performed on Varian software
>>>>> works
>>>>> perfectly.
>>>>>
>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>> creates
>>>>> streaks across the reconstruction as if they were way too bright.
>>>>> If the first few projections are excluded, the following projection
>>>>> will act
>>>>> the same way.
>>>>>
>>>>> The projections are corrected for beam hardening and all the
>>>>> projections
>>>>> have the expected attenuation.
>>>>> No "smearing" filters (like median) is used, and iterative
>>>>> reconstruction
>>>>> makes the same artifacts.
>>>>>
>>>>> Setting the value of the first and last projection to zero has the same
>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>> the
>>>>> artifacts.
>>>>>
>>>>> Have any of you had a similar problem? Am I missing something?
>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>
>>>>> Best regards
>>>>> Andreas
>>>>>
>>>>> __________________________________
>>>>>
>>>>> Andreas Gravgaard Andersen
>>>>>
>>>>> Department of Oncology,
>>>>>
>>>>> Aarhus University Hospital
>>>>>
>>>>> N?rrebrogade 44,
>>>>>
>>>>> 8000, Aarhus C
>>>>>
>>>>> Mail:     andreasg at phys.au.dk
>>>>>
>>>>> Cell:      +45 3165 8140
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 03:26:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 09:26:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
 <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
Message-ID: <CAF0oig2TSmAsSn=o3aLo6LEFDOSaKRtfknjMer24rcDKJ-0Fqg@mail.gmail.com>

Hi,
Thanks for sharing. There still seems to be some streak artefacts, do you
see the same in the Varian reconstruction?
I'm looking forward to the pull-request, I think we should try to make the
bzip2 optional.
Simon

On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the fast response Simon!
>
> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
> right all along!
> I just didn't get why it makes a difference. I think I do now, as the
> resulting image was flipped upside down and not left/right as I expected.
> [attached]
>
> The reconstruction is significantly better, I'll look into what should be
> included in the reader and what I should keep in my program to keep
> conformity with the other readers. Then I'll create a pull request.
>
> Just for the purpose of others hitting the same or a similar bug, I also
> attempted:
> I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
> back/forward projection, *but with no* significant improvement [attached]
>
> And:
> If you want you can download the data set from: [Dropbox link to 460MB zip
> <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep
> it up as long as Dropbox allows me)] Only the Acquisitions/subfolder is
> used along with the Scan.xml (Calibrations folder may be used in the future
> in my program, but I'm not sure if you can rely on the existence of the
> content).
>
> A MatLab XimReader is available: link
> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
> available from Varian bitbucket along a with a python version and a
> C#->matlab plugin
> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>).
> Otherwise my fork with the RTK-style reader is available from the same
> repository (I have also added Hnc support, thanks to the Geoff Hugo fork,
> so bzip2 is a new dependancy).
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> Hi,
>> You can try any iterative reconstruction, they can also handle short
>> scans. Start with a few iterations of rtksart or rtkconjugategradient.
>> However, the nature of the artifacts indicate more a problem in the
>> geometry in my opinion. I have seen such errors when, for example, rotating
>> in the wrong direction. I can have a look if you share the dataset.
>> Cheers,
>> Simon
>>
>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
>> andreasg at phys.au.dk> wrote:
>>
>>> Thanks for the suggestions, Simon and Cyril!
>>>
>>> I have been carefully looking though the geometry and from what I
>>> understand of the transformations matrices, the geometry looks correct/(as
>>> expected).
>>>
>>> HOWEVER: I found out that the reason for the Hnd to behave differently
>>> were because had used half-fan scans (full-arc).
>>> When I used a full-fan (half-arc) scan of Hnd projections the same
>>> artifacts occurs!
>>>
>>> Are there other (built-in) means of improving half-arc scans, than the
>>> parker short scan filter?
>>>
>>> Parker short scan does a decent job, but the result is still far from
>>> the quality of the Varian software reconstruction at least for the CatPhan.
>>>
>>> Best regards
>>> Andreas
>>>
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>>
>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>>
>>>> One suggestion since it works with the Hnd projections:
>>>> You can run rtkprojections twice (with the Hnd projections, then with
>>>> Xim projections) and output two projection stack files and two geometry
>>>> files, then compare the projection stack files by subtracting one to the
>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>>> are identical, then I do not see any reason why the reconstructions should
>>>> be different, so my guess is that you will find differences.
>>>>
>>>>
>>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>>
>>>>> Hi,
>>>>> I have almost never worked with Varian data but it looks like a
>>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>>> projections which results in assigning a bad geometry to each
>>>>> projection. How did you name your projections? Maybe check that the
>>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>>> an issue in the creation of the geometry file itself.
>>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>>> code when you feel it's ready.
>>>>> Simon
>>>>>
>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>>> <andreasg at phys.au.dk> wrote:
>>>>>
>>>>>> Dear RTK experts,
>>>>>>
>>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>>> format. I
>>>>>> have written the reader myself - very similar to the Hnd one already
>>>>>> available with RTK.
>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>>
>>>>>> The reader apparently works (Images and angles displays as expected
>>>>>> in UI),
>>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>>> image
>>>>>> that is smeared out around the high and low density areas [see
>>>>>> attached
>>>>>> image]
>>>>>>
>>>>>> I'm using half arc, full fan images with no bow-tie filter from
>>>>>> Scripps
>>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>>> SDD=3m.
>>>>>>
>>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>>> algorithm).
>>>>>> The reconstruction of the Xim projections performed on Varian
>>>>>> software works
>>>>>> perfectly.
>>>>>>
>>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>>> creates
>>>>>> streaks across the reconstruction as if they were way too bright.
>>>>>> If the first few projections are excluded, the following projection
>>>>>> will act
>>>>>> the same way.
>>>>>>
>>>>>> The projections are corrected for beam hardening and all the
>>>>>> projections
>>>>>> have the expected attenuation.
>>>>>> No "smearing" filters (like median) is used, and iterative
>>>>>> reconstruction
>>>>>> makes the same artifacts.
>>>>>>
>>>>>> Setting the value of the first and last projection to zero has the
>>>>>> same
>>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>>> the
>>>>>> artifacts.
>>>>>>
>>>>>> Have any of you had a similar problem? Am I missing something?
>>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>>
>>>>>> Best regards
>>>>>> Andreas
>>>>>>
>>>>>> __________________________________
>>>>>>
>>>>>> Andreas Gravgaard Andersen
>>>>>>
>>>>>> Department of Oncology,
>>>>>>
>>>>>> Aarhus University Hospital
>>>>>>
>>>>>> N?rrebrogade 44,
>>>>>>
>>>>>> 8000, Aarhus C
>>>>>>
>>>>>> Mail:     andreasg at phys.au.dk
>>>>>>
>>>>>> Cell:      +45 3165 8140
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:05:24 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:05:24 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
Message-ID: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>

Dear RTK users,
I have quickly tested calling the SimpleRTK python lib from Matlab and it
seems to work well:
http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
Therefore, I don't think we have to work on Matlab wrappings but let us
know if you think otherwise.
Future works include a simple installation mechanism for pre-compiled
SimpleRTK libraries. We'll keep you posted!
Simon
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From bottiger at gmail.com  Mon Sep 19 05:14:03 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 11:14:03 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
Message-ID: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>

Dear Simon

This look very interesting! Which platform did you successfully execute
this on?
I will give it a try at once (on windows) and let you know if I run into
any problems.

best

Arvid

On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> I have quickly tested calling the SimpleRTK python lib from Matlab and it
> seems to work well:
> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
> Therefore, I don't think we have to work on Matlab wrappings but let us
> know if you think otherwise.
> Future works include a simple installation mechanism for pre-compiled
> SimpleRTK libraries. We'll keep you posted!
> Simon
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:19:28 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:19:28 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
Message-ID: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>

The latest MacOS. It's nice if you can test it on other platforms, I'll try
to run it on Linux but I have to upgrade matlab first (I think python calls
are available starting with Matlab 2014).
Simon

On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Dear Simon
>
> This look very interesting! Which platform did you successfully execute
> this on?
> I will give it a try at once (on windows) and let you know if I run into
> any problems.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> Dear RTK users,
>> I have quickly tested calling the SimpleRTK python lib from Matlab and it
>> seems to work well:
>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>> Therefore, I don't think we have to work on Matlab wrappings but let us
>> know if you think otherwise.
>> Future works include a simple installation mechanism for pre-compiled
>> SimpleRTK libraries. We'll keep you posted!
>> Simon
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From bottiger at gmail.com  Mon Sep 19 08:30:32 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 14:30:32 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
Message-ID: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>

Hi again.

I've been trying to get it working. However, I did run into some problems
compiling SimpleRTK. The main issue seems to be that it depends on
SimpleRTKCommon - which I do not have.

Here is the last few lines from VS2013

> 5>LINK : fatal error LNK1181: cannot open input file
'..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib' [C:\Users\aplb\Work\RTK\RTK1.2-
> bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> 5>
> 5>      0 Warning(s)
> 5>      2 Error(s)
> 5>
> 5>  Time Elapsed 00:00:25.26
> ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
==========

I'm not quite sure what is going on, because the only reference I can find
to SimpleRTKCommon is the CMakeLists.txt on github:
https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt

best

Arvid

On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> The latest MacOS. It's nice if you can test it on other platforms, I'll
> try to run it on Linux but I have to upgrade matlab first (I think python
> calls are available starting with Matlab 2014).
> Simon
>
> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Dear Simon
>>
>> This look very interesting! Which platform did you successfully execute
>> this on?
>> I will give it a try at once (on windows) and let you know if I run into
>> any problems.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Dear RTK users,
>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>> it seems to work well:
>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>> know if you think otherwise.
>>> Future works include a simple installation mechanism for pre-compiled
>>> SimpleRTK libraries. We'll keep you posted!
>>> Simon
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 12:50:33 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 18:50:33 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
Message-ID: <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>

 SimpleRTKCommon is a library generated when compiling. Don't you have
another error before that which explains why it did not compile?
Simon

On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I've been trying to get it working. However, I did run into some problems
> compiling SimpleRTK. The main issue seems to be that it depends on
> SimpleRTKCommon - which I do not have.
>
> Here is the last few lines from VS2013
>
> > 5>LINK : fatal error LNK1181: cannot open input file '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
> [C:\Users\aplb\Work\RTK\RTK1.2-
> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> > 5>
> > 5>      0 Warning(s)
> > 5>      2 Error(s)
> > 5>
> > 5>  Time Elapsed 00:00:25.26
> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
> ==========
>
> I'm not quite sure what is going on, because the only reference I can find
> to SimpleRTKCommon is the CMakeLists.txt on github:
> https://github.com/SimonRit/RTK/blob/master/utilities/
> SimpleRTK/CMakeLists.txt
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>> try to run it on Linux but I have to upgrade matlab first (I think python
>> calls are available starting with Matlab 2014).
>> Simon
>>
>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Dear Simon
>>>
>>> This look very interesting! Which platform did you successfully execute
>>> this on?
>>> I will give it a try at once (on windows) and let you know if I run into
>>> any problems.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Dear RTK users,
>>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>>> it seems to work well:
>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>>> know if you think otherwise.
>>>> Future works include a simple installation mechanism for pre-compiled
>>>> SimpleRTK libraries. We'll keep you posted!
>>>> Simon
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 01:33:46 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 07:33:46 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
Message-ID: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>

I'm not an msvc specialist but your first line suggests that you have 
pasted only part of the log:

20>  Done Building Project 
"C:\Users\aplb\Work\RTK\RTK1.2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" 
(default targets) -- FAILED.

What you need to find out is why this build failed. If the build fails, 
the linking cannot work.
Cheers,
Simon

On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
> I did a complete rebuild, and here is the end of the output: 
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that 
> I'm trying to compile the version I just pulled from git earlier 
> today, since the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     SimpleRTKCommon is a library generated when compiling. Don't you
>     have another error before that which explains why it did not compile?
>     Simon
>
>     On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger
>     <bottiger at gmail.com <mailto:bottiger at gmail.com>> wrote:
>
>         Hi again.
>
>         I've been trying to get it working. However, I did run into
>         some problems compiling SimpleRTK. The main issue seems to be
>         that it depends on SimpleRTKCommon - which I do not have.
>
>         Here is the last few lines from VS2013
>
>         > 5>LINK : fatal error LNK1181: cannot open input file
>         '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>         [C:\Users\aplb\Work\RTK\RTK1.2-
>         > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>         > 5>
>         > 5>      0 Warning(s)
>         > 5>      2 Error(s)
>         > 5>
>         > 5>  Time Elapsed 00:00:25.26
>         > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0
>         skipped ==========
>
>         I'm not quite sure what is going on, because the only
>         reference I can find to SimpleRTKCommon is the CMakeLists.txt
>         on github:
>         https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt
>         <https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt>
>
>         best
>
>         Arvid
>
>         On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit
>         <simon.rit at creatis.insa-lyon.fr
>         <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>             The latest MacOS. It's nice if you can test it on other
>             platforms, I'll try to run it on Linux but I have to
>             upgrade matlab first (I think python calls are available
>             starting with Matlab 2014).
>             Simon
>
>             On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen
>             B?ttiger <bottiger at gmail.com <mailto:bottiger at gmail.com>>
>             wrote:
>
>                 Dear Simon
>
>                 This look very interesting! Which platform did you
>                 successfully execute this on?
>                 I will give it a try at once (on windows) and let you
>                 know if I run into any problems.
>
>                 best
>
>                 Arvid
>
>                 On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit
>                 <simon.rit at creatis.insa-lyon.fr
>                 <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>                     Dear RTK users,
>                     I have quickly tested calling the SimpleRTK python
>                     lib from Matlab and it seems to work well:
>                     http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>                     <http://wiki.openrtk.org/index.php/SimpleRTK#Matlab>
>                     Therefore, I don't think we have to work on Matlab
>                     wrappings but let us know if you think otherwise.
>                     Future works include a simple installation
>                     mechanism for pre-compiled SimpleRTK libraries.
>                     We'll keep you posted!
>                     Simon
>
>                     _______________________________________________
>                     Rtk-users mailing list
>                     Rtk-users at public.kitware.com
>                     <mailto:Rtk-users at public.kitware.com>
>                     http://public.kitware.com/mailman/listinfo/rtk-users
>                     <http://public.kitware.com/mailman/listinfo/rtk-users>
>
>
>
>
>
>

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From bottiger at gmail.com  Tue Sep 20 08:17:35 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Tue, 20 Sep 2016 14:17:35 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
Message-ID: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>

Hi again.

I understand, but could you please help me get in contact with the person
who knows something about the windows build (if any), I think there is
something wrong.

I have been investigating the build problems I had and found that in the
sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
opened it up and found the projects which I had problems building:
"SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.

When I then tried to build SimpleRTKCommon manually it just compiled
without any problems. However, when I followed up by building
"SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
find "SimpleRTKCommon-0.9.lib" - which I just build.

After some more investigation I realized that the SimpleRTKCommon is set to
build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects it
to be a static linked library (LIB). After changing SimpleRTKCommon to be
build as a static library - and changing the output location - I could
build SimpleRTKBasicFilters0.

However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
to a LIB as well I could build SimpleRTKBasicFilters1, then
SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.

I'm unsure if the intention is to build them as static or dynamic
libraries, but in any case the current build configuration doesn't work -
on my setup at least.

However, I should note than for some reason the "lua5" project did build
successfully out of the box. Whatever it does differently works.

best

Arvid



On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> I'm not an msvc specialist but your first line suggests that you have
> pasted only part of the log:
>
> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.
> 2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
> What you need to find out is why this build failed. If the build fails,
> the linking cannot work.
> Cheers,
> Simon
>
>
> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>
> I did a complete rebuild, and here is the end of the output:
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that I'm
> trying to compile the version I just pulled from git earlier today, since
> the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> SimpleRTKCommon is a library generated when compiling. Don't you have
>> another error before that which explains why it did not compile?
>> Simon
>>
>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Hi again.
>>>
>>> I've been trying to get it working. However, I did run into some
>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>> SimpleRTKCommon - which I do not have.
>>>
>>> Here is the last few lines from VS2013
>>>
>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>> > 5>
>>> > 5>      0 Warning(s)
>>> > 5>      2 Error(s)
>>> > 5>
>>> > 5>  Time Elapsed 00:00:25.26
>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>> ==========
>>>
>>> I'm not quite sure what is going on, because the only reference I can
>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>> RTK/CMakeLists.txt
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>>>> try to run it on Linux but I have to upgrade matlab first (I think python
>>>> calls are available starting with Matlab 2014).
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Dear Simon
>>>>>
>>>>> This look very interesting! Which platform did you successfully
>>>>> execute this on?
>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>> into any problems.
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Dear RTK users,
>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>> and it seems to work well:
>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>> us know if you think otherwise.
>>>>>> Future works include a simple installation mechanism for pre-compiled
>>>>>> SimpleRTK libraries. We'll keep you posted!
>>>>>> Simon
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 10:19:20 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 16:19:20 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
Message-ID: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>

Hi,
Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
I can't solve your problem but Kitware is going to look into an upgrade of
SimpleRTK in the coming days, I'll ask them if they know what is the issue.
If you look here:
http://my.cdash.org/viewNotes.php?buildid=1052065
this is a nightly build of SimpleRTK on Windows and it seems to work. I
don't see why it wouldn't work for you.
Simon

On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I understand, but could you please help me get in contact with the person
> who knows something about the windows build (if any), I think there is
> something wrong.
>
> I have been investigating the build problems I had and found that in the
> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
> opened it up and found the projects which I had problems building:
> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>
> When I then tried to build SimpleRTKCommon manually it just compiled
> without any problems. However, when I followed up by building
> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
> find "SimpleRTKCommon-0.9.lib" - which I just build.
>
> After some more investigation I realized that the SimpleRTKCommon is set
> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
> it to be a static linked library (LIB). After changing SimpleRTKCommon to
> be build as a static library - and changing the output location - I could
> build SimpleRTKBasicFilters0.
>
> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
> to a LIB as well I could build SimpleRTKBasicFilters1, then
> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>
> I'm unsure if the intention is to build them as static or dynamic
> libraries, but in any case the current build configuration doesn't work -
> on my setup at least.
>
> However, I should note than for some reason the "lua5" project did build
> successfully out of the box. Whatever it does differently works.
>
> best
>
> Arvid
>
>
>
> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> I'm not an msvc specialist but your first line suggests that you have
>> pasted only part of the log:
>>
>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
>> What you need to find out is why this build failed. If the build fails,
>> the linking cannot work.
>> Cheers,
>> Simon
>>
>>
>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>
>> I did a complete rebuild, and here is the end of the output:
>> http://pastebin.com/hvQ33WWg
>>
>> I have to admit I'm not sure what to make of it. I should note that I'm
>> trying to compile the version I just pulled from git earlier today, since
>> the other version I normally work with is really old.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>> another error before that which explains why it did not compile?
>>> Simon
>>>
>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>> bottiger at gmail.com> wrote:
>>>
>>>> Hi again.
>>>>
>>>> I've been trying to get it working. However, I did run into some
>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>> SimpleRTKCommon - which I do not have.
>>>>
>>>> Here is the last few lines from VS2013
>>>>
>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>> > 5>
>>>> > 5>      0 Warning(s)
>>>> > 5>      2 Error(s)
>>>> > 5>
>>>> > 5>  Time Elapsed 00:00:25.26
>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>> ==========
>>>>
>>>> I'm not quite sure what is going on, because the only reference I can
>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>> RTK/CMakeLists.txt
>>>>
>>>> best
>>>>
>>>> Arvid
>>>>
>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>> python calls are available starting with Matlab 2014).
>>>>> Simon
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>> bottiger at gmail.com> wrote:
>>>>>
>>>>>> Dear Simon
>>>>>>
>>>>>> This look very interesting! Which platform did you successfully
>>>>>> execute this on?
>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>> into any problems.
>>>>>>
>>>>>> best
>>>>>>
>>>>>> Arvid
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>
>>>>>>> Dear RTK users,
>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>> and it seems to work well:
>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>>> us know if you think otherwise.
>>>>>>> Future works include a simple installation mechanism for
>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>> Simon
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 02:40:50 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 08:40:50 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
Message-ID: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>

Dear RTK users,
RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
been released, about 7 months after RTK v1.2.0.

Release notes :
- Style updated (follow more closely latest ITK guidelines).
- Started using Travis CI, github pull requests should now be used for code
submission.
- New pre-processing functionalities:
  * CUDA polynomial gain correction,
  * scatter glare correction,
  * lag correction,
  * idark option,
  * removed threshold to positive values after i0 LUT.
- Improved CUDA forward and backprojection speed using projection slabs.
- Added motion-compensated forward and back projection operators in CUDA,
in both 3D and 4D.
- Added the rtkregularizedconjugategradient application, which performs 3D
regularized reconstruction by conjugate gradient + optional regularizations
(Positivity, TV, Wavelets).
- Made the rtkfourdrooster, rtkmcrooster and rtkregularizedconjugategradient
fully modular. Each regularization step can be made active or inactive.
- Added a filter to minimize the L0 norm of the temporal gradient (one-D
only).

Many thanks to the contributors, in alphabetical order for this release: Cyril
Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien
Jomier, S?bastien
Brousmiche, Simon Rit

As usual, be aware that we don't focus on releases since we have a public
github repository <http://github.com/SimonRit/RTK> that we try to keep
stable. I still recommend the use of the master HEAD over releases to enjoy
the new RTK developments before their release. We still have a few on-going
projects for which we will use and enhance RTK.

Simon (for the RTK consortium)
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 04:48:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 10:48:26 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
In-Reply-To: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
References: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
Message-ID: <CAF0oig0=5_KPN198JzsGQXDd07Nvw_Ew+qSGhguk0m27s3U-3Q@mail.gmail.com>

Sorry, I had forgotten to change the release number in the source file.
It's been corrected, you will have to move your tag locally or update your
file if you had already downloaded it.
Simon

On Thu, Sep 22, 2016 at 8:40 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
> been released, about 7 months after RTK v1.2.0.
>
> Release notes :
> - Style updated (follow more closely latest ITK guidelines).
> - Started using Travis CI, github pull requests should now be used for
> code submission.
> - New pre-processing functionalities:
>   * CUDA polynomial gain correction,
>   * scatter glare correction,
>   * lag correction,
>   * idark option,
>   * removed threshold to positive values after i0 LUT.
> - Improved CUDA forward and backprojection speed using projection slabs.
> - Added motion-compensated forward and back projection operators in CUDA,
> in both 3D and 4D.
> - Added the rtkregularizedconjugategradient application, which performs
> 3D regularized reconstruction by conjugate gradient + optional
> regularizations (Positivity, TV, Wavelets).
> - Made the rtkfourdrooster, rtkmcrooster and
> rtkregularizedconjugategradient fully modular. Each regularization step
> can be made active or inactive.
> - Added a filter to minimize the L0 norm of the temporal gradient (one-D
> only).
>
> Many thanks to the contributors, in alphabetical order for this release: Cyril
> Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien Jomier, S?bastien
> Brousmiche, Simon Rit
>
> As usual, be aware that we don't focus on releases since we have a public
> github repository <http://github.com/SimonRit/RTK> that we try to keep
> stable. I still recommend the use of the master HEAD over releases to
> enjoy the new RTK developments before their release. We still have a few
> on-going projects for which we will use and enhance RTK.
>
> Simon (for the RTK consortium)
>
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From bottiger at gmail.com  Fri Sep 23 04:29:06 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Fri, 23 Sep 2016 10:29:06 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
 <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
Message-ID: <CANBwxwEvaUrvd1X=74g=V2JmDwtrQKFDtyUdAZJn5CRCBCkb8g@mail.gmail.com>

Hi again.

I've been spending some more time with this, and feel I learned a little
bit more. I have now tested this on several machines with several compiler
versions (more or less all of them) and serveral cmake versions - all with
Windows 7.

I can actually reproduce the successful build you linked to, but this can
only be done if you do not include any of the language wrappings, like in
the build you linked to. Enable any of them, and the build will break. (see
attachment)

I suspect it must have been working in the past, but since none of them are
included in your test there have been a breaking change, and none of them
work anymore.

I am still trying to tweak then projects manually to build SimpleRTK with
some sort of language support, but still without any luck.

best

Arvid

On Tue, Sep 20, 2016 at 4:19 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
> at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
> I can't solve your problem but Kitware is going to look into an upgrade of
> SimpleRTK in the coming days, I'll ask them if they know what is the issue.
> If you look here:
> http://my.cdash.org/viewNotes.php?buildid=1052065
> this is a nightly build of SimpleRTK on Windows and it seems to work. I
> don't see why it wouldn't work for you.
> Simon
>
> On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Hi again.
>>
>> I understand, but could you please help me get in contact with the person
>> who knows something about the windows build (if any), I think there is
>> something wrong.
>>
>> I have been investigating the build problems I had and found that in the
>> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
>> opened it up and found the projects which I had problems building:
>> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>>
>> When I then tried to build SimpleRTKCommon manually it just compiled
>> without any problems. However, when I followed up by building
>> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
>> find "SimpleRTKCommon-0.9.lib" - which I just build.
>>
>> After some more investigation I realized that the SimpleRTKCommon is set
>> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
>> it to be a static linked library (LIB). After changing SimpleRTKCommon to
>> be build as a static library - and changing the output location - I could
>> build SimpleRTKBasicFilters0.
>>
>> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing
>> that to a LIB as well I could build SimpleRTKBasicFilters1, then
>> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>>
>> I'm unsure if the intention is to build them as static or dynamic
>> libraries, but in any case the current build configuration doesn't work -
>> on my setup at least.
>>
>> However, I should note than for some reason the "lua5" project did build
>> successfully out of the box. Whatever it does differently works.
>>
>> best
>>
>> Arvid
>>
>>
>>
>> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> I'm not an msvc specialist but your first line suggests that you have
>>> pasted only part of the log:
>>>
>>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) --
>>> FAILED.
>>> What you need to find out is why this build failed. If the build fails,
>>> the linking cannot work.
>>> Cheers,
>>> Simon
>>>
>>>
>>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>>
>>> I did a complete rebuild, and here is the end of the output:
>>> http://pastebin.com/hvQ33WWg
>>>
>>> I have to admit I'm not sure what to make of it. I should note that I'm
>>> trying to compile the version I just pulled from git earlier today, since
>>> the other version I normally work with is really old.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>>> another error before that which explains why it did not compile?
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Hi again.
>>>>>
>>>>> I've been trying to get it working. However, I did run into some
>>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>>> SimpleRTKCommon - which I do not have.
>>>>>
>>>>> Here is the last few lines from VS2013
>>>>>
>>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>>> > 5>
>>>>> > 5>      0 Warning(s)
>>>>> > 5>      2 Error(s)
>>>>> > 5>
>>>>> > 5>  Time Elapsed 00:00:25.26
>>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>>> ==========
>>>>>
>>>>> I'm not quite sure what is going on, because the only reference I can
>>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>>> RTK/CMakeLists.txt
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>>> python calls are available starting with Matlab 2014).
>>>>>> Simon
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>>> bottiger at gmail.com> wrote:
>>>>>>
>>>>>>> Dear Simon
>>>>>>>
>>>>>>> This look very interesting! Which platform did you successfully
>>>>>>> execute this on?
>>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>>> into any problems.
>>>>>>>
>>>>>>> best
>>>>>>>
>>>>>>> Arvid
>>>>>>>
>>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Dear RTK users,
>>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>>> and it seems to work well:
>>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but
>>>>>>>> let us know if you think otherwise.
>>>>>>>> Future works include a simple installation mechanism for
>>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
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From ajbatkinson at gmail.com  Wed Sep 28 08:11:12 2016
From: ajbatkinson at gmail.com (Abby Bryce Atkinson)
Date: Wed, 28 Sep 2016 13:11:12 +0100
Subject: [Rtk-users] 4DROOSTERReconstruction Example
Message-ID: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>

Hi,

I am trying to work through the 4DROOSTER example using the POPI patient
images (
http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) but
I am getting stuck when extracting the respiratory signal using the
amsterdam shroud.

I receive this error:


C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
--path .\Projections\ ^
More?                    --regexp '.*.his' ^
More?                    --output shroud.mha ^
More?                    --unsharp 650
ExceptionObject caught with writer->Update() in file
C:\RTK\applications\rtkamst
erdamshroud\rtkamsterdamshroud.cxx line 91

itk::ExceptionObject (0030E9E0)
Location: "void __thiscall itk::ImageFileWriter<class itk::Image<double,2>
>::Wr
ite(void)"
File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
Line: 284
Description: itk::ERROR: ImageFileWriter(03670318): Largest possible region
does
 not fully contain requested paste IO regionPaste IO region: ImageIORegion
(0030
EDD4)
  Dimension: 2
  Index: 0 0
  Size: 0 0
Largest possible region: ImageRegion (0030EE70)
  Dimension: 2
  Index: [0, 0]
  Size: [0, 0]


Can anyone help with a solution/tell me what I am doing wrong please?

Thanks,

Abby
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From simon.rit at creatis.insa-lyon.fr  Wed Sep 28 12:49:32 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 28 Sep 2016 18:49:32 +0200
Subject: [Rtk-users] 4DROOSTERReconstruction Example
In-Reply-To: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
References: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
Message-ID: <e23fc5ec-f7b4-846c-e349-f07564e2da8a@creatis.insa-lyon.fr>

Hi,

My guess is that the software does not find the projections. I would add 
the --verbose option and check that you actually input some projections. 
If not, I guess there is an issue with the path or the regexp in your 
command line.

Simon

On 28/09/2016 14:11, Abby Bryce Atkinson wrote:
> Hi,
>
> I am trying to work through the 4DROOSTER example using the POPI 
> patient images 
> (http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) 
> but I am getting stuck when extracting the respiratory signal using 
> the amsterdam shroud.
>
> I receive this error:
>
>
> C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
> --path .\Projections\ ^
> More?                    --regexp '.*.his' ^
> More?                    --output shroud.mha ^
> More?                    --unsharp 650
> ExceptionObject caught with writer->Update() in file 
> C:\RTK\applications\rtkamst
> erdamshroud\rtkamsterdamshroud.cxx line 91
>
> itk::ExceptionObject (0030E9E0)
> Location: "void __thiscall itk::ImageFileWriter<class 
> itk::Image<double,2> >::Wr
> ite(void)"
> File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
> Line: 284
> Description: itk::ERROR: ImageFileWriter(03670318): Largest possible 
> region does
>  not fully contain requested paste IO regionPaste IO region: 
> ImageIORegion (0030
> EDD4)
>   Dimension: 2
>   Index: 0 0
>   Size: 0 0
> Largest possible region: ImageRegion (0030EE70)
>   Dimension: 2
>   Index: [0, 0]
>   Size: [0, 0]
>
>
> Can anyone help with a solution/tell me what I am doing wrong please?
>
> Thanks,
>
> Abby
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users

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From signabdm at gmail.com  Mon Sep 12 06:58:59 2016
From: signabdm at gmail.com (Valeriy Signatulin)
Date: Mon, 12 Sep 2016 16:58:59 +0600
Subject: [Rtk-users] rotation of detector plane
Message-ID: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>

Hello RTK users.
Is it possible to specify rotation of detector plane in RTK ? (in
rtksimulategeom for example) If not, what is the best way to code this ?
By rotation of detector plane i mean twist, tilt, skew around the normal of
the detector as described in
http://www.ndt.net/article/v10n09/yisun/yisun.pdf page 6.
I'm trying to write the geometry calibration method described in this
article in RTK and i need to simulate these rotations to check the results.
Thanks.
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 12 08:40:31 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 12 Sep 2016 14:40:31 +0200
Subject: [Rtk-users] rotation of detector plane
In-Reply-To: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
References: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
Message-ID: <CAF0oig0C3zFcAaAhWHV9g+UY02i7cws7OU-7r2YadyAt3TH5GA@mail.gmail.com>

Hi,
You can do any rotation with RTK. The rotation is described 3 Euler angles,
see the geometry doc <http://www.openrtk.org/Doxygen/geometry.pdf>. From
the command line, that would be the --in_angle and out_angle that allow you
to modify the other angles than the standard angle for the position along
the circular rotation (GantryAngle). If you want to modify it per
projection, that's possible using C++ or Python code (AddProjection
<http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
method).
Good luck,
Simon

On Mon, Sep 12, 2016 at 12:58 PM, Valeriy Signatulin <signabdm at gmail.com>
wrote:

> Hello RTK users.
> Is it possible to specify rotation of detector plane in RTK ? (in
> rtksimulategeom for example) If not, what is the best way to code this ?
> By rotation of detector plane i mean twist, tilt, skew around the normal
> of the detector as described in http://www.ndt.net/article/
> v10n09/yisun/yisun.pdf page 6.
> I'm trying to write the geometry calibration method described in this
> article in RTK and i need to simulate these rotations to check the results.
> Thanks.
>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From andreasg at phys.au.dk  Tue Sep 13 13:06:46 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Tue, 13 Sep 2016 19:06:46 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
Message-ID: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>

Dear RTK experts,

I am reconstructing Varian ProBeam projections of the Xim image format. I
have written the reader myself - very similar to the Hnd one already
available with RTK.
Links to my fork: [XimReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkXimImageIO.cxx>,
XMLReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamXMLFileReader.cxx>,
GeometryReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamGeometryReader.cxx>
]

The reader apparently works (Images and angles displays as expected in UI),
however when reconstructing with a regular FDK* I get a reconstructed image
that is smeared out around the high and low density areas *[see attached
image]

I'm using half arc, full fan images with no bow-tie filter from Scripps
(~520 projections). Fixed detector and source (offset=0) with SID=2m,
SDD=3m.

*For the Hnd projections the reconstruction works perfectly (Same algorithm
<https://github.com/agravgaard/cbctrecon/blob/master/cbctrecon.cpp#L2726>).*
The reconstruction of the Xim projections performed on Varian software
works perfectly.

Without the Parker Short Scan Filter the first and last projections creates
streaks across the reconstruction as if they were way too bright.
If the first few projections are excluded, the following projection will
act the same way.

The projections are corrected for beam hardening and all the projections
have the expected attenuation.
No "smearing" filters (like median) is used, and iterative reconstruction
makes the same artifacts.

Setting the value of the first and last projection to zero has the same
effect as excluding. Changing the ramp filter only changes noise, not the
artifacts.

*Have any of you had a similar problem? *Am I missing something?
Any suggestions are welcome I'm running out of ideas.

Best regards
Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 13 16:18:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 13 Sep 2016 22:18:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
Message-ID: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>

Hi,
I have almost never worked with Varian data but it looks like a
geometry problem. Maybe the problem comes from a bad ordering of the
projections which results in assigning a bad geometry to each
projection. How did you name your projections? Maybe check that the
order matches that of the RTK geometry file. Otherwise, there might be
an issue in the creation of the geometry file itself.
All this sounds good, happy bug hunt and don't hesitate to share your
code when you feel it's ready.
Simon

On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
<andreasg at phys.au.dk> wrote:
> Dear RTK experts,
>
> I am reconstructing Varian ProBeam projections of the Xim image format. I
> have written the reader myself - very similar to the Hnd one already
> available with RTK.
> Links to my fork: [XimReader, XMLReader, GeometryReader]
>
> The reader apparently works (Images and angles displays as expected in UI),
> however when reconstructing with a regular FDK I get a reconstructed image
> that is smeared out around the high and low density areas [see attached
> image]
>
> I'm using half arc, full fan images with no bow-tie filter from Scripps
> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
> SDD=3m.
>
> For the Hnd projections the reconstruction works perfectly (Same algorithm).
> The reconstruction of the Xim projections performed on Varian software works
> perfectly.
>
> Without the Parker Short Scan Filter the first and last projections creates
> streaks across the reconstruction as if they were way too bright.
> If the first few projections are excluded, the following projection will act
> the same way.
>
> The projections are corrected for beam hardening and all the projections
> have the expected attenuation.
> No "smearing" filters (like median) is used, and iterative reconstruction
> makes the same artifacts.
>
> Setting the value of the first and last projection to zero has the same
> effect as excluding. Changing the ramp filter only changes noise, not the
> artifacts.
>
> Have any of you had a similar problem? Am I missing something?
> Any suggestions are welcome I'm running out of ideas.
>
> Best regards
> Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>


From cyril.mory at creatis.insa-lyon.fr  Wed Sep 14 03:10:42 2016
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 14 Sep 2016 09:10:42 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
Message-ID: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>

One suggestion since it works with the Hnd projections:
You can run rtkprojections twice (with the Hnd projections, then with 
Xim projections) and output two projection stack files and two geometry 
files, then compare the projection stack files by subtracting one to the 
other (with SimpleRTK or clitk) and the geometry files with diff. If 
they are identical, then I do not see any reason why the reconstructions 
should be different, so my guess is that you will find differences.

On 09/13/2016 10:18 PM, Simon Rit wrote:
> Hi,
> I have almost never worked with Varian data but it looks like a
> geometry problem. Maybe the problem comes from a bad ordering of the
> projections which results in assigning a bad geometry to each
> projection. How did you name your projections? Maybe check that the
> order matches that of the RTK geometry file. Otherwise, there might be
> an issue in the creation of the geometry file itself.
> All this sounds good, happy bug hunt and don't hesitate to share your
> code when you feel it's ready.
> Simon
>
> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
> <andreasg at phys.au.dk> wrote:
>> Dear RTK experts,
>>
>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>> have written the reader myself - very similar to the Hnd one already
>> available with RTK.
>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>
>> The reader apparently works (Images and angles displays as expected in UI),
>> however when reconstructing with a regular FDK I get a reconstructed image
>> that is smeared out around the high and low density areas [see attached
>> image]
>>
>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>> SDD=3m.
>>
>> For the Hnd projections the reconstruction works perfectly (Same algorithm).
>> The reconstruction of the Xim projections performed on Varian software works
>> perfectly.
>>
>> Without the Parker Short Scan Filter the first and last projections creates
>> streaks across the reconstruction as if they were way too bright.
>> If the first few projections are excluded, the following projection will act
>> the same way.
>>
>> The projections are corrected for beam hardening and all the projections
>> have the expected attenuation.
>> No "smearing" filters (like median) is used, and iterative reconstruction
>> makes the same artifacts.
>>
>> Setting the value of the first and last projection to zero has the same
>> effect as excluding. Changing the ramp filter only changes noise, not the
>> artifacts.
>>
>> Have any of you had a similar problem? Am I missing something?
>> Any suggestions are welcome I'm running out of ideas.
>>
>> Best regards
>> Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>



From andreasg at phys.au.dk  Fri Sep 16 08:56:34 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 14:56:34 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
Message-ID: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>

Thanks for the suggestions, Simon and Cyril!

I have been carefully looking though the geometry and from what I
understand of the transformations matrices, the geometry looks correct/(as
expected).

HOWEVER: I found out that the reason for the Hnd to behave differently were
because had used half-fan scans (full-arc).
When I used a full-fan (half-arc) scan of Hnd projections the same
artifacts occurs!

Are there other (built-in) means of improving half-arc scans, than the
parker short scan filter?

Parker short scan does a decent job, but the result is still far from the
quality of the Varian software reconstruction at least for the CatPhan.

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:

> One suggestion since it works with the Hnd projections:
> You can run rtkprojections twice (with the Hnd projections, then with Xim
> projections) and output two projection stack files and two geometry files,
> then compare the projection stack files by subtracting one to the other
> (with SimpleRTK or clitk) and the geometry files with diff. If they are
> identical, then I do not see any reason why the reconstructions should be
> different, so my guess is that you will find differences.
>
>
> On 09/13/2016 10:18 PM, Simon Rit wrote:
>
>> Hi,
>> I have almost never worked with Varian data but it looks like a
>> geometry problem. Maybe the problem comes from a bad ordering of the
>> projections which results in assigning a bad geometry to each
>> projection. How did you name your projections? Maybe check that the
>> order matches that of the RTK geometry file. Otherwise, there might be
>> an issue in the creation of the geometry file itself.
>> All this sounds good, happy bug hunt and don't hesitate to share your
>> code when you feel it's ready.
>> Simon
>>
>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>> <andreasg at phys.au.dk> wrote:
>>
>>> Dear RTK experts,
>>>
>>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>>> have written the reader myself - very similar to the Hnd one already
>>> available with RTK.
>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>
>>> The reader apparently works (Images and angles displays as expected in
>>> UI),
>>> however when reconstructing with a regular FDK I get a reconstructed
>>> image
>>> that is smeared out around the high and low density areas [see attached
>>> image]
>>>
>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>> SDD=3m.
>>>
>>> For the Hnd projections the reconstruction works perfectly (Same
>>> algorithm).
>>> The reconstruction of the Xim projections performed on Varian software
>>> works
>>> perfectly.
>>>
>>> Without the Parker Short Scan Filter the first and last projections
>>> creates
>>> streaks across the reconstruction as if they were way too bright.
>>> If the first few projections are excluded, the following projection will
>>> act
>>> the same way.
>>>
>>> The projections are corrected for beam hardening and all the projections
>>> have the expected attenuation.
>>> No "smearing" filters (like median) is used, and iterative reconstruction
>>> makes the same artifacts.
>>>
>>> Setting the value of the first and last projection to zero has the same
>>> effect as excluding. Changing the ramp filter only changes noise, not the
>>> artifacts.
>>>
>>> Have any of you had a similar problem? Am I missing something?
>>> Any suggestions are welcome I'm running out of ideas.
>>>
>>> Best regards
>>> Andreas
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Sep 16 10:13:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 16 Sep 2016 16:13:26 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
Message-ID: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>

Hi,
You can try any iterative reconstruction, they can also handle short scans.
Start with a few iterations of rtksart or rtkconjugategradient. However,
the nature of the artifacts indicate more a problem in the geometry in my
opinion. I have seen such errors when, for example, rotating in the wrong
direction. I can have a look if you share the dataset.
Cheers,
Simon

On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the suggestions, Simon and Cyril!
>
> I have been carefully looking though the geometry and from what I
> understand of the transformations matrices, the geometry looks correct/(as
> expected).
>
> HOWEVER: I found out that the reason for the Hnd to behave differently
> were because had used half-fan scans (full-arc).
> When I used a full-fan (half-arc) scan of Hnd projections the same
> artifacts occurs!
>
> Are there other (built-in) means of improving half-arc scans, than the
> parker short scan filter?
>
> Parker short scan does a decent job, but the result is still far from the
> quality of the Varian software reconstruction at least for the CatPhan.
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>
>> One suggestion since it works with the Hnd projections:
>> You can run rtkprojections twice (with the Hnd projections, then with Xim
>> projections) and output two projection stack files and two geometry files,
>> then compare the projection stack files by subtracting one to the other
>> (with SimpleRTK or clitk) and the geometry files with diff. If they are
>> identical, then I do not see any reason why the reconstructions should be
>> different, so my guess is that you will find differences.
>>
>>
>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>
>>> Hi,
>>> I have almost never worked with Varian data but it looks like a
>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>> projections which results in assigning a bad geometry to each
>>> projection. How did you name your projections? Maybe check that the
>>> order matches that of the RTK geometry file. Otherwise, there might be
>>> an issue in the creation of the geometry file itself.
>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>> code when you feel it's ready.
>>> Simon
>>>
>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>> <andreasg at phys.au.dk> wrote:
>>>
>>>> Dear RTK experts,
>>>>
>>>> I am reconstructing Varian ProBeam projections of the Xim image format.
>>>> I
>>>> have written the reader myself - very similar to the Hnd one already
>>>> available with RTK.
>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>
>>>> The reader apparently works (Images and angles displays as expected in
>>>> UI),
>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>> image
>>>> that is smeared out around the high and low density areas [see attached
>>>> image]
>>>>
>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>> SDD=3m.
>>>>
>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>> algorithm).
>>>> The reconstruction of the Xim projections performed on Varian software
>>>> works
>>>> perfectly.
>>>>
>>>> Without the Parker Short Scan Filter the first and last projections
>>>> creates
>>>> streaks across the reconstruction as if they were way too bright.
>>>> If the first few projections are excluded, the following projection
>>>> will act
>>>> the same way.
>>>>
>>>> The projections are corrected for beam hardening and all the projections
>>>> have the expected attenuation.
>>>> No "smearing" filters (like median) is used, and iterative
>>>> reconstruction
>>>> makes the same artifacts.
>>>>
>>>> Setting the value of the first and last projection to zero has the same
>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>> the
>>>> artifacts.
>>>>
>>>> Have any of you had a similar problem? Am I missing something?
>>>> Any suggestions are welcome I'm running out of ideas.
>>>>
>>>> Best regards
>>>> Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> N?rrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     andreasg at phys.au.dk
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From andreasg at phys.au.dk  Fri Sep 16 16:37:43 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 22:37:43 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
Message-ID: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>

Thanks for the fast response Simon!

I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
right all along!
I just didn't get why it makes a difference. I think I do now, as the
resulting image was flipped upside down and not left/right as I expected.
[attached]

The reconstruction is significantly better, I'll look into what should be
included in the reader and what I should keep in my program to keep
conformity with the other readers. Then I'll create a pull request.

Just for the purpose of others hitting the same or a similar bug, I also
attempted:
I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
back/forward projection, *but with no* significant improvement [attached]

And:
If you want you can download the data set from: [Dropbox link to 460MB zip
<https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep it
up as long as Dropbox allows me)] Only the Acquisitions/subfolder is used
along with the Scan.xml (Calibrations folder may be used in the future in
my program, but I'm not sure if you can rely on the existence of the
content).

A MatLab XimReader is available: link
<https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
available from Varian bitbucket along a with a python version and a
C#->matlab plugin
<https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). Otherwise
my fork with the RTK-style reader is available from the same repository (I
have also added Hnc support, thanks to the Geoff Hugo fork, so bzip2 is a
new dependancy).

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:

> Hi,
> You can try any iterative reconstruction, they can also handle short
> scans. Start with a few iterations of rtksart or rtkconjugategradient.
> However, the nature of the artifacts indicate more a problem in the
> geometry in my opinion. I have seen such errors when, for example, rotating
> in the wrong direction. I can have a look if you share the dataset.
> Cheers,
> Simon
>
> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
> andreasg at phys.au.dk> wrote:
>
>> Thanks for the suggestions, Simon and Cyril!
>>
>> I have been carefully looking though the geometry and from what I
>> understand of the transformations matrices, the geometry looks correct/(as
>> expected).
>>
>> HOWEVER: I found out that the reason for the Hnd to behave differently
>> were because had used half-fan scans (full-arc).
>> When I used a full-fan (half-arc) scan of Hnd projections the same
>> artifacts occurs!
>>
>> Are there other (built-in) means of improving half-arc scans, than the
>> parker short scan filter?
>>
>> Parker short scan does a decent job, but the result is still far from the
>> quality of the Varian software reconstruction at least for the CatPhan.
>>
>> Best regards
>> Andreas
>>
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>>
>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>
>>> One suggestion since it works with the Hnd projections:
>>> You can run rtkprojections twice (with the Hnd projections, then with
>>> Xim projections) and output two projection stack files and two geometry
>>> files, then compare the projection stack files by subtracting one to the
>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>> are identical, then I do not see any reason why the reconstructions should
>>> be different, so my guess is that you will find differences.
>>>
>>>
>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>
>>>> Hi,
>>>> I have almost never worked with Varian data but it looks like a
>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>> projections which results in assigning a bad geometry to each
>>>> projection. How did you name your projections? Maybe check that the
>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>> an issue in the creation of the geometry file itself.
>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>> code when you feel it's ready.
>>>> Simon
>>>>
>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>> <andreasg at phys.au.dk> wrote:
>>>>
>>>>> Dear RTK experts,
>>>>>
>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>> format. I
>>>>> have written the reader myself - very similar to the Hnd one already
>>>>> available with RTK.
>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>
>>>>> The reader apparently works (Images and angles displays as expected in
>>>>> UI),
>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>> image
>>>>> that is smeared out around the high and low density areas [see attached
>>>>> image]
>>>>>
>>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>> SDD=3m.
>>>>>
>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>> algorithm).
>>>>> The reconstruction of the Xim projections performed on Varian software
>>>>> works
>>>>> perfectly.
>>>>>
>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>> creates
>>>>> streaks across the reconstruction as if they were way too bright.
>>>>> If the first few projections are excluded, the following projection
>>>>> will act
>>>>> the same way.
>>>>>
>>>>> The projections are corrected for beam hardening and all the
>>>>> projections
>>>>> have the expected attenuation.
>>>>> No "smearing" filters (like median) is used, and iterative
>>>>> reconstruction
>>>>> makes the same artifacts.
>>>>>
>>>>> Setting the value of the first and last projection to zero has the same
>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>> the
>>>>> artifacts.
>>>>>
>>>>> Have any of you had a similar problem? Am I missing something?
>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>
>>>>> Best regards
>>>>> Andreas
>>>>>
>>>>> __________________________________
>>>>>
>>>>> Andreas Gravgaard Andersen
>>>>>
>>>>> Department of Oncology,
>>>>>
>>>>> Aarhus University Hospital
>>>>>
>>>>> N?rrebrogade 44,
>>>>>
>>>>> 8000, Aarhus C
>>>>>
>>>>> Mail:     andreasg at phys.au.dk
>>>>>
>>>>> Cell:      +45 3165 8140
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 03:26:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 09:26:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
 <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
Message-ID: <CAF0oig2TSmAsSn=o3aLo6LEFDOSaKRtfknjMer24rcDKJ-0Fqg@mail.gmail.com>

Hi,
Thanks for sharing. There still seems to be some streak artefacts, do you
see the same in the Varian reconstruction?
I'm looking forward to the pull-request, I think we should try to make the
bzip2 optional.
Simon

On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the fast response Simon!
>
> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
> right all along!
> I just didn't get why it makes a difference. I think I do now, as the
> resulting image was flipped upside down and not left/right as I expected.
> [attached]
>
> The reconstruction is significantly better, I'll look into what should be
> included in the reader and what I should keep in my program to keep
> conformity with the other readers. Then I'll create a pull request.
>
> Just for the purpose of others hitting the same or a similar bug, I also
> attempted:
> I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
> back/forward projection, *but with no* significant improvement [attached]
>
> And:
> If you want you can download the data set from: [Dropbox link to 460MB zip
> <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep
> it up as long as Dropbox allows me)] Only the Acquisitions/subfolder is
> used along with the Scan.xml (Calibrations folder may be used in the future
> in my program, but I'm not sure if you can rely on the existence of the
> content).
>
> A MatLab XimReader is available: link
> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
> available from Varian bitbucket along a with a python version and a
> C#->matlab plugin
> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>).
> Otherwise my fork with the RTK-style reader is available from the same
> repository (I have also added Hnc support, thanks to the Geoff Hugo fork,
> so bzip2 is a new dependancy).
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> Hi,
>> You can try any iterative reconstruction, they can also handle short
>> scans. Start with a few iterations of rtksart or rtkconjugategradient.
>> However, the nature of the artifacts indicate more a problem in the
>> geometry in my opinion. I have seen such errors when, for example, rotating
>> in the wrong direction. I can have a look if you share the dataset.
>> Cheers,
>> Simon
>>
>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
>> andreasg at phys.au.dk> wrote:
>>
>>> Thanks for the suggestions, Simon and Cyril!
>>>
>>> I have been carefully looking though the geometry and from what I
>>> understand of the transformations matrices, the geometry looks correct/(as
>>> expected).
>>>
>>> HOWEVER: I found out that the reason for the Hnd to behave differently
>>> were because had used half-fan scans (full-arc).
>>> When I used a full-fan (half-arc) scan of Hnd projections the same
>>> artifacts occurs!
>>>
>>> Are there other (built-in) means of improving half-arc scans, than the
>>> parker short scan filter?
>>>
>>> Parker short scan does a decent job, but the result is still far from
>>> the quality of the Varian software reconstruction at least for the CatPhan.
>>>
>>> Best regards
>>> Andreas
>>>
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>>
>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>>
>>>> One suggestion since it works with the Hnd projections:
>>>> You can run rtkprojections twice (with the Hnd projections, then with
>>>> Xim projections) and output two projection stack files and two geometry
>>>> files, then compare the projection stack files by subtracting one to the
>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>>> are identical, then I do not see any reason why the reconstructions should
>>>> be different, so my guess is that you will find differences.
>>>>
>>>>
>>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>>
>>>>> Hi,
>>>>> I have almost never worked with Varian data but it looks like a
>>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>>> projections which results in assigning a bad geometry to each
>>>>> projection. How did you name your projections? Maybe check that the
>>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>>> an issue in the creation of the geometry file itself.
>>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>>> code when you feel it's ready.
>>>>> Simon
>>>>>
>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>>> <andreasg at phys.au.dk> wrote:
>>>>>
>>>>>> Dear RTK experts,
>>>>>>
>>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>>> format. I
>>>>>> have written the reader myself - very similar to the Hnd one already
>>>>>> available with RTK.
>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>>
>>>>>> The reader apparently works (Images and angles displays as expected
>>>>>> in UI),
>>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>>> image
>>>>>> that is smeared out around the high and low density areas [see
>>>>>> attached
>>>>>> image]
>>>>>>
>>>>>> I'm using half arc, full fan images with no bow-tie filter from
>>>>>> Scripps
>>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>>> SDD=3m.
>>>>>>
>>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>>> algorithm).
>>>>>> The reconstruction of the Xim projections performed on Varian
>>>>>> software works
>>>>>> perfectly.
>>>>>>
>>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>>> creates
>>>>>> streaks across the reconstruction as if they were way too bright.
>>>>>> If the first few projections are excluded, the following projection
>>>>>> will act
>>>>>> the same way.
>>>>>>
>>>>>> The projections are corrected for beam hardening and all the
>>>>>> projections
>>>>>> have the expected attenuation.
>>>>>> No "smearing" filters (like median) is used, and iterative
>>>>>> reconstruction
>>>>>> makes the same artifacts.
>>>>>>
>>>>>> Setting the value of the first and last projection to zero has the
>>>>>> same
>>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>>> the
>>>>>> artifacts.
>>>>>>
>>>>>> Have any of you had a similar problem? Am I missing something?
>>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>>
>>>>>> Best regards
>>>>>> Andreas
>>>>>>
>>>>>> __________________________________
>>>>>>
>>>>>> Andreas Gravgaard Andersen
>>>>>>
>>>>>> Department of Oncology,
>>>>>>
>>>>>> Aarhus University Hospital
>>>>>>
>>>>>> N?rrebrogade 44,
>>>>>>
>>>>>> 8000, Aarhus C
>>>>>>
>>>>>> Mail:     andreasg at phys.au.dk
>>>>>>
>>>>>> Cell:      +45 3165 8140
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:05:24 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:05:24 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
Message-ID: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>

Dear RTK users,
I have quickly tested calling the SimpleRTK python lib from Matlab and it
seems to work well:
http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
Therefore, I don't think we have to work on Matlab wrappings but let us
know if you think otherwise.
Future works include a simple installation mechanism for pre-compiled
SimpleRTK libraries. We'll keep you posted!
Simon
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From bottiger at gmail.com  Mon Sep 19 05:14:03 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 11:14:03 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
Message-ID: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>

Dear Simon

This look very interesting! Which platform did you successfully execute
this on?
I will give it a try at once (on windows) and let you know if I run into
any problems.

best

Arvid

On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> I have quickly tested calling the SimpleRTK python lib from Matlab and it
> seems to work well:
> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
> Therefore, I don't think we have to work on Matlab wrappings but let us
> know if you think otherwise.
> Future works include a simple installation mechanism for pre-compiled
> SimpleRTK libraries. We'll keep you posted!
> Simon
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:19:28 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:19:28 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
Message-ID: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>

The latest MacOS. It's nice if you can test it on other platforms, I'll try
to run it on Linux but I have to upgrade matlab first (I think python calls
are available starting with Matlab 2014).
Simon

On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Dear Simon
>
> This look very interesting! Which platform did you successfully execute
> this on?
> I will give it a try at once (on windows) and let you know if I run into
> any problems.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> Dear RTK users,
>> I have quickly tested calling the SimpleRTK python lib from Matlab and it
>> seems to work well:
>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>> Therefore, I don't think we have to work on Matlab wrappings but let us
>> know if you think otherwise.
>> Future works include a simple installation mechanism for pre-compiled
>> SimpleRTK libraries. We'll keep you posted!
>> Simon
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From bottiger at gmail.com  Mon Sep 19 08:30:32 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 14:30:32 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
Message-ID: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>

Hi again.

I've been trying to get it working. However, I did run into some problems
compiling SimpleRTK. The main issue seems to be that it depends on
SimpleRTKCommon - which I do not have.

Here is the last few lines from VS2013

> 5>LINK : fatal error LNK1181: cannot open input file
'..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib' [C:\Users\aplb\Work\RTK\RTK1.2-
> bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> 5>
> 5>      0 Warning(s)
> 5>      2 Error(s)
> 5>
> 5>  Time Elapsed 00:00:25.26
> ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
==========

I'm not quite sure what is going on, because the only reference I can find
to SimpleRTKCommon is the CMakeLists.txt on github:
https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt

best

Arvid

On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> The latest MacOS. It's nice if you can test it on other platforms, I'll
> try to run it on Linux but I have to upgrade matlab first (I think python
> calls are available starting with Matlab 2014).
> Simon
>
> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Dear Simon
>>
>> This look very interesting! Which platform did you successfully execute
>> this on?
>> I will give it a try at once (on windows) and let you know if I run into
>> any problems.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Dear RTK users,
>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>> it seems to work well:
>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>> know if you think otherwise.
>>> Future works include a simple installation mechanism for pre-compiled
>>> SimpleRTK libraries. We'll keep you posted!
>>> Simon
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 12:50:33 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 18:50:33 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
Message-ID: <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>

 SimpleRTKCommon is a library generated when compiling. Don't you have
another error before that which explains why it did not compile?
Simon

On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I've been trying to get it working. However, I did run into some problems
> compiling SimpleRTK. The main issue seems to be that it depends on
> SimpleRTKCommon - which I do not have.
>
> Here is the last few lines from VS2013
>
> > 5>LINK : fatal error LNK1181: cannot open input file '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
> [C:\Users\aplb\Work\RTK\RTK1.2-
> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> > 5>
> > 5>      0 Warning(s)
> > 5>      2 Error(s)
> > 5>
> > 5>  Time Elapsed 00:00:25.26
> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
> ==========
>
> I'm not quite sure what is going on, because the only reference I can find
> to SimpleRTKCommon is the CMakeLists.txt on github:
> https://github.com/SimonRit/RTK/blob/master/utilities/
> SimpleRTK/CMakeLists.txt
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>> try to run it on Linux but I have to upgrade matlab first (I think python
>> calls are available starting with Matlab 2014).
>> Simon
>>
>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Dear Simon
>>>
>>> This look very interesting! Which platform did you successfully execute
>>> this on?
>>> I will give it a try at once (on windows) and let you know if I run into
>>> any problems.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Dear RTK users,
>>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>>> it seems to work well:
>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>>> know if you think otherwise.
>>>> Future works include a simple installation mechanism for pre-compiled
>>>> SimpleRTK libraries. We'll keep you posted!
>>>> Simon
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 01:33:46 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 07:33:46 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
Message-ID: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>

I'm not an msvc specialist but your first line suggests that you have 
pasted only part of the log:

20>  Done Building Project 
"C:\Users\aplb\Work\RTK\RTK1.2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" 
(default targets) -- FAILED.

What you need to find out is why this build failed. If the build fails, 
the linking cannot work.
Cheers,
Simon

On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
> I did a complete rebuild, and here is the end of the output: 
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that 
> I'm trying to compile the version I just pulled from git earlier 
> today, since the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     SimpleRTKCommon is a library generated when compiling. Don't you
>     have another error before that which explains why it did not compile?
>     Simon
>
>     On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger
>     <bottiger at gmail.com <mailto:bottiger at gmail.com>> wrote:
>
>         Hi again.
>
>         I've been trying to get it working. However, I did run into
>         some problems compiling SimpleRTK. The main issue seems to be
>         that it depends on SimpleRTKCommon - which I do not have.
>
>         Here is the last few lines from VS2013
>
>         > 5>LINK : fatal error LNK1181: cannot open input file
>         '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>         [C:\Users\aplb\Work\RTK\RTK1.2-
>         > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>         > 5>
>         > 5>      0 Warning(s)
>         > 5>      2 Error(s)
>         > 5>
>         > 5>  Time Elapsed 00:00:25.26
>         > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0
>         skipped ==========
>
>         I'm not quite sure what is going on, because the only
>         reference I can find to SimpleRTKCommon is the CMakeLists.txt
>         on github:
>         https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt
>         <https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt>
>
>         best
>
>         Arvid
>
>         On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit
>         <simon.rit at creatis.insa-lyon.fr
>         <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>             The latest MacOS. It's nice if you can test it on other
>             platforms, I'll try to run it on Linux but I have to
>             upgrade matlab first (I think python calls are available
>             starting with Matlab 2014).
>             Simon
>
>             On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen
>             B?ttiger <bottiger at gmail.com <mailto:bottiger at gmail.com>>
>             wrote:
>
>                 Dear Simon
>
>                 This look very interesting! Which platform did you
>                 successfully execute this on?
>                 I will give it a try at once (on windows) and let you
>                 know if I run into any problems.
>
>                 best
>
>                 Arvid
>
>                 On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit
>                 <simon.rit at creatis.insa-lyon.fr
>                 <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>                     Dear RTK users,
>                     I have quickly tested calling the SimpleRTK python
>                     lib from Matlab and it seems to work well:
>                     http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>                     <http://wiki.openrtk.org/index.php/SimpleRTK#Matlab>
>                     Therefore, I don't think we have to work on Matlab
>                     wrappings but let us know if you think otherwise.
>                     Future works include a simple installation
>                     mechanism for pre-compiled SimpleRTK libraries.
>                     We'll keep you posted!
>                     Simon
>
>                     _______________________________________________
>                     Rtk-users mailing list
>                     Rtk-users at public.kitware.com
>                     <mailto:Rtk-users at public.kitware.com>
>                     http://public.kitware.com/mailman/listinfo/rtk-users
>                     <http://public.kitware.com/mailman/listinfo/rtk-users>
>
>
>
>
>
>

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From bottiger at gmail.com  Tue Sep 20 08:17:35 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Tue, 20 Sep 2016 14:17:35 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
Message-ID: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>

Hi again.

I understand, but could you please help me get in contact with the person
who knows something about the windows build (if any), I think there is
something wrong.

I have been investigating the build problems I had and found that in the
sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
opened it up and found the projects which I had problems building:
"SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.

When I then tried to build SimpleRTKCommon manually it just compiled
without any problems. However, when I followed up by building
"SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
find "SimpleRTKCommon-0.9.lib" - which I just build.

After some more investigation I realized that the SimpleRTKCommon is set to
build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects it
to be a static linked library (LIB). After changing SimpleRTKCommon to be
build as a static library - and changing the output location - I could
build SimpleRTKBasicFilters0.

However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
to a LIB as well I could build SimpleRTKBasicFilters1, then
SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.

I'm unsure if the intention is to build them as static or dynamic
libraries, but in any case the current build configuration doesn't work -
on my setup at least.

However, I should note than for some reason the "lua5" project did build
successfully out of the box. Whatever it does differently works.

best

Arvid



On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> I'm not an msvc specialist but your first line suggests that you have
> pasted only part of the log:
>
> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.
> 2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
> What you need to find out is why this build failed. If the build fails,
> the linking cannot work.
> Cheers,
> Simon
>
>
> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>
> I did a complete rebuild, and here is the end of the output:
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that I'm
> trying to compile the version I just pulled from git earlier today, since
> the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> SimpleRTKCommon is a library generated when compiling. Don't you have
>> another error before that which explains why it did not compile?
>> Simon
>>
>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Hi again.
>>>
>>> I've been trying to get it working. However, I did run into some
>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>> SimpleRTKCommon - which I do not have.
>>>
>>> Here is the last few lines from VS2013
>>>
>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>> > 5>
>>> > 5>      0 Warning(s)
>>> > 5>      2 Error(s)
>>> > 5>
>>> > 5>  Time Elapsed 00:00:25.26
>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>> ==========
>>>
>>> I'm not quite sure what is going on, because the only reference I can
>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>> RTK/CMakeLists.txt
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>>>> try to run it on Linux but I have to upgrade matlab first (I think python
>>>> calls are available starting with Matlab 2014).
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Dear Simon
>>>>>
>>>>> This look very interesting! Which platform did you successfully
>>>>> execute this on?
>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>> into any problems.
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Dear RTK users,
>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>> and it seems to work well:
>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>> us know if you think otherwise.
>>>>>> Future works include a simple installation mechanism for pre-compiled
>>>>>> SimpleRTK libraries. We'll keep you posted!
>>>>>> Simon
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 10:19:20 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 16:19:20 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
Message-ID: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>

Hi,
Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
I can't solve your problem but Kitware is going to look into an upgrade of
SimpleRTK in the coming days, I'll ask them if they know what is the issue.
If you look here:
http://my.cdash.org/viewNotes.php?buildid=1052065
this is a nightly build of SimpleRTK on Windows and it seems to work. I
don't see why it wouldn't work for you.
Simon

On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I understand, but could you please help me get in contact with the person
> who knows something about the windows build (if any), I think there is
> something wrong.
>
> I have been investigating the build problems I had and found that in the
> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
> opened it up and found the projects which I had problems building:
> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>
> When I then tried to build SimpleRTKCommon manually it just compiled
> without any problems. However, when I followed up by building
> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
> find "SimpleRTKCommon-0.9.lib" - which I just build.
>
> After some more investigation I realized that the SimpleRTKCommon is set
> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
> it to be a static linked library (LIB). After changing SimpleRTKCommon to
> be build as a static library - and changing the output location - I could
> build SimpleRTKBasicFilters0.
>
> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
> to a LIB as well I could build SimpleRTKBasicFilters1, then
> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>
> I'm unsure if the intention is to build them as static or dynamic
> libraries, but in any case the current build configuration doesn't work -
> on my setup at least.
>
> However, I should note than for some reason the "lua5" project did build
> successfully out of the box. Whatever it does differently works.
>
> best
>
> Arvid
>
>
>
> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> I'm not an msvc specialist but your first line suggests that you have
>> pasted only part of the log:
>>
>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
>> What you need to find out is why this build failed. If the build fails,
>> the linking cannot work.
>> Cheers,
>> Simon
>>
>>
>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>
>> I did a complete rebuild, and here is the end of the output:
>> http://pastebin.com/hvQ33WWg
>>
>> I have to admit I'm not sure what to make of it. I should note that I'm
>> trying to compile the version I just pulled from git earlier today, since
>> the other version I normally work with is really old.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>> another error before that which explains why it did not compile?
>>> Simon
>>>
>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>> bottiger at gmail.com> wrote:
>>>
>>>> Hi again.
>>>>
>>>> I've been trying to get it working. However, I did run into some
>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>> SimpleRTKCommon - which I do not have.
>>>>
>>>> Here is the last few lines from VS2013
>>>>
>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>> > 5>
>>>> > 5>      0 Warning(s)
>>>> > 5>      2 Error(s)
>>>> > 5>
>>>> > 5>  Time Elapsed 00:00:25.26
>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>> ==========
>>>>
>>>> I'm not quite sure what is going on, because the only reference I can
>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>> RTK/CMakeLists.txt
>>>>
>>>> best
>>>>
>>>> Arvid
>>>>
>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>> python calls are available starting with Matlab 2014).
>>>>> Simon
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>> bottiger at gmail.com> wrote:
>>>>>
>>>>>> Dear Simon
>>>>>>
>>>>>> This look very interesting! Which platform did you successfully
>>>>>> execute this on?
>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>> into any problems.
>>>>>>
>>>>>> best
>>>>>>
>>>>>> Arvid
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>
>>>>>>> Dear RTK users,
>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>> and it seems to work well:
>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>>> us know if you think otherwise.
>>>>>>> Future works include a simple installation mechanism for
>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>> Simon
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 02:40:50 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 08:40:50 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
Message-ID: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>

Dear RTK users,
RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
been released, about 7 months after RTK v1.2.0.

Release notes :
- Style updated (follow more closely latest ITK guidelines).
- Started using Travis CI, github pull requests should now be used for code
submission.
- New pre-processing functionalities:
  * CUDA polynomial gain correction,
  * scatter glare correction,
  * lag correction,
  * idark option,
  * removed threshold to positive values after i0 LUT.
- Improved CUDA forward and backprojection speed using projection slabs.
- Added motion-compensated forward and back projection operators in CUDA,
in both 3D and 4D.
- Added the rtkregularizedconjugategradient application, which performs 3D
regularized reconstruction by conjugate gradient + optional regularizations
(Positivity, TV, Wavelets).
- Made the rtkfourdrooster, rtkmcrooster and rtkregularizedconjugategradient
fully modular. Each regularization step can be made active or inactive.
- Added a filter to minimize the L0 norm of the temporal gradient (one-D
only).

Many thanks to the contributors, in alphabetical order for this release: Cyril
Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien
Jomier, S?bastien
Brousmiche, Simon Rit

As usual, be aware that we don't focus on releases since we have a public
github repository <http://github.com/SimonRit/RTK> that we try to keep
stable. I still recommend the use of the master HEAD over releases to enjoy
the new RTK developments before their release. We still have a few on-going
projects for which we will use and enhance RTK.

Simon (for the RTK consortium)
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 04:48:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 10:48:26 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
In-Reply-To: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
References: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
Message-ID: <CAF0oig0=5_KPN198JzsGQXDd07Nvw_Ew+qSGhguk0m27s3U-3Q@mail.gmail.com>

Sorry, I had forgotten to change the release number in the source file.
It's been corrected, you will have to move your tag locally or update your
file if you had already downloaded it.
Simon

On Thu, Sep 22, 2016 at 8:40 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
> been released, about 7 months after RTK v1.2.0.
>
> Release notes :
> - Style updated (follow more closely latest ITK guidelines).
> - Started using Travis CI, github pull requests should now be used for
> code submission.
> - New pre-processing functionalities:
>   * CUDA polynomial gain correction,
>   * scatter glare correction,
>   * lag correction,
>   * idark option,
>   * removed threshold to positive values after i0 LUT.
> - Improved CUDA forward and backprojection speed using projection slabs.
> - Added motion-compensated forward and back projection operators in CUDA,
> in both 3D and 4D.
> - Added the rtkregularizedconjugategradient application, which performs
> 3D regularized reconstruction by conjugate gradient + optional
> regularizations (Positivity, TV, Wavelets).
> - Made the rtkfourdrooster, rtkmcrooster and
> rtkregularizedconjugategradient fully modular. Each regularization step
> can be made active or inactive.
> - Added a filter to minimize the L0 norm of the temporal gradient (one-D
> only).
>
> Many thanks to the contributors, in alphabetical order for this release: Cyril
> Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien Jomier, S?bastien
> Brousmiche, Simon Rit
>
> As usual, be aware that we don't focus on releases since we have a public
> github repository <http://github.com/SimonRit/RTK> that we try to keep
> stable. I still recommend the use of the master HEAD over releases to
> enjoy the new RTK developments before their release. We still have a few
> on-going projects for which we will use and enhance RTK.
>
> Simon (for the RTK consortium)
>
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From bottiger at gmail.com  Fri Sep 23 04:29:06 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Fri, 23 Sep 2016 10:29:06 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
 <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
Message-ID: <CANBwxwEvaUrvd1X=74g=V2JmDwtrQKFDtyUdAZJn5CRCBCkb8g@mail.gmail.com>

Hi again.

I've been spending some more time with this, and feel I learned a little
bit more. I have now tested this on several machines with several compiler
versions (more or less all of them) and serveral cmake versions - all with
Windows 7.

I can actually reproduce the successful build you linked to, but this can
only be done if you do not include any of the language wrappings, like in
the build you linked to. Enable any of them, and the build will break. (see
attachment)

I suspect it must have been working in the past, but since none of them are
included in your test there have been a breaking change, and none of them
work anymore.

I am still trying to tweak then projects manually to build SimpleRTK with
some sort of language support, but still without any luck.

best

Arvid

On Tue, Sep 20, 2016 at 4:19 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
> at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
> I can't solve your problem but Kitware is going to look into an upgrade of
> SimpleRTK in the coming days, I'll ask them if they know what is the issue.
> If you look here:
> http://my.cdash.org/viewNotes.php?buildid=1052065
> this is a nightly build of SimpleRTK on Windows and it seems to work. I
> don't see why it wouldn't work for you.
> Simon
>
> On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Hi again.
>>
>> I understand, but could you please help me get in contact with the person
>> who knows something about the windows build (if any), I think there is
>> something wrong.
>>
>> I have been investigating the build problems I had and found that in the
>> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
>> opened it up and found the projects which I had problems building:
>> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>>
>> When I then tried to build SimpleRTKCommon manually it just compiled
>> without any problems. However, when I followed up by building
>> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
>> find "SimpleRTKCommon-0.9.lib" - which I just build.
>>
>> After some more investigation I realized that the SimpleRTKCommon is set
>> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
>> it to be a static linked library (LIB). After changing SimpleRTKCommon to
>> be build as a static library - and changing the output location - I could
>> build SimpleRTKBasicFilters0.
>>
>> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing
>> that to a LIB as well I could build SimpleRTKBasicFilters1, then
>> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>>
>> I'm unsure if the intention is to build them as static or dynamic
>> libraries, but in any case the current build configuration doesn't work -
>> on my setup at least.
>>
>> However, I should note than for some reason the "lua5" project did build
>> successfully out of the box. Whatever it does differently works.
>>
>> best
>>
>> Arvid
>>
>>
>>
>> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> I'm not an msvc specialist but your first line suggests that you have
>>> pasted only part of the log:
>>>
>>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) --
>>> FAILED.
>>> What you need to find out is why this build failed. If the build fails,
>>> the linking cannot work.
>>> Cheers,
>>> Simon
>>>
>>>
>>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>>
>>> I did a complete rebuild, and here is the end of the output:
>>> http://pastebin.com/hvQ33WWg
>>>
>>> I have to admit I'm not sure what to make of it. I should note that I'm
>>> trying to compile the version I just pulled from git earlier today, since
>>> the other version I normally work with is really old.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>>> another error before that which explains why it did not compile?
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Hi again.
>>>>>
>>>>> I've been trying to get it working. However, I did run into some
>>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>>> SimpleRTKCommon - which I do not have.
>>>>>
>>>>> Here is the last few lines from VS2013
>>>>>
>>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>>> > 5>
>>>>> > 5>      0 Warning(s)
>>>>> > 5>      2 Error(s)
>>>>> > 5>
>>>>> > 5>  Time Elapsed 00:00:25.26
>>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>>> ==========
>>>>>
>>>>> I'm not quite sure what is going on, because the only reference I can
>>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>>> RTK/CMakeLists.txt
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>>> python calls are available starting with Matlab 2014).
>>>>>> Simon
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>>> bottiger at gmail.com> wrote:
>>>>>>
>>>>>>> Dear Simon
>>>>>>>
>>>>>>> This look very interesting! Which platform did you successfully
>>>>>>> execute this on?
>>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>>> into any problems.
>>>>>>>
>>>>>>> best
>>>>>>>
>>>>>>> Arvid
>>>>>>>
>>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Dear RTK users,
>>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>>> and it seems to work well:
>>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but
>>>>>>>> let us know if you think otherwise.
>>>>>>>> Future works include a simple installation mechanism for
>>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
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From ajbatkinson at gmail.com  Wed Sep 28 08:11:12 2016
From: ajbatkinson at gmail.com (Abby Bryce Atkinson)
Date: Wed, 28 Sep 2016 13:11:12 +0100
Subject: [Rtk-users] 4DROOSTERReconstruction Example
Message-ID: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>

Hi,

I am trying to work through the 4DROOSTER example using the POPI patient
images (
http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) but
I am getting stuck when extracting the respiratory signal using the
amsterdam shroud.

I receive this error:


C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
--path .\Projections\ ^
More?                    --regexp '.*.his' ^
More?                    --output shroud.mha ^
More?                    --unsharp 650
ExceptionObject caught with writer->Update() in file
C:\RTK\applications\rtkamst
erdamshroud\rtkamsterdamshroud.cxx line 91

itk::ExceptionObject (0030E9E0)
Location: "void __thiscall itk::ImageFileWriter<class itk::Image<double,2>
>::Wr
ite(void)"
File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
Line: 284
Description: itk::ERROR: ImageFileWriter(03670318): Largest possible region
does
 not fully contain requested paste IO regionPaste IO region: ImageIORegion
(0030
EDD4)
  Dimension: 2
  Index: 0 0
  Size: 0 0
Largest possible region: ImageRegion (0030EE70)
  Dimension: 2
  Index: [0, 0]
  Size: [0, 0]


Can anyone help with a solution/tell me what I am doing wrong please?

Thanks,

Abby
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From simon.rit at creatis.insa-lyon.fr  Wed Sep 28 12:49:32 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 28 Sep 2016 18:49:32 +0200
Subject: [Rtk-users] 4DROOSTERReconstruction Example
In-Reply-To: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
References: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
Message-ID: <e23fc5ec-f7b4-846c-e349-f07564e2da8a@creatis.insa-lyon.fr>

Hi,

My guess is that the software does not find the projections. I would add 
the --verbose option and check that you actually input some projections. 
If not, I guess there is an issue with the path or the regexp in your 
command line.

Simon

On 28/09/2016 14:11, Abby Bryce Atkinson wrote:
> Hi,
>
> I am trying to work through the 4DROOSTER example using the POPI 
> patient images 
> (http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) 
> but I am getting stuck when extracting the respiratory signal using 
> the amsterdam shroud.
>
> I receive this error:
>
>
> C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
> --path .\Projections\ ^
> More?                    --regexp '.*.his' ^
> More?                    --output shroud.mha ^
> More?                    --unsharp 650
> ExceptionObject caught with writer->Update() in file 
> C:\RTK\applications\rtkamst
> erdamshroud\rtkamsterdamshroud.cxx line 91
>
> itk::ExceptionObject (0030E9E0)
> Location: "void __thiscall itk::ImageFileWriter<class 
> itk::Image<double,2> >::Wr
> ite(void)"
> File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
> Line: 284
> Description: itk::ERROR: ImageFileWriter(03670318): Largest possible 
> region does
>  not fully contain requested paste IO regionPaste IO region: 
> ImageIORegion (0030
> EDD4)
>   Dimension: 2
>   Index: 0 0
>   Size: 0 0
> Largest possible region: ImageRegion (0030EE70)
>   Dimension: 2
>   Index: [0, 0]
>   Size: [0, 0]
>
>
> Can anyone help with a solution/tell me what I am doing wrong please?
>
> Thanks,
>
> Abby
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users

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From signabdm at gmail.com  Mon Sep 12 06:58:59 2016
From: signabdm at gmail.com (Valeriy Signatulin)
Date: Mon, 12 Sep 2016 16:58:59 +0600
Subject: [Rtk-users] rotation of detector plane
Message-ID: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>

Hello RTK users.
Is it possible to specify rotation of detector plane in RTK ? (in
rtksimulategeom for example) If not, what is the best way to code this ?
By rotation of detector plane i mean twist, tilt, skew around the normal of
the detector as described in
http://www.ndt.net/article/v10n09/yisun/yisun.pdf page 6.
I'm trying to write the geometry calibration method described in this
article in RTK and i need to simulate these rotations to check the results.
Thanks.
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 12 08:40:31 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 12 Sep 2016 14:40:31 +0200
Subject: [Rtk-users] rotation of detector plane
In-Reply-To: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
References: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
Message-ID: <CAF0oig0C3zFcAaAhWHV9g+UY02i7cws7OU-7r2YadyAt3TH5GA@mail.gmail.com>

Hi,
You can do any rotation with RTK. The rotation is described 3 Euler angles,
see the geometry doc <http://www.openrtk.org/Doxygen/geometry.pdf>. From
the command line, that would be the --in_angle and out_angle that allow you
to modify the other angles than the standard angle for the position along
the circular rotation (GantryAngle). If you want to modify it per
projection, that's possible using C++ or Python code (AddProjection
<http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
method).
Good luck,
Simon

On Mon, Sep 12, 2016 at 12:58 PM, Valeriy Signatulin <signabdm at gmail.com>
wrote:

> Hello RTK users.
> Is it possible to specify rotation of detector plane in RTK ? (in
> rtksimulategeom for example) If not, what is the best way to code this ?
> By rotation of detector plane i mean twist, tilt, skew around the normal
> of the detector as described in http://www.ndt.net/article/
> v10n09/yisun/yisun.pdf page 6.
> I'm trying to write the geometry calibration method described in this
> article in RTK and i need to simulate these rotations to check the results.
> Thanks.
>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From andreasg at phys.au.dk  Tue Sep 13 13:06:46 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Tue, 13 Sep 2016 19:06:46 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
Message-ID: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>

Dear RTK experts,

I am reconstructing Varian ProBeam projections of the Xim image format. I
have written the reader myself - very similar to the Hnd one already
available with RTK.
Links to my fork: [XimReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkXimImageIO.cxx>,
XMLReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamXMLFileReader.cxx>,
GeometryReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamGeometryReader.cxx>
]

The reader apparently works (Images and angles displays as expected in UI),
however when reconstructing with a regular FDK* I get a reconstructed image
that is smeared out around the high and low density areas *[see attached
image]

I'm using half arc, full fan images with no bow-tie filter from Scripps
(~520 projections). Fixed detector and source (offset=0) with SID=2m,
SDD=3m.

*For the Hnd projections the reconstruction works perfectly (Same algorithm
<https://github.com/agravgaard/cbctrecon/blob/master/cbctrecon.cpp#L2726>).*
The reconstruction of the Xim projections performed on Varian software
works perfectly.

Without the Parker Short Scan Filter the first and last projections creates
streaks across the reconstruction as if they were way too bright.
If the first few projections are excluded, the following projection will
act the same way.

The projections are corrected for beam hardening and all the projections
have the expected attenuation.
No "smearing" filters (like median) is used, and iterative reconstruction
makes the same artifacts.

Setting the value of the first and last projection to zero has the same
effect as excluding. Changing the ramp filter only changes noise, not the
artifacts.

*Have any of you had a similar problem? *Am I missing something?
Any suggestions are welcome I'm running out of ideas.

Best regards
Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 13 16:18:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 13 Sep 2016 22:18:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
Message-ID: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>

Hi,
I have almost never worked with Varian data but it looks like a
geometry problem. Maybe the problem comes from a bad ordering of the
projections which results in assigning a bad geometry to each
projection. How did you name your projections? Maybe check that the
order matches that of the RTK geometry file. Otherwise, there might be
an issue in the creation of the geometry file itself.
All this sounds good, happy bug hunt and don't hesitate to share your
code when you feel it's ready.
Simon

On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
<andreasg at phys.au.dk> wrote:
> Dear RTK experts,
>
> I am reconstructing Varian ProBeam projections of the Xim image format. I
> have written the reader myself - very similar to the Hnd one already
> available with RTK.
> Links to my fork: [XimReader, XMLReader, GeometryReader]
>
> The reader apparently works (Images and angles displays as expected in UI),
> however when reconstructing with a regular FDK I get a reconstructed image
> that is smeared out around the high and low density areas [see attached
> image]
>
> I'm using half arc, full fan images with no bow-tie filter from Scripps
> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
> SDD=3m.
>
> For the Hnd projections the reconstruction works perfectly (Same algorithm).
> The reconstruction of the Xim projections performed on Varian software works
> perfectly.
>
> Without the Parker Short Scan Filter the first and last projections creates
> streaks across the reconstruction as if they were way too bright.
> If the first few projections are excluded, the following projection will act
> the same way.
>
> The projections are corrected for beam hardening and all the projections
> have the expected attenuation.
> No "smearing" filters (like median) is used, and iterative reconstruction
> makes the same artifacts.
>
> Setting the value of the first and last projection to zero has the same
> effect as excluding. Changing the ramp filter only changes noise, not the
> artifacts.
>
> Have any of you had a similar problem? Am I missing something?
> Any suggestions are welcome I'm running out of ideas.
>
> Best regards
> Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>


From cyril.mory at creatis.insa-lyon.fr  Wed Sep 14 03:10:42 2016
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 14 Sep 2016 09:10:42 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
Message-ID: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>

One suggestion since it works with the Hnd projections:
You can run rtkprojections twice (with the Hnd projections, then with 
Xim projections) and output two projection stack files and two geometry 
files, then compare the projection stack files by subtracting one to the 
other (with SimpleRTK or clitk) and the geometry files with diff. If 
they are identical, then I do not see any reason why the reconstructions 
should be different, so my guess is that you will find differences.

On 09/13/2016 10:18 PM, Simon Rit wrote:
> Hi,
> I have almost never worked with Varian data but it looks like a
> geometry problem. Maybe the problem comes from a bad ordering of the
> projections which results in assigning a bad geometry to each
> projection. How did you name your projections? Maybe check that the
> order matches that of the RTK geometry file. Otherwise, there might be
> an issue in the creation of the geometry file itself.
> All this sounds good, happy bug hunt and don't hesitate to share your
> code when you feel it's ready.
> Simon
>
> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
> <andreasg at phys.au.dk> wrote:
>> Dear RTK experts,
>>
>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>> have written the reader myself - very similar to the Hnd one already
>> available with RTK.
>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>
>> The reader apparently works (Images and angles displays as expected in UI),
>> however when reconstructing with a regular FDK I get a reconstructed image
>> that is smeared out around the high and low density areas [see attached
>> image]
>>
>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>> SDD=3m.
>>
>> For the Hnd projections the reconstruction works perfectly (Same algorithm).
>> The reconstruction of the Xim projections performed on Varian software works
>> perfectly.
>>
>> Without the Parker Short Scan Filter the first and last projections creates
>> streaks across the reconstruction as if they were way too bright.
>> If the first few projections are excluded, the following projection will act
>> the same way.
>>
>> The projections are corrected for beam hardening and all the projections
>> have the expected attenuation.
>> No "smearing" filters (like median) is used, and iterative reconstruction
>> makes the same artifacts.
>>
>> Setting the value of the first and last projection to zero has the same
>> effect as excluding. Changing the ramp filter only changes noise, not the
>> artifacts.
>>
>> Have any of you had a similar problem? Am I missing something?
>> Any suggestions are welcome I'm running out of ideas.
>>
>> Best regards
>> Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>



From andreasg at phys.au.dk  Fri Sep 16 08:56:34 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 14:56:34 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
Message-ID: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>

Thanks for the suggestions, Simon and Cyril!

I have been carefully looking though the geometry and from what I
understand of the transformations matrices, the geometry looks correct/(as
expected).

HOWEVER: I found out that the reason for the Hnd to behave differently were
because had used half-fan scans (full-arc).
When I used a full-fan (half-arc) scan of Hnd projections the same
artifacts occurs!

Are there other (built-in) means of improving half-arc scans, than the
parker short scan filter?

Parker short scan does a decent job, but the result is still far from the
quality of the Varian software reconstruction at least for the CatPhan.

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:

> One suggestion since it works with the Hnd projections:
> You can run rtkprojections twice (with the Hnd projections, then with Xim
> projections) and output two projection stack files and two geometry files,
> then compare the projection stack files by subtracting one to the other
> (with SimpleRTK or clitk) and the geometry files with diff. If they are
> identical, then I do not see any reason why the reconstructions should be
> different, so my guess is that you will find differences.
>
>
> On 09/13/2016 10:18 PM, Simon Rit wrote:
>
>> Hi,
>> I have almost never worked with Varian data but it looks like a
>> geometry problem. Maybe the problem comes from a bad ordering of the
>> projections which results in assigning a bad geometry to each
>> projection. How did you name your projections? Maybe check that the
>> order matches that of the RTK geometry file. Otherwise, there might be
>> an issue in the creation of the geometry file itself.
>> All this sounds good, happy bug hunt and don't hesitate to share your
>> code when you feel it's ready.
>> Simon
>>
>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>> <andreasg at phys.au.dk> wrote:
>>
>>> Dear RTK experts,
>>>
>>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>>> have written the reader myself - very similar to the Hnd one already
>>> available with RTK.
>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>
>>> The reader apparently works (Images and angles displays as expected in
>>> UI),
>>> however when reconstructing with a regular FDK I get a reconstructed
>>> image
>>> that is smeared out around the high and low density areas [see attached
>>> image]
>>>
>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>> SDD=3m.
>>>
>>> For the Hnd projections the reconstruction works perfectly (Same
>>> algorithm).
>>> The reconstruction of the Xim projections performed on Varian software
>>> works
>>> perfectly.
>>>
>>> Without the Parker Short Scan Filter the first and last projections
>>> creates
>>> streaks across the reconstruction as if they were way too bright.
>>> If the first few projections are excluded, the following projection will
>>> act
>>> the same way.
>>>
>>> The projections are corrected for beam hardening and all the projections
>>> have the expected attenuation.
>>> No "smearing" filters (like median) is used, and iterative reconstruction
>>> makes the same artifacts.
>>>
>>> Setting the value of the first and last projection to zero has the same
>>> effect as excluding. Changing the ramp filter only changes noise, not the
>>> artifacts.
>>>
>>> Have any of you had a similar problem? Am I missing something?
>>> Any suggestions are welcome I'm running out of ideas.
>>>
>>> Best regards
>>> Andreas
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Sep 16 10:13:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 16 Sep 2016 16:13:26 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
Message-ID: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>

Hi,
You can try any iterative reconstruction, they can also handle short scans.
Start with a few iterations of rtksart or rtkconjugategradient. However,
the nature of the artifacts indicate more a problem in the geometry in my
opinion. I have seen such errors when, for example, rotating in the wrong
direction. I can have a look if you share the dataset.
Cheers,
Simon

On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the suggestions, Simon and Cyril!
>
> I have been carefully looking though the geometry and from what I
> understand of the transformations matrices, the geometry looks correct/(as
> expected).
>
> HOWEVER: I found out that the reason for the Hnd to behave differently
> were because had used half-fan scans (full-arc).
> When I used a full-fan (half-arc) scan of Hnd projections the same
> artifacts occurs!
>
> Are there other (built-in) means of improving half-arc scans, than the
> parker short scan filter?
>
> Parker short scan does a decent job, but the result is still far from the
> quality of the Varian software reconstruction at least for the CatPhan.
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>
>> One suggestion since it works with the Hnd projections:
>> You can run rtkprojections twice (with the Hnd projections, then with Xim
>> projections) and output two projection stack files and two geometry files,
>> then compare the projection stack files by subtracting one to the other
>> (with SimpleRTK or clitk) and the geometry files with diff. If they are
>> identical, then I do not see any reason why the reconstructions should be
>> different, so my guess is that you will find differences.
>>
>>
>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>
>>> Hi,
>>> I have almost never worked with Varian data but it looks like a
>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>> projections which results in assigning a bad geometry to each
>>> projection. How did you name your projections? Maybe check that the
>>> order matches that of the RTK geometry file. Otherwise, there might be
>>> an issue in the creation of the geometry file itself.
>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>> code when you feel it's ready.
>>> Simon
>>>
>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>> <andreasg at phys.au.dk> wrote:
>>>
>>>> Dear RTK experts,
>>>>
>>>> I am reconstructing Varian ProBeam projections of the Xim image format.
>>>> I
>>>> have written the reader myself - very similar to the Hnd one already
>>>> available with RTK.
>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>
>>>> The reader apparently works (Images and angles displays as expected in
>>>> UI),
>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>> image
>>>> that is smeared out around the high and low density areas [see attached
>>>> image]
>>>>
>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>> SDD=3m.
>>>>
>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>> algorithm).
>>>> The reconstruction of the Xim projections performed on Varian software
>>>> works
>>>> perfectly.
>>>>
>>>> Without the Parker Short Scan Filter the first and last projections
>>>> creates
>>>> streaks across the reconstruction as if they were way too bright.
>>>> If the first few projections are excluded, the following projection
>>>> will act
>>>> the same way.
>>>>
>>>> The projections are corrected for beam hardening and all the projections
>>>> have the expected attenuation.
>>>> No "smearing" filters (like median) is used, and iterative
>>>> reconstruction
>>>> makes the same artifacts.
>>>>
>>>> Setting the value of the first and last projection to zero has the same
>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>> the
>>>> artifacts.
>>>>
>>>> Have any of you had a similar problem? Am I missing something?
>>>> Any suggestions are welcome I'm running out of ideas.
>>>>
>>>> Best regards
>>>> Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> N?rrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     andreasg at phys.au.dk
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From andreasg at phys.au.dk  Fri Sep 16 16:37:43 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 22:37:43 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
Message-ID: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>

Thanks for the fast response Simon!

I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
right all along!
I just didn't get why it makes a difference. I think I do now, as the
resulting image was flipped upside down and not left/right as I expected.
[attached]

The reconstruction is significantly better, I'll look into what should be
included in the reader and what I should keep in my program to keep
conformity with the other readers. Then I'll create a pull request.

Just for the purpose of others hitting the same or a similar bug, I also
attempted:
I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
back/forward projection, *but with no* significant improvement [attached]

And:
If you want you can download the data set from: [Dropbox link to 460MB zip
<https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep it
up as long as Dropbox allows me)] Only the Acquisitions/subfolder is used
along with the Scan.xml (Calibrations folder may be used in the future in
my program, but I'm not sure if you can rely on the existence of the
content).

A MatLab XimReader is available: link
<https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
available from Varian bitbucket along a with a python version and a
C#->matlab plugin
<https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). Otherwise
my fork with the RTK-style reader is available from the same repository (I
have also added Hnc support, thanks to the Geoff Hugo fork, so bzip2 is a
new dependancy).

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:

> Hi,
> You can try any iterative reconstruction, they can also handle short
> scans. Start with a few iterations of rtksart or rtkconjugategradient.
> However, the nature of the artifacts indicate more a problem in the
> geometry in my opinion. I have seen such errors when, for example, rotating
> in the wrong direction. I can have a look if you share the dataset.
> Cheers,
> Simon
>
> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
> andreasg at phys.au.dk> wrote:
>
>> Thanks for the suggestions, Simon and Cyril!
>>
>> I have been carefully looking though the geometry and from what I
>> understand of the transformations matrices, the geometry looks correct/(as
>> expected).
>>
>> HOWEVER: I found out that the reason for the Hnd to behave differently
>> were because had used half-fan scans (full-arc).
>> When I used a full-fan (half-arc) scan of Hnd projections the same
>> artifacts occurs!
>>
>> Are there other (built-in) means of improving half-arc scans, than the
>> parker short scan filter?
>>
>> Parker short scan does a decent job, but the result is still far from the
>> quality of the Varian software reconstruction at least for the CatPhan.
>>
>> Best regards
>> Andreas
>>
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>>
>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>
>>> One suggestion since it works with the Hnd projections:
>>> You can run rtkprojections twice (with the Hnd projections, then with
>>> Xim projections) and output two projection stack files and two geometry
>>> files, then compare the projection stack files by subtracting one to the
>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>> are identical, then I do not see any reason why the reconstructions should
>>> be different, so my guess is that you will find differences.
>>>
>>>
>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>
>>>> Hi,
>>>> I have almost never worked with Varian data but it looks like a
>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>> projections which results in assigning a bad geometry to each
>>>> projection. How did you name your projections? Maybe check that the
>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>> an issue in the creation of the geometry file itself.
>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>> code when you feel it's ready.
>>>> Simon
>>>>
>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>> <andreasg at phys.au.dk> wrote:
>>>>
>>>>> Dear RTK experts,
>>>>>
>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>> format. I
>>>>> have written the reader myself - very similar to the Hnd one already
>>>>> available with RTK.
>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>
>>>>> The reader apparently works (Images and angles displays as expected in
>>>>> UI),
>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>> image
>>>>> that is smeared out around the high and low density areas [see attached
>>>>> image]
>>>>>
>>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>> SDD=3m.
>>>>>
>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>> algorithm).
>>>>> The reconstruction of the Xim projections performed on Varian software
>>>>> works
>>>>> perfectly.
>>>>>
>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>> creates
>>>>> streaks across the reconstruction as if they were way too bright.
>>>>> If the first few projections are excluded, the following projection
>>>>> will act
>>>>> the same way.
>>>>>
>>>>> The projections are corrected for beam hardening and all the
>>>>> projections
>>>>> have the expected attenuation.
>>>>> No "smearing" filters (like median) is used, and iterative
>>>>> reconstruction
>>>>> makes the same artifacts.
>>>>>
>>>>> Setting the value of the first and last projection to zero has the same
>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>> the
>>>>> artifacts.
>>>>>
>>>>> Have any of you had a similar problem? Am I missing something?
>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>
>>>>> Best regards
>>>>> Andreas
>>>>>
>>>>> __________________________________
>>>>>
>>>>> Andreas Gravgaard Andersen
>>>>>
>>>>> Department of Oncology,
>>>>>
>>>>> Aarhus University Hospital
>>>>>
>>>>> N?rrebrogade 44,
>>>>>
>>>>> 8000, Aarhus C
>>>>>
>>>>> Mail:     andreasg at phys.au.dk
>>>>>
>>>>> Cell:      +45 3165 8140
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 03:26:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 09:26:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
 <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
Message-ID: <CAF0oig2TSmAsSn=o3aLo6LEFDOSaKRtfknjMer24rcDKJ-0Fqg@mail.gmail.com>

Hi,
Thanks for sharing. There still seems to be some streak artefacts, do you
see the same in the Varian reconstruction?
I'm looking forward to the pull-request, I think we should try to make the
bzip2 optional.
Simon

On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the fast response Simon!
>
> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
> right all along!
> I just didn't get why it makes a difference. I think I do now, as the
> resulting image was flipped upside down and not left/right as I expected.
> [attached]
>
> The reconstruction is significantly better, I'll look into what should be
> included in the reader and what I should keep in my program to keep
> conformity with the other readers. Then I'll create a pull request.
>
> Just for the purpose of others hitting the same or a similar bug, I also
> attempted:
> I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
> back/forward projection, *but with no* significant improvement [attached]
>
> And:
> If you want you can download the data set from: [Dropbox link to 460MB zip
> <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep
> it up as long as Dropbox allows me)] Only the Acquisitions/subfolder is
> used along with the Scan.xml (Calibrations folder may be used in the future
> in my program, but I'm not sure if you can rely on the existence of the
> content).
>
> A MatLab XimReader is available: link
> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
> available from Varian bitbucket along a with a python version and a
> C#->matlab plugin
> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>).
> Otherwise my fork with the RTK-style reader is available from the same
> repository (I have also added Hnc support, thanks to the Geoff Hugo fork,
> so bzip2 is a new dependancy).
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> Hi,
>> You can try any iterative reconstruction, they can also handle short
>> scans. Start with a few iterations of rtksart or rtkconjugategradient.
>> However, the nature of the artifacts indicate more a problem in the
>> geometry in my opinion. I have seen such errors when, for example, rotating
>> in the wrong direction. I can have a look if you share the dataset.
>> Cheers,
>> Simon
>>
>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
>> andreasg at phys.au.dk> wrote:
>>
>>> Thanks for the suggestions, Simon and Cyril!
>>>
>>> I have been carefully looking though the geometry and from what I
>>> understand of the transformations matrices, the geometry looks correct/(as
>>> expected).
>>>
>>> HOWEVER: I found out that the reason for the Hnd to behave differently
>>> were because had used half-fan scans (full-arc).
>>> When I used a full-fan (half-arc) scan of Hnd projections the same
>>> artifacts occurs!
>>>
>>> Are there other (built-in) means of improving half-arc scans, than the
>>> parker short scan filter?
>>>
>>> Parker short scan does a decent job, but the result is still far from
>>> the quality of the Varian software reconstruction at least for the CatPhan.
>>>
>>> Best regards
>>> Andreas
>>>
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>>
>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>>
>>>> One suggestion since it works with the Hnd projections:
>>>> You can run rtkprojections twice (with the Hnd projections, then with
>>>> Xim projections) and output two projection stack files and two geometry
>>>> files, then compare the projection stack files by subtracting one to the
>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>>> are identical, then I do not see any reason why the reconstructions should
>>>> be different, so my guess is that you will find differences.
>>>>
>>>>
>>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>>
>>>>> Hi,
>>>>> I have almost never worked with Varian data but it looks like a
>>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>>> projections which results in assigning a bad geometry to each
>>>>> projection. How did you name your projections? Maybe check that the
>>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>>> an issue in the creation of the geometry file itself.
>>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>>> code when you feel it's ready.
>>>>> Simon
>>>>>
>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>>> <andreasg at phys.au.dk> wrote:
>>>>>
>>>>>> Dear RTK experts,
>>>>>>
>>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>>> format. I
>>>>>> have written the reader myself - very similar to the Hnd one already
>>>>>> available with RTK.
>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>>
>>>>>> The reader apparently works (Images and angles displays as expected
>>>>>> in UI),
>>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>>> image
>>>>>> that is smeared out around the high and low density areas [see
>>>>>> attached
>>>>>> image]
>>>>>>
>>>>>> I'm using half arc, full fan images with no bow-tie filter from
>>>>>> Scripps
>>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>>> SDD=3m.
>>>>>>
>>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>>> algorithm).
>>>>>> The reconstruction of the Xim projections performed on Varian
>>>>>> software works
>>>>>> perfectly.
>>>>>>
>>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>>> creates
>>>>>> streaks across the reconstruction as if they were way too bright.
>>>>>> If the first few projections are excluded, the following projection
>>>>>> will act
>>>>>> the same way.
>>>>>>
>>>>>> The projections are corrected for beam hardening and all the
>>>>>> projections
>>>>>> have the expected attenuation.
>>>>>> No "smearing" filters (like median) is used, and iterative
>>>>>> reconstruction
>>>>>> makes the same artifacts.
>>>>>>
>>>>>> Setting the value of the first and last projection to zero has the
>>>>>> same
>>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>>> the
>>>>>> artifacts.
>>>>>>
>>>>>> Have any of you had a similar problem? Am I missing something?
>>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>>
>>>>>> Best regards
>>>>>> Andreas
>>>>>>
>>>>>> __________________________________
>>>>>>
>>>>>> Andreas Gravgaard Andersen
>>>>>>
>>>>>> Department of Oncology,
>>>>>>
>>>>>> Aarhus University Hospital
>>>>>>
>>>>>> N?rrebrogade 44,
>>>>>>
>>>>>> 8000, Aarhus C
>>>>>>
>>>>>> Mail:     andreasg at phys.au.dk
>>>>>>
>>>>>> Cell:      +45 3165 8140
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:05:24 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:05:24 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
Message-ID: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>

Dear RTK users,
I have quickly tested calling the SimpleRTK python lib from Matlab and it
seems to work well:
http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
Therefore, I don't think we have to work on Matlab wrappings but let us
know if you think otherwise.
Future works include a simple installation mechanism for pre-compiled
SimpleRTK libraries. We'll keep you posted!
Simon
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From bottiger at gmail.com  Mon Sep 19 05:14:03 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 11:14:03 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
Message-ID: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>

Dear Simon

This look very interesting! Which platform did you successfully execute
this on?
I will give it a try at once (on windows) and let you know if I run into
any problems.

best

Arvid

On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> I have quickly tested calling the SimpleRTK python lib from Matlab and it
> seems to work well:
> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
> Therefore, I don't think we have to work on Matlab wrappings but let us
> know if you think otherwise.
> Future works include a simple installation mechanism for pre-compiled
> SimpleRTK libraries. We'll keep you posted!
> Simon
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:19:28 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:19:28 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
Message-ID: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>

The latest MacOS. It's nice if you can test it on other platforms, I'll try
to run it on Linux but I have to upgrade matlab first (I think python calls
are available starting with Matlab 2014).
Simon

On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Dear Simon
>
> This look very interesting! Which platform did you successfully execute
> this on?
> I will give it a try at once (on windows) and let you know if I run into
> any problems.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> Dear RTK users,
>> I have quickly tested calling the SimpleRTK python lib from Matlab and it
>> seems to work well:
>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>> Therefore, I don't think we have to work on Matlab wrappings but let us
>> know if you think otherwise.
>> Future works include a simple installation mechanism for pre-compiled
>> SimpleRTK libraries. We'll keep you posted!
>> Simon
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From bottiger at gmail.com  Mon Sep 19 08:30:32 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 14:30:32 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
Message-ID: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>

Hi again.

I've been trying to get it working. However, I did run into some problems
compiling SimpleRTK. The main issue seems to be that it depends on
SimpleRTKCommon - which I do not have.

Here is the last few lines from VS2013

> 5>LINK : fatal error LNK1181: cannot open input file
'..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib' [C:\Users\aplb\Work\RTK\RTK1.2-
> bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> 5>
> 5>      0 Warning(s)
> 5>      2 Error(s)
> 5>
> 5>  Time Elapsed 00:00:25.26
> ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
==========

I'm not quite sure what is going on, because the only reference I can find
to SimpleRTKCommon is the CMakeLists.txt on github:
https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt

best

Arvid

On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> The latest MacOS. It's nice if you can test it on other platforms, I'll
> try to run it on Linux but I have to upgrade matlab first (I think python
> calls are available starting with Matlab 2014).
> Simon
>
> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Dear Simon
>>
>> This look very interesting! Which platform did you successfully execute
>> this on?
>> I will give it a try at once (on windows) and let you know if I run into
>> any problems.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Dear RTK users,
>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>> it seems to work well:
>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>> know if you think otherwise.
>>> Future works include a simple installation mechanism for pre-compiled
>>> SimpleRTK libraries. We'll keep you posted!
>>> Simon
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 12:50:33 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 18:50:33 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
Message-ID: <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>

 SimpleRTKCommon is a library generated when compiling. Don't you have
another error before that which explains why it did not compile?
Simon

On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I've been trying to get it working. However, I did run into some problems
> compiling SimpleRTK. The main issue seems to be that it depends on
> SimpleRTKCommon - which I do not have.
>
> Here is the last few lines from VS2013
>
> > 5>LINK : fatal error LNK1181: cannot open input file '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
> [C:\Users\aplb\Work\RTK\RTK1.2-
> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> > 5>
> > 5>      0 Warning(s)
> > 5>      2 Error(s)
> > 5>
> > 5>  Time Elapsed 00:00:25.26
> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
> ==========
>
> I'm not quite sure what is going on, because the only reference I can find
> to SimpleRTKCommon is the CMakeLists.txt on github:
> https://github.com/SimonRit/RTK/blob/master/utilities/
> SimpleRTK/CMakeLists.txt
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>> try to run it on Linux but I have to upgrade matlab first (I think python
>> calls are available starting with Matlab 2014).
>> Simon
>>
>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Dear Simon
>>>
>>> This look very interesting! Which platform did you successfully execute
>>> this on?
>>> I will give it a try at once (on windows) and let you know if I run into
>>> any problems.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Dear RTK users,
>>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>>> it seems to work well:
>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>>> know if you think otherwise.
>>>> Future works include a simple installation mechanism for pre-compiled
>>>> SimpleRTK libraries. We'll keep you posted!
>>>> Simon
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 01:33:46 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 07:33:46 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
Message-ID: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>

I'm not an msvc specialist but your first line suggests that you have 
pasted only part of the log:

20>  Done Building Project 
"C:\Users\aplb\Work\RTK\RTK1.2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" 
(default targets) -- FAILED.

What you need to find out is why this build failed. If the build fails, 
the linking cannot work.
Cheers,
Simon

On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
> I did a complete rebuild, and here is the end of the output: 
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that 
> I'm trying to compile the version I just pulled from git earlier 
> today, since the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     SimpleRTKCommon is a library generated when compiling. Don't you
>     have another error before that which explains why it did not compile?
>     Simon
>
>     On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger
>     <bottiger at gmail.com <mailto:bottiger at gmail.com>> wrote:
>
>         Hi again.
>
>         I've been trying to get it working. However, I did run into
>         some problems compiling SimpleRTK. The main issue seems to be
>         that it depends on SimpleRTKCommon - which I do not have.
>
>         Here is the last few lines from VS2013
>
>         > 5>LINK : fatal error LNK1181: cannot open input file
>         '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>         [C:\Users\aplb\Work\RTK\RTK1.2-
>         > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>         > 5>
>         > 5>      0 Warning(s)
>         > 5>      2 Error(s)
>         > 5>
>         > 5>  Time Elapsed 00:00:25.26
>         > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0
>         skipped ==========
>
>         I'm not quite sure what is going on, because the only
>         reference I can find to SimpleRTKCommon is the CMakeLists.txt
>         on github:
>         https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt
>         <https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt>
>
>         best
>
>         Arvid
>
>         On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit
>         <simon.rit at creatis.insa-lyon.fr
>         <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>             The latest MacOS. It's nice if you can test it on other
>             platforms, I'll try to run it on Linux but I have to
>             upgrade matlab first (I think python calls are available
>             starting with Matlab 2014).
>             Simon
>
>             On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen
>             B?ttiger <bottiger at gmail.com <mailto:bottiger at gmail.com>>
>             wrote:
>
>                 Dear Simon
>
>                 This look very interesting! Which platform did you
>                 successfully execute this on?
>                 I will give it a try at once (on windows) and let you
>                 know if I run into any problems.
>
>                 best
>
>                 Arvid
>
>                 On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit
>                 <simon.rit at creatis.insa-lyon.fr
>                 <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>                     Dear RTK users,
>                     I have quickly tested calling the SimpleRTK python
>                     lib from Matlab and it seems to work well:
>                     http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>                     <http://wiki.openrtk.org/index.php/SimpleRTK#Matlab>
>                     Therefore, I don't think we have to work on Matlab
>                     wrappings but let us know if you think otherwise.
>                     Future works include a simple installation
>                     mechanism for pre-compiled SimpleRTK libraries.
>                     We'll keep you posted!
>                     Simon
>
>                     _______________________________________________
>                     Rtk-users mailing list
>                     Rtk-users at public.kitware.com
>                     <mailto:Rtk-users at public.kitware.com>
>                     http://public.kitware.com/mailman/listinfo/rtk-users
>                     <http://public.kitware.com/mailman/listinfo/rtk-users>
>
>
>
>
>
>

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From bottiger at gmail.com  Tue Sep 20 08:17:35 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Tue, 20 Sep 2016 14:17:35 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
Message-ID: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>

Hi again.

I understand, but could you please help me get in contact with the person
who knows something about the windows build (if any), I think there is
something wrong.

I have been investigating the build problems I had and found that in the
sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
opened it up and found the projects which I had problems building:
"SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.

When I then tried to build SimpleRTKCommon manually it just compiled
without any problems. However, when I followed up by building
"SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
find "SimpleRTKCommon-0.9.lib" - which I just build.

After some more investigation I realized that the SimpleRTKCommon is set to
build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects it
to be a static linked library (LIB). After changing SimpleRTKCommon to be
build as a static library - and changing the output location - I could
build SimpleRTKBasicFilters0.

However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
to a LIB as well I could build SimpleRTKBasicFilters1, then
SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.

I'm unsure if the intention is to build them as static or dynamic
libraries, but in any case the current build configuration doesn't work -
on my setup at least.

However, I should note than for some reason the "lua5" project did build
successfully out of the box. Whatever it does differently works.

best

Arvid



On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> I'm not an msvc specialist but your first line suggests that you have
> pasted only part of the log:
>
> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.
> 2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
> What you need to find out is why this build failed. If the build fails,
> the linking cannot work.
> Cheers,
> Simon
>
>
> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>
> I did a complete rebuild, and here is the end of the output:
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that I'm
> trying to compile the version I just pulled from git earlier today, since
> the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> SimpleRTKCommon is a library generated when compiling. Don't you have
>> another error before that which explains why it did not compile?
>> Simon
>>
>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Hi again.
>>>
>>> I've been trying to get it working. However, I did run into some
>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>> SimpleRTKCommon - which I do not have.
>>>
>>> Here is the last few lines from VS2013
>>>
>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>> > 5>
>>> > 5>      0 Warning(s)
>>> > 5>      2 Error(s)
>>> > 5>
>>> > 5>  Time Elapsed 00:00:25.26
>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>> ==========
>>>
>>> I'm not quite sure what is going on, because the only reference I can
>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>> RTK/CMakeLists.txt
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>>>> try to run it on Linux but I have to upgrade matlab first (I think python
>>>> calls are available starting with Matlab 2014).
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Dear Simon
>>>>>
>>>>> This look very interesting! Which platform did you successfully
>>>>> execute this on?
>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>> into any problems.
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Dear RTK users,
>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>> and it seems to work well:
>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>> us know if you think otherwise.
>>>>>> Future works include a simple installation mechanism for pre-compiled
>>>>>> SimpleRTK libraries. We'll keep you posted!
>>>>>> Simon
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 10:19:20 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 16:19:20 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
Message-ID: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>

Hi,
Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
I can't solve your problem but Kitware is going to look into an upgrade of
SimpleRTK in the coming days, I'll ask them if they know what is the issue.
If you look here:
http://my.cdash.org/viewNotes.php?buildid=1052065
this is a nightly build of SimpleRTK on Windows and it seems to work. I
don't see why it wouldn't work for you.
Simon

On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I understand, but could you please help me get in contact with the person
> who knows something about the windows build (if any), I think there is
> something wrong.
>
> I have been investigating the build problems I had and found that in the
> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
> opened it up and found the projects which I had problems building:
> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>
> When I then tried to build SimpleRTKCommon manually it just compiled
> without any problems. However, when I followed up by building
> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
> find "SimpleRTKCommon-0.9.lib" - which I just build.
>
> After some more investigation I realized that the SimpleRTKCommon is set
> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
> it to be a static linked library (LIB). After changing SimpleRTKCommon to
> be build as a static library - and changing the output location - I could
> build SimpleRTKBasicFilters0.
>
> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
> to a LIB as well I could build SimpleRTKBasicFilters1, then
> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>
> I'm unsure if the intention is to build them as static or dynamic
> libraries, but in any case the current build configuration doesn't work -
> on my setup at least.
>
> However, I should note than for some reason the "lua5" project did build
> successfully out of the box. Whatever it does differently works.
>
> best
>
> Arvid
>
>
>
> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> I'm not an msvc specialist but your first line suggests that you have
>> pasted only part of the log:
>>
>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
>> What you need to find out is why this build failed. If the build fails,
>> the linking cannot work.
>> Cheers,
>> Simon
>>
>>
>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>
>> I did a complete rebuild, and here is the end of the output:
>> http://pastebin.com/hvQ33WWg
>>
>> I have to admit I'm not sure what to make of it. I should note that I'm
>> trying to compile the version I just pulled from git earlier today, since
>> the other version I normally work with is really old.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>> another error before that which explains why it did not compile?
>>> Simon
>>>
>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>> bottiger at gmail.com> wrote:
>>>
>>>> Hi again.
>>>>
>>>> I've been trying to get it working. However, I did run into some
>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>> SimpleRTKCommon - which I do not have.
>>>>
>>>> Here is the last few lines from VS2013
>>>>
>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>> > 5>
>>>> > 5>      0 Warning(s)
>>>> > 5>      2 Error(s)
>>>> > 5>
>>>> > 5>  Time Elapsed 00:00:25.26
>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>> ==========
>>>>
>>>> I'm not quite sure what is going on, because the only reference I can
>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>> RTK/CMakeLists.txt
>>>>
>>>> best
>>>>
>>>> Arvid
>>>>
>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>> python calls are available starting with Matlab 2014).
>>>>> Simon
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>> bottiger at gmail.com> wrote:
>>>>>
>>>>>> Dear Simon
>>>>>>
>>>>>> This look very interesting! Which platform did you successfully
>>>>>> execute this on?
>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>> into any problems.
>>>>>>
>>>>>> best
>>>>>>
>>>>>> Arvid
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>
>>>>>>> Dear RTK users,
>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>> and it seems to work well:
>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>>> us know if you think otherwise.
>>>>>>> Future works include a simple installation mechanism for
>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>> Simon
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 02:40:50 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 08:40:50 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
Message-ID: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>

Dear RTK users,
RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
been released, about 7 months after RTK v1.2.0.

Release notes :
- Style updated (follow more closely latest ITK guidelines).
- Started using Travis CI, github pull requests should now be used for code
submission.
- New pre-processing functionalities:
  * CUDA polynomial gain correction,
  * scatter glare correction,
  * lag correction,
  * idark option,
  * removed threshold to positive values after i0 LUT.
- Improved CUDA forward and backprojection speed using projection slabs.
- Added motion-compensated forward and back projection operators in CUDA,
in both 3D and 4D.
- Added the rtkregularizedconjugategradient application, which performs 3D
regularized reconstruction by conjugate gradient + optional regularizations
(Positivity, TV, Wavelets).
- Made the rtkfourdrooster, rtkmcrooster and rtkregularizedconjugategradient
fully modular. Each regularization step can be made active or inactive.
- Added a filter to minimize the L0 norm of the temporal gradient (one-D
only).

Many thanks to the contributors, in alphabetical order for this release: Cyril
Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien
Jomier, S?bastien
Brousmiche, Simon Rit

As usual, be aware that we don't focus on releases since we have a public
github repository <http://github.com/SimonRit/RTK> that we try to keep
stable. I still recommend the use of the master HEAD over releases to enjoy
the new RTK developments before their release. We still have a few on-going
projects for which we will use and enhance RTK.

Simon (for the RTK consortium)
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 04:48:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 10:48:26 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
In-Reply-To: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
References: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
Message-ID: <CAF0oig0=5_KPN198JzsGQXDd07Nvw_Ew+qSGhguk0m27s3U-3Q@mail.gmail.com>

Sorry, I had forgotten to change the release number in the source file.
It's been corrected, you will have to move your tag locally or update your
file if you had already downloaded it.
Simon

On Thu, Sep 22, 2016 at 8:40 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
> been released, about 7 months after RTK v1.2.0.
>
> Release notes :
> - Style updated (follow more closely latest ITK guidelines).
> - Started using Travis CI, github pull requests should now be used for
> code submission.
> - New pre-processing functionalities:
>   * CUDA polynomial gain correction,
>   * scatter glare correction,
>   * lag correction,
>   * idark option,
>   * removed threshold to positive values after i0 LUT.
> - Improved CUDA forward and backprojection speed using projection slabs.
> - Added motion-compensated forward and back projection operators in CUDA,
> in both 3D and 4D.
> - Added the rtkregularizedconjugategradient application, which performs
> 3D regularized reconstruction by conjugate gradient + optional
> regularizations (Positivity, TV, Wavelets).
> - Made the rtkfourdrooster, rtkmcrooster and
> rtkregularizedconjugategradient fully modular. Each regularization step
> can be made active or inactive.
> - Added a filter to minimize the L0 norm of the temporal gradient (one-D
> only).
>
> Many thanks to the contributors, in alphabetical order for this release: Cyril
> Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien Jomier, S?bastien
> Brousmiche, Simon Rit
>
> As usual, be aware that we don't focus on releases since we have a public
> github repository <http://github.com/SimonRit/RTK> that we try to keep
> stable. I still recommend the use of the master HEAD over releases to
> enjoy the new RTK developments before their release. We still have a few
> on-going projects for which we will use and enhance RTK.
>
> Simon (for the RTK consortium)
>
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From bottiger at gmail.com  Fri Sep 23 04:29:06 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Fri, 23 Sep 2016 10:29:06 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
 <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
Message-ID: <CANBwxwEvaUrvd1X=74g=V2JmDwtrQKFDtyUdAZJn5CRCBCkb8g@mail.gmail.com>

Hi again.

I've been spending some more time with this, and feel I learned a little
bit more. I have now tested this on several machines with several compiler
versions (more or less all of them) and serveral cmake versions - all with
Windows 7.

I can actually reproduce the successful build you linked to, but this can
only be done if you do not include any of the language wrappings, like in
the build you linked to. Enable any of them, and the build will break. (see
attachment)

I suspect it must have been working in the past, but since none of them are
included in your test there have been a breaking change, and none of them
work anymore.

I am still trying to tweak then projects manually to build SimpleRTK with
some sort of language support, but still without any luck.

best

Arvid

On Tue, Sep 20, 2016 at 4:19 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
> at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
> I can't solve your problem but Kitware is going to look into an upgrade of
> SimpleRTK in the coming days, I'll ask them if they know what is the issue.
> If you look here:
> http://my.cdash.org/viewNotes.php?buildid=1052065
> this is a nightly build of SimpleRTK on Windows and it seems to work. I
> don't see why it wouldn't work for you.
> Simon
>
> On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Hi again.
>>
>> I understand, but could you please help me get in contact with the person
>> who knows something about the windows build (if any), I think there is
>> something wrong.
>>
>> I have been investigating the build problems I had and found that in the
>> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
>> opened it up and found the projects which I had problems building:
>> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>>
>> When I then tried to build SimpleRTKCommon manually it just compiled
>> without any problems. However, when I followed up by building
>> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
>> find "SimpleRTKCommon-0.9.lib" - which I just build.
>>
>> After some more investigation I realized that the SimpleRTKCommon is set
>> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
>> it to be a static linked library (LIB). After changing SimpleRTKCommon to
>> be build as a static library - and changing the output location - I could
>> build SimpleRTKBasicFilters0.
>>
>> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing
>> that to a LIB as well I could build SimpleRTKBasicFilters1, then
>> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>>
>> I'm unsure if the intention is to build them as static or dynamic
>> libraries, but in any case the current build configuration doesn't work -
>> on my setup at least.
>>
>> However, I should note than for some reason the "lua5" project did build
>> successfully out of the box. Whatever it does differently works.
>>
>> best
>>
>> Arvid
>>
>>
>>
>> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> I'm not an msvc specialist but your first line suggests that you have
>>> pasted only part of the log:
>>>
>>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) --
>>> FAILED.
>>> What you need to find out is why this build failed. If the build fails,
>>> the linking cannot work.
>>> Cheers,
>>> Simon
>>>
>>>
>>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>>
>>> I did a complete rebuild, and here is the end of the output:
>>> http://pastebin.com/hvQ33WWg
>>>
>>> I have to admit I'm not sure what to make of it. I should note that I'm
>>> trying to compile the version I just pulled from git earlier today, since
>>> the other version I normally work with is really old.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>>> another error before that which explains why it did not compile?
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Hi again.
>>>>>
>>>>> I've been trying to get it working. However, I did run into some
>>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>>> SimpleRTKCommon - which I do not have.
>>>>>
>>>>> Here is the last few lines from VS2013
>>>>>
>>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>>> > 5>
>>>>> > 5>      0 Warning(s)
>>>>> > 5>      2 Error(s)
>>>>> > 5>
>>>>> > 5>  Time Elapsed 00:00:25.26
>>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>>> ==========
>>>>>
>>>>> I'm not quite sure what is going on, because the only reference I can
>>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>>> RTK/CMakeLists.txt
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>>> python calls are available starting with Matlab 2014).
>>>>>> Simon
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>>> bottiger at gmail.com> wrote:
>>>>>>
>>>>>>> Dear Simon
>>>>>>>
>>>>>>> This look very interesting! Which platform did you successfully
>>>>>>> execute this on?
>>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>>> into any problems.
>>>>>>>
>>>>>>> best
>>>>>>>
>>>>>>> Arvid
>>>>>>>
>>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Dear RTK users,
>>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>>> and it seems to work well:
>>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but
>>>>>>>> let us know if you think otherwise.
>>>>>>>> Future works include a simple installation mechanism for
>>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
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From ajbatkinson at gmail.com  Wed Sep 28 08:11:12 2016
From: ajbatkinson at gmail.com (Abby Bryce Atkinson)
Date: Wed, 28 Sep 2016 13:11:12 +0100
Subject: [Rtk-users] 4DROOSTERReconstruction Example
Message-ID: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>

Hi,

I am trying to work through the 4DROOSTER example using the POPI patient
images (
http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) but
I am getting stuck when extracting the respiratory signal using the
amsterdam shroud.

I receive this error:


C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
--path .\Projections\ ^
More?                    --regexp '.*.his' ^
More?                    --output shroud.mha ^
More?                    --unsharp 650
ExceptionObject caught with writer->Update() in file
C:\RTK\applications\rtkamst
erdamshroud\rtkamsterdamshroud.cxx line 91

itk::ExceptionObject (0030E9E0)
Location: "void __thiscall itk::ImageFileWriter<class itk::Image<double,2>
>::Wr
ite(void)"
File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
Line: 284
Description: itk::ERROR: ImageFileWriter(03670318): Largest possible region
does
 not fully contain requested paste IO regionPaste IO region: ImageIORegion
(0030
EDD4)
  Dimension: 2
  Index: 0 0
  Size: 0 0
Largest possible region: ImageRegion (0030EE70)
  Dimension: 2
  Index: [0, 0]
  Size: [0, 0]


Can anyone help with a solution/tell me what I am doing wrong please?

Thanks,

Abby
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From simon.rit at creatis.insa-lyon.fr  Wed Sep 28 12:49:32 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 28 Sep 2016 18:49:32 +0200
Subject: [Rtk-users] 4DROOSTERReconstruction Example
In-Reply-To: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
References: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
Message-ID: <e23fc5ec-f7b4-846c-e349-f07564e2da8a@creatis.insa-lyon.fr>

Hi,

My guess is that the software does not find the projections. I would add 
the --verbose option and check that you actually input some projections. 
If not, I guess there is an issue with the path or the regexp in your 
command line.

Simon

On 28/09/2016 14:11, Abby Bryce Atkinson wrote:
> Hi,
>
> I am trying to work through the 4DROOSTER example using the POPI 
> patient images 
> (http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) 
> but I am getting stuck when extracting the respiratory signal using 
> the amsterdam shroud.
>
> I receive this error:
>
>
> C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
> --path .\Projections\ ^
> More?                    --regexp '.*.his' ^
> More?                    --output shroud.mha ^
> More?                    --unsharp 650
> ExceptionObject caught with writer->Update() in file 
> C:\RTK\applications\rtkamst
> erdamshroud\rtkamsterdamshroud.cxx line 91
>
> itk::ExceptionObject (0030E9E0)
> Location: "void __thiscall itk::ImageFileWriter<class 
> itk::Image<double,2> >::Wr
> ite(void)"
> File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
> Line: 284
> Description: itk::ERROR: ImageFileWriter(03670318): Largest possible 
> region does
>  not fully contain requested paste IO regionPaste IO region: 
> ImageIORegion (0030
> EDD4)
>   Dimension: 2
>   Index: 0 0
>   Size: 0 0
> Largest possible region: ImageRegion (0030EE70)
>   Dimension: 2
>   Index: [0, 0]
>   Size: [0, 0]
>
>
> Can anyone help with a solution/tell me what I am doing wrong please?
>
> Thanks,
>
> Abby
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users

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From signabdm at gmail.com  Mon Sep 12 06:58:59 2016
From: signabdm at gmail.com (Valeriy Signatulin)
Date: Mon, 12 Sep 2016 16:58:59 +0600
Subject: [Rtk-users] rotation of detector plane
Message-ID: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>

Hello RTK users.
Is it possible to specify rotation of detector plane in RTK ? (in
rtksimulategeom for example) If not, what is the best way to code this ?
By rotation of detector plane i mean twist, tilt, skew around the normal of
the detector as described in
http://www.ndt.net/article/v10n09/yisun/yisun.pdf page 6.
I'm trying to write the geometry calibration method described in this
article in RTK and i need to simulate these rotations to check the results.
Thanks.
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 12 08:40:31 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 12 Sep 2016 14:40:31 +0200
Subject: [Rtk-users] rotation of detector plane
In-Reply-To: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
References: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
Message-ID: <CAF0oig0C3zFcAaAhWHV9g+UY02i7cws7OU-7r2YadyAt3TH5GA@mail.gmail.com>

Hi,
You can do any rotation with RTK. The rotation is described 3 Euler angles,
see the geometry doc <http://www.openrtk.org/Doxygen/geometry.pdf>. From
the command line, that would be the --in_angle and out_angle that allow you
to modify the other angles than the standard angle for the position along
the circular rotation (GantryAngle). If you want to modify it per
projection, that's possible using C++ or Python code (AddProjection
<http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
method).
Good luck,
Simon

On Mon, Sep 12, 2016 at 12:58 PM, Valeriy Signatulin <signabdm at gmail.com>
wrote:

> Hello RTK users.
> Is it possible to specify rotation of detector plane in RTK ? (in
> rtksimulategeom for example) If not, what is the best way to code this ?
> By rotation of detector plane i mean twist, tilt, skew around the normal
> of the detector as described in http://www.ndt.net/article/
> v10n09/yisun/yisun.pdf page 6.
> I'm trying to write the geometry calibration method described in this
> article in RTK and i need to simulate these rotations to check the results.
> Thanks.
>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From andreasg at phys.au.dk  Tue Sep 13 13:06:46 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Tue, 13 Sep 2016 19:06:46 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
Message-ID: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>

Dear RTK experts,

I am reconstructing Varian ProBeam projections of the Xim image format. I
have written the reader myself - very similar to the Hnd one already
available with RTK.
Links to my fork: [XimReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkXimImageIO.cxx>,
XMLReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamXMLFileReader.cxx>,
GeometryReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamGeometryReader.cxx>
]

The reader apparently works (Images and angles displays as expected in UI),
however when reconstructing with a regular FDK* I get a reconstructed image
that is smeared out around the high and low density areas *[see attached
image]

I'm using half arc, full fan images with no bow-tie filter from Scripps
(~520 projections). Fixed detector and source (offset=0) with SID=2m,
SDD=3m.

*For the Hnd projections the reconstruction works perfectly (Same algorithm
<https://github.com/agravgaard/cbctrecon/blob/master/cbctrecon.cpp#L2726>).*
The reconstruction of the Xim projections performed on Varian software
works perfectly.

Without the Parker Short Scan Filter the first and last projections creates
streaks across the reconstruction as if they were way too bright.
If the first few projections are excluded, the following projection will
act the same way.

The projections are corrected for beam hardening and all the projections
have the expected attenuation.
No "smearing" filters (like median) is used, and iterative reconstruction
makes the same artifacts.

Setting the value of the first and last projection to zero has the same
effect as excluding. Changing the ramp filter only changes noise, not the
artifacts.

*Have any of you had a similar problem? *Am I missing something?
Any suggestions are welcome I'm running out of ideas.

Best regards
Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 13 16:18:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 13 Sep 2016 22:18:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
Message-ID: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>

Hi,
I have almost never worked with Varian data but it looks like a
geometry problem. Maybe the problem comes from a bad ordering of the
projections which results in assigning a bad geometry to each
projection. How did you name your projections? Maybe check that the
order matches that of the RTK geometry file. Otherwise, there might be
an issue in the creation of the geometry file itself.
All this sounds good, happy bug hunt and don't hesitate to share your
code when you feel it's ready.
Simon

On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
<andreasg at phys.au.dk> wrote:
> Dear RTK experts,
>
> I am reconstructing Varian ProBeam projections of the Xim image format. I
> have written the reader myself - very similar to the Hnd one already
> available with RTK.
> Links to my fork: [XimReader, XMLReader, GeometryReader]
>
> The reader apparently works (Images and angles displays as expected in UI),
> however when reconstructing with a regular FDK I get a reconstructed image
> that is smeared out around the high and low density areas [see attached
> image]
>
> I'm using half arc, full fan images with no bow-tie filter from Scripps
> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
> SDD=3m.
>
> For the Hnd projections the reconstruction works perfectly (Same algorithm).
> The reconstruction of the Xim projections performed on Varian software works
> perfectly.
>
> Without the Parker Short Scan Filter the first and last projections creates
> streaks across the reconstruction as if they were way too bright.
> If the first few projections are excluded, the following projection will act
> the same way.
>
> The projections are corrected for beam hardening and all the projections
> have the expected attenuation.
> No "smearing" filters (like median) is used, and iterative reconstruction
> makes the same artifacts.
>
> Setting the value of the first and last projection to zero has the same
> effect as excluding. Changing the ramp filter only changes noise, not the
> artifacts.
>
> Have any of you had a similar problem? Am I missing something?
> Any suggestions are welcome I'm running out of ideas.
>
> Best regards
> Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>


From cyril.mory at creatis.insa-lyon.fr  Wed Sep 14 03:10:42 2016
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 14 Sep 2016 09:10:42 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
Message-ID: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>

One suggestion since it works with the Hnd projections:
You can run rtkprojections twice (with the Hnd projections, then with 
Xim projections) and output two projection stack files and two geometry 
files, then compare the projection stack files by subtracting one to the 
other (with SimpleRTK or clitk) and the geometry files with diff. If 
they are identical, then I do not see any reason why the reconstructions 
should be different, so my guess is that you will find differences.

On 09/13/2016 10:18 PM, Simon Rit wrote:
> Hi,
> I have almost never worked with Varian data but it looks like a
> geometry problem. Maybe the problem comes from a bad ordering of the
> projections which results in assigning a bad geometry to each
> projection. How did you name your projections? Maybe check that the
> order matches that of the RTK geometry file. Otherwise, there might be
> an issue in the creation of the geometry file itself.
> All this sounds good, happy bug hunt and don't hesitate to share your
> code when you feel it's ready.
> Simon
>
> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
> <andreasg at phys.au.dk> wrote:
>> Dear RTK experts,
>>
>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>> have written the reader myself - very similar to the Hnd one already
>> available with RTK.
>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>
>> The reader apparently works (Images and angles displays as expected in UI),
>> however when reconstructing with a regular FDK I get a reconstructed image
>> that is smeared out around the high and low density areas [see attached
>> image]
>>
>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>> SDD=3m.
>>
>> For the Hnd projections the reconstruction works perfectly (Same algorithm).
>> The reconstruction of the Xim projections performed on Varian software works
>> perfectly.
>>
>> Without the Parker Short Scan Filter the first and last projections creates
>> streaks across the reconstruction as if they were way too bright.
>> If the first few projections are excluded, the following projection will act
>> the same way.
>>
>> The projections are corrected for beam hardening and all the projections
>> have the expected attenuation.
>> No "smearing" filters (like median) is used, and iterative reconstruction
>> makes the same artifacts.
>>
>> Setting the value of the first and last projection to zero has the same
>> effect as excluding. Changing the ramp filter only changes noise, not the
>> artifacts.
>>
>> Have any of you had a similar problem? Am I missing something?
>> Any suggestions are welcome I'm running out of ideas.
>>
>> Best regards
>> Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>



From andreasg at phys.au.dk  Fri Sep 16 08:56:34 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 14:56:34 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
Message-ID: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>

Thanks for the suggestions, Simon and Cyril!

I have been carefully looking though the geometry and from what I
understand of the transformations matrices, the geometry looks correct/(as
expected).

HOWEVER: I found out that the reason for the Hnd to behave differently were
because had used half-fan scans (full-arc).
When I used a full-fan (half-arc) scan of Hnd projections the same
artifacts occurs!

Are there other (built-in) means of improving half-arc scans, than the
parker short scan filter?

Parker short scan does a decent job, but the result is still far from the
quality of the Varian software reconstruction at least for the CatPhan.

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:

> One suggestion since it works with the Hnd projections:
> You can run rtkprojections twice (with the Hnd projections, then with Xim
> projections) and output two projection stack files and two geometry files,
> then compare the projection stack files by subtracting one to the other
> (with SimpleRTK or clitk) and the geometry files with diff. If they are
> identical, then I do not see any reason why the reconstructions should be
> different, so my guess is that you will find differences.
>
>
> On 09/13/2016 10:18 PM, Simon Rit wrote:
>
>> Hi,
>> I have almost never worked with Varian data but it looks like a
>> geometry problem. Maybe the problem comes from a bad ordering of the
>> projections which results in assigning a bad geometry to each
>> projection. How did you name your projections? Maybe check that the
>> order matches that of the RTK geometry file. Otherwise, there might be
>> an issue in the creation of the geometry file itself.
>> All this sounds good, happy bug hunt and don't hesitate to share your
>> code when you feel it's ready.
>> Simon
>>
>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>> <andreasg at phys.au.dk> wrote:
>>
>>> Dear RTK experts,
>>>
>>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>>> have written the reader myself - very similar to the Hnd one already
>>> available with RTK.
>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>
>>> The reader apparently works (Images and angles displays as expected in
>>> UI),
>>> however when reconstructing with a regular FDK I get a reconstructed
>>> image
>>> that is smeared out around the high and low density areas [see attached
>>> image]
>>>
>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>> SDD=3m.
>>>
>>> For the Hnd projections the reconstruction works perfectly (Same
>>> algorithm).
>>> The reconstruction of the Xim projections performed on Varian software
>>> works
>>> perfectly.
>>>
>>> Without the Parker Short Scan Filter the first and last projections
>>> creates
>>> streaks across the reconstruction as if they were way too bright.
>>> If the first few projections are excluded, the following projection will
>>> act
>>> the same way.
>>>
>>> The projections are corrected for beam hardening and all the projections
>>> have the expected attenuation.
>>> No "smearing" filters (like median) is used, and iterative reconstruction
>>> makes the same artifacts.
>>>
>>> Setting the value of the first and last projection to zero has the same
>>> effect as excluding. Changing the ramp filter only changes noise, not the
>>> artifacts.
>>>
>>> Have any of you had a similar problem? Am I missing something?
>>> Any suggestions are welcome I'm running out of ideas.
>>>
>>> Best regards
>>> Andreas
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Sep 16 10:13:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 16 Sep 2016 16:13:26 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
Message-ID: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>

Hi,
You can try any iterative reconstruction, they can also handle short scans.
Start with a few iterations of rtksart or rtkconjugategradient. However,
the nature of the artifacts indicate more a problem in the geometry in my
opinion. I have seen such errors when, for example, rotating in the wrong
direction. I can have a look if you share the dataset.
Cheers,
Simon

On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the suggestions, Simon and Cyril!
>
> I have been carefully looking though the geometry and from what I
> understand of the transformations matrices, the geometry looks correct/(as
> expected).
>
> HOWEVER: I found out that the reason for the Hnd to behave differently
> were because had used half-fan scans (full-arc).
> When I used a full-fan (half-arc) scan of Hnd projections the same
> artifacts occurs!
>
> Are there other (built-in) means of improving half-arc scans, than the
> parker short scan filter?
>
> Parker short scan does a decent job, but the result is still far from the
> quality of the Varian software reconstruction at least for the CatPhan.
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>
>> One suggestion since it works with the Hnd projections:
>> You can run rtkprojections twice (with the Hnd projections, then with Xim
>> projections) and output two projection stack files and two geometry files,
>> then compare the projection stack files by subtracting one to the other
>> (with SimpleRTK or clitk) and the geometry files with diff. If they are
>> identical, then I do not see any reason why the reconstructions should be
>> different, so my guess is that you will find differences.
>>
>>
>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>
>>> Hi,
>>> I have almost never worked with Varian data but it looks like a
>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>> projections which results in assigning a bad geometry to each
>>> projection. How did you name your projections? Maybe check that the
>>> order matches that of the RTK geometry file. Otherwise, there might be
>>> an issue in the creation of the geometry file itself.
>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>> code when you feel it's ready.
>>> Simon
>>>
>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>> <andreasg at phys.au.dk> wrote:
>>>
>>>> Dear RTK experts,
>>>>
>>>> I am reconstructing Varian ProBeam projections of the Xim image format.
>>>> I
>>>> have written the reader myself - very similar to the Hnd one already
>>>> available with RTK.
>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>
>>>> The reader apparently works (Images and angles displays as expected in
>>>> UI),
>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>> image
>>>> that is smeared out around the high and low density areas [see attached
>>>> image]
>>>>
>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>> SDD=3m.
>>>>
>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>> algorithm).
>>>> The reconstruction of the Xim projections performed on Varian software
>>>> works
>>>> perfectly.
>>>>
>>>> Without the Parker Short Scan Filter the first and last projections
>>>> creates
>>>> streaks across the reconstruction as if they were way too bright.
>>>> If the first few projections are excluded, the following projection
>>>> will act
>>>> the same way.
>>>>
>>>> The projections are corrected for beam hardening and all the projections
>>>> have the expected attenuation.
>>>> No "smearing" filters (like median) is used, and iterative
>>>> reconstruction
>>>> makes the same artifacts.
>>>>
>>>> Setting the value of the first and last projection to zero has the same
>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>> the
>>>> artifacts.
>>>>
>>>> Have any of you had a similar problem? Am I missing something?
>>>> Any suggestions are welcome I'm running out of ideas.
>>>>
>>>> Best regards
>>>> Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> N?rrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     andreasg at phys.au.dk
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From andreasg at phys.au.dk  Fri Sep 16 16:37:43 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 22:37:43 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
Message-ID: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>

Thanks for the fast response Simon!

I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
right all along!
I just didn't get why it makes a difference. I think I do now, as the
resulting image was flipped upside down and not left/right as I expected.
[attached]

The reconstruction is significantly better, I'll look into what should be
included in the reader and what I should keep in my program to keep
conformity with the other readers. Then I'll create a pull request.

Just for the purpose of others hitting the same or a similar bug, I also
attempted:
I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
back/forward projection, *but with no* significant improvement [attached]

And:
If you want you can download the data set from: [Dropbox link to 460MB zip
<https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep it
up as long as Dropbox allows me)] Only the Acquisitions/subfolder is used
along with the Scan.xml (Calibrations folder may be used in the future in
my program, but I'm not sure if you can rely on the existence of the
content).

A MatLab XimReader is available: link
<https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
available from Varian bitbucket along a with a python version and a
C#->matlab plugin
<https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). Otherwise
my fork with the RTK-style reader is available from the same repository (I
have also added Hnc support, thanks to the Geoff Hugo fork, so bzip2 is a
new dependancy).

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:

> Hi,
> You can try any iterative reconstruction, they can also handle short
> scans. Start with a few iterations of rtksart or rtkconjugategradient.
> However, the nature of the artifacts indicate more a problem in the
> geometry in my opinion. I have seen such errors when, for example, rotating
> in the wrong direction. I can have a look if you share the dataset.
> Cheers,
> Simon
>
> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
> andreasg at phys.au.dk> wrote:
>
>> Thanks for the suggestions, Simon and Cyril!
>>
>> I have been carefully looking though the geometry and from what I
>> understand of the transformations matrices, the geometry looks correct/(as
>> expected).
>>
>> HOWEVER: I found out that the reason for the Hnd to behave differently
>> were because had used half-fan scans (full-arc).
>> When I used a full-fan (half-arc) scan of Hnd projections the same
>> artifacts occurs!
>>
>> Are there other (built-in) means of improving half-arc scans, than the
>> parker short scan filter?
>>
>> Parker short scan does a decent job, but the result is still far from the
>> quality of the Varian software reconstruction at least for the CatPhan.
>>
>> Best regards
>> Andreas
>>
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>>
>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>
>>> One suggestion since it works with the Hnd projections:
>>> You can run rtkprojections twice (with the Hnd projections, then with
>>> Xim projections) and output two projection stack files and two geometry
>>> files, then compare the projection stack files by subtracting one to the
>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>> are identical, then I do not see any reason why the reconstructions should
>>> be different, so my guess is that you will find differences.
>>>
>>>
>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>
>>>> Hi,
>>>> I have almost never worked with Varian data but it looks like a
>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>> projections which results in assigning a bad geometry to each
>>>> projection. How did you name your projections? Maybe check that the
>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>> an issue in the creation of the geometry file itself.
>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>> code when you feel it's ready.
>>>> Simon
>>>>
>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>> <andreasg at phys.au.dk> wrote:
>>>>
>>>>> Dear RTK experts,
>>>>>
>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>> format. I
>>>>> have written the reader myself - very similar to the Hnd one already
>>>>> available with RTK.
>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>
>>>>> The reader apparently works (Images and angles displays as expected in
>>>>> UI),
>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>> image
>>>>> that is smeared out around the high and low density areas [see attached
>>>>> image]
>>>>>
>>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>> SDD=3m.
>>>>>
>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>> algorithm).
>>>>> The reconstruction of the Xim projections performed on Varian software
>>>>> works
>>>>> perfectly.
>>>>>
>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>> creates
>>>>> streaks across the reconstruction as if they were way too bright.
>>>>> If the first few projections are excluded, the following projection
>>>>> will act
>>>>> the same way.
>>>>>
>>>>> The projections are corrected for beam hardening and all the
>>>>> projections
>>>>> have the expected attenuation.
>>>>> No "smearing" filters (like median) is used, and iterative
>>>>> reconstruction
>>>>> makes the same artifacts.
>>>>>
>>>>> Setting the value of the first and last projection to zero has the same
>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>> the
>>>>> artifacts.
>>>>>
>>>>> Have any of you had a similar problem? Am I missing something?
>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>
>>>>> Best regards
>>>>> Andreas
>>>>>
>>>>> __________________________________
>>>>>
>>>>> Andreas Gravgaard Andersen
>>>>>
>>>>> Department of Oncology,
>>>>>
>>>>> Aarhus University Hospital
>>>>>
>>>>> N?rrebrogade 44,
>>>>>
>>>>> 8000, Aarhus C
>>>>>
>>>>> Mail:     andreasg at phys.au.dk
>>>>>
>>>>> Cell:      +45 3165 8140
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 03:26:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 09:26:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
 <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
Message-ID: <CAF0oig2TSmAsSn=o3aLo6LEFDOSaKRtfknjMer24rcDKJ-0Fqg@mail.gmail.com>

Hi,
Thanks for sharing. There still seems to be some streak artefacts, do you
see the same in the Varian reconstruction?
I'm looking forward to the pull-request, I think we should try to make the
bzip2 optional.
Simon

On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the fast response Simon!
>
> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
> right all along!
> I just didn't get why it makes a difference. I think I do now, as the
> resulting image was flipped upside down and not left/right as I expected.
> [attached]
>
> The reconstruction is significantly better, I'll look into what should be
> included in the reader and what I should keep in my program to keep
> conformity with the other readers. Then I'll create a pull request.
>
> Just for the purpose of others hitting the same or a similar bug, I also
> attempted:
> I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
> back/forward projection, *but with no* significant improvement [attached]
>
> And:
> If you want you can download the data set from: [Dropbox link to 460MB zip
> <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep
> it up as long as Dropbox allows me)] Only the Acquisitions/subfolder is
> used along with the Scan.xml (Calibrations folder may be used in the future
> in my program, but I'm not sure if you can rely on the existence of the
> content).
>
> A MatLab XimReader is available: link
> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
> available from Varian bitbucket along a with a python version and a
> C#->matlab plugin
> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>).
> Otherwise my fork with the RTK-style reader is available from the same
> repository (I have also added Hnc support, thanks to the Geoff Hugo fork,
> so bzip2 is a new dependancy).
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> Hi,
>> You can try any iterative reconstruction, they can also handle short
>> scans. Start with a few iterations of rtksart or rtkconjugategradient.
>> However, the nature of the artifacts indicate more a problem in the
>> geometry in my opinion. I have seen such errors when, for example, rotating
>> in the wrong direction. I can have a look if you share the dataset.
>> Cheers,
>> Simon
>>
>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
>> andreasg at phys.au.dk> wrote:
>>
>>> Thanks for the suggestions, Simon and Cyril!
>>>
>>> I have been carefully looking though the geometry and from what I
>>> understand of the transformations matrices, the geometry looks correct/(as
>>> expected).
>>>
>>> HOWEVER: I found out that the reason for the Hnd to behave differently
>>> were because had used half-fan scans (full-arc).
>>> When I used a full-fan (half-arc) scan of Hnd projections the same
>>> artifacts occurs!
>>>
>>> Are there other (built-in) means of improving half-arc scans, than the
>>> parker short scan filter?
>>>
>>> Parker short scan does a decent job, but the result is still far from
>>> the quality of the Varian software reconstruction at least for the CatPhan.
>>>
>>> Best regards
>>> Andreas
>>>
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>>
>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>>
>>>> One suggestion since it works with the Hnd projections:
>>>> You can run rtkprojections twice (with the Hnd projections, then with
>>>> Xim projections) and output two projection stack files and two geometry
>>>> files, then compare the projection stack files by subtracting one to the
>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>>> are identical, then I do not see any reason why the reconstructions should
>>>> be different, so my guess is that you will find differences.
>>>>
>>>>
>>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>>
>>>>> Hi,
>>>>> I have almost never worked with Varian data but it looks like a
>>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>>> projections which results in assigning a bad geometry to each
>>>>> projection. How did you name your projections? Maybe check that the
>>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>>> an issue in the creation of the geometry file itself.
>>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>>> code when you feel it's ready.
>>>>> Simon
>>>>>
>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>>> <andreasg at phys.au.dk> wrote:
>>>>>
>>>>>> Dear RTK experts,
>>>>>>
>>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>>> format. I
>>>>>> have written the reader myself - very similar to the Hnd one already
>>>>>> available with RTK.
>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>>
>>>>>> The reader apparently works (Images and angles displays as expected
>>>>>> in UI),
>>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>>> image
>>>>>> that is smeared out around the high and low density areas [see
>>>>>> attached
>>>>>> image]
>>>>>>
>>>>>> I'm using half arc, full fan images with no bow-tie filter from
>>>>>> Scripps
>>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>>> SDD=3m.
>>>>>>
>>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>>> algorithm).
>>>>>> The reconstruction of the Xim projections performed on Varian
>>>>>> software works
>>>>>> perfectly.
>>>>>>
>>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>>> creates
>>>>>> streaks across the reconstruction as if they were way too bright.
>>>>>> If the first few projections are excluded, the following projection
>>>>>> will act
>>>>>> the same way.
>>>>>>
>>>>>> The projections are corrected for beam hardening and all the
>>>>>> projections
>>>>>> have the expected attenuation.
>>>>>> No "smearing" filters (like median) is used, and iterative
>>>>>> reconstruction
>>>>>> makes the same artifacts.
>>>>>>
>>>>>> Setting the value of the first and last projection to zero has the
>>>>>> same
>>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>>> the
>>>>>> artifacts.
>>>>>>
>>>>>> Have any of you had a similar problem? Am I missing something?
>>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>>
>>>>>> Best regards
>>>>>> Andreas
>>>>>>
>>>>>> __________________________________
>>>>>>
>>>>>> Andreas Gravgaard Andersen
>>>>>>
>>>>>> Department of Oncology,
>>>>>>
>>>>>> Aarhus University Hospital
>>>>>>
>>>>>> N?rrebrogade 44,
>>>>>>
>>>>>> 8000, Aarhus C
>>>>>>
>>>>>> Mail:     andreasg at phys.au.dk
>>>>>>
>>>>>> Cell:      +45 3165 8140
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:05:24 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:05:24 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
Message-ID: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>

Dear RTK users,
I have quickly tested calling the SimpleRTK python lib from Matlab and it
seems to work well:
http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
Therefore, I don't think we have to work on Matlab wrappings but let us
know if you think otherwise.
Future works include a simple installation mechanism for pre-compiled
SimpleRTK libraries. We'll keep you posted!
Simon
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From bottiger at gmail.com  Mon Sep 19 05:14:03 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 11:14:03 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
Message-ID: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>

Dear Simon

This look very interesting! Which platform did you successfully execute
this on?
I will give it a try at once (on windows) and let you know if I run into
any problems.

best

Arvid

On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> I have quickly tested calling the SimpleRTK python lib from Matlab and it
> seems to work well:
> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
> Therefore, I don't think we have to work on Matlab wrappings but let us
> know if you think otherwise.
> Future works include a simple installation mechanism for pre-compiled
> SimpleRTK libraries. We'll keep you posted!
> Simon
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:19:28 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:19:28 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
Message-ID: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>

The latest MacOS. It's nice if you can test it on other platforms, I'll try
to run it on Linux but I have to upgrade matlab first (I think python calls
are available starting with Matlab 2014).
Simon

On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Dear Simon
>
> This look very interesting! Which platform did you successfully execute
> this on?
> I will give it a try at once (on windows) and let you know if I run into
> any problems.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> Dear RTK users,
>> I have quickly tested calling the SimpleRTK python lib from Matlab and it
>> seems to work well:
>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>> Therefore, I don't think we have to work on Matlab wrappings but let us
>> know if you think otherwise.
>> Future works include a simple installation mechanism for pre-compiled
>> SimpleRTK libraries. We'll keep you posted!
>> Simon
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From bottiger at gmail.com  Mon Sep 19 08:30:32 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 14:30:32 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
Message-ID: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>

Hi again.

I've been trying to get it working. However, I did run into some problems
compiling SimpleRTK. The main issue seems to be that it depends on
SimpleRTKCommon - which I do not have.

Here is the last few lines from VS2013

> 5>LINK : fatal error LNK1181: cannot open input file
'..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib' [C:\Users\aplb\Work\RTK\RTK1.2-
> bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> 5>
> 5>      0 Warning(s)
> 5>      2 Error(s)
> 5>
> 5>  Time Elapsed 00:00:25.26
> ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
==========

I'm not quite sure what is going on, because the only reference I can find
to SimpleRTKCommon is the CMakeLists.txt on github:
https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt

best

Arvid

On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> The latest MacOS. It's nice if you can test it on other platforms, I'll
> try to run it on Linux but I have to upgrade matlab first (I think python
> calls are available starting with Matlab 2014).
> Simon
>
> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Dear Simon
>>
>> This look very interesting! Which platform did you successfully execute
>> this on?
>> I will give it a try at once (on windows) and let you know if I run into
>> any problems.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Dear RTK users,
>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>> it seems to work well:
>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>> know if you think otherwise.
>>> Future works include a simple installation mechanism for pre-compiled
>>> SimpleRTK libraries. We'll keep you posted!
>>> Simon
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 12:50:33 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 18:50:33 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
Message-ID: <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>

 SimpleRTKCommon is a library generated when compiling. Don't you have
another error before that which explains why it did not compile?
Simon

On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I've been trying to get it working. However, I did run into some problems
> compiling SimpleRTK. The main issue seems to be that it depends on
> SimpleRTKCommon - which I do not have.
>
> Here is the last few lines from VS2013
>
> > 5>LINK : fatal error LNK1181: cannot open input file '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
> [C:\Users\aplb\Work\RTK\RTK1.2-
> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> > 5>
> > 5>      0 Warning(s)
> > 5>      2 Error(s)
> > 5>
> > 5>  Time Elapsed 00:00:25.26
> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
> ==========
>
> I'm not quite sure what is going on, because the only reference I can find
> to SimpleRTKCommon is the CMakeLists.txt on github:
> https://github.com/SimonRit/RTK/blob/master/utilities/
> SimpleRTK/CMakeLists.txt
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>> try to run it on Linux but I have to upgrade matlab first (I think python
>> calls are available starting with Matlab 2014).
>> Simon
>>
>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Dear Simon
>>>
>>> This look very interesting! Which platform did you successfully execute
>>> this on?
>>> I will give it a try at once (on windows) and let you know if I run into
>>> any problems.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Dear RTK users,
>>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>>> it seems to work well:
>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>>> know if you think otherwise.
>>>> Future works include a simple installation mechanism for pre-compiled
>>>> SimpleRTK libraries. We'll keep you posted!
>>>> Simon
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 01:33:46 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 07:33:46 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
Message-ID: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>

I'm not an msvc specialist but your first line suggests that you have 
pasted only part of the log:

20>  Done Building Project 
"C:\Users\aplb\Work\RTK\RTK1.2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" 
(default targets) -- FAILED.

What you need to find out is why this build failed. If the build fails, 
the linking cannot work.
Cheers,
Simon

On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
> I did a complete rebuild, and here is the end of the output: 
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that 
> I'm trying to compile the version I just pulled from git earlier 
> today, since the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     SimpleRTKCommon is a library generated when compiling. Don't you
>     have another error before that which explains why it did not compile?
>     Simon
>
>     On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger
>     <bottiger at gmail.com <mailto:bottiger at gmail.com>> wrote:
>
>         Hi again.
>
>         I've been trying to get it working. However, I did run into
>         some problems compiling SimpleRTK. The main issue seems to be
>         that it depends on SimpleRTKCommon - which I do not have.
>
>         Here is the last few lines from VS2013
>
>         > 5>LINK : fatal error LNK1181: cannot open input file
>         '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>         [C:\Users\aplb\Work\RTK\RTK1.2-
>         > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>         > 5>
>         > 5>      0 Warning(s)
>         > 5>      2 Error(s)
>         > 5>
>         > 5>  Time Elapsed 00:00:25.26
>         > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0
>         skipped ==========
>
>         I'm not quite sure what is going on, because the only
>         reference I can find to SimpleRTKCommon is the CMakeLists.txt
>         on github:
>         https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt
>         <https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt>
>
>         best
>
>         Arvid
>
>         On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit
>         <simon.rit at creatis.insa-lyon.fr
>         <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>             The latest MacOS. It's nice if you can test it on other
>             platforms, I'll try to run it on Linux but I have to
>             upgrade matlab first (I think python calls are available
>             starting with Matlab 2014).
>             Simon
>
>             On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen
>             B?ttiger <bottiger at gmail.com <mailto:bottiger at gmail.com>>
>             wrote:
>
>                 Dear Simon
>
>                 This look very interesting! Which platform did you
>                 successfully execute this on?
>                 I will give it a try at once (on windows) and let you
>                 know if I run into any problems.
>
>                 best
>
>                 Arvid
>
>                 On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit
>                 <simon.rit at creatis.insa-lyon.fr
>                 <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>                     Dear RTK users,
>                     I have quickly tested calling the SimpleRTK python
>                     lib from Matlab and it seems to work well:
>                     http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>                     <http://wiki.openrtk.org/index.php/SimpleRTK#Matlab>
>                     Therefore, I don't think we have to work on Matlab
>                     wrappings but let us know if you think otherwise.
>                     Future works include a simple installation
>                     mechanism for pre-compiled SimpleRTK libraries.
>                     We'll keep you posted!
>                     Simon
>
>                     _______________________________________________
>                     Rtk-users mailing list
>                     Rtk-users at public.kitware.com
>                     <mailto:Rtk-users at public.kitware.com>
>                     http://public.kitware.com/mailman/listinfo/rtk-users
>                     <http://public.kitware.com/mailman/listinfo/rtk-users>
>
>
>
>
>
>

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From bottiger at gmail.com  Tue Sep 20 08:17:35 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Tue, 20 Sep 2016 14:17:35 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
Message-ID: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>

Hi again.

I understand, but could you please help me get in contact with the person
who knows something about the windows build (if any), I think there is
something wrong.

I have been investigating the build problems I had and found that in the
sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
opened it up and found the projects which I had problems building:
"SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.

When I then tried to build SimpleRTKCommon manually it just compiled
without any problems. However, when I followed up by building
"SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
find "SimpleRTKCommon-0.9.lib" - which I just build.

After some more investigation I realized that the SimpleRTKCommon is set to
build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects it
to be a static linked library (LIB). After changing SimpleRTKCommon to be
build as a static library - and changing the output location - I could
build SimpleRTKBasicFilters0.

However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
to a LIB as well I could build SimpleRTKBasicFilters1, then
SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.

I'm unsure if the intention is to build them as static or dynamic
libraries, but in any case the current build configuration doesn't work -
on my setup at least.

However, I should note than for some reason the "lua5" project did build
successfully out of the box. Whatever it does differently works.

best

Arvid



On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> I'm not an msvc specialist but your first line suggests that you have
> pasted only part of the log:
>
> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.
> 2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
> What you need to find out is why this build failed. If the build fails,
> the linking cannot work.
> Cheers,
> Simon
>
>
> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>
> I did a complete rebuild, and here is the end of the output:
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that I'm
> trying to compile the version I just pulled from git earlier today, since
> the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> SimpleRTKCommon is a library generated when compiling. Don't you have
>> another error before that which explains why it did not compile?
>> Simon
>>
>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Hi again.
>>>
>>> I've been trying to get it working. However, I did run into some
>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>> SimpleRTKCommon - which I do not have.
>>>
>>> Here is the last few lines from VS2013
>>>
>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>> > 5>
>>> > 5>      0 Warning(s)
>>> > 5>      2 Error(s)
>>> > 5>
>>> > 5>  Time Elapsed 00:00:25.26
>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>> ==========
>>>
>>> I'm not quite sure what is going on, because the only reference I can
>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>> RTK/CMakeLists.txt
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>>>> try to run it on Linux but I have to upgrade matlab first (I think python
>>>> calls are available starting with Matlab 2014).
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Dear Simon
>>>>>
>>>>> This look very interesting! Which platform did you successfully
>>>>> execute this on?
>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>> into any problems.
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Dear RTK users,
>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>> and it seems to work well:
>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>> us know if you think otherwise.
>>>>>> Future works include a simple installation mechanism for pre-compiled
>>>>>> SimpleRTK libraries. We'll keep you posted!
>>>>>> Simon
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 10:19:20 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 16:19:20 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
Message-ID: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>

Hi,
Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
I can't solve your problem but Kitware is going to look into an upgrade of
SimpleRTK in the coming days, I'll ask them if they know what is the issue.
If you look here:
http://my.cdash.org/viewNotes.php?buildid=1052065
this is a nightly build of SimpleRTK on Windows and it seems to work. I
don't see why it wouldn't work for you.
Simon

On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I understand, but could you please help me get in contact with the person
> who knows something about the windows build (if any), I think there is
> something wrong.
>
> I have been investigating the build problems I had and found that in the
> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
> opened it up and found the projects which I had problems building:
> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>
> When I then tried to build SimpleRTKCommon manually it just compiled
> without any problems. However, when I followed up by building
> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
> find "SimpleRTKCommon-0.9.lib" - which I just build.
>
> After some more investigation I realized that the SimpleRTKCommon is set
> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
> it to be a static linked library (LIB). After changing SimpleRTKCommon to
> be build as a static library - and changing the output location - I could
> build SimpleRTKBasicFilters0.
>
> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
> to a LIB as well I could build SimpleRTKBasicFilters1, then
> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>
> I'm unsure if the intention is to build them as static or dynamic
> libraries, but in any case the current build configuration doesn't work -
> on my setup at least.
>
> However, I should note than for some reason the "lua5" project did build
> successfully out of the box. Whatever it does differently works.
>
> best
>
> Arvid
>
>
>
> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> I'm not an msvc specialist but your first line suggests that you have
>> pasted only part of the log:
>>
>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
>> What you need to find out is why this build failed. If the build fails,
>> the linking cannot work.
>> Cheers,
>> Simon
>>
>>
>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>
>> I did a complete rebuild, and here is the end of the output:
>> http://pastebin.com/hvQ33WWg
>>
>> I have to admit I'm not sure what to make of it. I should note that I'm
>> trying to compile the version I just pulled from git earlier today, since
>> the other version I normally work with is really old.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>> another error before that which explains why it did not compile?
>>> Simon
>>>
>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>> bottiger at gmail.com> wrote:
>>>
>>>> Hi again.
>>>>
>>>> I've been trying to get it working. However, I did run into some
>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>> SimpleRTKCommon - which I do not have.
>>>>
>>>> Here is the last few lines from VS2013
>>>>
>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>> > 5>
>>>> > 5>      0 Warning(s)
>>>> > 5>      2 Error(s)
>>>> > 5>
>>>> > 5>  Time Elapsed 00:00:25.26
>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>> ==========
>>>>
>>>> I'm not quite sure what is going on, because the only reference I can
>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>> RTK/CMakeLists.txt
>>>>
>>>> best
>>>>
>>>> Arvid
>>>>
>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>> python calls are available starting with Matlab 2014).
>>>>> Simon
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>> bottiger at gmail.com> wrote:
>>>>>
>>>>>> Dear Simon
>>>>>>
>>>>>> This look very interesting! Which platform did you successfully
>>>>>> execute this on?
>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>> into any problems.
>>>>>>
>>>>>> best
>>>>>>
>>>>>> Arvid
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>
>>>>>>> Dear RTK users,
>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>> and it seems to work well:
>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>>> us know if you think otherwise.
>>>>>>> Future works include a simple installation mechanism for
>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>> Simon
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 02:40:50 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 08:40:50 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
Message-ID: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>

Dear RTK users,
RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
been released, about 7 months after RTK v1.2.0.

Release notes :
- Style updated (follow more closely latest ITK guidelines).
- Started using Travis CI, github pull requests should now be used for code
submission.
- New pre-processing functionalities:
  * CUDA polynomial gain correction,
  * scatter glare correction,
  * lag correction,
  * idark option,
  * removed threshold to positive values after i0 LUT.
- Improved CUDA forward and backprojection speed using projection slabs.
- Added motion-compensated forward and back projection operators in CUDA,
in both 3D and 4D.
- Added the rtkregularizedconjugategradient application, which performs 3D
regularized reconstruction by conjugate gradient + optional regularizations
(Positivity, TV, Wavelets).
- Made the rtkfourdrooster, rtkmcrooster and rtkregularizedconjugategradient
fully modular. Each regularization step can be made active or inactive.
- Added a filter to minimize the L0 norm of the temporal gradient (one-D
only).

Many thanks to the contributors, in alphabetical order for this release: Cyril
Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien
Jomier, S?bastien
Brousmiche, Simon Rit

As usual, be aware that we don't focus on releases since we have a public
github repository <http://github.com/SimonRit/RTK> that we try to keep
stable. I still recommend the use of the master HEAD over releases to enjoy
the new RTK developments before their release. We still have a few on-going
projects for which we will use and enhance RTK.

Simon (for the RTK consortium)
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 04:48:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 10:48:26 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
In-Reply-To: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
References: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
Message-ID: <CAF0oig0=5_KPN198JzsGQXDd07Nvw_Ew+qSGhguk0m27s3U-3Q@mail.gmail.com>

Sorry, I had forgotten to change the release number in the source file.
It's been corrected, you will have to move your tag locally or update your
file if you had already downloaded it.
Simon

On Thu, Sep 22, 2016 at 8:40 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
> been released, about 7 months after RTK v1.2.0.
>
> Release notes :
> - Style updated (follow more closely latest ITK guidelines).
> - Started using Travis CI, github pull requests should now be used for
> code submission.
> - New pre-processing functionalities:
>   * CUDA polynomial gain correction,
>   * scatter glare correction,
>   * lag correction,
>   * idark option,
>   * removed threshold to positive values after i0 LUT.
> - Improved CUDA forward and backprojection speed using projection slabs.
> - Added motion-compensated forward and back projection operators in CUDA,
> in both 3D and 4D.
> - Added the rtkregularizedconjugategradient application, which performs
> 3D regularized reconstruction by conjugate gradient + optional
> regularizations (Positivity, TV, Wavelets).
> - Made the rtkfourdrooster, rtkmcrooster and
> rtkregularizedconjugategradient fully modular. Each regularization step
> can be made active or inactive.
> - Added a filter to minimize the L0 norm of the temporal gradient (one-D
> only).
>
> Many thanks to the contributors, in alphabetical order for this release: Cyril
> Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien Jomier, S?bastien
> Brousmiche, Simon Rit
>
> As usual, be aware that we don't focus on releases since we have a public
> github repository <http://github.com/SimonRit/RTK> that we try to keep
> stable. I still recommend the use of the master HEAD over releases to
> enjoy the new RTK developments before their release. We still have a few
> on-going projects for which we will use and enhance RTK.
>
> Simon (for the RTK consortium)
>
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From bottiger at gmail.com  Fri Sep 23 04:29:06 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Fri, 23 Sep 2016 10:29:06 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
 <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
Message-ID: <CANBwxwEvaUrvd1X=74g=V2JmDwtrQKFDtyUdAZJn5CRCBCkb8g@mail.gmail.com>

Hi again.

I've been spending some more time with this, and feel I learned a little
bit more. I have now tested this on several machines with several compiler
versions (more or less all of them) and serveral cmake versions - all with
Windows 7.

I can actually reproduce the successful build you linked to, but this can
only be done if you do not include any of the language wrappings, like in
the build you linked to. Enable any of them, and the build will break. (see
attachment)

I suspect it must have been working in the past, but since none of them are
included in your test there have been a breaking change, and none of them
work anymore.

I am still trying to tweak then projects manually to build SimpleRTK with
some sort of language support, but still without any luck.

best

Arvid

On Tue, Sep 20, 2016 at 4:19 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
> at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
> I can't solve your problem but Kitware is going to look into an upgrade of
> SimpleRTK in the coming days, I'll ask them if they know what is the issue.
> If you look here:
> http://my.cdash.org/viewNotes.php?buildid=1052065
> this is a nightly build of SimpleRTK on Windows and it seems to work. I
> don't see why it wouldn't work for you.
> Simon
>
> On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Hi again.
>>
>> I understand, but could you please help me get in contact with the person
>> who knows something about the windows build (if any), I think there is
>> something wrong.
>>
>> I have been investigating the build problems I had and found that in the
>> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
>> opened it up and found the projects which I had problems building:
>> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>>
>> When I then tried to build SimpleRTKCommon manually it just compiled
>> without any problems. However, when I followed up by building
>> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
>> find "SimpleRTKCommon-0.9.lib" - which I just build.
>>
>> After some more investigation I realized that the SimpleRTKCommon is set
>> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
>> it to be a static linked library (LIB). After changing SimpleRTKCommon to
>> be build as a static library - and changing the output location - I could
>> build SimpleRTKBasicFilters0.
>>
>> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing
>> that to a LIB as well I could build SimpleRTKBasicFilters1, then
>> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>>
>> I'm unsure if the intention is to build them as static or dynamic
>> libraries, but in any case the current build configuration doesn't work -
>> on my setup at least.
>>
>> However, I should note than for some reason the "lua5" project did build
>> successfully out of the box. Whatever it does differently works.
>>
>> best
>>
>> Arvid
>>
>>
>>
>> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> I'm not an msvc specialist but your first line suggests that you have
>>> pasted only part of the log:
>>>
>>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) --
>>> FAILED.
>>> What you need to find out is why this build failed. If the build fails,
>>> the linking cannot work.
>>> Cheers,
>>> Simon
>>>
>>>
>>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>>
>>> I did a complete rebuild, and here is the end of the output:
>>> http://pastebin.com/hvQ33WWg
>>>
>>> I have to admit I'm not sure what to make of it. I should note that I'm
>>> trying to compile the version I just pulled from git earlier today, since
>>> the other version I normally work with is really old.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>>> another error before that which explains why it did not compile?
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Hi again.
>>>>>
>>>>> I've been trying to get it working. However, I did run into some
>>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>>> SimpleRTKCommon - which I do not have.
>>>>>
>>>>> Here is the last few lines from VS2013
>>>>>
>>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>>> > 5>
>>>>> > 5>      0 Warning(s)
>>>>> > 5>      2 Error(s)
>>>>> > 5>
>>>>> > 5>  Time Elapsed 00:00:25.26
>>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>>> ==========
>>>>>
>>>>> I'm not quite sure what is going on, because the only reference I can
>>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>>> RTK/CMakeLists.txt
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>>> python calls are available starting with Matlab 2014).
>>>>>> Simon
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>>> bottiger at gmail.com> wrote:
>>>>>>
>>>>>>> Dear Simon
>>>>>>>
>>>>>>> This look very interesting! Which platform did you successfully
>>>>>>> execute this on?
>>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>>> into any problems.
>>>>>>>
>>>>>>> best
>>>>>>>
>>>>>>> Arvid
>>>>>>>
>>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Dear RTK users,
>>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>>> and it seems to work well:
>>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but
>>>>>>>> let us know if you think otherwise.
>>>>>>>> Future works include a simple installation mechanism for
>>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
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From ajbatkinson at gmail.com  Wed Sep 28 08:11:12 2016
From: ajbatkinson at gmail.com (Abby Bryce Atkinson)
Date: Wed, 28 Sep 2016 13:11:12 +0100
Subject: [Rtk-users] 4DROOSTERReconstruction Example
Message-ID: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>

Hi,

I am trying to work through the 4DROOSTER example using the POPI patient
images (
http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) but
I am getting stuck when extracting the respiratory signal using the
amsterdam shroud.

I receive this error:


C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
--path .\Projections\ ^
More?                    --regexp '.*.his' ^
More?                    --output shroud.mha ^
More?                    --unsharp 650
ExceptionObject caught with writer->Update() in file
C:\RTK\applications\rtkamst
erdamshroud\rtkamsterdamshroud.cxx line 91

itk::ExceptionObject (0030E9E0)
Location: "void __thiscall itk::ImageFileWriter<class itk::Image<double,2>
>::Wr
ite(void)"
File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
Line: 284
Description: itk::ERROR: ImageFileWriter(03670318): Largest possible region
does
 not fully contain requested paste IO regionPaste IO region: ImageIORegion
(0030
EDD4)
  Dimension: 2
  Index: 0 0
  Size: 0 0
Largest possible region: ImageRegion (0030EE70)
  Dimension: 2
  Index: [0, 0]
  Size: [0, 0]


Can anyone help with a solution/tell me what I am doing wrong please?

Thanks,

Abby
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From simon.rit at creatis.insa-lyon.fr  Wed Sep 28 12:49:32 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 28 Sep 2016 18:49:32 +0200
Subject: [Rtk-users] 4DROOSTERReconstruction Example
In-Reply-To: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
References: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
Message-ID: <e23fc5ec-f7b4-846c-e349-f07564e2da8a@creatis.insa-lyon.fr>

Hi,

My guess is that the software does not find the projections. I would add 
the --verbose option and check that you actually input some projections. 
If not, I guess there is an issue with the path or the regexp in your 
command line.

Simon

On 28/09/2016 14:11, Abby Bryce Atkinson wrote:
> Hi,
>
> I am trying to work through the 4DROOSTER example using the POPI 
> patient images 
> (http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) 
> but I am getting stuck when extracting the respiratory signal using 
> the amsterdam shroud.
>
> I receive this error:
>
>
> C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
> --path .\Projections\ ^
> More?                    --regexp '.*.his' ^
> More?                    --output shroud.mha ^
> More?                    --unsharp 650
> ExceptionObject caught with writer->Update() in file 
> C:\RTK\applications\rtkamst
> erdamshroud\rtkamsterdamshroud.cxx line 91
>
> itk::ExceptionObject (0030E9E0)
> Location: "void __thiscall itk::ImageFileWriter<class 
> itk::Image<double,2> >::Wr
> ite(void)"
> File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
> Line: 284
> Description: itk::ERROR: ImageFileWriter(03670318): Largest possible 
> region does
>  not fully contain requested paste IO regionPaste IO region: 
> ImageIORegion (0030
> EDD4)
>   Dimension: 2
>   Index: 0 0
>   Size: 0 0
> Largest possible region: ImageRegion (0030EE70)
>   Dimension: 2
>   Index: [0, 0]
>   Size: [0, 0]
>
>
> Can anyone help with a solution/tell me what I am doing wrong please?
>
> Thanks,
>
> Abby
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users

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From signabdm at gmail.com  Mon Sep 12 06:58:59 2016
From: signabdm at gmail.com (Valeriy Signatulin)
Date: Mon, 12 Sep 2016 16:58:59 +0600
Subject: [Rtk-users] rotation of detector plane
Message-ID: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>

Hello RTK users.
Is it possible to specify rotation of detector plane in RTK ? (in
rtksimulategeom for example) If not, what is the best way to code this ?
By rotation of detector plane i mean twist, tilt, skew around the normal of
the detector as described in
http://www.ndt.net/article/v10n09/yisun/yisun.pdf page 6.
I'm trying to write the geometry calibration method described in this
article in RTK and i need to simulate these rotations to check the results.
Thanks.
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 12 08:40:31 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 12 Sep 2016 14:40:31 +0200
Subject: [Rtk-users] rotation of detector plane
In-Reply-To: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
References: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
Message-ID: <CAF0oig0C3zFcAaAhWHV9g+UY02i7cws7OU-7r2YadyAt3TH5GA@mail.gmail.com>

Hi,
You can do any rotation with RTK. The rotation is described 3 Euler angles,
see the geometry doc <http://www.openrtk.org/Doxygen/geometry.pdf>. From
the command line, that would be the --in_angle and out_angle that allow you
to modify the other angles than the standard angle for the position along
the circular rotation (GantryAngle). If you want to modify it per
projection, that's possible using C++ or Python code (AddProjection
<http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
method).
Good luck,
Simon

On Mon, Sep 12, 2016 at 12:58 PM, Valeriy Signatulin <signabdm at gmail.com>
wrote:

> Hello RTK users.
> Is it possible to specify rotation of detector plane in RTK ? (in
> rtksimulategeom for example) If not, what is the best way to code this ?
> By rotation of detector plane i mean twist, tilt, skew around the normal
> of the detector as described in http://www.ndt.net/article/
> v10n09/yisun/yisun.pdf page 6.
> I'm trying to write the geometry calibration method described in this
> article in RTK and i need to simulate these rotations to check the results.
> Thanks.
>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From andreasg at phys.au.dk  Tue Sep 13 13:06:46 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Tue, 13 Sep 2016 19:06:46 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
Message-ID: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>

Dear RTK experts,

I am reconstructing Varian ProBeam projections of the Xim image format. I
have written the reader myself - very similar to the Hnd one already
available with RTK.
Links to my fork: [XimReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkXimImageIO.cxx>,
XMLReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamXMLFileReader.cxx>,
GeometryReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamGeometryReader.cxx>
]

The reader apparently works (Images and angles displays as expected in UI),
however when reconstructing with a regular FDK* I get a reconstructed image
that is smeared out around the high and low density areas *[see attached
image]

I'm using half arc, full fan images with no bow-tie filter from Scripps
(~520 projections). Fixed detector and source (offset=0) with SID=2m,
SDD=3m.

*For the Hnd projections the reconstruction works perfectly (Same algorithm
<https://github.com/agravgaard/cbctrecon/blob/master/cbctrecon.cpp#L2726>).*
The reconstruction of the Xim projections performed on Varian software
works perfectly.

Without the Parker Short Scan Filter the first and last projections creates
streaks across the reconstruction as if they were way too bright.
If the first few projections are excluded, the following projection will
act the same way.

The projections are corrected for beam hardening and all the projections
have the expected attenuation.
No "smearing" filters (like median) is used, and iterative reconstruction
makes the same artifacts.

Setting the value of the first and last projection to zero has the same
effect as excluding. Changing the ramp filter only changes noise, not the
artifacts.

*Have any of you had a similar problem? *Am I missing something?
Any suggestions are welcome I'm running out of ideas.

Best regards
Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 13 16:18:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 13 Sep 2016 22:18:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
Message-ID: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>

Hi,
I have almost never worked with Varian data but it looks like a
geometry problem. Maybe the problem comes from a bad ordering of the
projections which results in assigning a bad geometry to each
projection. How did you name your projections? Maybe check that the
order matches that of the RTK geometry file. Otherwise, there might be
an issue in the creation of the geometry file itself.
All this sounds good, happy bug hunt and don't hesitate to share your
code when you feel it's ready.
Simon

On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
<andreasg at phys.au.dk> wrote:
> Dear RTK experts,
>
> I am reconstructing Varian ProBeam projections of the Xim image format. I
> have written the reader myself - very similar to the Hnd one already
> available with RTK.
> Links to my fork: [XimReader, XMLReader, GeometryReader]
>
> The reader apparently works (Images and angles displays as expected in UI),
> however when reconstructing with a regular FDK I get a reconstructed image
> that is smeared out around the high and low density areas [see attached
> image]
>
> I'm using half arc, full fan images with no bow-tie filter from Scripps
> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
> SDD=3m.
>
> For the Hnd projections the reconstruction works perfectly (Same algorithm).
> The reconstruction of the Xim projections performed on Varian software works
> perfectly.
>
> Without the Parker Short Scan Filter the first and last projections creates
> streaks across the reconstruction as if they were way too bright.
> If the first few projections are excluded, the following projection will act
> the same way.
>
> The projections are corrected for beam hardening and all the projections
> have the expected attenuation.
> No "smearing" filters (like median) is used, and iterative reconstruction
> makes the same artifacts.
>
> Setting the value of the first and last projection to zero has the same
> effect as excluding. Changing the ramp filter only changes noise, not the
> artifacts.
>
> Have any of you had a similar problem? Am I missing something?
> Any suggestions are welcome I'm running out of ideas.
>
> Best regards
> Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>


From cyril.mory at creatis.insa-lyon.fr  Wed Sep 14 03:10:42 2016
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 14 Sep 2016 09:10:42 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
Message-ID: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>

One suggestion since it works with the Hnd projections:
You can run rtkprojections twice (with the Hnd projections, then with 
Xim projections) and output two projection stack files and two geometry 
files, then compare the projection stack files by subtracting one to the 
other (with SimpleRTK or clitk) and the geometry files with diff. If 
they are identical, then I do not see any reason why the reconstructions 
should be different, so my guess is that you will find differences.

On 09/13/2016 10:18 PM, Simon Rit wrote:
> Hi,
> I have almost never worked with Varian data but it looks like a
> geometry problem. Maybe the problem comes from a bad ordering of the
> projections which results in assigning a bad geometry to each
> projection. How did you name your projections? Maybe check that the
> order matches that of the RTK geometry file. Otherwise, there might be
> an issue in the creation of the geometry file itself.
> All this sounds good, happy bug hunt and don't hesitate to share your
> code when you feel it's ready.
> Simon
>
> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
> <andreasg at phys.au.dk> wrote:
>> Dear RTK experts,
>>
>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>> have written the reader myself - very similar to the Hnd one already
>> available with RTK.
>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>
>> The reader apparently works (Images and angles displays as expected in UI),
>> however when reconstructing with a regular FDK I get a reconstructed image
>> that is smeared out around the high and low density areas [see attached
>> image]
>>
>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>> SDD=3m.
>>
>> For the Hnd projections the reconstruction works perfectly (Same algorithm).
>> The reconstruction of the Xim projections performed on Varian software works
>> perfectly.
>>
>> Without the Parker Short Scan Filter the first and last projections creates
>> streaks across the reconstruction as if they were way too bright.
>> If the first few projections are excluded, the following projection will act
>> the same way.
>>
>> The projections are corrected for beam hardening and all the projections
>> have the expected attenuation.
>> No "smearing" filters (like median) is used, and iterative reconstruction
>> makes the same artifacts.
>>
>> Setting the value of the first and last projection to zero has the same
>> effect as excluding. Changing the ramp filter only changes noise, not the
>> artifacts.
>>
>> Have any of you had a similar problem? Am I missing something?
>> Any suggestions are welcome I'm running out of ideas.
>>
>> Best regards
>> Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>



From andreasg at phys.au.dk  Fri Sep 16 08:56:34 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 14:56:34 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
Message-ID: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>

Thanks for the suggestions, Simon and Cyril!

I have been carefully looking though the geometry and from what I
understand of the transformations matrices, the geometry looks correct/(as
expected).

HOWEVER: I found out that the reason for the Hnd to behave differently were
because had used half-fan scans (full-arc).
When I used a full-fan (half-arc) scan of Hnd projections the same
artifacts occurs!

Are there other (built-in) means of improving half-arc scans, than the
parker short scan filter?

Parker short scan does a decent job, but the result is still far from the
quality of the Varian software reconstruction at least for the CatPhan.

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:

> One suggestion since it works with the Hnd projections:
> You can run rtkprojections twice (with the Hnd projections, then with Xim
> projections) and output two projection stack files and two geometry files,
> then compare the projection stack files by subtracting one to the other
> (with SimpleRTK or clitk) and the geometry files with diff. If they are
> identical, then I do not see any reason why the reconstructions should be
> different, so my guess is that you will find differences.
>
>
> On 09/13/2016 10:18 PM, Simon Rit wrote:
>
>> Hi,
>> I have almost never worked with Varian data but it looks like a
>> geometry problem. Maybe the problem comes from a bad ordering of the
>> projections which results in assigning a bad geometry to each
>> projection. How did you name your projections? Maybe check that the
>> order matches that of the RTK geometry file. Otherwise, there might be
>> an issue in the creation of the geometry file itself.
>> All this sounds good, happy bug hunt and don't hesitate to share your
>> code when you feel it's ready.
>> Simon
>>
>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>> <andreasg at phys.au.dk> wrote:
>>
>>> Dear RTK experts,
>>>
>>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>>> have written the reader myself - very similar to the Hnd one already
>>> available with RTK.
>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>
>>> The reader apparently works (Images and angles displays as expected in
>>> UI),
>>> however when reconstructing with a regular FDK I get a reconstructed
>>> image
>>> that is smeared out around the high and low density areas [see attached
>>> image]
>>>
>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>> SDD=3m.
>>>
>>> For the Hnd projections the reconstruction works perfectly (Same
>>> algorithm).
>>> The reconstruction of the Xim projections performed on Varian software
>>> works
>>> perfectly.
>>>
>>> Without the Parker Short Scan Filter the first and last projections
>>> creates
>>> streaks across the reconstruction as if they were way too bright.
>>> If the first few projections are excluded, the following projection will
>>> act
>>> the same way.
>>>
>>> The projections are corrected for beam hardening and all the projections
>>> have the expected attenuation.
>>> No "smearing" filters (like median) is used, and iterative reconstruction
>>> makes the same artifacts.
>>>
>>> Setting the value of the first and last projection to zero has the same
>>> effect as excluding. Changing the ramp filter only changes noise, not the
>>> artifacts.
>>>
>>> Have any of you had a similar problem? Am I missing something?
>>> Any suggestions are welcome I'm running out of ideas.
>>>
>>> Best regards
>>> Andreas
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Sep 16 10:13:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 16 Sep 2016 16:13:26 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
Message-ID: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>

Hi,
You can try any iterative reconstruction, they can also handle short scans.
Start with a few iterations of rtksart or rtkconjugategradient. However,
the nature of the artifacts indicate more a problem in the geometry in my
opinion. I have seen such errors when, for example, rotating in the wrong
direction. I can have a look if you share the dataset.
Cheers,
Simon

On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the suggestions, Simon and Cyril!
>
> I have been carefully looking though the geometry and from what I
> understand of the transformations matrices, the geometry looks correct/(as
> expected).
>
> HOWEVER: I found out that the reason for the Hnd to behave differently
> were because had used half-fan scans (full-arc).
> When I used a full-fan (half-arc) scan of Hnd projections the same
> artifacts occurs!
>
> Are there other (built-in) means of improving half-arc scans, than the
> parker short scan filter?
>
> Parker short scan does a decent job, but the result is still far from the
> quality of the Varian software reconstruction at least for the CatPhan.
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>
>> One suggestion since it works with the Hnd projections:
>> You can run rtkprojections twice (with the Hnd projections, then with Xim
>> projections) and output two projection stack files and two geometry files,
>> then compare the projection stack files by subtracting one to the other
>> (with SimpleRTK or clitk) and the geometry files with diff. If they are
>> identical, then I do not see any reason why the reconstructions should be
>> different, so my guess is that you will find differences.
>>
>>
>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>
>>> Hi,
>>> I have almost never worked with Varian data but it looks like a
>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>> projections which results in assigning a bad geometry to each
>>> projection. How did you name your projections? Maybe check that the
>>> order matches that of the RTK geometry file. Otherwise, there might be
>>> an issue in the creation of the geometry file itself.
>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>> code when you feel it's ready.
>>> Simon
>>>
>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>> <andreasg at phys.au.dk> wrote:
>>>
>>>> Dear RTK experts,
>>>>
>>>> I am reconstructing Varian ProBeam projections of the Xim image format.
>>>> I
>>>> have written the reader myself - very similar to the Hnd one already
>>>> available with RTK.
>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>
>>>> The reader apparently works (Images and angles displays as expected in
>>>> UI),
>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>> image
>>>> that is smeared out around the high and low density areas [see attached
>>>> image]
>>>>
>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>> SDD=3m.
>>>>
>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>> algorithm).
>>>> The reconstruction of the Xim projections performed on Varian software
>>>> works
>>>> perfectly.
>>>>
>>>> Without the Parker Short Scan Filter the first and last projections
>>>> creates
>>>> streaks across the reconstruction as if they were way too bright.
>>>> If the first few projections are excluded, the following projection
>>>> will act
>>>> the same way.
>>>>
>>>> The projections are corrected for beam hardening and all the projections
>>>> have the expected attenuation.
>>>> No "smearing" filters (like median) is used, and iterative
>>>> reconstruction
>>>> makes the same artifacts.
>>>>
>>>> Setting the value of the first and last projection to zero has the same
>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>> the
>>>> artifacts.
>>>>
>>>> Have any of you had a similar problem? Am I missing something?
>>>> Any suggestions are welcome I'm running out of ideas.
>>>>
>>>> Best regards
>>>> Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> N?rrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     andreasg at phys.au.dk
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From andreasg at phys.au.dk  Fri Sep 16 16:37:43 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 22:37:43 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
Message-ID: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>

Thanks for the fast response Simon!

I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
right all along!
I just didn't get why it makes a difference. I think I do now, as the
resulting image was flipped upside down and not left/right as I expected.
[attached]

The reconstruction is significantly better, I'll look into what should be
included in the reader and what I should keep in my program to keep
conformity with the other readers. Then I'll create a pull request.

Just for the purpose of others hitting the same or a similar bug, I also
attempted:
I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
back/forward projection, *but with no* significant improvement [attached]

And:
If you want you can download the data set from: [Dropbox link to 460MB zip
<https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep it
up as long as Dropbox allows me)] Only the Acquisitions/subfolder is used
along with the Scan.xml (Calibrations folder may be used in the future in
my program, but I'm not sure if you can rely on the existence of the
content).

A MatLab XimReader is available: link
<https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
available from Varian bitbucket along a with a python version and a
C#->matlab plugin
<https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). Otherwise
my fork with the RTK-style reader is available from the same repository (I
have also added Hnc support, thanks to the Geoff Hugo fork, so bzip2 is a
new dependancy).

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:

> Hi,
> You can try any iterative reconstruction, they can also handle short
> scans. Start with a few iterations of rtksart or rtkconjugategradient.
> However, the nature of the artifacts indicate more a problem in the
> geometry in my opinion. I have seen such errors when, for example, rotating
> in the wrong direction. I can have a look if you share the dataset.
> Cheers,
> Simon
>
> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
> andreasg at phys.au.dk> wrote:
>
>> Thanks for the suggestions, Simon and Cyril!
>>
>> I have been carefully looking though the geometry and from what I
>> understand of the transformations matrices, the geometry looks correct/(as
>> expected).
>>
>> HOWEVER: I found out that the reason for the Hnd to behave differently
>> were because had used half-fan scans (full-arc).
>> When I used a full-fan (half-arc) scan of Hnd projections the same
>> artifacts occurs!
>>
>> Are there other (built-in) means of improving half-arc scans, than the
>> parker short scan filter?
>>
>> Parker short scan does a decent job, but the result is still far from the
>> quality of the Varian software reconstruction at least for the CatPhan.
>>
>> Best regards
>> Andreas
>>
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>>
>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>
>>> One suggestion since it works with the Hnd projections:
>>> You can run rtkprojections twice (with the Hnd projections, then with
>>> Xim projections) and output two projection stack files and two geometry
>>> files, then compare the projection stack files by subtracting one to the
>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>> are identical, then I do not see any reason why the reconstructions should
>>> be different, so my guess is that you will find differences.
>>>
>>>
>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>
>>>> Hi,
>>>> I have almost never worked with Varian data but it looks like a
>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>> projections which results in assigning a bad geometry to each
>>>> projection. How did you name your projections? Maybe check that the
>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>> an issue in the creation of the geometry file itself.
>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>> code when you feel it's ready.
>>>> Simon
>>>>
>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>> <andreasg at phys.au.dk> wrote:
>>>>
>>>>> Dear RTK experts,
>>>>>
>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>> format. I
>>>>> have written the reader myself - very similar to the Hnd one already
>>>>> available with RTK.
>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>
>>>>> The reader apparently works (Images and angles displays as expected in
>>>>> UI),
>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>> image
>>>>> that is smeared out around the high and low density areas [see attached
>>>>> image]
>>>>>
>>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>> SDD=3m.
>>>>>
>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>> algorithm).
>>>>> The reconstruction of the Xim projections performed on Varian software
>>>>> works
>>>>> perfectly.
>>>>>
>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>> creates
>>>>> streaks across the reconstruction as if they were way too bright.
>>>>> If the first few projections are excluded, the following projection
>>>>> will act
>>>>> the same way.
>>>>>
>>>>> The projections are corrected for beam hardening and all the
>>>>> projections
>>>>> have the expected attenuation.
>>>>> No "smearing" filters (like median) is used, and iterative
>>>>> reconstruction
>>>>> makes the same artifacts.
>>>>>
>>>>> Setting the value of the first and last projection to zero has the same
>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>> the
>>>>> artifacts.
>>>>>
>>>>> Have any of you had a similar problem? Am I missing something?
>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>
>>>>> Best regards
>>>>> Andreas
>>>>>
>>>>> __________________________________
>>>>>
>>>>> Andreas Gravgaard Andersen
>>>>>
>>>>> Department of Oncology,
>>>>>
>>>>> Aarhus University Hospital
>>>>>
>>>>> N?rrebrogade 44,
>>>>>
>>>>> 8000, Aarhus C
>>>>>
>>>>> Mail:     andreasg at phys.au.dk
>>>>>
>>>>> Cell:      +45 3165 8140
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 03:26:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 09:26:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
 <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
Message-ID: <CAF0oig2TSmAsSn=o3aLo6LEFDOSaKRtfknjMer24rcDKJ-0Fqg@mail.gmail.com>

Hi,
Thanks for sharing. There still seems to be some streak artefacts, do you
see the same in the Varian reconstruction?
I'm looking forward to the pull-request, I think we should try to make the
bzip2 optional.
Simon

On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the fast response Simon!
>
> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
> right all along!
> I just didn't get why it makes a difference. I think I do now, as the
> resulting image was flipped upside down and not left/right as I expected.
> [attached]
>
> The reconstruction is significantly better, I'll look into what should be
> included in the reader and what I should keep in my program to keep
> conformity with the other readers. Then I'll create a pull request.
>
> Just for the purpose of others hitting the same or a similar bug, I also
> attempted:
> I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
> back/forward projection, *but with no* significant improvement [attached]
>
> And:
> If you want you can download the data set from: [Dropbox link to 460MB zip
> <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep
> it up as long as Dropbox allows me)] Only the Acquisitions/subfolder is
> used along with the Scan.xml (Calibrations folder may be used in the future
> in my program, but I'm not sure if you can rely on the existence of the
> content).
>
> A MatLab XimReader is available: link
> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
> available from Varian bitbucket along a with a python version and a
> C#->matlab plugin
> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>).
> Otherwise my fork with the RTK-style reader is available from the same
> repository (I have also added Hnc support, thanks to the Geoff Hugo fork,
> so bzip2 is a new dependancy).
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> Hi,
>> You can try any iterative reconstruction, they can also handle short
>> scans. Start with a few iterations of rtksart or rtkconjugategradient.
>> However, the nature of the artifacts indicate more a problem in the
>> geometry in my opinion. I have seen such errors when, for example, rotating
>> in the wrong direction. I can have a look if you share the dataset.
>> Cheers,
>> Simon
>>
>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
>> andreasg at phys.au.dk> wrote:
>>
>>> Thanks for the suggestions, Simon and Cyril!
>>>
>>> I have been carefully looking though the geometry and from what I
>>> understand of the transformations matrices, the geometry looks correct/(as
>>> expected).
>>>
>>> HOWEVER: I found out that the reason for the Hnd to behave differently
>>> were because had used half-fan scans (full-arc).
>>> When I used a full-fan (half-arc) scan of Hnd projections the same
>>> artifacts occurs!
>>>
>>> Are there other (built-in) means of improving half-arc scans, than the
>>> parker short scan filter?
>>>
>>> Parker short scan does a decent job, but the result is still far from
>>> the quality of the Varian software reconstruction at least for the CatPhan.
>>>
>>> Best regards
>>> Andreas
>>>
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>>
>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>>
>>>> One suggestion since it works with the Hnd projections:
>>>> You can run rtkprojections twice (with the Hnd projections, then with
>>>> Xim projections) and output two projection stack files and two geometry
>>>> files, then compare the projection stack files by subtracting one to the
>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>>> are identical, then I do not see any reason why the reconstructions should
>>>> be different, so my guess is that you will find differences.
>>>>
>>>>
>>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>>
>>>>> Hi,
>>>>> I have almost never worked with Varian data but it looks like a
>>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>>> projections which results in assigning a bad geometry to each
>>>>> projection. How did you name your projections? Maybe check that the
>>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>>> an issue in the creation of the geometry file itself.
>>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>>> code when you feel it's ready.
>>>>> Simon
>>>>>
>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>>> <andreasg at phys.au.dk> wrote:
>>>>>
>>>>>> Dear RTK experts,
>>>>>>
>>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>>> format. I
>>>>>> have written the reader myself - very similar to the Hnd one already
>>>>>> available with RTK.
>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>>
>>>>>> The reader apparently works (Images and angles displays as expected
>>>>>> in UI),
>>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>>> image
>>>>>> that is smeared out around the high and low density areas [see
>>>>>> attached
>>>>>> image]
>>>>>>
>>>>>> I'm using half arc, full fan images with no bow-tie filter from
>>>>>> Scripps
>>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>>> SDD=3m.
>>>>>>
>>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>>> algorithm).
>>>>>> The reconstruction of the Xim projections performed on Varian
>>>>>> software works
>>>>>> perfectly.
>>>>>>
>>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>>> creates
>>>>>> streaks across the reconstruction as if they were way too bright.
>>>>>> If the first few projections are excluded, the following projection
>>>>>> will act
>>>>>> the same way.
>>>>>>
>>>>>> The projections are corrected for beam hardening and all the
>>>>>> projections
>>>>>> have the expected attenuation.
>>>>>> No "smearing" filters (like median) is used, and iterative
>>>>>> reconstruction
>>>>>> makes the same artifacts.
>>>>>>
>>>>>> Setting the value of the first and last projection to zero has the
>>>>>> same
>>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>>> the
>>>>>> artifacts.
>>>>>>
>>>>>> Have any of you had a similar problem? Am I missing something?
>>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>>
>>>>>> Best regards
>>>>>> Andreas
>>>>>>
>>>>>> __________________________________
>>>>>>
>>>>>> Andreas Gravgaard Andersen
>>>>>>
>>>>>> Department of Oncology,
>>>>>>
>>>>>> Aarhus University Hospital
>>>>>>
>>>>>> N?rrebrogade 44,
>>>>>>
>>>>>> 8000, Aarhus C
>>>>>>
>>>>>> Mail:     andreasg at phys.au.dk
>>>>>>
>>>>>> Cell:      +45 3165 8140
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:05:24 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:05:24 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
Message-ID: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>

Dear RTK users,
I have quickly tested calling the SimpleRTK python lib from Matlab and it
seems to work well:
http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
Therefore, I don't think we have to work on Matlab wrappings but let us
know if you think otherwise.
Future works include a simple installation mechanism for pre-compiled
SimpleRTK libraries. We'll keep you posted!
Simon
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From bottiger at gmail.com  Mon Sep 19 05:14:03 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 11:14:03 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
Message-ID: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>

Dear Simon

This look very interesting! Which platform did you successfully execute
this on?
I will give it a try at once (on windows) and let you know if I run into
any problems.

best

Arvid

On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> I have quickly tested calling the SimpleRTK python lib from Matlab and it
> seems to work well:
> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
> Therefore, I don't think we have to work on Matlab wrappings but let us
> know if you think otherwise.
> Future works include a simple installation mechanism for pre-compiled
> SimpleRTK libraries. We'll keep you posted!
> Simon
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:19:28 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:19:28 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
Message-ID: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>

The latest MacOS. It's nice if you can test it on other platforms, I'll try
to run it on Linux but I have to upgrade matlab first (I think python calls
are available starting with Matlab 2014).
Simon

On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Dear Simon
>
> This look very interesting! Which platform did you successfully execute
> this on?
> I will give it a try at once (on windows) and let you know if I run into
> any problems.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> Dear RTK users,
>> I have quickly tested calling the SimpleRTK python lib from Matlab and it
>> seems to work well:
>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>> Therefore, I don't think we have to work on Matlab wrappings but let us
>> know if you think otherwise.
>> Future works include a simple installation mechanism for pre-compiled
>> SimpleRTK libraries. We'll keep you posted!
>> Simon
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From bottiger at gmail.com  Mon Sep 19 08:30:32 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 14:30:32 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
Message-ID: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>

Hi again.

I've been trying to get it working. However, I did run into some problems
compiling SimpleRTK. The main issue seems to be that it depends on
SimpleRTKCommon - which I do not have.

Here is the last few lines from VS2013

> 5>LINK : fatal error LNK1181: cannot open input file
'..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib' [C:\Users\aplb\Work\RTK\RTK1.2-
> bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> 5>
> 5>      0 Warning(s)
> 5>      2 Error(s)
> 5>
> 5>  Time Elapsed 00:00:25.26
> ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
==========

I'm not quite sure what is going on, because the only reference I can find
to SimpleRTKCommon is the CMakeLists.txt on github:
https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt

best

Arvid

On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> The latest MacOS. It's nice if you can test it on other platforms, I'll
> try to run it on Linux but I have to upgrade matlab first (I think python
> calls are available starting with Matlab 2014).
> Simon
>
> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Dear Simon
>>
>> This look very interesting! Which platform did you successfully execute
>> this on?
>> I will give it a try at once (on windows) and let you know if I run into
>> any problems.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Dear RTK users,
>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>> it seems to work well:
>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>> know if you think otherwise.
>>> Future works include a simple installation mechanism for pre-compiled
>>> SimpleRTK libraries. We'll keep you posted!
>>> Simon
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 12:50:33 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 18:50:33 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
Message-ID: <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>

 SimpleRTKCommon is a library generated when compiling. Don't you have
another error before that which explains why it did not compile?
Simon

On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I've been trying to get it working. However, I did run into some problems
> compiling SimpleRTK. The main issue seems to be that it depends on
> SimpleRTKCommon - which I do not have.
>
> Here is the last few lines from VS2013
>
> > 5>LINK : fatal error LNK1181: cannot open input file '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
> [C:\Users\aplb\Work\RTK\RTK1.2-
> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> > 5>
> > 5>      0 Warning(s)
> > 5>      2 Error(s)
> > 5>
> > 5>  Time Elapsed 00:00:25.26
> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
> ==========
>
> I'm not quite sure what is going on, because the only reference I can find
> to SimpleRTKCommon is the CMakeLists.txt on github:
> https://github.com/SimonRit/RTK/blob/master/utilities/
> SimpleRTK/CMakeLists.txt
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>> try to run it on Linux but I have to upgrade matlab first (I think python
>> calls are available starting with Matlab 2014).
>> Simon
>>
>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Dear Simon
>>>
>>> This look very interesting! Which platform did you successfully execute
>>> this on?
>>> I will give it a try at once (on windows) and let you know if I run into
>>> any problems.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Dear RTK users,
>>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>>> it seems to work well:
>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>>> know if you think otherwise.
>>>> Future works include a simple installation mechanism for pre-compiled
>>>> SimpleRTK libraries. We'll keep you posted!
>>>> Simon
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 01:33:46 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 07:33:46 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
Message-ID: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>

I'm not an msvc specialist but your first line suggests that you have 
pasted only part of the log:

20>  Done Building Project 
"C:\Users\aplb\Work\RTK\RTK1.2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" 
(default targets) -- FAILED.

What you need to find out is why this build failed. If the build fails, 
the linking cannot work.
Cheers,
Simon

On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
> I did a complete rebuild, and here is the end of the output: 
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that 
> I'm trying to compile the version I just pulled from git earlier 
> today, since the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     SimpleRTKCommon is a library generated when compiling. Don't you
>     have another error before that which explains why it did not compile?
>     Simon
>
>     On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger
>     <bottiger at gmail.com <mailto:bottiger at gmail.com>> wrote:
>
>         Hi again.
>
>         I've been trying to get it working. However, I did run into
>         some problems compiling SimpleRTK. The main issue seems to be
>         that it depends on SimpleRTKCommon - which I do not have.
>
>         Here is the last few lines from VS2013
>
>         > 5>LINK : fatal error LNK1181: cannot open input file
>         '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>         [C:\Users\aplb\Work\RTK\RTK1.2-
>         > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>         > 5>
>         > 5>      0 Warning(s)
>         > 5>      2 Error(s)
>         > 5>
>         > 5>  Time Elapsed 00:00:25.26
>         > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0
>         skipped ==========
>
>         I'm not quite sure what is going on, because the only
>         reference I can find to SimpleRTKCommon is the CMakeLists.txt
>         on github:
>         https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt
>         <https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt>
>
>         best
>
>         Arvid
>
>         On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit
>         <simon.rit at creatis.insa-lyon.fr
>         <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>             The latest MacOS. It's nice if you can test it on other
>             platforms, I'll try to run it on Linux but I have to
>             upgrade matlab first (I think python calls are available
>             starting with Matlab 2014).
>             Simon
>
>             On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen
>             B?ttiger <bottiger at gmail.com <mailto:bottiger at gmail.com>>
>             wrote:
>
>                 Dear Simon
>
>                 This look very interesting! Which platform did you
>                 successfully execute this on?
>                 I will give it a try at once (on windows) and let you
>                 know if I run into any problems.
>
>                 best
>
>                 Arvid
>
>                 On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit
>                 <simon.rit at creatis.insa-lyon.fr
>                 <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>                     Dear RTK users,
>                     I have quickly tested calling the SimpleRTK python
>                     lib from Matlab and it seems to work well:
>                     http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>                     <http://wiki.openrtk.org/index.php/SimpleRTK#Matlab>
>                     Therefore, I don't think we have to work on Matlab
>                     wrappings but let us know if you think otherwise.
>                     Future works include a simple installation
>                     mechanism for pre-compiled SimpleRTK libraries.
>                     We'll keep you posted!
>                     Simon
>
>                     _______________________________________________
>                     Rtk-users mailing list
>                     Rtk-users at public.kitware.com
>                     <mailto:Rtk-users at public.kitware.com>
>                     http://public.kitware.com/mailman/listinfo/rtk-users
>                     <http://public.kitware.com/mailman/listinfo/rtk-users>
>
>
>
>
>
>

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From bottiger at gmail.com  Tue Sep 20 08:17:35 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Tue, 20 Sep 2016 14:17:35 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
Message-ID: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>

Hi again.

I understand, but could you please help me get in contact with the person
who knows something about the windows build (if any), I think there is
something wrong.

I have been investigating the build problems I had and found that in the
sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
opened it up and found the projects which I had problems building:
"SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.

When I then tried to build SimpleRTKCommon manually it just compiled
without any problems. However, when I followed up by building
"SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
find "SimpleRTKCommon-0.9.lib" - which I just build.

After some more investigation I realized that the SimpleRTKCommon is set to
build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects it
to be a static linked library (LIB). After changing SimpleRTKCommon to be
build as a static library - and changing the output location - I could
build SimpleRTKBasicFilters0.

However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
to a LIB as well I could build SimpleRTKBasicFilters1, then
SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.

I'm unsure if the intention is to build them as static or dynamic
libraries, but in any case the current build configuration doesn't work -
on my setup at least.

However, I should note than for some reason the "lua5" project did build
successfully out of the box. Whatever it does differently works.

best

Arvid



On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> I'm not an msvc specialist but your first line suggests that you have
> pasted only part of the log:
>
> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.
> 2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
> What you need to find out is why this build failed. If the build fails,
> the linking cannot work.
> Cheers,
> Simon
>
>
> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>
> I did a complete rebuild, and here is the end of the output:
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that I'm
> trying to compile the version I just pulled from git earlier today, since
> the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> SimpleRTKCommon is a library generated when compiling. Don't you have
>> another error before that which explains why it did not compile?
>> Simon
>>
>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Hi again.
>>>
>>> I've been trying to get it working. However, I did run into some
>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>> SimpleRTKCommon - which I do not have.
>>>
>>> Here is the last few lines from VS2013
>>>
>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>> > 5>
>>> > 5>      0 Warning(s)
>>> > 5>      2 Error(s)
>>> > 5>
>>> > 5>  Time Elapsed 00:00:25.26
>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>> ==========
>>>
>>> I'm not quite sure what is going on, because the only reference I can
>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>> RTK/CMakeLists.txt
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>>>> try to run it on Linux but I have to upgrade matlab first (I think python
>>>> calls are available starting with Matlab 2014).
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Dear Simon
>>>>>
>>>>> This look very interesting! Which platform did you successfully
>>>>> execute this on?
>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>> into any problems.
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Dear RTK users,
>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>> and it seems to work well:
>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>> us know if you think otherwise.
>>>>>> Future works include a simple installation mechanism for pre-compiled
>>>>>> SimpleRTK libraries. We'll keep you posted!
>>>>>> Simon
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 10:19:20 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 16:19:20 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
Message-ID: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>

Hi,
Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
I can't solve your problem but Kitware is going to look into an upgrade of
SimpleRTK in the coming days, I'll ask them if they know what is the issue.
If you look here:
http://my.cdash.org/viewNotes.php?buildid=1052065
this is a nightly build of SimpleRTK on Windows and it seems to work. I
don't see why it wouldn't work for you.
Simon

On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I understand, but could you please help me get in contact with the person
> who knows something about the windows build (if any), I think there is
> something wrong.
>
> I have been investigating the build problems I had and found that in the
> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
> opened it up and found the projects which I had problems building:
> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>
> When I then tried to build SimpleRTKCommon manually it just compiled
> without any problems. However, when I followed up by building
> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
> find "SimpleRTKCommon-0.9.lib" - which I just build.
>
> After some more investigation I realized that the SimpleRTKCommon is set
> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
> it to be a static linked library (LIB). After changing SimpleRTKCommon to
> be build as a static library - and changing the output location - I could
> build SimpleRTKBasicFilters0.
>
> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
> to a LIB as well I could build SimpleRTKBasicFilters1, then
> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>
> I'm unsure if the intention is to build them as static or dynamic
> libraries, but in any case the current build configuration doesn't work -
> on my setup at least.
>
> However, I should note than for some reason the "lua5" project did build
> successfully out of the box. Whatever it does differently works.
>
> best
>
> Arvid
>
>
>
> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> I'm not an msvc specialist but your first line suggests that you have
>> pasted only part of the log:
>>
>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
>> What you need to find out is why this build failed. If the build fails,
>> the linking cannot work.
>> Cheers,
>> Simon
>>
>>
>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>
>> I did a complete rebuild, and here is the end of the output:
>> http://pastebin.com/hvQ33WWg
>>
>> I have to admit I'm not sure what to make of it. I should note that I'm
>> trying to compile the version I just pulled from git earlier today, since
>> the other version I normally work with is really old.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>> another error before that which explains why it did not compile?
>>> Simon
>>>
>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>> bottiger at gmail.com> wrote:
>>>
>>>> Hi again.
>>>>
>>>> I've been trying to get it working. However, I did run into some
>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>> SimpleRTKCommon - which I do not have.
>>>>
>>>> Here is the last few lines from VS2013
>>>>
>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>> > 5>
>>>> > 5>      0 Warning(s)
>>>> > 5>      2 Error(s)
>>>> > 5>
>>>> > 5>  Time Elapsed 00:00:25.26
>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>> ==========
>>>>
>>>> I'm not quite sure what is going on, because the only reference I can
>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>> RTK/CMakeLists.txt
>>>>
>>>> best
>>>>
>>>> Arvid
>>>>
>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>> python calls are available starting with Matlab 2014).
>>>>> Simon
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>> bottiger at gmail.com> wrote:
>>>>>
>>>>>> Dear Simon
>>>>>>
>>>>>> This look very interesting! Which platform did you successfully
>>>>>> execute this on?
>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>> into any problems.
>>>>>>
>>>>>> best
>>>>>>
>>>>>> Arvid
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>
>>>>>>> Dear RTK users,
>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>> and it seems to work well:
>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>>> us know if you think otherwise.
>>>>>>> Future works include a simple installation mechanism for
>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>> Simon
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 02:40:50 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 08:40:50 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
Message-ID: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>

Dear RTK users,
RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
been released, about 7 months after RTK v1.2.0.

Release notes :
- Style updated (follow more closely latest ITK guidelines).
- Started using Travis CI, github pull requests should now be used for code
submission.
- New pre-processing functionalities:
  * CUDA polynomial gain correction,
  * scatter glare correction,
  * lag correction,
  * idark option,
  * removed threshold to positive values after i0 LUT.
- Improved CUDA forward and backprojection speed using projection slabs.
- Added motion-compensated forward and back projection operators in CUDA,
in both 3D and 4D.
- Added the rtkregularizedconjugategradient application, which performs 3D
regularized reconstruction by conjugate gradient + optional regularizations
(Positivity, TV, Wavelets).
- Made the rtkfourdrooster, rtkmcrooster and rtkregularizedconjugategradient
fully modular. Each regularization step can be made active or inactive.
- Added a filter to minimize the L0 norm of the temporal gradient (one-D
only).

Many thanks to the contributors, in alphabetical order for this release: Cyril
Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien
Jomier, S?bastien
Brousmiche, Simon Rit

As usual, be aware that we don't focus on releases since we have a public
github repository <http://github.com/SimonRit/RTK> that we try to keep
stable. I still recommend the use of the master HEAD over releases to enjoy
the new RTK developments before their release. We still have a few on-going
projects for which we will use and enhance RTK.

Simon (for the RTK consortium)
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 04:48:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 10:48:26 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
In-Reply-To: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
References: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
Message-ID: <CAF0oig0=5_KPN198JzsGQXDd07Nvw_Ew+qSGhguk0m27s3U-3Q@mail.gmail.com>

Sorry, I had forgotten to change the release number in the source file.
It's been corrected, you will have to move your tag locally or update your
file if you had already downloaded it.
Simon

On Thu, Sep 22, 2016 at 8:40 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
> been released, about 7 months after RTK v1.2.0.
>
> Release notes :
> - Style updated (follow more closely latest ITK guidelines).
> - Started using Travis CI, github pull requests should now be used for
> code submission.
> - New pre-processing functionalities:
>   * CUDA polynomial gain correction,
>   * scatter glare correction,
>   * lag correction,
>   * idark option,
>   * removed threshold to positive values after i0 LUT.
> - Improved CUDA forward and backprojection speed using projection slabs.
> - Added motion-compensated forward and back projection operators in CUDA,
> in both 3D and 4D.
> - Added the rtkregularizedconjugategradient application, which performs
> 3D regularized reconstruction by conjugate gradient + optional
> regularizations (Positivity, TV, Wavelets).
> - Made the rtkfourdrooster, rtkmcrooster and
> rtkregularizedconjugategradient fully modular. Each regularization step
> can be made active or inactive.
> - Added a filter to minimize the L0 norm of the temporal gradient (one-D
> only).
>
> Many thanks to the contributors, in alphabetical order for this release: Cyril
> Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien Jomier, S?bastien
> Brousmiche, Simon Rit
>
> As usual, be aware that we don't focus on releases since we have a public
> github repository <http://github.com/SimonRit/RTK> that we try to keep
> stable. I still recommend the use of the master HEAD over releases to
> enjoy the new RTK developments before their release. We still have a few
> on-going projects for which we will use and enhance RTK.
>
> Simon (for the RTK consortium)
>
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From bottiger at gmail.com  Fri Sep 23 04:29:06 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Fri, 23 Sep 2016 10:29:06 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
 <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
Message-ID: <CANBwxwEvaUrvd1X=74g=V2JmDwtrQKFDtyUdAZJn5CRCBCkb8g@mail.gmail.com>

Hi again.

I've been spending some more time with this, and feel I learned a little
bit more. I have now tested this on several machines with several compiler
versions (more or less all of them) and serveral cmake versions - all with
Windows 7.

I can actually reproduce the successful build you linked to, but this can
only be done if you do not include any of the language wrappings, like in
the build you linked to. Enable any of them, and the build will break. (see
attachment)

I suspect it must have been working in the past, but since none of them are
included in your test there have been a breaking change, and none of them
work anymore.

I am still trying to tweak then projects manually to build SimpleRTK with
some sort of language support, but still without any luck.

best

Arvid

On Tue, Sep 20, 2016 at 4:19 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
> at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
> I can't solve your problem but Kitware is going to look into an upgrade of
> SimpleRTK in the coming days, I'll ask them if they know what is the issue.
> If you look here:
> http://my.cdash.org/viewNotes.php?buildid=1052065
> this is a nightly build of SimpleRTK on Windows and it seems to work. I
> don't see why it wouldn't work for you.
> Simon
>
> On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Hi again.
>>
>> I understand, but could you please help me get in contact with the person
>> who knows something about the windows build (if any), I think there is
>> something wrong.
>>
>> I have been investigating the build problems I had and found that in the
>> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
>> opened it up and found the projects which I had problems building:
>> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>>
>> When I then tried to build SimpleRTKCommon manually it just compiled
>> without any problems. However, when I followed up by building
>> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
>> find "SimpleRTKCommon-0.9.lib" - which I just build.
>>
>> After some more investigation I realized that the SimpleRTKCommon is set
>> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
>> it to be a static linked library (LIB). After changing SimpleRTKCommon to
>> be build as a static library - and changing the output location - I could
>> build SimpleRTKBasicFilters0.
>>
>> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing
>> that to a LIB as well I could build SimpleRTKBasicFilters1, then
>> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>>
>> I'm unsure if the intention is to build them as static or dynamic
>> libraries, but in any case the current build configuration doesn't work -
>> on my setup at least.
>>
>> However, I should note than for some reason the "lua5" project did build
>> successfully out of the box. Whatever it does differently works.
>>
>> best
>>
>> Arvid
>>
>>
>>
>> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> I'm not an msvc specialist but your first line suggests that you have
>>> pasted only part of the log:
>>>
>>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) --
>>> FAILED.
>>> What you need to find out is why this build failed. If the build fails,
>>> the linking cannot work.
>>> Cheers,
>>> Simon
>>>
>>>
>>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>>
>>> I did a complete rebuild, and here is the end of the output:
>>> http://pastebin.com/hvQ33WWg
>>>
>>> I have to admit I'm not sure what to make of it. I should note that I'm
>>> trying to compile the version I just pulled from git earlier today, since
>>> the other version I normally work with is really old.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>>> another error before that which explains why it did not compile?
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Hi again.
>>>>>
>>>>> I've been trying to get it working. However, I did run into some
>>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>>> SimpleRTKCommon - which I do not have.
>>>>>
>>>>> Here is the last few lines from VS2013
>>>>>
>>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>>> > 5>
>>>>> > 5>      0 Warning(s)
>>>>> > 5>      2 Error(s)
>>>>> > 5>
>>>>> > 5>  Time Elapsed 00:00:25.26
>>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>>> ==========
>>>>>
>>>>> I'm not quite sure what is going on, because the only reference I can
>>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>>> RTK/CMakeLists.txt
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>>> python calls are available starting with Matlab 2014).
>>>>>> Simon
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>>> bottiger at gmail.com> wrote:
>>>>>>
>>>>>>> Dear Simon
>>>>>>>
>>>>>>> This look very interesting! Which platform did you successfully
>>>>>>> execute this on?
>>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>>> into any problems.
>>>>>>>
>>>>>>> best
>>>>>>>
>>>>>>> Arvid
>>>>>>>
>>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Dear RTK users,
>>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>>> and it seems to work well:
>>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but
>>>>>>>> let us know if you think otherwise.
>>>>>>>> Future works include a simple installation mechanism for
>>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
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From ajbatkinson at gmail.com  Wed Sep 28 08:11:12 2016
From: ajbatkinson at gmail.com (Abby Bryce Atkinson)
Date: Wed, 28 Sep 2016 13:11:12 +0100
Subject: [Rtk-users] 4DROOSTERReconstruction Example
Message-ID: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>

Hi,

I am trying to work through the 4DROOSTER example using the POPI patient
images (
http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) but
I am getting stuck when extracting the respiratory signal using the
amsterdam shroud.

I receive this error:


C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
--path .\Projections\ ^
More?                    --regexp '.*.his' ^
More?                    --output shroud.mha ^
More?                    --unsharp 650
ExceptionObject caught with writer->Update() in file
C:\RTK\applications\rtkamst
erdamshroud\rtkamsterdamshroud.cxx line 91

itk::ExceptionObject (0030E9E0)
Location: "void __thiscall itk::ImageFileWriter<class itk::Image<double,2>
>::Wr
ite(void)"
File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
Line: 284
Description: itk::ERROR: ImageFileWriter(03670318): Largest possible region
does
 not fully contain requested paste IO regionPaste IO region: ImageIORegion
(0030
EDD4)
  Dimension: 2
  Index: 0 0
  Size: 0 0
Largest possible region: ImageRegion (0030EE70)
  Dimension: 2
  Index: [0, 0]
  Size: [0, 0]


Can anyone help with a solution/tell me what I am doing wrong please?

Thanks,

Abby
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From simon.rit at creatis.insa-lyon.fr  Wed Sep 28 12:49:32 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 28 Sep 2016 18:49:32 +0200
Subject: [Rtk-users] 4DROOSTERReconstruction Example
In-Reply-To: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
References: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
Message-ID: <e23fc5ec-f7b4-846c-e349-f07564e2da8a@creatis.insa-lyon.fr>

Hi,

My guess is that the software does not find the projections. I would add 
the --verbose option and check that you actually input some projections. 
If not, I guess there is an issue with the path or the regexp in your 
command line.

Simon

On 28/09/2016 14:11, Abby Bryce Atkinson wrote:
> Hi,
>
> I am trying to work through the 4DROOSTER example using the POPI 
> patient images 
> (http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) 
> but I am getting stuck when extracting the respiratory signal using 
> the amsterdam shroud.
>
> I receive this error:
>
>
> C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
> --path .\Projections\ ^
> More?                    --regexp '.*.his' ^
> More?                    --output shroud.mha ^
> More?                    --unsharp 650
> ExceptionObject caught with writer->Update() in file 
> C:\RTK\applications\rtkamst
> erdamshroud\rtkamsterdamshroud.cxx line 91
>
> itk::ExceptionObject (0030E9E0)
> Location: "void __thiscall itk::ImageFileWriter<class 
> itk::Image<double,2> >::Wr
> ite(void)"
> File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
> Line: 284
> Description: itk::ERROR: ImageFileWriter(03670318): Largest possible 
> region does
>  not fully contain requested paste IO regionPaste IO region: 
> ImageIORegion (0030
> EDD4)
>   Dimension: 2
>   Index: 0 0
>   Size: 0 0
> Largest possible region: ImageRegion (0030EE70)
>   Dimension: 2
>   Index: [0, 0]
>   Size: [0, 0]
>
>
> Can anyone help with a solution/tell me what I am doing wrong please?
>
> Thanks,
>
> Abby
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users

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From signabdm at gmail.com  Mon Sep 12 06:58:59 2016
From: signabdm at gmail.com (Valeriy Signatulin)
Date: Mon, 12 Sep 2016 16:58:59 +0600
Subject: [Rtk-users] rotation of detector plane
Message-ID: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>

Hello RTK users.
Is it possible to specify rotation of detector plane in RTK ? (in
rtksimulategeom for example) If not, what is the best way to code this ?
By rotation of detector plane i mean twist, tilt, skew around the normal of
the detector as described in
http://www.ndt.net/article/v10n09/yisun/yisun.pdf page 6.
I'm trying to write the geometry calibration method described in this
article in RTK and i need to simulate these rotations to check the results.
Thanks.
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 12 08:40:31 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 12 Sep 2016 14:40:31 +0200
Subject: [Rtk-users] rotation of detector plane
In-Reply-To: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
References: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
Message-ID: <CAF0oig0C3zFcAaAhWHV9g+UY02i7cws7OU-7r2YadyAt3TH5GA@mail.gmail.com>

Hi,
You can do any rotation with RTK. The rotation is described 3 Euler angles,
see the geometry doc <http://www.openrtk.org/Doxygen/geometry.pdf>. From
the command line, that would be the --in_angle and out_angle that allow you
to modify the other angles than the standard angle for the position along
the circular rotation (GantryAngle). If you want to modify it per
projection, that's possible using C++ or Python code (AddProjection
<http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
method).
Good luck,
Simon

On Mon, Sep 12, 2016 at 12:58 PM, Valeriy Signatulin <signabdm at gmail.com>
wrote:

> Hello RTK users.
> Is it possible to specify rotation of detector plane in RTK ? (in
> rtksimulategeom for example) If not, what is the best way to code this ?
> By rotation of detector plane i mean twist, tilt, skew around the normal
> of the detector as described in http://www.ndt.net/article/
> v10n09/yisun/yisun.pdf page 6.
> I'm trying to write the geometry calibration method described in this
> article in RTK and i need to simulate these rotations to check the results.
> Thanks.
>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From andreasg at phys.au.dk  Tue Sep 13 13:06:46 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Tue, 13 Sep 2016 19:06:46 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
Message-ID: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>

Dear RTK experts,

I am reconstructing Varian ProBeam projections of the Xim image format. I
have written the reader myself - very similar to the Hnd one already
available with RTK.
Links to my fork: [XimReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkXimImageIO.cxx>,
XMLReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamXMLFileReader.cxx>,
GeometryReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamGeometryReader.cxx>
]

The reader apparently works (Images and angles displays as expected in UI),
however when reconstructing with a regular FDK* I get a reconstructed image
that is smeared out around the high and low density areas *[see attached
image]

I'm using half arc, full fan images with no bow-tie filter from Scripps
(~520 projections). Fixed detector and source (offset=0) with SID=2m,
SDD=3m.

*For the Hnd projections the reconstruction works perfectly (Same algorithm
<https://github.com/agravgaard/cbctrecon/blob/master/cbctrecon.cpp#L2726>).*
The reconstruction of the Xim projections performed on Varian software
works perfectly.

Without the Parker Short Scan Filter the first and last projections creates
streaks across the reconstruction as if they were way too bright.
If the first few projections are excluded, the following projection will
act the same way.

The projections are corrected for beam hardening and all the projections
have the expected attenuation.
No "smearing" filters (like median) is used, and iterative reconstruction
makes the same artifacts.

Setting the value of the first and last projection to zero has the same
effect as excluding. Changing the ramp filter only changes noise, not the
artifacts.

*Have any of you had a similar problem? *Am I missing something?
Any suggestions are welcome I'm running out of ideas.

Best regards
Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 13 16:18:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 13 Sep 2016 22:18:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
Message-ID: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>

Hi,
I have almost never worked with Varian data but it looks like a
geometry problem. Maybe the problem comes from a bad ordering of the
projections which results in assigning a bad geometry to each
projection. How did you name your projections? Maybe check that the
order matches that of the RTK geometry file. Otherwise, there might be
an issue in the creation of the geometry file itself.
All this sounds good, happy bug hunt and don't hesitate to share your
code when you feel it's ready.
Simon

On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
<andreasg at phys.au.dk> wrote:
> Dear RTK experts,
>
> I am reconstructing Varian ProBeam projections of the Xim image format. I
> have written the reader myself - very similar to the Hnd one already
> available with RTK.
> Links to my fork: [XimReader, XMLReader, GeometryReader]
>
> The reader apparently works (Images and angles displays as expected in UI),
> however when reconstructing with a regular FDK I get a reconstructed image
> that is smeared out around the high and low density areas [see attached
> image]
>
> I'm using half arc, full fan images with no bow-tie filter from Scripps
> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
> SDD=3m.
>
> For the Hnd projections the reconstruction works perfectly (Same algorithm).
> The reconstruction of the Xim projections performed on Varian software works
> perfectly.
>
> Without the Parker Short Scan Filter the first and last projections creates
> streaks across the reconstruction as if they were way too bright.
> If the first few projections are excluded, the following projection will act
> the same way.
>
> The projections are corrected for beam hardening and all the projections
> have the expected attenuation.
> No "smearing" filters (like median) is used, and iterative reconstruction
> makes the same artifacts.
>
> Setting the value of the first and last projection to zero has the same
> effect as excluding. Changing the ramp filter only changes noise, not the
> artifacts.
>
> Have any of you had a similar problem? Am I missing something?
> Any suggestions are welcome I'm running out of ideas.
>
> Best regards
> Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>


From cyril.mory at creatis.insa-lyon.fr  Wed Sep 14 03:10:42 2016
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 14 Sep 2016 09:10:42 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
Message-ID: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>

One suggestion since it works with the Hnd projections:
You can run rtkprojections twice (with the Hnd projections, then with 
Xim projections) and output two projection stack files and two geometry 
files, then compare the projection stack files by subtracting one to the 
other (with SimpleRTK or clitk) and the geometry files with diff. If 
they are identical, then I do not see any reason why the reconstructions 
should be different, so my guess is that you will find differences.

On 09/13/2016 10:18 PM, Simon Rit wrote:
> Hi,
> I have almost never worked with Varian data but it looks like a
> geometry problem. Maybe the problem comes from a bad ordering of the
> projections which results in assigning a bad geometry to each
> projection. How did you name your projections? Maybe check that the
> order matches that of the RTK geometry file. Otherwise, there might be
> an issue in the creation of the geometry file itself.
> All this sounds good, happy bug hunt and don't hesitate to share your
> code when you feel it's ready.
> Simon
>
> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
> <andreasg at phys.au.dk> wrote:
>> Dear RTK experts,
>>
>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>> have written the reader myself - very similar to the Hnd one already
>> available with RTK.
>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>
>> The reader apparently works (Images and angles displays as expected in UI),
>> however when reconstructing with a regular FDK I get a reconstructed image
>> that is smeared out around the high and low density areas [see attached
>> image]
>>
>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>> SDD=3m.
>>
>> For the Hnd projections the reconstruction works perfectly (Same algorithm).
>> The reconstruction of the Xim projections performed on Varian software works
>> perfectly.
>>
>> Without the Parker Short Scan Filter the first and last projections creates
>> streaks across the reconstruction as if they were way too bright.
>> If the first few projections are excluded, the following projection will act
>> the same way.
>>
>> The projections are corrected for beam hardening and all the projections
>> have the expected attenuation.
>> No "smearing" filters (like median) is used, and iterative reconstruction
>> makes the same artifacts.
>>
>> Setting the value of the first and last projection to zero has the same
>> effect as excluding. Changing the ramp filter only changes noise, not the
>> artifacts.
>>
>> Have any of you had a similar problem? Am I missing something?
>> Any suggestions are welcome I'm running out of ideas.
>>
>> Best regards
>> Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>



From andreasg at phys.au.dk  Fri Sep 16 08:56:34 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 14:56:34 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
Message-ID: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>

Thanks for the suggestions, Simon and Cyril!

I have been carefully looking though the geometry and from what I
understand of the transformations matrices, the geometry looks correct/(as
expected).

HOWEVER: I found out that the reason for the Hnd to behave differently were
because had used half-fan scans (full-arc).
When I used a full-fan (half-arc) scan of Hnd projections the same
artifacts occurs!

Are there other (built-in) means of improving half-arc scans, than the
parker short scan filter?

Parker short scan does a decent job, but the result is still far from the
quality of the Varian software reconstruction at least for the CatPhan.

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:

> One suggestion since it works with the Hnd projections:
> You can run rtkprojections twice (with the Hnd projections, then with Xim
> projections) and output two projection stack files and two geometry files,
> then compare the projection stack files by subtracting one to the other
> (with SimpleRTK or clitk) and the geometry files with diff. If they are
> identical, then I do not see any reason why the reconstructions should be
> different, so my guess is that you will find differences.
>
>
> On 09/13/2016 10:18 PM, Simon Rit wrote:
>
>> Hi,
>> I have almost never worked with Varian data but it looks like a
>> geometry problem. Maybe the problem comes from a bad ordering of the
>> projections which results in assigning a bad geometry to each
>> projection. How did you name your projections? Maybe check that the
>> order matches that of the RTK geometry file. Otherwise, there might be
>> an issue in the creation of the geometry file itself.
>> All this sounds good, happy bug hunt and don't hesitate to share your
>> code when you feel it's ready.
>> Simon
>>
>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>> <andreasg at phys.au.dk> wrote:
>>
>>> Dear RTK experts,
>>>
>>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>>> have written the reader myself - very similar to the Hnd one already
>>> available with RTK.
>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>
>>> The reader apparently works (Images and angles displays as expected in
>>> UI),
>>> however when reconstructing with a regular FDK I get a reconstructed
>>> image
>>> that is smeared out around the high and low density areas [see attached
>>> image]
>>>
>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>> SDD=3m.
>>>
>>> For the Hnd projections the reconstruction works perfectly (Same
>>> algorithm).
>>> The reconstruction of the Xim projections performed on Varian software
>>> works
>>> perfectly.
>>>
>>> Without the Parker Short Scan Filter the first and last projections
>>> creates
>>> streaks across the reconstruction as if they were way too bright.
>>> If the first few projections are excluded, the following projection will
>>> act
>>> the same way.
>>>
>>> The projections are corrected for beam hardening and all the projections
>>> have the expected attenuation.
>>> No "smearing" filters (like median) is used, and iterative reconstruction
>>> makes the same artifacts.
>>>
>>> Setting the value of the first and last projection to zero has the same
>>> effect as excluding. Changing the ramp filter only changes noise, not the
>>> artifacts.
>>>
>>> Have any of you had a similar problem? Am I missing something?
>>> Any suggestions are welcome I'm running out of ideas.
>>>
>>> Best regards
>>> Andreas
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Sep 16 10:13:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 16 Sep 2016 16:13:26 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
Message-ID: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>

Hi,
You can try any iterative reconstruction, they can also handle short scans.
Start with a few iterations of rtksart or rtkconjugategradient. However,
the nature of the artifacts indicate more a problem in the geometry in my
opinion. I have seen such errors when, for example, rotating in the wrong
direction. I can have a look if you share the dataset.
Cheers,
Simon

On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the suggestions, Simon and Cyril!
>
> I have been carefully looking though the geometry and from what I
> understand of the transformations matrices, the geometry looks correct/(as
> expected).
>
> HOWEVER: I found out that the reason for the Hnd to behave differently
> were because had used half-fan scans (full-arc).
> When I used a full-fan (half-arc) scan of Hnd projections the same
> artifacts occurs!
>
> Are there other (built-in) means of improving half-arc scans, than the
> parker short scan filter?
>
> Parker short scan does a decent job, but the result is still far from the
> quality of the Varian software reconstruction at least for the CatPhan.
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>
>> One suggestion since it works with the Hnd projections:
>> You can run rtkprojections twice (with the Hnd projections, then with Xim
>> projections) and output two projection stack files and two geometry files,
>> then compare the projection stack files by subtracting one to the other
>> (with SimpleRTK or clitk) and the geometry files with diff. If they are
>> identical, then I do not see any reason why the reconstructions should be
>> different, so my guess is that you will find differences.
>>
>>
>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>
>>> Hi,
>>> I have almost never worked with Varian data but it looks like a
>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>> projections which results in assigning a bad geometry to each
>>> projection. How did you name your projections? Maybe check that the
>>> order matches that of the RTK geometry file. Otherwise, there might be
>>> an issue in the creation of the geometry file itself.
>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>> code when you feel it's ready.
>>> Simon
>>>
>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>> <andreasg at phys.au.dk> wrote:
>>>
>>>> Dear RTK experts,
>>>>
>>>> I am reconstructing Varian ProBeam projections of the Xim image format.
>>>> I
>>>> have written the reader myself - very similar to the Hnd one already
>>>> available with RTK.
>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>
>>>> The reader apparently works (Images and angles displays as expected in
>>>> UI),
>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>> image
>>>> that is smeared out around the high and low density areas [see attached
>>>> image]
>>>>
>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>> SDD=3m.
>>>>
>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>> algorithm).
>>>> The reconstruction of the Xim projections performed on Varian software
>>>> works
>>>> perfectly.
>>>>
>>>> Without the Parker Short Scan Filter the first and last projections
>>>> creates
>>>> streaks across the reconstruction as if they were way too bright.
>>>> If the first few projections are excluded, the following projection
>>>> will act
>>>> the same way.
>>>>
>>>> The projections are corrected for beam hardening and all the projections
>>>> have the expected attenuation.
>>>> No "smearing" filters (like median) is used, and iterative
>>>> reconstruction
>>>> makes the same artifacts.
>>>>
>>>> Setting the value of the first and last projection to zero has the same
>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>> the
>>>> artifacts.
>>>>
>>>> Have any of you had a similar problem? Am I missing something?
>>>> Any suggestions are welcome I'm running out of ideas.
>>>>
>>>> Best regards
>>>> Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> N?rrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     andreasg at phys.au.dk
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From andreasg at phys.au.dk  Fri Sep 16 16:37:43 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 22:37:43 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
Message-ID: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>

Thanks for the fast response Simon!

I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
right all along!
I just didn't get why it makes a difference. I think I do now, as the
resulting image was flipped upside down and not left/right as I expected.
[attached]

The reconstruction is significantly better, I'll look into what should be
included in the reader and what I should keep in my program to keep
conformity with the other readers. Then I'll create a pull request.

Just for the purpose of others hitting the same or a similar bug, I also
attempted:
I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
back/forward projection, *but with no* significant improvement [attached]

And:
If you want you can download the data set from: [Dropbox link to 460MB zip
<https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep it
up as long as Dropbox allows me)] Only the Acquisitions/subfolder is used
along with the Scan.xml (Calibrations folder may be used in the future in
my program, but I'm not sure if you can rely on the existence of the
content).

A MatLab XimReader is available: link
<https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
available from Varian bitbucket along a with a python version and a
C#->matlab plugin
<https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). Otherwise
my fork with the RTK-style reader is available from the same repository (I
have also added Hnc support, thanks to the Geoff Hugo fork, so bzip2 is a
new dependancy).

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:

> Hi,
> You can try any iterative reconstruction, they can also handle short
> scans. Start with a few iterations of rtksart or rtkconjugategradient.
> However, the nature of the artifacts indicate more a problem in the
> geometry in my opinion. I have seen such errors when, for example, rotating
> in the wrong direction. I can have a look if you share the dataset.
> Cheers,
> Simon
>
> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
> andreasg at phys.au.dk> wrote:
>
>> Thanks for the suggestions, Simon and Cyril!
>>
>> I have been carefully looking though the geometry and from what I
>> understand of the transformations matrices, the geometry looks correct/(as
>> expected).
>>
>> HOWEVER: I found out that the reason for the Hnd to behave differently
>> were because had used half-fan scans (full-arc).
>> When I used a full-fan (half-arc) scan of Hnd projections the same
>> artifacts occurs!
>>
>> Are there other (built-in) means of improving half-arc scans, than the
>> parker short scan filter?
>>
>> Parker short scan does a decent job, but the result is still far from the
>> quality of the Varian software reconstruction at least for the CatPhan.
>>
>> Best regards
>> Andreas
>>
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>>
>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>
>>> One suggestion since it works with the Hnd projections:
>>> You can run rtkprojections twice (with the Hnd projections, then with
>>> Xim projections) and output two projection stack files and two geometry
>>> files, then compare the projection stack files by subtracting one to the
>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>> are identical, then I do not see any reason why the reconstructions should
>>> be different, so my guess is that you will find differences.
>>>
>>>
>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>
>>>> Hi,
>>>> I have almost never worked with Varian data but it looks like a
>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>> projections which results in assigning a bad geometry to each
>>>> projection. How did you name your projections? Maybe check that the
>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>> an issue in the creation of the geometry file itself.
>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>> code when you feel it's ready.
>>>> Simon
>>>>
>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>> <andreasg at phys.au.dk> wrote:
>>>>
>>>>> Dear RTK experts,
>>>>>
>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>> format. I
>>>>> have written the reader myself - very similar to the Hnd one already
>>>>> available with RTK.
>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>
>>>>> The reader apparently works (Images and angles displays as expected in
>>>>> UI),
>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>> image
>>>>> that is smeared out around the high and low density areas [see attached
>>>>> image]
>>>>>
>>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>> SDD=3m.
>>>>>
>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>> algorithm).
>>>>> The reconstruction of the Xim projections performed on Varian software
>>>>> works
>>>>> perfectly.
>>>>>
>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>> creates
>>>>> streaks across the reconstruction as if they were way too bright.
>>>>> If the first few projections are excluded, the following projection
>>>>> will act
>>>>> the same way.
>>>>>
>>>>> The projections are corrected for beam hardening and all the
>>>>> projections
>>>>> have the expected attenuation.
>>>>> No "smearing" filters (like median) is used, and iterative
>>>>> reconstruction
>>>>> makes the same artifacts.
>>>>>
>>>>> Setting the value of the first and last projection to zero has the same
>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>> the
>>>>> artifacts.
>>>>>
>>>>> Have any of you had a similar problem? Am I missing something?
>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>
>>>>> Best regards
>>>>> Andreas
>>>>>
>>>>> __________________________________
>>>>>
>>>>> Andreas Gravgaard Andersen
>>>>>
>>>>> Department of Oncology,
>>>>>
>>>>> Aarhus University Hospital
>>>>>
>>>>> N?rrebrogade 44,
>>>>>
>>>>> 8000, Aarhus C
>>>>>
>>>>> Mail:     andreasg at phys.au.dk
>>>>>
>>>>> Cell:      +45 3165 8140
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 03:26:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 09:26:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
 <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
Message-ID: <CAF0oig2TSmAsSn=o3aLo6LEFDOSaKRtfknjMer24rcDKJ-0Fqg@mail.gmail.com>

Hi,
Thanks for sharing. There still seems to be some streak artefacts, do you
see the same in the Varian reconstruction?
I'm looking forward to the pull-request, I think we should try to make the
bzip2 optional.
Simon

On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the fast response Simon!
>
> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
> right all along!
> I just didn't get why it makes a difference. I think I do now, as the
> resulting image was flipped upside down and not left/right as I expected.
> [attached]
>
> The reconstruction is significantly better, I'll look into what should be
> included in the reader and what I should keep in my program to keep
> conformity with the other readers. Then I'll create a pull request.
>
> Just for the purpose of others hitting the same or a similar bug, I also
> attempted:
> I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
> back/forward projection, *but with no* significant improvement [attached]
>
> And:
> If you want you can download the data set from: [Dropbox link to 460MB zip
> <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep
> it up as long as Dropbox allows me)] Only the Acquisitions/subfolder is
> used along with the Scan.xml (Calibrations folder may be used in the future
> in my program, but I'm not sure if you can rely on the existence of the
> content).
>
> A MatLab XimReader is available: link
> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
> available from Varian bitbucket along a with a python version and a
> C#->matlab plugin
> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>).
> Otherwise my fork with the RTK-style reader is available from the same
> repository (I have also added Hnc support, thanks to the Geoff Hugo fork,
> so bzip2 is a new dependancy).
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> Hi,
>> You can try any iterative reconstruction, they can also handle short
>> scans. Start with a few iterations of rtksart or rtkconjugategradient.
>> However, the nature of the artifacts indicate more a problem in the
>> geometry in my opinion. I have seen such errors when, for example, rotating
>> in the wrong direction. I can have a look if you share the dataset.
>> Cheers,
>> Simon
>>
>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
>> andreasg at phys.au.dk> wrote:
>>
>>> Thanks for the suggestions, Simon and Cyril!
>>>
>>> I have been carefully looking though the geometry and from what I
>>> understand of the transformations matrices, the geometry looks correct/(as
>>> expected).
>>>
>>> HOWEVER: I found out that the reason for the Hnd to behave differently
>>> were because had used half-fan scans (full-arc).
>>> When I used a full-fan (half-arc) scan of Hnd projections the same
>>> artifacts occurs!
>>>
>>> Are there other (built-in) means of improving half-arc scans, than the
>>> parker short scan filter?
>>>
>>> Parker short scan does a decent job, but the result is still far from
>>> the quality of the Varian software reconstruction at least for the CatPhan.
>>>
>>> Best regards
>>> Andreas
>>>
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>>
>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>>
>>>> One suggestion since it works with the Hnd projections:
>>>> You can run rtkprojections twice (with the Hnd projections, then with
>>>> Xim projections) and output two projection stack files and two geometry
>>>> files, then compare the projection stack files by subtracting one to the
>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>>> are identical, then I do not see any reason why the reconstructions should
>>>> be different, so my guess is that you will find differences.
>>>>
>>>>
>>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>>
>>>>> Hi,
>>>>> I have almost never worked with Varian data but it looks like a
>>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>>> projections which results in assigning a bad geometry to each
>>>>> projection. How did you name your projections? Maybe check that the
>>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>>> an issue in the creation of the geometry file itself.
>>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>>> code when you feel it's ready.
>>>>> Simon
>>>>>
>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>>> <andreasg at phys.au.dk> wrote:
>>>>>
>>>>>> Dear RTK experts,
>>>>>>
>>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>>> format. I
>>>>>> have written the reader myself - very similar to the Hnd one already
>>>>>> available with RTK.
>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>>
>>>>>> The reader apparently works (Images and angles displays as expected
>>>>>> in UI),
>>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>>> image
>>>>>> that is smeared out around the high and low density areas [see
>>>>>> attached
>>>>>> image]
>>>>>>
>>>>>> I'm using half arc, full fan images with no bow-tie filter from
>>>>>> Scripps
>>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>>> SDD=3m.
>>>>>>
>>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>>> algorithm).
>>>>>> The reconstruction of the Xim projections performed on Varian
>>>>>> software works
>>>>>> perfectly.
>>>>>>
>>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>>> creates
>>>>>> streaks across the reconstruction as if they were way too bright.
>>>>>> If the first few projections are excluded, the following projection
>>>>>> will act
>>>>>> the same way.
>>>>>>
>>>>>> The projections are corrected for beam hardening and all the
>>>>>> projections
>>>>>> have the expected attenuation.
>>>>>> No "smearing" filters (like median) is used, and iterative
>>>>>> reconstruction
>>>>>> makes the same artifacts.
>>>>>>
>>>>>> Setting the value of the first and last projection to zero has the
>>>>>> same
>>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>>> the
>>>>>> artifacts.
>>>>>>
>>>>>> Have any of you had a similar problem? Am I missing something?
>>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>>
>>>>>> Best regards
>>>>>> Andreas
>>>>>>
>>>>>> __________________________________
>>>>>>
>>>>>> Andreas Gravgaard Andersen
>>>>>>
>>>>>> Department of Oncology,
>>>>>>
>>>>>> Aarhus University Hospital
>>>>>>
>>>>>> N?rrebrogade 44,
>>>>>>
>>>>>> 8000, Aarhus C
>>>>>>
>>>>>> Mail:     andreasg at phys.au.dk
>>>>>>
>>>>>> Cell:      +45 3165 8140
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:05:24 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:05:24 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
Message-ID: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>

Dear RTK users,
I have quickly tested calling the SimpleRTK python lib from Matlab and it
seems to work well:
http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
Therefore, I don't think we have to work on Matlab wrappings but let us
know if you think otherwise.
Future works include a simple installation mechanism for pre-compiled
SimpleRTK libraries. We'll keep you posted!
Simon
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From bottiger at gmail.com  Mon Sep 19 05:14:03 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 11:14:03 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
Message-ID: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>

Dear Simon

This look very interesting! Which platform did you successfully execute
this on?
I will give it a try at once (on windows) and let you know if I run into
any problems.

best

Arvid

On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> I have quickly tested calling the SimpleRTK python lib from Matlab and it
> seems to work well:
> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
> Therefore, I don't think we have to work on Matlab wrappings but let us
> know if you think otherwise.
> Future works include a simple installation mechanism for pre-compiled
> SimpleRTK libraries. We'll keep you posted!
> Simon
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:19:28 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:19:28 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
Message-ID: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>

The latest MacOS. It's nice if you can test it on other platforms, I'll try
to run it on Linux but I have to upgrade matlab first (I think python calls
are available starting with Matlab 2014).
Simon

On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Dear Simon
>
> This look very interesting! Which platform did you successfully execute
> this on?
> I will give it a try at once (on windows) and let you know if I run into
> any problems.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> Dear RTK users,
>> I have quickly tested calling the SimpleRTK python lib from Matlab and it
>> seems to work well:
>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>> Therefore, I don't think we have to work on Matlab wrappings but let us
>> know if you think otherwise.
>> Future works include a simple installation mechanism for pre-compiled
>> SimpleRTK libraries. We'll keep you posted!
>> Simon
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From bottiger at gmail.com  Mon Sep 19 08:30:32 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 14:30:32 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
Message-ID: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>

Hi again.

I've been trying to get it working. However, I did run into some problems
compiling SimpleRTK. The main issue seems to be that it depends on
SimpleRTKCommon - which I do not have.

Here is the last few lines from VS2013

> 5>LINK : fatal error LNK1181: cannot open input file
'..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib' [C:\Users\aplb\Work\RTK\RTK1.2-
> bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> 5>
> 5>      0 Warning(s)
> 5>      2 Error(s)
> 5>
> 5>  Time Elapsed 00:00:25.26
> ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
==========

I'm not quite sure what is going on, because the only reference I can find
to SimpleRTKCommon is the CMakeLists.txt on github:
https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt

best

Arvid

On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> The latest MacOS. It's nice if you can test it on other platforms, I'll
> try to run it on Linux but I have to upgrade matlab first (I think python
> calls are available starting with Matlab 2014).
> Simon
>
> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Dear Simon
>>
>> This look very interesting! Which platform did you successfully execute
>> this on?
>> I will give it a try at once (on windows) and let you know if I run into
>> any problems.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Dear RTK users,
>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>> it seems to work well:
>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>> know if you think otherwise.
>>> Future works include a simple installation mechanism for pre-compiled
>>> SimpleRTK libraries. We'll keep you posted!
>>> Simon
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 12:50:33 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 18:50:33 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
Message-ID: <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>

 SimpleRTKCommon is a library generated when compiling. Don't you have
another error before that which explains why it did not compile?
Simon

On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I've been trying to get it working. However, I did run into some problems
> compiling SimpleRTK. The main issue seems to be that it depends on
> SimpleRTKCommon - which I do not have.
>
> Here is the last few lines from VS2013
>
> > 5>LINK : fatal error LNK1181: cannot open input file '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
> [C:\Users\aplb\Work\RTK\RTK1.2-
> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> > 5>
> > 5>      0 Warning(s)
> > 5>      2 Error(s)
> > 5>
> > 5>  Time Elapsed 00:00:25.26
> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
> ==========
>
> I'm not quite sure what is going on, because the only reference I can find
> to SimpleRTKCommon is the CMakeLists.txt on github:
> https://github.com/SimonRit/RTK/blob/master/utilities/
> SimpleRTK/CMakeLists.txt
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>> try to run it on Linux but I have to upgrade matlab first (I think python
>> calls are available starting with Matlab 2014).
>> Simon
>>
>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Dear Simon
>>>
>>> This look very interesting! Which platform did you successfully execute
>>> this on?
>>> I will give it a try at once (on windows) and let you know if I run into
>>> any problems.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Dear RTK users,
>>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>>> it seems to work well:
>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>>> know if you think otherwise.
>>>> Future works include a simple installation mechanism for pre-compiled
>>>> SimpleRTK libraries. We'll keep you posted!
>>>> Simon
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 01:33:46 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 07:33:46 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
Message-ID: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>

I'm not an msvc specialist but your first line suggests that you have 
pasted only part of the log:

20>  Done Building Project 
"C:\Users\aplb\Work\RTK\RTK1.2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" 
(default targets) -- FAILED.

What you need to find out is why this build failed. If the build fails, 
the linking cannot work.
Cheers,
Simon

On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
> I did a complete rebuild, and here is the end of the output: 
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that 
> I'm trying to compile the version I just pulled from git earlier 
> today, since the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     SimpleRTKCommon is a library generated when compiling. Don't you
>     have another error before that which explains why it did not compile?
>     Simon
>
>     On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger
>     <bottiger at gmail.com <mailto:bottiger at gmail.com>> wrote:
>
>         Hi again.
>
>         I've been trying to get it working. However, I did run into
>         some problems compiling SimpleRTK. The main issue seems to be
>         that it depends on SimpleRTKCommon - which I do not have.
>
>         Here is the last few lines from VS2013
>
>         > 5>LINK : fatal error LNK1181: cannot open input file
>         '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>         [C:\Users\aplb\Work\RTK\RTK1.2-
>         > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>         > 5>
>         > 5>      0 Warning(s)
>         > 5>      2 Error(s)
>         > 5>
>         > 5>  Time Elapsed 00:00:25.26
>         > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0
>         skipped ==========
>
>         I'm not quite sure what is going on, because the only
>         reference I can find to SimpleRTKCommon is the CMakeLists.txt
>         on github:
>         https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt
>         <https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt>
>
>         best
>
>         Arvid
>
>         On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit
>         <simon.rit at creatis.insa-lyon.fr
>         <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>             The latest MacOS. It's nice if you can test it on other
>             platforms, I'll try to run it on Linux but I have to
>             upgrade matlab first (I think python calls are available
>             starting with Matlab 2014).
>             Simon
>
>             On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen
>             B?ttiger <bottiger at gmail.com <mailto:bottiger at gmail.com>>
>             wrote:
>
>                 Dear Simon
>
>                 This look very interesting! Which platform did you
>                 successfully execute this on?
>                 I will give it a try at once (on windows) and let you
>                 know if I run into any problems.
>
>                 best
>
>                 Arvid
>
>                 On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit
>                 <simon.rit at creatis.insa-lyon.fr
>                 <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>                     Dear RTK users,
>                     I have quickly tested calling the SimpleRTK python
>                     lib from Matlab and it seems to work well:
>                     http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>                     <http://wiki.openrtk.org/index.php/SimpleRTK#Matlab>
>                     Therefore, I don't think we have to work on Matlab
>                     wrappings but let us know if you think otherwise.
>                     Future works include a simple installation
>                     mechanism for pre-compiled SimpleRTK libraries.
>                     We'll keep you posted!
>                     Simon
>
>                     _______________________________________________
>                     Rtk-users mailing list
>                     Rtk-users at public.kitware.com
>                     <mailto:Rtk-users at public.kitware.com>
>                     http://public.kitware.com/mailman/listinfo/rtk-users
>                     <http://public.kitware.com/mailman/listinfo/rtk-users>
>
>
>
>
>
>

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From bottiger at gmail.com  Tue Sep 20 08:17:35 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Tue, 20 Sep 2016 14:17:35 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
Message-ID: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>

Hi again.

I understand, but could you please help me get in contact with the person
who knows something about the windows build (if any), I think there is
something wrong.

I have been investigating the build problems I had and found that in the
sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
opened it up and found the projects which I had problems building:
"SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.

When I then tried to build SimpleRTKCommon manually it just compiled
without any problems. However, when I followed up by building
"SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
find "SimpleRTKCommon-0.9.lib" - which I just build.

After some more investigation I realized that the SimpleRTKCommon is set to
build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects it
to be a static linked library (LIB). After changing SimpleRTKCommon to be
build as a static library - and changing the output location - I could
build SimpleRTKBasicFilters0.

However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
to a LIB as well I could build SimpleRTKBasicFilters1, then
SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.

I'm unsure if the intention is to build them as static or dynamic
libraries, but in any case the current build configuration doesn't work -
on my setup at least.

However, I should note than for some reason the "lua5" project did build
successfully out of the box. Whatever it does differently works.

best

Arvid



On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> I'm not an msvc specialist but your first line suggests that you have
> pasted only part of the log:
>
> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.
> 2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
> What you need to find out is why this build failed. If the build fails,
> the linking cannot work.
> Cheers,
> Simon
>
>
> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>
> I did a complete rebuild, and here is the end of the output:
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that I'm
> trying to compile the version I just pulled from git earlier today, since
> the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> SimpleRTKCommon is a library generated when compiling. Don't you have
>> another error before that which explains why it did not compile?
>> Simon
>>
>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Hi again.
>>>
>>> I've been trying to get it working. However, I did run into some
>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>> SimpleRTKCommon - which I do not have.
>>>
>>> Here is the last few lines from VS2013
>>>
>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>> > 5>
>>> > 5>      0 Warning(s)
>>> > 5>      2 Error(s)
>>> > 5>
>>> > 5>  Time Elapsed 00:00:25.26
>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>> ==========
>>>
>>> I'm not quite sure what is going on, because the only reference I can
>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>> RTK/CMakeLists.txt
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>>>> try to run it on Linux but I have to upgrade matlab first (I think python
>>>> calls are available starting with Matlab 2014).
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Dear Simon
>>>>>
>>>>> This look very interesting! Which platform did you successfully
>>>>> execute this on?
>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>> into any problems.
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Dear RTK users,
>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>> and it seems to work well:
>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>> us know if you think otherwise.
>>>>>> Future works include a simple installation mechanism for pre-compiled
>>>>>> SimpleRTK libraries. We'll keep you posted!
>>>>>> Simon
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 10:19:20 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 16:19:20 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
Message-ID: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>

Hi,
Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
I can't solve your problem but Kitware is going to look into an upgrade of
SimpleRTK in the coming days, I'll ask them if they know what is the issue.
If you look here:
http://my.cdash.org/viewNotes.php?buildid=1052065
this is a nightly build of SimpleRTK on Windows and it seems to work. I
don't see why it wouldn't work for you.
Simon

On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I understand, but could you please help me get in contact with the person
> who knows something about the windows build (if any), I think there is
> something wrong.
>
> I have been investigating the build problems I had and found that in the
> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
> opened it up and found the projects which I had problems building:
> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>
> When I then tried to build SimpleRTKCommon manually it just compiled
> without any problems. However, when I followed up by building
> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
> find "SimpleRTKCommon-0.9.lib" - which I just build.
>
> After some more investigation I realized that the SimpleRTKCommon is set
> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
> it to be a static linked library (LIB). After changing SimpleRTKCommon to
> be build as a static library - and changing the output location - I could
> build SimpleRTKBasicFilters0.
>
> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
> to a LIB as well I could build SimpleRTKBasicFilters1, then
> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>
> I'm unsure if the intention is to build them as static or dynamic
> libraries, but in any case the current build configuration doesn't work -
> on my setup at least.
>
> However, I should note than for some reason the "lua5" project did build
> successfully out of the box. Whatever it does differently works.
>
> best
>
> Arvid
>
>
>
> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> I'm not an msvc specialist but your first line suggests that you have
>> pasted only part of the log:
>>
>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
>> What you need to find out is why this build failed. If the build fails,
>> the linking cannot work.
>> Cheers,
>> Simon
>>
>>
>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>
>> I did a complete rebuild, and here is the end of the output:
>> http://pastebin.com/hvQ33WWg
>>
>> I have to admit I'm not sure what to make of it. I should note that I'm
>> trying to compile the version I just pulled from git earlier today, since
>> the other version I normally work with is really old.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>> another error before that which explains why it did not compile?
>>> Simon
>>>
>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>> bottiger at gmail.com> wrote:
>>>
>>>> Hi again.
>>>>
>>>> I've been trying to get it working. However, I did run into some
>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>> SimpleRTKCommon - which I do not have.
>>>>
>>>> Here is the last few lines from VS2013
>>>>
>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>> > 5>
>>>> > 5>      0 Warning(s)
>>>> > 5>      2 Error(s)
>>>> > 5>
>>>> > 5>  Time Elapsed 00:00:25.26
>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>> ==========
>>>>
>>>> I'm not quite sure what is going on, because the only reference I can
>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>> RTK/CMakeLists.txt
>>>>
>>>> best
>>>>
>>>> Arvid
>>>>
>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>> python calls are available starting with Matlab 2014).
>>>>> Simon
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>> bottiger at gmail.com> wrote:
>>>>>
>>>>>> Dear Simon
>>>>>>
>>>>>> This look very interesting! Which platform did you successfully
>>>>>> execute this on?
>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>> into any problems.
>>>>>>
>>>>>> best
>>>>>>
>>>>>> Arvid
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>
>>>>>>> Dear RTK users,
>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>> and it seems to work well:
>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>>> us know if you think otherwise.
>>>>>>> Future works include a simple installation mechanism for
>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>> Simon
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 02:40:50 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 08:40:50 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
Message-ID: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>

Dear RTK users,
RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
been released, about 7 months after RTK v1.2.0.

Release notes :
- Style updated (follow more closely latest ITK guidelines).
- Started using Travis CI, github pull requests should now be used for code
submission.
- New pre-processing functionalities:
  * CUDA polynomial gain correction,
  * scatter glare correction,
  * lag correction,
  * idark option,
  * removed threshold to positive values after i0 LUT.
- Improved CUDA forward and backprojection speed using projection slabs.
- Added motion-compensated forward and back projection operators in CUDA,
in both 3D and 4D.
- Added the rtkregularizedconjugategradient application, which performs 3D
regularized reconstruction by conjugate gradient + optional regularizations
(Positivity, TV, Wavelets).
- Made the rtkfourdrooster, rtkmcrooster and rtkregularizedconjugategradient
fully modular. Each regularization step can be made active or inactive.
- Added a filter to minimize the L0 norm of the temporal gradient (one-D
only).

Many thanks to the contributors, in alphabetical order for this release: Cyril
Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien
Jomier, S?bastien
Brousmiche, Simon Rit

As usual, be aware that we don't focus on releases since we have a public
github repository <http://github.com/SimonRit/RTK> that we try to keep
stable. I still recommend the use of the master HEAD over releases to enjoy
the new RTK developments before their release. We still have a few on-going
projects for which we will use and enhance RTK.

Simon (for the RTK consortium)
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 04:48:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 10:48:26 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
In-Reply-To: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
References: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
Message-ID: <CAF0oig0=5_KPN198JzsGQXDd07Nvw_Ew+qSGhguk0m27s3U-3Q@mail.gmail.com>

Sorry, I had forgotten to change the release number in the source file.
It's been corrected, you will have to move your tag locally or update your
file if you had already downloaded it.
Simon

On Thu, Sep 22, 2016 at 8:40 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
> been released, about 7 months after RTK v1.2.0.
>
> Release notes :
> - Style updated (follow more closely latest ITK guidelines).
> - Started using Travis CI, github pull requests should now be used for
> code submission.
> - New pre-processing functionalities:
>   * CUDA polynomial gain correction,
>   * scatter glare correction,
>   * lag correction,
>   * idark option,
>   * removed threshold to positive values after i0 LUT.
> - Improved CUDA forward and backprojection speed using projection slabs.
> - Added motion-compensated forward and back projection operators in CUDA,
> in both 3D and 4D.
> - Added the rtkregularizedconjugategradient application, which performs
> 3D regularized reconstruction by conjugate gradient + optional
> regularizations (Positivity, TV, Wavelets).
> - Made the rtkfourdrooster, rtkmcrooster and
> rtkregularizedconjugategradient fully modular. Each regularization step
> can be made active or inactive.
> - Added a filter to minimize the L0 norm of the temporal gradient (one-D
> only).
>
> Many thanks to the contributors, in alphabetical order for this release: Cyril
> Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien Jomier, S?bastien
> Brousmiche, Simon Rit
>
> As usual, be aware that we don't focus on releases since we have a public
> github repository <http://github.com/SimonRit/RTK> that we try to keep
> stable. I still recommend the use of the master HEAD over releases to
> enjoy the new RTK developments before their release. We still have a few
> on-going projects for which we will use and enhance RTK.
>
> Simon (for the RTK consortium)
>
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From bottiger at gmail.com  Fri Sep 23 04:29:06 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Fri, 23 Sep 2016 10:29:06 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
 <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
Message-ID: <CANBwxwEvaUrvd1X=74g=V2JmDwtrQKFDtyUdAZJn5CRCBCkb8g@mail.gmail.com>

Hi again.

I've been spending some more time with this, and feel I learned a little
bit more. I have now tested this on several machines with several compiler
versions (more or less all of them) and serveral cmake versions - all with
Windows 7.

I can actually reproduce the successful build you linked to, but this can
only be done if you do not include any of the language wrappings, like in
the build you linked to. Enable any of them, and the build will break. (see
attachment)

I suspect it must have been working in the past, but since none of them are
included in your test there have been a breaking change, and none of them
work anymore.

I am still trying to tweak then projects manually to build SimpleRTK with
some sort of language support, but still without any luck.

best

Arvid

On Tue, Sep 20, 2016 at 4:19 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
> at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
> I can't solve your problem but Kitware is going to look into an upgrade of
> SimpleRTK in the coming days, I'll ask them if they know what is the issue.
> If you look here:
> http://my.cdash.org/viewNotes.php?buildid=1052065
> this is a nightly build of SimpleRTK on Windows and it seems to work. I
> don't see why it wouldn't work for you.
> Simon
>
> On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Hi again.
>>
>> I understand, but could you please help me get in contact with the person
>> who knows something about the windows build (if any), I think there is
>> something wrong.
>>
>> I have been investigating the build problems I had and found that in the
>> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
>> opened it up and found the projects which I had problems building:
>> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>>
>> When I then tried to build SimpleRTKCommon manually it just compiled
>> without any problems. However, when I followed up by building
>> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
>> find "SimpleRTKCommon-0.9.lib" - which I just build.
>>
>> After some more investigation I realized that the SimpleRTKCommon is set
>> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
>> it to be a static linked library (LIB). After changing SimpleRTKCommon to
>> be build as a static library - and changing the output location - I could
>> build SimpleRTKBasicFilters0.
>>
>> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing
>> that to a LIB as well I could build SimpleRTKBasicFilters1, then
>> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>>
>> I'm unsure if the intention is to build them as static or dynamic
>> libraries, but in any case the current build configuration doesn't work -
>> on my setup at least.
>>
>> However, I should note than for some reason the "lua5" project did build
>> successfully out of the box. Whatever it does differently works.
>>
>> best
>>
>> Arvid
>>
>>
>>
>> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> I'm not an msvc specialist but your first line suggests that you have
>>> pasted only part of the log:
>>>
>>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) --
>>> FAILED.
>>> What you need to find out is why this build failed. If the build fails,
>>> the linking cannot work.
>>> Cheers,
>>> Simon
>>>
>>>
>>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>>
>>> I did a complete rebuild, and here is the end of the output:
>>> http://pastebin.com/hvQ33WWg
>>>
>>> I have to admit I'm not sure what to make of it. I should note that I'm
>>> trying to compile the version I just pulled from git earlier today, since
>>> the other version I normally work with is really old.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>>> another error before that which explains why it did not compile?
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Hi again.
>>>>>
>>>>> I've been trying to get it working. However, I did run into some
>>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>>> SimpleRTKCommon - which I do not have.
>>>>>
>>>>> Here is the last few lines from VS2013
>>>>>
>>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>>> > 5>
>>>>> > 5>      0 Warning(s)
>>>>> > 5>      2 Error(s)
>>>>> > 5>
>>>>> > 5>  Time Elapsed 00:00:25.26
>>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>>> ==========
>>>>>
>>>>> I'm not quite sure what is going on, because the only reference I can
>>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>>> RTK/CMakeLists.txt
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>>> python calls are available starting with Matlab 2014).
>>>>>> Simon
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>>> bottiger at gmail.com> wrote:
>>>>>>
>>>>>>> Dear Simon
>>>>>>>
>>>>>>> This look very interesting! Which platform did you successfully
>>>>>>> execute this on?
>>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>>> into any problems.
>>>>>>>
>>>>>>> best
>>>>>>>
>>>>>>> Arvid
>>>>>>>
>>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Dear RTK users,
>>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>>> and it seems to work well:
>>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but
>>>>>>>> let us know if you think otherwise.
>>>>>>>> Future works include a simple installation mechanism for
>>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
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From ajbatkinson at gmail.com  Wed Sep 28 08:11:12 2016
From: ajbatkinson at gmail.com (Abby Bryce Atkinson)
Date: Wed, 28 Sep 2016 13:11:12 +0100
Subject: [Rtk-users] 4DROOSTERReconstruction Example
Message-ID: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>

Hi,

I am trying to work through the 4DROOSTER example using the POPI patient
images (
http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) but
I am getting stuck when extracting the respiratory signal using the
amsterdam shroud.

I receive this error:


C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
--path .\Projections\ ^
More?                    --regexp '.*.his' ^
More?                    --output shroud.mha ^
More?                    --unsharp 650
ExceptionObject caught with writer->Update() in file
C:\RTK\applications\rtkamst
erdamshroud\rtkamsterdamshroud.cxx line 91

itk::ExceptionObject (0030E9E0)
Location: "void __thiscall itk::ImageFileWriter<class itk::Image<double,2>
>::Wr
ite(void)"
File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
Line: 284
Description: itk::ERROR: ImageFileWriter(03670318): Largest possible region
does
 not fully contain requested paste IO regionPaste IO region: ImageIORegion
(0030
EDD4)
  Dimension: 2
  Index: 0 0
  Size: 0 0
Largest possible region: ImageRegion (0030EE70)
  Dimension: 2
  Index: [0, 0]
  Size: [0, 0]


Can anyone help with a solution/tell me what I am doing wrong please?

Thanks,

Abby
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From simon.rit at creatis.insa-lyon.fr  Wed Sep 28 12:49:32 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 28 Sep 2016 18:49:32 +0200
Subject: [Rtk-users] 4DROOSTERReconstruction Example
In-Reply-To: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
References: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
Message-ID: <e23fc5ec-f7b4-846c-e349-f07564e2da8a@creatis.insa-lyon.fr>

Hi,

My guess is that the software does not find the projections. I would add 
the --verbose option and check that you actually input some projections. 
If not, I guess there is an issue with the path or the regexp in your 
command line.

Simon

On 28/09/2016 14:11, Abby Bryce Atkinson wrote:
> Hi,
>
> I am trying to work through the 4DROOSTER example using the POPI 
> patient images 
> (http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) 
> but I am getting stuck when extracting the respiratory signal using 
> the amsterdam shroud.
>
> I receive this error:
>
>
> C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
> --path .\Projections\ ^
> More?                    --regexp '.*.his' ^
> More?                    --output shroud.mha ^
> More?                    --unsharp 650
> ExceptionObject caught with writer->Update() in file 
> C:\RTK\applications\rtkamst
> erdamshroud\rtkamsterdamshroud.cxx line 91
>
> itk::ExceptionObject (0030E9E0)
> Location: "void __thiscall itk::ImageFileWriter<class 
> itk::Image<double,2> >::Wr
> ite(void)"
> File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
> Line: 284
> Description: itk::ERROR: ImageFileWriter(03670318): Largest possible 
> region does
>  not fully contain requested paste IO regionPaste IO region: 
> ImageIORegion (0030
> EDD4)
>   Dimension: 2
>   Index: 0 0
>   Size: 0 0
> Largest possible region: ImageRegion (0030EE70)
>   Dimension: 2
>   Index: [0, 0]
>   Size: [0, 0]
>
>
> Can anyone help with a solution/tell me what I am doing wrong please?
>
> Thanks,
>
> Abby
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users

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From signabdm at gmail.com  Mon Sep 12 06:58:59 2016
From: signabdm at gmail.com (Valeriy Signatulin)
Date: Mon, 12 Sep 2016 16:58:59 +0600
Subject: [Rtk-users] rotation of detector plane
Message-ID: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>

Hello RTK users.
Is it possible to specify rotation of detector plane in RTK ? (in
rtksimulategeom for example) If not, what is the best way to code this ?
By rotation of detector plane i mean twist, tilt, skew around the normal of
the detector as described in
http://www.ndt.net/article/v10n09/yisun/yisun.pdf page 6.
I'm trying to write the geometry calibration method described in this
article in RTK and i need to simulate these rotations to check the results.
Thanks.
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 12 08:40:31 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 12 Sep 2016 14:40:31 +0200
Subject: [Rtk-users] rotation of detector plane
In-Reply-To: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
References: <CAJE4RPhWj7NyU9vAyuR9dKZh2F0QoGrRFCoVmcUz5SAcsLuh3Q@mail.gmail.com>
Message-ID: <CAF0oig0C3zFcAaAhWHV9g+UY02i7cws7OU-7r2YadyAt3TH5GA@mail.gmail.com>

Hi,
You can do any rotation with RTK. The rotation is described 3 Euler angles,
see the geometry doc <http://www.openrtk.org/Doxygen/geometry.pdf>. From
the command line, that would be the --in_angle and out_angle that allow you
to modify the other angles than the standard angle for the position along
the circular rotation (GantryAngle). If you want to modify it per
projection, that's possible using C++ or Python code (AddProjection
<http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
method).
Good luck,
Simon

On Mon, Sep 12, 2016 at 12:58 PM, Valeriy Signatulin <signabdm at gmail.com>
wrote:

> Hello RTK users.
> Is it possible to specify rotation of detector plane in RTK ? (in
> rtksimulategeom for example) If not, what is the best way to code this ?
> By rotation of detector plane i mean twist, tilt, skew around the normal
> of the detector as described in http://www.ndt.net/article/
> v10n09/yisun/yisun.pdf page 6.
> I'm trying to write the geometry calibration method described in this
> article in RTK and i need to simulate these rotations to check the results.
> Thanks.
>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From andreasg at phys.au.dk  Tue Sep 13 13:06:46 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Tue, 13 Sep 2016 19:06:46 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
Message-ID: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>

Dear RTK experts,

I am reconstructing Varian ProBeam projections of the Xim image format. I
have written the reader myself - very similar to the Hnd one already
available with RTK.
Links to my fork: [XimReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkXimImageIO.cxx>,
XMLReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamXMLFileReader.cxx>,
GeometryReader
<https://github.com/agravgaard/RTK/blob/master/code/rtkVarianProBeamGeometryReader.cxx>
]

The reader apparently works (Images and angles displays as expected in UI),
however when reconstructing with a regular FDK* I get a reconstructed image
that is smeared out around the high and low density areas *[see attached
image]

I'm using half arc, full fan images with no bow-tie filter from Scripps
(~520 projections). Fixed detector and source (offset=0) with SID=2m,
SDD=3m.

*For the Hnd projections the reconstruction works perfectly (Same algorithm
<https://github.com/agravgaard/cbctrecon/blob/master/cbctrecon.cpp#L2726>).*
The reconstruction of the Xim projections performed on Varian software
works perfectly.

Without the Parker Short Scan Filter the first and last projections creates
streaks across the reconstruction as if they were way too bright.
If the first few projections are excluded, the following projection will
act the same way.

The projections are corrected for beam hardening and all the projections
have the expected attenuation.
No "smearing" filters (like median) is used, and iterative reconstruction
makes the same artifacts.

Setting the value of the first and last projection to zero has the same
effect as excluding. Changing the ramp filter only changes noise, not the
artifacts.

*Have any of you had a similar problem? *Am I missing something?
Any suggestions are welcome I'm running out of ideas.

Best regards
Andreas

__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 13 16:18:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 13 Sep 2016 22:18:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
Message-ID: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>

Hi,
I have almost never worked with Varian data but it looks like a
geometry problem. Maybe the problem comes from a bad ordering of the
projections which results in assigning a bad geometry to each
projection. How did you name your projections? Maybe check that the
order matches that of the RTK geometry file. Otherwise, there might be
an issue in the creation of the geometry file itself.
All this sounds good, happy bug hunt and don't hesitate to share your
code when you feel it's ready.
Simon

On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
<andreasg at phys.au.dk> wrote:
> Dear RTK experts,
>
> I am reconstructing Varian ProBeam projections of the Xim image format. I
> have written the reader myself - very similar to the Hnd one already
> available with RTK.
> Links to my fork: [XimReader, XMLReader, GeometryReader]
>
> The reader apparently works (Images and angles displays as expected in UI),
> however when reconstructing with a regular FDK I get a reconstructed image
> that is smeared out around the high and low density areas [see attached
> image]
>
> I'm using half arc, full fan images with no bow-tie filter from Scripps
> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
> SDD=3m.
>
> For the Hnd projections the reconstruction works perfectly (Same algorithm).
> The reconstruction of the Xim projections performed on Varian software works
> perfectly.
>
> Without the Parker Short Scan Filter the first and last projections creates
> streaks across the reconstruction as if they were way too bright.
> If the first few projections are excluded, the following projection will act
> the same way.
>
> The projections are corrected for beam hardening and all the projections
> have the expected attenuation.
> No "smearing" filters (like median) is used, and iterative reconstruction
> makes the same artifacts.
>
> Setting the value of the first and last projection to zero has the same
> effect as excluding. Changing the ramp filter only changes noise, not the
> artifacts.
>
> Have any of you had a similar problem? Am I missing something?
> Any suggestions are welcome I'm running out of ideas.
>
> Best regards
> Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>


From cyril.mory at creatis.insa-lyon.fr  Wed Sep 14 03:10:42 2016
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 14 Sep 2016 09:10:42 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
Message-ID: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>

One suggestion since it works with the Hnd projections:
You can run rtkprojections twice (with the Hnd projections, then with 
Xim projections) and output two projection stack files and two geometry 
files, then compare the projection stack files by subtracting one to the 
other (with SimpleRTK or clitk) and the geometry files with diff. If 
they are identical, then I do not see any reason why the reconstructions 
should be different, so my guess is that you will find differences.

On 09/13/2016 10:18 PM, Simon Rit wrote:
> Hi,
> I have almost never worked with Varian data but it looks like a
> geometry problem. Maybe the problem comes from a bad ordering of the
> projections which results in assigning a bad geometry to each
> projection. How did you name your projections? Maybe check that the
> order matches that of the RTK geometry file. Otherwise, there might be
> an issue in the creation of the geometry file itself.
> All this sounds good, happy bug hunt and don't hesitate to share your
> code when you feel it's ready.
> Simon
>
> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
> <andreasg at phys.au.dk> wrote:
>> Dear RTK experts,
>>
>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>> have written the reader myself - very similar to the Hnd one already
>> available with RTK.
>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>
>> The reader apparently works (Images and angles displays as expected in UI),
>> however when reconstructing with a regular FDK I get a reconstructed image
>> that is smeared out around the high and low density areas [see attached
>> image]
>>
>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>> SDD=3m.
>>
>> For the Hnd projections the reconstruction works perfectly (Same algorithm).
>> The reconstruction of the Xim projections performed on Varian software works
>> perfectly.
>>
>> Without the Parker Short Scan Filter the first and last projections creates
>> streaks across the reconstruction as if they were way too bright.
>> If the first few projections are excluded, the following projection will act
>> the same way.
>>
>> The projections are corrected for beam hardening and all the projections
>> have the expected attenuation.
>> No "smearing" filters (like median) is used, and iterative reconstruction
>> makes the same artifacts.
>>
>> Setting the value of the first and last projection to zero has the same
>> effect as excluding. Changing the ramp filter only changes noise, not the
>> artifacts.
>>
>> Have any of you had a similar problem? Am I missing something?
>> Any suggestions are welcome I'm running out of ideas.
>>
>> Best regards
>> Andreas
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>



From andreasg at phys.au.dk  Fri Sep 16 08:56:34 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 14:56:34 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
Message-ID: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>

Thanks for the suggestions, Simon and Cyril!

I have been carefully looking though the geometry and from what I
understand of the transformations matrices, the geometry looks correct/(as
expected).

HOWEVER: I found out that the reason for the Hnd to behave differently were
because had used half-fan scans (full-arc).
When I used a full-fan (half-arc) scan of Hnd projections the same
artifacts occurs!

Are there other (built-in) means of improving half-arc scans, than the
parker short scan filter?

Parker short scan does a decent job, but the result is still far from the
quality of the Varian software reconstruction at least for the CatPhan.

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:

> One suggestion since it works with the Hnd projections:
> You can run rtkprojections twice (with the Hnd projections, then with Xim
> projections) and output two projection stack files and two geometry files,
> then compare the projection stack files by subtracting one to the other
> (with SimpleRTK or clitk) and the geometry files with diff. If they are
> identical, then I do not see any reason why the reconstructions should be
> different, so my guess is that you will find differences.
>
>
> On 09/13/2016 10:18 PM, Simon Rit wrote:
>
>> Hi,
>> I have almost never worked with Varian data but it looks like a
>> geometry problem. Maybe the problem comes from a bad ordering of the
>> projections which results in assigning a bad geometry to each
>> projection. How did you name your projections? Maybe check that the
>> order matches that of the RTK geometry file. Otherwise, there might be
>> an issue in the creation of the geometry file itself.
>> All this sounds good, happy bug hunt and don't hesitate to share your
>> code when you feel it's ready.
>> Simon
>>
>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>> <andreasg at phys.au.dk> wrote:
>>
>>> Dear RTK experts,
>>>
>>> I am reconstructing Varian ProBeam projections of the Xim image format. I
>>> have written the reader myself - very similar to the Hnd one already
>>> available with RTK.
>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>
>>> The reader apparently works (Images and angles displays as expected in
>>> UI),
>>> however when reconstructing with a regular FDK I get a reconstructed
>>> image
>>> that is smeared out around the high and low density areas [see attached
>>> image]
>>>
>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>> SDD=3m.
>>>
>>> For the Hnd projections the reconstruction works perfectly (Same
>>> algorithm).
>>> The reconstruction of the Xim projections performed on Varian software
>>> works
>>> perfectly.
>>>
>>> Without the Parker Short Scan Filter the first and last projections
>>> creates
>>> streaks across the reconstruction as if they were way too bright.
>>> If the first few projections are excluded, the following projection will
>>> act
>>> the same way.
>>>
>>> The projections are corrected for beam hardening and all the projections
>>> have the expected attenuation.
>>> No "smearing" filters (like median) is used, and iterative reconstruction
>>> makes the same artifacts.
>>>
>>> Setting the value of the first and last projection to zero has the same
>>> effect as excluding. Changing the ramp filter only changes noise, not the
>>> artifacts.
>>>
>>> Have any of you had a similar problem? Am I missing something?
>>> Any suggestions are welcome I'm running out of ideas.
>>>
>>> Best regards
>>> Andreas
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Sep 16 10:13:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 16 Sep 2016 16:13:26 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
Message-ID: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>

Hi,
You can try any iterative reconstruction, they can also handle short scans.
Start with a few iterations of rtksart or rtkconjugategradient. However,
the nature of the artifacts indicate more a problem in the geometry in my
opinion. I have seen such errors when, for example, rotating in the wrong
direction. I can have a look if you share the dataset.
Cheers,
Simon

On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the suggestions, Simon and Cyril!
>
> I have been carefully looking though the geometry and from what I
> understand of the transformations matrices, the geometry looks correct/(as
> expected).
>
> HOWEVER: I found out that the reason for the Hnd to behave differently
> were because had used half-fan scans (full-arc).
> When I used a full-fan (half-arc) scan of Hnd projections the same
> artifacts occurs!
>
> Are there other (built-in) means of improving half-arc scans, than the
> parker short scan filter?
>
> Parker short scan does a decent job, but the result is still far from the
> quality of the Varian software reconstruction at least for the CatPhan.
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>
>> One suggestion since it works with the Hnd projections:
>> You can run rtkprojections twice (with the Hnd projections, then with Xim
>> projections) and output two projection stack files and two geometry files,
>> then compare the projection stack files by subtracting one to the other
>> (with SimpleRTK or clitk) and the geometry files with diff. If they are
>> identical, then I do not see any reason why the reconstructions should be
>> different, so my guess is that you will find differences.
>>
>>
>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>
>>> Hi,
>>> I have almost never worked with Varian data but it looks like a
>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>> projections which results in assigning a bad geometry to each
>>> projection. How did you name your projections? Maybe check that the
>>> order matches that of the RTK geometry file. Otherwise, there might be
>>> an issue in the creation of the geometry file itself.
>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>> code when you feel it's ready.
>>> Simon
>>>
>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>> <andreasg at phys.au.dk> wrote:
>>>
>>>> Dear RTK experts,
>>>>
>>>> I am reconstructing Varian ProBeam projections of the Xim image format.
>>>> I
>>>> have written the reader myself - very similar to the Hnd one already
>>>> available with RTK.
>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>
>>>> The reader apparently works (Images and angles displays as expected in
>>>> UI),
>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>> image
>>>> that is smeared out around the high and low density areas [see attached
>>>> image]
>>>>
>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>> SDD=3m.
>>>>
>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>> algorithm).
>>>> The reconstruction of the Xim projections performed on Varian software
>>>> works
>>>> perfectly.
>>>>
>>>> Without the Parker Short Scan Filter the first and last projections
>>>> creates
>>>> streaks across the reconstruction as if they were way too bright.
>>>> If the first few projections are excluded, the following projection
>>>> will act
>>>> the same way.
>>>>
>>>> The projections are corrected for beam hardening and all the projections
>>>> have the expected attenuation.
>>>> No "smearing" filters (like median) is used, and iterative
>>>> reconstruction
>>>> makes the same artifacts.
>>>>
>>>> Setting the value of the first and last projection to zero has the same
>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>> the
>>>> artifacts.
>>>>
>>>> Have any of you had a similar problem? Am I missing something?
>>>> Any suggestions are welcome I'm running out of ideas.
>>>>
>>>> Best regards
>>>> Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> N?rrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     andreasg at phys.au.dk
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From andreasg at phys.au.dk  Fri Sep 16 16:37:43 2016
From: andreasg at phys.au.dk (Andreas Gravgaard Andersen)
Date: Fri, 16 Sep 2016 22:37:43 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
Message-ID: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>

Thanks for the fast response Simon!

I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
right all along!
I just didn't get why it makes a difference. I think I do now, as the
resulting image was flipped upside down and not left/right as I expected.
[attached]

The reconstruction is significantly better, I'll look into what should be
included in the reader and what I should keep in my program to keep
conformity with the other readers. Then I'll create a pull request.

Just for the purpose of others hitting the same or a similar bug, I also
attempted:
I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
back/forward projection, *but with no* significant improvement [attached]

And:
If you want you can download the data set from: [Dropbox link to 460MB zip
<https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep it
up as long as Dropbox allows me)] Only the Acquisitions/subfolder is used
along with the Scan.xml (Calibrations folder may be used in the future in
my program, but I'm not sure if you can rely on the existence of the
content).

A MatLab XimReader is available: link
<https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
available from Varian bitbucket along a with a python version and a
C#->matlab plugin
<https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). Otherwise
my fork with the RTK-style reader is available from the same repository (I
have also added Hnc support, thanks to the Geoff Hugo fork, so bzip2 is a
new dependancy).

Best regards
Andreas


__________________________________

Andreas Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

N?rrebrogade 44,

8000, Aarhus C

Mail:     andreasg at phys.au.dk

Cell:      +45 3165 8140



2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:

> Hi,
> You can try any iterative reconstruction, they can also handle short
> scans. Start with a few iterations of rtksart or rtkconjugategradient.
> However, the nature of the artifacts indicate more a problem in the
> geometry in my opinion. I have seen such errors when, for example, rotating
> in the wrong direction. I can have a look if you share the dataset.
> Cheers,
> Simon
>
> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
> andreasg at phys.au.dk> wrote:
>
>> Thanks for the suggestions, Simon and Cyril!
>>
>> I have been carefully looking though the geometry and from what I
>> understand of the transformations matrices, the geometry looks correct/(as
>> expected).
>>
>> HOWEVER: I found out that the reason for the Hnd to behave differently
>> were because had used half-fan scans (full-arc).
>> When I used a full-fan (half-arc) scan of Hnd projections the same
>> artifacts occurs!
>>
>> Are there other (built-in) means of improving half-arc scans, than the
>> parker short scan filter?
>>
>> Parker short scan does a decent job, but the result is still far from the
>> quality of the Varian software reconstruction at least for the CatPhan.
>>
>> Best regards
>> Andreas
>>
>>
>> __________________________________
>>
>> Andreas Gravgaard Andersen
>>
>> Department of Oncology,
>>
>> Aarhus University Hospital
>>
>> N?rrebrogade 44,
>>
>> 8000, Aarhus C
>>
>> Mail:     andreasg at phys.au.dk
>>
>> Cell:      +45 3165 8140
>>
>>
>>
>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>
>>> One suggestion since it works with the Hnd projections:
>>> You can run rtkprojections twice (with the Hnd projections, then with
>>> Xim projections) and output two projection stack files and two geometry
>>> files, then compare the projection stack files by subtracting one to the
>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>> are identical, then I do not see any reason why the reconstructions should
>>> be different, so my guess is that you will find differences.
>>>
>>>
>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>
>>>> Hi,
>>>> I have almost never worked with Varian data but it looks like a
>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>> projections which results in assigning a bad geometry to each
>>>> projection. How did you name your projections? Maybe check that the
>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>> an issue in the creation of the geometry file itself.
>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>> code when you feel it's ready.
>>>> Simon
>>>>
>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>> <andreasg at phys.au.dk> wrote:
>>>>
>>>>> Dear RTK experts,
>>>>>
>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>> format. I
>>>>> have written the reader myself - very similar to the Hnd one already
>>>>> available with RTK.
>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>
>>>>> The reader apparently works (Images and angles displays as expected in
>>>>> UI),
>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>> image
>>>>> that is smeared out around the high and low density areas [see attached
>>>>> image]
>>>>>
>>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>> SDD=3m.
>>>>>
>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>> algorithm).
>>>>> The reconstruction of the Xim projections performed on Varian software
>>>>> works
>>>>> perfectly.
>>>>>
>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>> creates
>>>>> streaks across the reconstruction as if they were way too bright.
>>>>> If the first few projections are excluded, the following projection
>>>>> will act
>>>>> the same way.
>>>>>
>>>>> The projections are corrected for beam hardening and all the
>>>>> projections
>>>>> have the expected attenuation.
>>>>> No "smearing" filters (like median) is used, and iterative
>>>>> reconstruction
>>>>> makes the same artifacts.
>>>>>
>>>>> Setting the value of the first and last projection to zero has the same
>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>> the
>>>>> artifacts.
>>>>>
>>>>> Have any of you had a similar problem? Am I missing something?
>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>
>>>>> Best regards
>>>>> Andreas
>>>>>
>>>>> __________________________________
>>>>>
>>>>> Andreas Gravgaard Andersen
>>>>>
>>>>> Department of Oncology,
>>>>>
>>>>> Aarhus University Hospital
>>>>>
>>>>> N?rrebrogade 44,
>>>>>
>>>>> 8000, Aarhus C
>>>>>
>>>>> Mail:     andreasg at phys.au.dk
>>>>>
>>>>> Cell:      +45 3165 8140
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 03:26:55 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 09:26:55 +0200
Subject: [Rtk-users] Fwd: Have you encountered this artifact?
In-Reply-To: <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
References: <CAE0aawF5eMdrFzhg1O_G7ZtJBAGgTjNVuuF4G8p9z2HRVgd5Aw@mail.gmail.com>
 <CAE0aawFD+e9yDcrNBb4SSSRCH=Z8tRr5o=kJFwnwkD6B82H7tg@mail.gmail.com>
 <CAF0oig0UDTOnbawo3a+Wq__KzHvKtjB2PbC3nv8hxo6DuR8Zcg@mail.gmail.com>
 <d66e67dd-fd42-9661-978b-eada3c71b41d@creatis.insa-lyon.fr>
 <CAE0aawHWLrjHQMYKgzHXGzrtprA0kPTJk5mcUGptL-ou4UgJYg@mail.gmail.com>
 <CAF0oig16F9R45km2d9goYR6kcq_3PbRsJh8Gv4u9dD4_KrRD=w@mail.gmail.com>
 <CAE0aawEW7BFp3RORAWGRhFMipnckUEp0ZG165+WYemPswkprsA@mail.gmail.com>
Message-ID: <CAF0oig2TSmAsSn=o3aLo6LEFDOSaKRtfknjMer24rcDKJ-0Fqg@mail.gmail.com>

Hi,
Thanks for sharing. There still seems to be some streak artefacts, do you
see the same in the Varian reconstruction?
I'm looking forward to the pull-request, I think we should try to make the
bzip2 optional.
Simon

On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the fast response Simon!
>
> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
> right all along!
> I just didn't get why it makes a difference. I think I do now, as the
> resulting image was flipped upside down and not left/right as I expected.
> [attached]
>
> The reconstruction is significantly better, I'll look into what should be
> included in the reader and what I should keep in my program to keep
> conformity with the other readers. Then I'll create a pull request.
>
> Just for the purpose of others hitting the same or a similar bug, I also
> attempted:
> I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
> back/forward projection, *but with no* significant improvement [attached]
>
> And:
> If you want you can download the data set from: [Dropbox link to 460MB zip
> <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep
> it up as long as Dropbox allows me)] Only the Acquisitions/subfolder is
> used along with the Scan.xml (Calibrations folder may be used in the future
> in my program, but I'm not sure if you can rely on the existence of the
> content).
>
> A MatLab XimReader is available: link
> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
> available from Varian bitbucket along a with a python version and a
> C#->matlab plugin
> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>).
> Otherwise my fork with the RTK-style reader is available from the same
> repository (I have also added Hnc support, thanks to the Geoff Hugo fork,
> so bzip2 is a new dependancy).
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> N?rrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> Hi,
>> You can try any iterative reconstruction, they can also handle short
>> scans. Start with a few iterations of rtksart or rtkconjugategradient.
>> However, the nature of the artifacts indicate more a problem in the
>> geometry in my opinion. I have seen such errors when, for example, rotating
>> in the wrong direction. I can have a look if you share the dataset.
>> Cheers,
>> Simon
>>
>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
>> andreasg at phys.au.dk> wrote:
>>
>>> Thanks for the suggestions, Simon and Cyril!
>>>
>>> I have been carefully looking though the geometry and from what I
>>> understand of the transformations matrices, the geometry looks correct/(as
>>> expected).
>>>
>>> HOWEVER: I found out that the reason for the Hnd to behave differently
>>> were because had used half-fan scans (full-arc).
>>> When I used a full-fan (half-arc) scan of Hnd projections the same
>>> artifacts occurs!
>>>
>>> Are there other (built-in) means of improving half-arc scans, than the
>>> parker short scan filter?
>>>
>>> Parker short scan does a decent job, but the result is still far from
>>> the quality of the Varian software reconstruction at least for the CatPhan.
>>>
>>> Best regards
>>> Andreas
>>>
>>>
>>> __________________________________
>>>
>>> Andreas Gravgaard Andersen
>>>
>>> Department of Oncology,
>>>
>>> Aarhus University Hospital
>>>
>>> N?rrebrogade 44,
>>>
>>> 8000, Aarhus C
>>>
>>> Mail:     andreasg at phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
>>>
>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>>>
>>>> One suggestion since it works with the Hnd projections:
>>>> You can run rtkprojections twice (with the Hnd projections, then with
>>>> Xim projections) and output two projection stack files and two geometry
>>>> files, then compare the projection stack files by subtracting one to the
>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they
>>>> are identical, then I do not see any reason why the reconstructions should
>>>> be different, so my guess is that you will find differences.
>>>>
>>>>
>>>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>>>
>>>>> Hi,
>>>>> I have almost never worked with Varian data but it looks like a
>>>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>>>> projections which results in assigning a bad geometry to each
>>>>> projection. How did you name your projections? Maybe check that the
>>>>> order matches that of the RTK geometry file. Otherwise, there might be
>>>>> an issue in the creation of the geometry file itself.
>>>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>>>> code when you feel it's ready.
>>>>> Simon
>>>>>
>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>>>> <andreasg at phys.au.dk> wrote:
>>>>>
>>>>>> Dear RTK experts,
>>>>>>
>>>>>> I am reconstructing Varian ProBeam projections of the Xim image
>>>>>> format. I
>>>>>> have written the reader myself - very similar to the Hnd one already
>>>>>> available with RTK.
>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>>>
>>>>>> The reader apparently works (Images and angles displays as expected
>>>>>> in UI),
>>>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>>>> image
>>>>>> that is smeared out around the high and low density areas [see
>>>>>> attached
>>>>>> image]
>>>>>>
>>>>>> I'm using half arc, full fan images with no bow-tie filter from
>>>>>> Scripps
>>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>>>> SDD=3m.
>>>>>>
>>>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>>>> algorithm).
>>>>>> The reconstruction of the Xim projections performed on Varian
>>>>>> software works
>>>>>> perfectly.
>>>>>>
>>>>>> Without the Parker Short Scan Filter the first and last projections
>>>>>> creates
>>>>>> streaks across the reconstruction as if they were way too bright.
>>>>>> If the first few projections are excluded, the following projection
>>>>>> will act
>>>>>> the same way.
>>>>>>
>>>>>> The projections are corrected for beam hardening and all the
>>>>>> projections
>>>>>> have the expected attenuation.
>>>>>> No "smearing" filters (like median) is used, and iterative
>>>>>> reconstruction
>>>>>> makes the same artifacts.
>>>>>>
>>>>>> Setting the value of the first and last projection to zero has the
>>>>>> same
>>>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>>>> the
>>>>>> artifacts.
>>>>>>
>>>>>> Have any of you had a similar problem? Am I missing something?
>>>>>> Any suggestions are welcome I'm running out of ideas.
>>>>>>
>>>>>> Best regards
>>>>>> Andreas
>>>>>>
>>>>>> __________________________________
>>>>>>
>>>>>> Andreas Gravgaard Andersen
>>>>>>
>>>>>> Department of Oncology,
>>>>>>
>>>>>> Aarhus University Hospital
>>>>>>
>>>>>> N?rrebrogade 44,
>>>>>>
>>>>>> 8000, Aarhus C
>>>>>>
>>>>>> Mail:     andreasg at phys.au.dk
>>>>>>
>>>>>> Cell:      +45 3165 8140
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:05:24 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:05:24 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
Message-ID: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>

Dear RTK users,
I have quickly tested calling the SimpleRTK python lib from Matlab and it
seems to work well:
http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
Therefore, I don't think we have to work on Matlab wrappings but let us
know if you think otherwise.
Future works include a simple installation mechanism for pre-compiled
SimpleRTK libraries. We'll keep you posted!
Simon
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From bottiger at gmail.com  Mon Sep 19 05:14:03 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 11:14:03 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
Message-ID: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>

Dear Simon

This look very interesting! Which platform did you successfully execute
this on?
I will give it a try at once (on windows) and let you know if I run into
any problems.

best

Arvid

On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> I have quickly tested calling the SimpleRTK python lib from Matlab and it
> seems to work well:
> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
> Therefore, I don't think we have to work on Matlab wrappings but let us
> know if you think otherwise.
> Future works include a simple installation mechanism for pre-compiled
> SimpleRTK libraries. We'll keep you posted!
> Simon
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 05:19:28 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 11:19:28 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
Message-ID: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>

The latest MacOS. It's nice if you can test it on other platforms, I'll try
to run it on Linux but I have to upgrade matlab first (I think python calls
are available starting with Matlab 2014).
Simon

On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Dear Simon
>
> This look very interesting! Which platform did you successfully execute
> this on?
> I will give it a try at once (on windows) and let you know if I run into
> any problems.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> Dear RTK users,
>> I have quickly tested calling the SimpleRTK python lib from Matlab and it
>> seems to work well:
>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>> Therefore, I don't think we have to work on Matlab wrappings but let us
>> know if you think otherwise.
>> Future works include a simple installation mechanism for pre-compiled
>> SimpleRTK libraries. We'll keep you posted!
>> Simon
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From bottiger at gmail.com  Mon Sep 19 08:30:32 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Mon, 19 Sep 2016 14:30:32 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
Message-ID: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>

Hi again.

I've been trying to get it working. However, I did run into some problems
compiling SimpleRTK. The main issue seems to be that it depends on
SimpleRTKCommon - which I do not have.

Here is the last few lines from VS2013

> 5>LINK : fatal error LNK1181: cannot open input file
'..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib' [C:\Users\aplb\Work\RTK\RTK1.2-
> bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> 5>
> 5>      0 Warning(s)
> 5>      2 Error(s)
> 5>
> 5>  Time Elapsed 00:00:25.26
> ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
==========

I'm not quite sure what is going on, because the only reference I can find
to SimpleRTKCommon is the CMakeLists.txt on github:
https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt

best

Arvid

On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> The latest MacOS. It's nice if you can test it on other platforms, I'll
> try to run it on Linux but I have to upgrade matlab first (I think python
> calls are available starting with Matlab 2014).
> Simon
>
> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Dear Simon
>>
>> This look very interesting! Which platform did you successfully execute
>> this on?
>> I will give it a try at once (on windows) and let you know if I run into
>> any problems.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Dear RTK users,
>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>> it seems to work well:
>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>> know if you think otherwise.
>>> Future works include a simple installation mechanism for pre-compiled
>>> SimpleRTK libraries. We'll keep you posted!
>>> Simon
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Mon Sep 19 12:50:33 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 19 Sep 2016 18:50:33 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
Message-ID: <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>

 SimpleRTKCommon is a library generated when compiling. Don't you have
another error before that which explains why it did not compile?
Simon

On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I've been trying to get it working. However, I did run into some problems
> compiling SimpleRTK. The main issue seems to be that it depends on
> SimpleRTKCommon - which I do not have.
>
> Here is the last few lines from VS2013
>
> > 5>LINK : fatal error LNK1181: cannot open input file '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
> [C:\Users\aplb\Work\RTK\RTK1.2-
> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
> > 5>
> > 5>      0 Warning(s)
> > 5>      2 Error(s)
> > 5>
> > 5>  Time Elapsed 00:00:25.26
> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
> ==========
>
> I'm not quite sure what is going on, because the only reference I can find
> to SimpleRTKCommon is the CMakeLists.txt on github:
> https://github.com/SimonRit/RTK/blob/master/utilities/
> SimpleRTK/CMakeLists.txt
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <simon.rit at creatis.insa-lyon.
> fr> wrote:
>
>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>> try to run it on Linux but I have to upgrade matlab first (I think python
>> calls are available starting with Matlab 2014).
>> Simon
>>
>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Dear Simon
>>>
>>> This look very interesting! Which platform did you successfully execute
>>> this on?
>>> I will give it a try at once (on windows) and let you know if I run into
>>> any problems.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Dear RTK users,
>>>> I have quickly tested calling the SimpleRTK python lib from Matlab and
>>>> it seems to work well:
>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>> Therefore, I don't think we have to work on Matlab wrappings but let us
>>>> know if you think otherwise.
>>>> Future works include a simple installation mechanism for pre-compiled
>>>> SimpleRTK libraries. We'll keep you posted!
>>>> Simon
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 01:33:46 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 07:33:46 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
Message-ID: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>

I'm not an msvc specialist but your first line suggests that you have 
pasted only part of the log:

20>  Done Building Project 
"C:\Users\aplb\Work\RTK\RTK1.2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" 
(default targets) -- FAILED.

What you need to find out is why this build failed. If the build fails, 
the linking cannot work.
Cheers,
Simon

On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
> I did a complete rebuild, and here is the end of the output: 
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that 
> I'm trying to compile the version I just pulled from git earlier 
> today, since the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     SimpleRTKCommon is a library generated when compiling. Don't you
>     have another error before that which explains why it did not compile?
>     Simon
>
>     On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger
>     <bottiger at gmail.com <mailto:bottiger at gmail.com>> wrote:
>
>         Hi again.
>
>         I've been trying to get it working. However, I did run into
>         some problems compiling SimpleRTK. The main issue seems to be
>         that it depends on SimpleRTKCommon - which I do not have.
>
>         Here is the last few lines from VS2013
>
>         > 5>LINK : fatal error LNK1181: cannot open input file
>         '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>         [C:\Users\aplb\Work\RTK\RTK1.2-
>         > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>         > 5>
>         > 5>      0 Warning(s)
>         > 5>      2 Error(s)
>         > 5>
>         > 5>  Time Elapsed 00:00:25.26
>         > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0
>         skipped ==========
>
>         I'm not quite sure what is going on, because the only
>         reference I can find to SimpleRTKCommon is the CMakeLists.txt
>         on github:
>         https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt
>         <https://github.com/SimonRit/RTK/blob/master/utilities/SimpleRTK/CMakeLists.txt>
>
>         best
>
>         Arvid
>
>         On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit
>         <simon.rit at creatis.insa-lyon.fr
>         <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>             The latest MacOS. It's nice if you can test it on other
>             platforms, I'll try to run it on Linux but I have to
>             upgrade matlab first (I think python calls are available
>             starting with Matlab 2014).
>             Simon
>
>             On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen
>             B?ttiger <bottiger at gmail.com <mailto:bottiger at gmail.com>>
>             wrote:
>
>                 Dear Simon
>
>                 This look very interesting! Which platform did you
>                 successfully execute this on?
>                 I will give it a try at once (on windows) and let you
>                 know if I run into any problems.
>
>                 best
>
>                 Arvid
>
>                 On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit
>                 <simon.rit at creatis.insa-lyon.fr
>                 <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>                     Dear RTK users,
>                     I have quickly tested calling the SimpleRTK python
>                     lib from Matlab and it seems to work well:
>                     http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>                     <http://wiki.openrtk.org/index.php/SimpleRTK#Matlab>
>                     Therefore, I don't think we have to work on Matlab
>                     wrappings but let us know if you think otherwise.
>                     Future works include a simple installation
>                     mechanism for pre-compiled SimpleRTK libraries.
>                     We'll keep you posted!
>                     Simon
>
>                     _______________________________________________
>                     Rtk-users mailing list
>                     Rtk-users at public.kitware.com
>                     <mailto:Rtk-users at public.kitware.com>
>                     http://public.kitware.com/mailman/listinfo/rtk-users
>                     <http://public.kitware.com/mailman/listinfo/rtk-users>
>
>
>
>
>
>

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From bottiger at gmail.com  Tue Sep 20 08:17:35 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Tue, 20 Sep 2016 14:17:35 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
Message-ID: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>

Hi again.

I understand, but could you please help me get in contact with the person
who knows something about the windows build (if any), I think there is
something wrong.

I have been investigating the build problems I had and found that in the
sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
opened it up and found the projects which I had problems building:
"SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.

When I then tried to build SimpleRTKCommon manually it just compiled
without any problems. However, when I followed up by building
"SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
find "SimpleRTKCommon-0.9.lib" - which I just build.

After some more investigation I realized that the SimpleRTKCommon is set to
build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects it
to be a static linked library (LIB). After changing SimpleRTKCommon to be
build as a static library - and changing the output location - I could
build SimpleRTKBasicFilters0.

However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
to a LIB as well I could build SimpleRTKBasicFilters1, then
SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.

I'm unsure if the intention is to build them as static or dynamic
libraries, but in any case the current build configuration doesn't work -
on my setup at least.

However, I should note than for some reason the "lua5" project did build
successfully out of the box. Whatever it does differently works.

best

Arvid



On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> I'm not an msvc specialist but your first line suggests that you have
> pasted only part of the log:
>
> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.
> 2-bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
> What you need to find out is why this build failed. If the build fails,
> the linking cannot work.
> Cheers,
> Simon
>
>
> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>
> I did a complete rebuild, and here is the end of the output:
> http://pastebin.com/hvQ33WWg
>
> I have to admit I'm not sure what to make of it. I should note that I'm
> trying to compile the version I just pulled from git earlier today, since
> the other version I normally work with is really old.
>
> best
>
> Arvid
>
> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> SimpleRTKCommon is a library generated when compiling. Don't you have
>> another error before that which explains why it did not compile?
>> Simon
>>
>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>> bottiger at gmail.com> wrote:
>>
>>> Hi again.
>>>
>>> I've been trying to get it working. However, I did run into some
>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>> SimpleRTKCommon - which I do not have.
>>>
>>> Here is the last few lines from VS2013
>>>
>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>> > 5>
>>> > 5>      0 Warning(s)
>>> > 5>      2 Error(s)
>>> > 5>
>>> > 5>  Time Elapsed 00:00:25.26
>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>> ==========
>>>
>>> I'm not quite sure what is going on, because the only reference I can
>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>> RTK/CMakeLists.txt
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> The latest MacOS. It's nice if you can test it on other platforms, I'll
>>>> try to run it on Linux but I have to upgrade matlab first (I think python
>>>> calls are available starting with Matlab 2014).
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Dear Simon
>>>>>
>>>>> This look very interesting! Which platform did you successfully
>>>>> execute this on?
>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>> into any problems.
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Dear RTK users,
>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>> and it seems to work well:
>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>> us know if you think otherwise.
>>>>>> Future works include a simple installation mechanism for pre-compiled
>>>>>> SimpleRTK libraries. We'll keep you posted!
>>>>>> Simon
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
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From simon.rit at creatis.insa-lyon.fr  Tue Sep 20 10:19:20 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 20 Sep 2016 16:19:20 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
Message-ID: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>

Hi,
Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
I can't solve your problem but Kitware is going to look into an upgrade of
SimpleRTK in the coming days, I'll ask them if they know what is the issue.
If you look here:
http://my.cdash.org/viewNotes.php?buildid=1052065
this is a nightly build of SimpleRTK on Windows and it seems to work. I
don't see why it wouldn't work for you.
Simon

On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
bottiger at gmail.com> wrote:

> Hi again.
>
> I understand, but could you please help me get in contact with the person
> who knows something about the windows build (if any), I think there is
> something wrong.
>
> I have been investigating the build problems I had and found that in the
> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
> opened it up and found the projects which I had problems building:
> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>
> When I then tried to build SimpleRTKCommon manually it just compiled
> without any problems. However, when I followed up by building
> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
> find "SimpleRTKCommon-0.9.lib" - which I just build.
>
> After some more investigation I realized that the SimpleRTKCommon is set
> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
> it to be a static linked library (LIB). After changing SimpleRTKCommon to
> be build as a static library - and changing the output location - I could
> build SimpleRTKBasicFilters0.
>
> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing that
> to a LIB as well I could build SimpleRTKBasicFilters1, then
> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>
> I'm unsure if the intention is to build them as static or dynamic
> libraries, but in any case the current build configuration doesn't work -
> on my setup at least.
>
> However, I should note than for some reason the "lua5" project did build
> successfully out of the box. Whatever it does differently works.
>
> best
>
> Arvid
>
>
>
> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> I'm not an msvc specialist but your first line suggests that you have
>> pasted only part of the log:
>>
>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) -- FAILED.
>> What you need to find out is why this build failed. If the build fails,
>> the linking cannot work.
>> Cheers,
>> Simon
>>
>>
>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>
>> I did a complete rebuild, and here is the end of the output:
>> http://pastebin.com/hvQ33WWg
>>
>> I have to admit I'm not sure what to make of it. I should note that I'm
>> trying to compile the version I just pulled from git earlier today, since
>> the other version I normally work with is really old.
>>
>> best
>>
>> Arvid
>>
>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>> another error before that which explains why it did not compile?
>>> Simon
>>>
>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>> bottiger at gmail.com> wrote:
>>>
>>>> Hi again.
>>>>
>>>> I've been trying to get it working. However, I did run into some
>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>> SimpleRTKCommon - which I do not have.
>>>>
>>>> Here is the last few lines from VS2013
>>>>
>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>> > 5>
>>>> > 5>      0 Warning(s)
>>>> > 5>      2 Error(s)
>>>> > 5>
>>>> > 5>  Time Elapsed 00:00:25.26
>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>> ==========
>>>>
>>>> I'm not quite sure what is going on, because the only reference I can
>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>> RTK/CMakeLists.txt
>>>>
>>>> best
>>>>
>>>> Arvid
>>>>
>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>> python calls are available starting with Matlab 2014).
>>>>> Simon
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>> bottiger at gmail.com> wrote:
>>>>>
>>>>>> Dear Simon
>>>>>>
>>>>>> This look very interesting! Which platform did you successfully
>>>>>> execute this on?
>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>> into any problems.
>>>>>>
>>>>>> best
>>>>>>
>>>>>> Arvid
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>
>>>>>>> Dear RTK users,
>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>> and it seems to work well:
>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but let
>>>>>>> us know if you think otherwise.
>>>>>>> Future works include a simple installation mechanism for
>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>> Simon
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 02:40:50 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 08:40:50 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
Message-ID: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>

Dear RTK users,
RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
been released, about 7 months after RTK v1.2.0.

Release notes :
- Style updated (follow more closely latest ITK guidelines).
- Started using Travis CI, github pull requests should now be used for code
submission.
- New pre-processing functionalities:
  * CUDA polynomial gain correction,
  * scatter glare correction,
  * lag correction,
  * idark option,
  * removed threshold to positive values after i0 LUT.
- Improved CUDA forward and backprojection speed using projection slabs.
- Added motion-compensated forward and back projection operators in CUDA,
in both 3D and 4D.
- Added the rtkregularizedconjugategradient application, which performs 3D
regularized reconstruction by conjugate gradient + optional regularizations
(Positivity, TV, Wavelets).
- Made the rtkfourdrooster, rtkmcrooster and rtkregularizedconjugategradient
fully modular. Each regularization step can be made active or inactive.
- Added a filter to minimize the L0 norm of the temporal gradient (one-D
only).

Many thanks to the contributors, in alphabetical order for this release: Cyril
Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien
Jomier, S?bastien
Brousmiche, Simon Rit

As usual, be aware that we don't focus on releases since we have a public
github repository <http://github.com/SimonRit/RTK> that we try to keep
stable. I still recommend the use of the master HEAD over releases to enjoy
the new RTK developments before their release. We still have a few on-going
projects for which we will use and enhance RTK.

Simon (for the RTK consortium)
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From simon.rit at creatis.insa-lyon.fr  Thu Sep 22 04:48:26 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 22 Sep 2016 10:48:26 +0200
Subject: [Rtk-users] Release of RTK v1.3.0
In-Reply-To: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
References: <CAF0oig3dRSS898BN_6TOiigo1e4vMSgJ7k66ygMqLhVCzJh6Pw@mail.gmail.com>
Message-ID: <CAF0oig0=5_KPN198JzsGQXDd07Nvw_Ew+qSGhguk0m27s3U-3Q@mail.gmail.com>

Sorry, I had forgotten to change the release number in the source file.
It's been corrected, you will have to move your tag locally or update your
file if you had already downloaded it.
Simon

On Thu, Sep 22, 2016 at 8:40 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Dear RTK users,
> RTK v1.3.0 <https://github.com/SimonRit/RTK/archive/v1.3.0.zip> has just
> been released, about 7 months after RTK v1.2.0.
>
> Release notes :
> - Style updated (follow more closely latest ITK guidelines).
> - Started using Travis CI, github pull requests should now be used for
> code submission.
> - New pre-processing functionalities:
>   * CUDA polynomial gain correction,
>   * scatter glare correction,
>   * lag correction,
>   * idark option,
>   * removed threshold to positive values after i0 LUT.
> - Improved CUDA forward and backprojection speed using projection slabs.
> - Added motion-compensated forward and back projection operators in CUDA,
> in both 3D and 4D.
> - Added the rtkregularizedconjugategradient application, which performs
> 3D regularized reconstruction by conjugate gradient + optional
> regularizations (Positivity, TV, Wavelets).
> - Made the rtkfourdrooster, rtkmcrooster and
> rtkregularizedconjugategradient fully modular. Each regularization step
> can be made active or inactive.
> - Added a filter to minimize the L0 norm of the temporal gradient (one-D
> only).
>
> Many thanks to the contributors, in alphabetical order for this release: Cyril
> Mory, Deepak Roy Chittajallu, Fabien Momey, Hans Johnson, Julien Jomier, S?bastien
> Brousmiche, Simon Rit
>
> As usual, be aware that we don't focus on releases since we have a public
> github repository <http://github.com/SimonRit/RTK> that we try to keep
> stable. I still recommend the use of the master HEAD over releases to
> enjoy the new RTK developments before their release. We still have a few
> on-going projects for which we will use and enhance RTK.
>
> Simon (for the RTK consortium)
>
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From bottiger at gmail.com  Fri Sep 23 04:29:06 2016
From: bottiger at gmail.com (=?UTF-8?Q?Arvid_Piehl_Lauritsen_B=C3=B6ttiger?=)
Date: Fri, 23 Sep 2016 10:29:06 +0200
Subject: [Rtk-users] SimpleRTK + Matlab
In-Reply-To: <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
References: <CAF0oig3ez108e=Jup2bxnODn9dmb_9TNdJfxy1b1HGFXpAX4gg@mail.gmail.com>
 <CANBwxwF-ymODBcKpGXJMQByVH3osx5-DOYSD9FUrwja5+q5rFQ@mail.gmail.com>
 <CAF0oig2z4QJ8RHN0rFz_urjtvm+XqE7C_sL43PRTPJ9ZYZKZKQ@mail.gmail.com>
 <CANBwxwGM4b02VNx64T-hHLQw5r2OvHUDG6RM1O565Y2O78=XaA@mail.gmail.com>
 <CAF0oig3tTetkmhHrAzLSGn4J-c_UM7trzLep7SM=F9Zg28Z4gg@mail.gmail.com>
 <CANBwxwHMRfbR+4MPaDE671DNY_-yxn+ZoaqyEgU74iSH1q2qyA@mail.gmail.com>
 <06d4327e-9fd4-bf08-565d-5304f577b521@creatis.insa-lyon.fr>
 <CANBwxwFRTpF6nUHpVQZD3-_Dq5KSfBsA3EdfjPV5ay1sBS+P3Q@mail.gmail.com>
 <CAF0oig1-XwojFgagikAK6PbHpga7U+_oEvTGgE0yeorMoVuOuA@mail.gmail.com>
Message-ID: <CANBwxwEvaUrvd1X=74g=V2JmDwtrQKFDtyUdAZJn5CRCBCkb8g@mail.gmail.com>

Hi again.

I've been spending some more time with this, and feel I learned a little
bit more. I have now tested this on several machines with several compiler
versions (more or less all of them) and serveral cmake versions - all with
Windows 7.

I can actually reproduce the successful build you linked to, but this can
only be done if you do not include any of the language wrappings, like in
the build you linked to. Enable any of them, and the build will break. (see
attachment)

I suspect it must have been working in the past, but since none of them are
included in your test there have been a breaking change, and none of them
work anymore.

I am still trying to tweak then projects manually to build SimpleRTK with
some sort of language support, but still without any luck.

best

Arvid

On Tue, Sep 20, 2016 at 4:19 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Sorry, I won't be able to help but I'd advise to tick on WRAP_PYTHON only
> at first in cmake, not the other languages (i.e., tick off WRAP_LUA).
> I can't solve your problem but Kitware is going to look into an upgrade of
> SimpleRTK in the coming days, I'll ask them if they know what is the issue.
> If you look here:
> http://my.cdash.org/viewNotes.php?buildid=1052065
> this is a nightly build of SimpleRTK on Windows and it seems to work. I
> don't see why it wouldn't work for you.
> Simon
>
> On Tue, Sep 20, 2016 at 2:17 PM, Arvid Piehl Lauritsen B?ttiger <
> bottiger at gmail.com> wrote:
>
>> Hi again.
>>
>> I understand, but could you please help me get in contact with the person
>> who knows something about the windows build (if any), I think there is
>> something wrong.
>>
>> I have been investigating the build problems I had and found that in the
>> sub folder "SimpleRTK-build" there is a solutions file with SimpleRTK. I
>> opened it up and found the projects which I had problems building:
>> "SimpleRTKCommon", "SimpleRTKBasicFilters0", "SimpleRTKBasicFilters1" etc.
>>
>> When I then tried to build SimpleRTKCommon manually it just compiled
>> without any problems. However, when I followed up by building
>> "SimpleRTKBasicFilters0" it gave me an error which stated that it couldn't
>> find "SimpleRTKCommon-0.9.lib" - which I just build.
>>
>> After some more investigation I realized that the SimpleRTKCommon is set
>> to build a dynamic linked library (DLL), and SimpleRTKBasicFilters0 expects
>> it to be a static linked library (LIB). After changing SimpleRTKCommon to
>> be build as a static library - and changing the output location - I could
>> build SimpleRTKBasicFilters0.
>>
>> However, SimpleRTKBasicFilters0 is also build as an DLL, but changing
>> that to a LIB as well I could build SimpleRTKBasicFilters1, then
>> SimpleRTKBasicFilters2 and then SimpleRTKBasicFilters3. You get the point.
>>
>> I'm unsure if the intention is to build them as static or dynamic
>> libraries, but in any case the current build configuration doesn't work -
>> on my setup at least.
>>
>> However, I should note than for some reason the "lua5" project did build
>> successfully out of the box. Whatever it does differently works.
>>
>> best
>>
>> Arvid
>>
>>
>>
>> On Tue, Sep 20, 2016 at 7:33 AM, Simon Rit <simon.rit at creatis.insa-lyon.f
>> r> wrote:
>>
>>> I'm not an msvc specialist but your first line suggests that you have
>>> pasted only part of the log:
>>>
>>> 20>  Done Building Project "C:\Users\aplb\Work\RTK\RTK1.2
>>> -bin-vs13\SimpleRTK-build\ALL_BUILD.vcxproj" (default targets) --
>>> FAILED.
>>> What you need to find out is why this build failed. If the build fails,
>>> the linking cannot work.
>>> Cheers,
>>> Simon
>>>
>>>
>>> On 19/09/2016 19:44, Arvid Piehl Lauritsen B?ttiger wrote:
>>>
>>> I did a complete rebuild, and here is the end of the output:
>>> http://pastebin.com/hvQ33WWg
>>>
>>> I have to admit I'm not sure what to make of it. I should note that I'm
>>> trying to compile the version I just pulled from git earlier today, since
>>> the other version I normally work with is really old.
>>>
>>> best
>>>
>>> Arvid
>>>
>>> On Mon, Sep 19, 2016 at 6:50 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> SimpleRTKCommon is a library generated when compiling. Don't you have
>>>> another error before that which explains why it did not compile?
>>>> Simon
>>>>
>>>> On Mon, Sep 19, 2016 at 2:30 PM, Arvid Piehl Lauritsen B?ttiger <
>>>> bottiger at gmail.com> wrote:
>>>>
>>>>> Hi again.
>>>>>
>>>>> I've been trying to get it working. However, I did run into some
>>>>> problems compiling SimpleRTK. The main issue seems to be that it depends on
>>>>> SimpleRTKCommon - which I do not have.
>>>>>
>>>>> Here is the last few lines from VS2013
>>>>>
>>>>> > 5>LINK : fatal error LNK1181: cannot open input file
>>>>> '..\..\..\lib\Debug\SimpleRTKCommon-0.9.lib'
>>>>> [C:\Users\aplb\Work\RTK\RTK1.2-
>>>>> > bin-vs13\SimpleRTK-build\Code\IO\src\SimpleRTKIO.vcxproj]
>>>>> > 5>
>>>>> > 5>      0 Warning(s)
>>>>> > 5>      2 Error(s)
>>>>> > 5>
>>>>> > 5>  Time Elapsed 00:00:25.26
>>>>> > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped
>>>>> ==========
>>>>>
>>>>> I'm not quite sure what is going on, because the only reference I can
>>>>> find to SimpleRTKCommon is the CMakeLists.txt on github:
>>>>> https://github.com/SimonRit/RTK/blob/master/utilities/Simple
>>>>> RTK/CMakeLists.txt
>>>>>
>>>>> best
>>>>>
>>>>> Arvid
>>>>>
>>>>> On Mon, Sep 19, 2016 at 11:19 AM, Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> The latest MacOS. It's nice if you can test it on other platforms,
>>>>>> I'll try to run it on Linux but I have to upgrade matlab first (I think
>>>>>> python calls are available starting with Matlab 2014).
>>>>>> Simon
>>>>>>
>>>>>> On Mon, Sep 19, 2016 at 11:14 AM, Arvid Piehl Lauritsen B?ttiger <
>>>>>> bottiger at gmail.com> wrote:
>>>>>>
>>>>>>> Dear Simon
>>>>>>>
>>>>>>> This look very interesting! Which platform did you successfully
>>>>>>> execute this on?
>>>>>>> I will give it a try at once (on windows) and let you know if I run
>>>>>>> into any problems.
>>>>>>>
>>>>>>> best
>>>>>>>
>>>>>>> Arvid
>>>>>>>
>>>>>>> On Mon, Sep 19, 2016 at 11:05 AM, Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Dear RTK users,
>>>>>>>> I have quickly tested calling the SimpleRTK python lib from Matlab
>>>>>>>> and it seems to work well:
>>>>>>>> http://wiki.openrtk.org/index.php/SimpleRTK#Matlab
>>>>>>>> Therefore, I don't think we have to work on Matlab wrappings but
>>>>>>>> let us know if you think otherwise.
>>>>>>>> Future works include a simple installation mechanism for
>>>>>>>> pre-compiled SimpleRTK libraries. We'll keep you posted!
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
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From ajbatkinson at gmail.com  Wed Sep 28 08:11:12 2016
From: ajbatkinson at gmail.com (Abby Bryce Atkinson)
Date: Wed, 28 Sep 2016 13:11:12 +0100
Subject: [Rtk-users] 4DROOSTERReconstruction Example
Message-ID: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>

Hi,

I am trying to work through the 4DROOSTER example using the POPI patient
images (
http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) but
I am getting stuck when extracting the respiratory signal using the
amsterdam shroud.

I receive this error:


C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
--path .\Projections\ ^
More?                    --regexp '.*.his' ^
More?                    --output shroud.mha ^
More?                    --unsharp 650
ExceptionObject caught with writer->Update() in file
C:\RTK\applications\rtkamst
erdamshroud\rtkamsterdamshroud.cxx line 91

itk::ExceptionObject (0030E9E0)
Location: "void __thiscall itk::ImageFileWriter<class itk::Image<double,2>
>::Wr
ite(void)"
File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
Line: 284
Description: itk::ERROR: ImageFileWriter(03670318): Largest possible region
does
 not fully contain requested paste IO regionPaste IO region: ImageIORegion
(0030
EDD4)
  Dimension: 2
  Index: 0 0
  Size: 0 0
Largest possible region: ImageRegion (0030EE70)
  Dimension: 2
  Index: [0, 0]
  Size: [0, 0]


Can anyone help with a solution/tell me what I am doing wrong please?

Thanks,

Abby
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From simon.rit at creatis.insa-lyon.fr  Wed Sep 28 12:49:32 2016
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 28 Sep 2016 18:49:32 +0200
Subject: [Rtk-users] 4DROOSTERReconstruction Example
In-Reply-To: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
References: <CAByUD3urmt6bGrAm-nVc3y07UoSetDYG7U4KoSs3hqkOeaTJLQ@mail.gmail.com>
Message-ID: <e23fc5ec-f7b4-846c-e349-f07564e2da8a@creatis.insa-lyon.fr>

Hi,

My guess is that the software does not find the projections. I would add 
the --verbose option and check that you actually input some projections. 
If not, I guess there is an issue with the path or the regexp in your 
command line.

Simon

On 28/09/2016 14:11, Abby Bryce Atkinson wrote:
> Hi,
>
> I am trying to work through the 4DROOSTER example using the POPI 
> patient images 
> (http://wiki.openrtk.org/index.php/RTK/Examples/4DROOSTERReconstruction) 
> but I am getting stuck when extracting the respiratory signal using 
> the amsterdam shroud.
>
> I receive this error:
>
>
> C:\ReconstructionRTK\4DROOSTERReconstruction>rtkamsterdamshroud
> --path .\Projections\ ^
> More?                    --regexp '.*.his' ^
> More?                    --output shroud.mha ^
> More?                    --unsharp 650
> ExceptionObject caught with writer->Update() in file 
> C:\RTK\applications\rtkamst
> erdamshroud\rtkamsterdamshroud.cxx line 91
>
> itk::ExceptionObject (0030E9E0)
> Location: "void __thiscall itk::ImageFileWriter<class 
> itk::Image<double,2> >::Wr
> ite(void)"
> File: c:\itk\modules\io\imagebase\include\itkImageFileWriter.hxx
> Line: 284
> Description: itk::ERROR: ImageFileWriter(03670318): Largest possible 
> region does
>  not fully contain requested paste IO regionPaste IO region: 
> ImageIORegion (0030
> EDD4)
>   Dimension: 2
>   Index: 0 0
>   Size: 0 0
> Largest possible region: ImageRegion (0030EE70)
>   Dimension: 2
>   Index: [0, 0]
>   Size: [0, 0]
>
>
> Can anyone help with a solution/tell me what I am doing wrong please?
>
> Thanks,
>
> Abby
>
>
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> Rtk-users at public.kitware.com
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