From henrydaviscope at gmail.com  Wed Apr  1 13:53:15 2020
From: henrydaviscope at gmail.com (Henry Cope)
Date: Wed, 1 Apr 2020 13:53:15 -0400
Subject: [Rtk-users] Converting 3D Image to 2d image
Message-ID: <CAG9ZuF8FzwWOiD+e2wO6Gzy=4gBEpx+u8Mhh39MgSusYK2wN9w@mail.gmail.com>

Good Afternoon,

I'm currently trying to create a program to read a given 3D image, perform
one forward projection from a varying rotation (Only one slice is made),
convert that to a 2D image and write it to a PNG file. I've modified the
base rtkforwardprojection.cxx program by adding code from
ImageReadExtractWrite.cxx to convert to a 2d image. However, when I attempt
to output to a PNG file, I receive the error:

Description:  Could not create IO object for writing file projectedImage.png
  Tried to create one of the following:
DCMImagXImageIO
    GDCMImageIO
    HisImageIO
    HncImageIO
    HndImageIO
    ImagXImageIO
    MetaImageIO
    OraImageIO
    TIFFImageIO
    XRadImageIO
    XimImageIO
You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

When I look on the ITK wiki, it states that png is a supported file type,
so I'm wondering what I'm doing wrong

Henry
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200401/53655587/attachment.html>

From simon.rit at creatis.insa-lyon.fr  Wed Apr  1 17:57:37 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 1 Apr 2020 23:57:37 +0200
Subject: [Rtk-users] Converting 3D Image to 2d image
In-Reply-To: <CAG9ZuF8FzwWOiD+e2wO6Gzy=4gBEpx+u8Mhh39MgSusYK2wN9w@mail.gmail.com>
References: <CAG9ZuF8FzwWOiD+e2wO6Gzy=4gBEpx+u8Mhh39MgSusYK2wN9w@mail.gmail.com>
Message-ID: <CAF0oig3ioWMJ8-=Xqy+Pu_s+TAPSGPHLZx2pi-nTEDkDbdVYpQ@mail.gmail.com>

Hi,
Yes, it should. Have you built the default ITK modules? If yes, I'm not
sure what's going on but you can ask on itk discourse
<http://discourse.itk.org/>.
Simon

On Wed, Apr 1, 2020 at 7:53 PM Henry Cope <henrydaviscope at gmail.com> wrote:

> Good Afternoon,
>
> I'm currently trying to create a program to read a given 3D image, perform
> one forward projection from a varying rotation (Only one slice is made),
> convert that to a 2D image and write it to a PNG file. I've modified the
> base rtkforwardprojection.cxx program by adding code from
> ImageReadExtractWrite.cxx to convert to a 2d image. However, when I
> attempt to output to a PNG file, I receive the error:
>
> Description:  Could not create IO object for writing file
> projectedImage.png
>   Tried to create one of the following:
> DCMImagXImageIO
>     GDCMImageIO
>     HisImageIO
>     HncImageIO
>     HndImageIO
>     ImagXImageIO
>     MetaImageIO
>     OraImageIO
>     TIFFImageIO
>     XRadImageIO
>     XimImageIO
> You probably failed to set a file suffix, or
>     set the suffix to an unsupported type.
>
> When I look on the ITK wiki, it states that png is a supported file type,
> so I'm wondering what I'm doing wrong
>
> Henry
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200401/5ad6b668/attachment.html>

From henrydaviscope at gmail.com  Thu Apr  2 11:04:48 2020
From: henrydaviscope at gmail.com (Henry Cope)
Date: Thu, 2 Apr 2020 11:04:48 -0400
Subject: [Rtk-users] Converting 3D Image to 2d image
In-Reply-To: <CAF0oig3ioWMJ8-=Xqy+Pu_s+TAPSGPHLZx2pi-nTEDkDbdVYpQ@mail.gmail.com>
References: <CAG9ZuF8FzwWOiD+e2wO6Gzy=4gBEpx+u8Mhh39MgSusYK2wN9w@mail.gmail.com>
 <CAF0oig3ioWMJ8-=Xqy+Pu_s+TAPSGPHLZx2pi-nTEDkDbdVYpQ@mail.gmail.com>
Message-ID: <CAG9ZuF_6R_48KenekVkM7nEKB5wjoEwij6HbJQxdCHHimCsN5Q@mail.gmail.com>

Hello Simon,

Yes, I just build the ITK modules and the problem still persists. I'll go
post my question to ITK discourse.

Henry

On Wed, Apr 1, 2020 at 5:55 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Yes, it should. Have you built the default ITK modules? If yes, I'm not
> sure what's going on but you can ask on itk discourse
> <http://discourse.itk.org/>.
> Simon
>
> On Wed, Apr 1, 2020 at 7:53 PM Henry Cope <henrydaviscope at gmail.com>
> wrote:
>
>> Good Afternoon,
>>
>> I'm currently trying to create a program to read a given 3D image,
>> perform one forward projection from a varying rotation (Only one slice is
>> made), convert that to a 2D image and write it to a PNG file. I've modified
>> the base rtkforwardprojection.cxx program by adding code from
>> ImageReadExtractWrite.cxx to convert to a 2d image. However, when I
>> attempt to output to a PNG file, I receive the error:
>>
>> Description:  Could not create IO object for writing file
>> projectedImage.png
>>   Tried to create one of the following:
>> DCMImagXImageIO
>>     GDCMImageIO
>>     HisImageIO
>>     HncImageIO
>>     HndImageIO
>>     ImagXImageIO
>>     MetaImageIO
>>     OraImageIO
>>     TIFFImageIO
>>     XRadImageIO
>>     XimImageIO
>> You probably failed to set a file suffix, or
>>     set the suffix to an unsupported type.
>>
>> When I look on the ITK wiki, it states that png is a supported file type,
>> so I'm wondering what I'm doing wrong
>>
>> Henry
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200402/5b2d8160/attachment.html>

From henrydaviscope at gmail.com  Tue Apr  7 14:42:57 2020
From: henrydaviscope at gmail.com (Henry Cope)
Date: Tue, 7 Apr 2020 14:42:57 -0400
Subject: [Rtk-users] 3D CT scan to 2D DRR
Message-ID: <CAG9ZuF_dLFUD6LmSoSkuODRQxPdF7u51=cC7BDm2U0wRO=FbOA@mail.gmail.com>

Hello,

I'm working on a project to turn a 3D CT scan into a 2D DRR. I'm starting
with the rtk forward projection, and then adding things like simulated
geometry and a slice extraction filter to it. Currently, all I get as my
DRR output is a black PNG. I'm not sure where I'm going wrong.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200407/f1267e65/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: DRRprojection.cxx
Type: application/octet-stream
Size: 4914 bytes
Desc: not available
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200407/f1267e65/attachment.obj>

From simon.rit at creatis.insa-lyon.fr  Tue Apr  7 16:58:21 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 7 Apr 2020 22:58:21 +0200
Subject: [Rtk-users] 3D CT scan to 2D DRR
In-Reply-To: <CAG9ZuF_dLFUD6LmSoSkuODRQxPdF7u51=cC7BDm2U0wRO=FbOA@mail.gmail.com>
References: <CAG9ZuF_dLFUD6LmSoSkuODRQxPdF7u51=cC7BDm2U0wRO=FbOA@mail.gmail.com>
Message-ID: <CAF0oig1D+a5b4B8ckoHa3-=Yd-O62XGeT9B7Gm++XCB63_-6AA@mail.gmail.com>

Hi,
There can be two reasons:
- you are working with unsigned short as input and output. This is tricky
because you must be sure that your pixel values will cover the range
between 0 and 255. For example, if your phantom has values between 0 and 1,
conversion to unsigned short will blank it. I would start with float pixel
type at first to be sure that this is not the problem. You can use tif
instead of png since it supports float.
- the geometry must be such that your source and detector rotate around
your image. The center of rotation is the point (0,0,0) (in distance unit).
Check that this point is indeed in your input target.mhd image. There is a
documentation for the geometry here
<http://www.openrtk.org/Doxygen/DocGeo3D.html>.
If you don't succeed, please provide the target.mhd (without raw) and we
can check what's going on.
Simon

On Tue, Apr 7, 2020 at 8:43 PM Henry Cope <henrydaviscope at gmail.com> wrote:

> Hello,
>
> I'm working on a project to turn a 3D CT scan into a 2D DRR. I'm starting
> with the rtk forward projection, and then adding things like simulated
> geometry and a slice extraction filter to it. Currently, all I get as my
> DRR output is a black PNG. I'm not sure where I'm going wrong.
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200407/56be56e9/attachment.html>

From henrydaviscope at gmail.com  Tue Apr  7 17:29:58 2020
From: henrydaviscope at gmail.com (Henry Cope)
Date: Tue, 7 Apr 2020 17:29:58 -0400
Subject: [Rtk-users] 3D CT scan to 2D DRR
In-Reply-To: <CAF0oig1D+a5b4B8ckoHa3-=Yd-O62XGeT9B7Gm++XCB63_-6AA@mail.gmail.com>
References: <CAG9ZuF_dLFUD6LmSoSkuODRQxPdF7u51=cC7BDm2U0wRO=FbOA@mail.gmail.com>
 <CAF0oig1D+a5b4B8ckoHa3-=Yd-O62XGeT9B7Gm++XCB63_-6AA@mail.gmail.com>
Message-ID: <CAG9ZuF-GgquH_OKJxDcU4Ut_f1j6E_0Oetwf1Km_KPvBR7zvCQ@mail.gmail.com>

Good Evening Simon,

Thank you, I changed InputPixelType to Float and everything worked.

Henry

On Tue, Apr 7, 2020 at 4:56 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> There can be two reasons:
> - you are working with unsigned short as input and output. This is tricky
> because you must be sure that your pixel values will cover the range
> between 0 and 255. For example, if your phantom has values between 0 and 1,
> conversion to unsigned short will blank it. I would start with float pixel
> type at first to be sure that this is not the problem. You can use tif
> instead of png since it supports float.
> - the geometry must be such that your source and detector rotate around
> your image. The center of rotation is the point (0,0,0) (in distance unit).
> Check that this point is indeed in your input target.mhd image. There is a
> documentation for the geometry here
> <http://www.openrtk.org/Doxygen/DocGeo3D.html>.
> If you don't succeed, please provide the target.mhd (without raw) and we
> can check what's going on.
> Simon
>
> On Tue, Apr 7, 2020 at 8:43 PM Henry Cope <henrydaviscope at gmail.com>
> wrote:
>
>> Hello,
>>
>> I'm working on a project to turn a 3D CT scan into a 2D DRR. I'm starting
>> with the rtk forward projection, and then adding things like simulated
>> geometry and a slice extraction filter to it. Currently, all I get as my
>> DRR output is a black PNG. I'm not sure where I'm going wrong.
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200407/71c8e02f/attachment.html>

From simon.rit at creatis.insa-lyon.fr  Wed Apr  8 11:59:33 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 8 Apr 2020 17:59:33 +0200
Subject: [Rtk-users] 3D CT scan to 2D DRR
In-Reply-To: <CAG9ZuF-Ep5PRTdFgdW2ysbKpCDryn6M8-ptjEjoSU=EGefTidg@mail.gmail.com>
References: <CAG9ZuF_dLFUD6LmSoSkuODRQxPdF7u51=cC7BDm2U0wRO=FbOA@mail.gmail.com>
 <CAF0oig1D+a5b4B8ckoHa3-=Yd-O62XGeT9B7Gm++XCB63_-6AA@mail.gmail.com>
 <CAG9ZuF-GgquH_OKJxDcU4Ut_f1j6E_0Oetwf1Km_KPvBR7zvCQ@mail.gmail.com>
 <CAG9ZuF-FRbqQ=BO0Y7RNcPuk_+W9e1ofpf2v_4YNMM53h1vnHQ@mail.gmail.com>
 <CAF0oig1NhCh9c44Er80vMGaWkYv-_Ok2g3hQLYxfxzRJNS2oeQ@mail.gmail.com>
 <CAG9ZuF-6X+NeOw58jQAg7WJaWuwPGyEk9sveqQ_mgUzGTPDb7A@mail.gmail.com>
 <CAF0oig1afpHZPiXyM6TG7Ah8XYug24580=hOuhnyfMG5zUr8uQ@mail.gmail.com>
 <CAG9ZuF-Ep5PRTdFgdW2ysbKpCDryn6M8-ptjEjoSU=EGefTidg@mail.gmail.com>
Message-ID: <CAF0oig3Z2yqUbafngHJyCXQsGWYG77Gcd+2nQh+i8teMNDaEng@mail.gmail.com>

Great!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200408/e5b50665/attachment.html>

From vl at xris.eu  Wed Apr 15 12:21:59 2020
From: vl at xris.eu (vincent)
Date: Wed, 15 Apr 2020 18:21:59 +0200
Subject: [Rtk-users] Rotation before and during rktprojections
Message-ID: <b3c31f1b-0a7c-67da-d8b2-b63f3fb5a5b6@xris.eu>

Hi RTK community,

I hope everyone is doing well in those hard times.

I have a panel that is rotated by 90? on the CT system.? I used to 
rotate the images back in the right orientation before building the 
sinogram with rtkprojections, but then I thought I might give a try at 
the "newdirection" option.? Using the matrix [0 1 0 ; 1 0 0 ; 0 0 1] 
gives the expected results.? So far so good. But when I try to 
reconstruct the latter with the same geometric parameters than for the 
pre-rotated projections, I obtain a very blurry result (vs a sharp one 
in the first case).? I am obviously missing something, and I would 
suspect I am not giving the right information to the rtkfdk 
application.? So far, here is what I have tried:

-keep the projections in the initial orientation, but give the 
"newdirection" option to the rtkfdk application,

-specify the "newdirection" in both rtkprojections and rtkfdk,

-turn to you for advice !

I thank you very much in advance for any help you might be able to give.

Best regards,

Vincent


From simon.rit at creatis.insa-lyon.fr  Wed Apr 15 14:13:35 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 15 Apr 2020 20:13:35 +0200
Subject: [Rtk-users] Rotation before and during rktprojections
In-Reply-To: <b3c31f1b-0a7c-67da-d8b2-b63f3fb5a5b6@xris.eu>
References: <b3c31f1b-0a7c-67da-d8b2-b63f3fb5a5b6@xris.eu>
Message-ID: <CAF0oig1H=yihYbGNKCLxjJPx0GtCXH5sW-9GzQiSbROos50Bhg@mail.gmail.com>

Hi Vincent,
Everything you did is correct but rtkfdk always applies the ramp filter
along the first dimension and does not check if this corresponds to the
direction orthogonal to the rotation axis. For your case, it is probably
not so difficult to adapt the code. When there is a small rotation, it is
debatable whether one should ignore the rotation for the ramp filter,
resample the image, or recalculate the filter in 2D (see our recent
publication here <https://doi.org/10.1088/1361-6560/ab7875> which has not
been implemented in RTK). I have opened an issue on github
<https://github.com/SimonRit/RTK/issues/335>, hopefully we'll find time to
fix this in the future (at least raise an exception above a parametrable
rotation threshold).
Best regards,
Simon

On Wed, Apr 15, 2020 at 7:00 PM vincent <vl at xris.eu> wrote:

> Hi RTK community,
>
> I hope everyone is doing well in those hard times.
>
> I have a panel that is rotated by 90? on the CT system.  I used to
> rotate the images back in the right orientation before building the
> sinogram with rtkprojections, but then I thought I might give a try at
> the "newdirection" option.  Using the matrix [0 1 0 ; 1 0 0 ; 0 0 1]
> gives the expected results.  So far so good. But when I try to
> reconstruct the latter with the same geometric parameters than for the
> pre-rotated projections, I obtain a very blurry result (vs a sharp one
> in the first case).  I am obviously missing something, and I would
> suspect I am not giving the right information to the rtkfdk
> application.  So far, here is what I have tried:
>
> -keep the projections in the initial orientation, but give the
> "newdirection" option to the rtkfdk application,
>
> -specify the "newdirection" in both rtkprojections and rtkfdk,
>
> -turn to you for advice !
>
> I thank you very much in advance for any help you might be able to give.
>
> Best regards,
>
> Vincent
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200415/bdbf0654/attachment.html>

From henrydaviscope at gmail.com  Wed Apr 15 17:15:25 2020
From: henrydaviscope at gmail.com (Henry Cope)
Date: Wed, 15 Apr 2020 17:15:25 -0400
Subject: [Rtk-users] fatal error LNK1104 and C1083
Message-ID: <CAG9ZuF-7Yk0jfN-ut19dHGf8+54naOY4VViUy5BO3JRwDaj+Xw@mail.gmail.com>

I'm unsure if this is an ITK or RTK forum question so I've posted it to
both.
I'm attempting to build ITK with the RTK module selected. I am attempting
this on Windows, with RTK 2.1.0 and ITK 5.1.0. I was able to successfully
build ITK without the RTK module. I was also able to successfully build RTK
as an external library.
When I attempt to build ITK with the RTK module selected with either
Release x64 or Build x64, I am met with these errors:

fatal error C1083: Cannot open include file: 'gdcmImageReader.h' : No such
file or directory
fatal error C1083: Cannot open include file: 'gdcmAttribute.h' : No such
file or directory
fatal error C1083: Cannot open include file: 'gdcmDataSet.h' : No such file
or directory
LINK: fatal error LNK1181: cannot open input file:
'../../../../lib/Release/itkRTK-5.1.lib'
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200415/cc7e75b6/attachment.html>

From simon.rit at creatis.insa-lyon.fr  Wed Apr 15 17:20:40 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 15 Apr 2020 23:20:40 +0200
Subject: [Rtk-users] fatal error LNK1104 and C1083
In-Reply-To: <CAG9ZuF-7Yk0jfN-ut19dHGf8+54naOY4VViUy5BO3JRwDaj+Xw@mail.gmail.com>
References: <CAG9ZuF-7Yk0jfN-ut19dHGf8+54naOY4VViUy5BO3JRwDaj+Xw@mail.gmail.com>
Message-ID: <CAF0oig0LtpVCY4Sm607UmvkM7=TOn0M=rB6c2WQGZ1xD84uduA@mail.gmail.com>

Hi,
So ITK 5.1 has not been released yet. It seems that you're using the HEAD
of the master branch? Because this has been fixed today (I hope), it's a
change from ITK impacting RTK:
https://github.com/SimonRit/RTK/commit/957d049eff68011723e9c6ff0e63fc404343f8fb
Simon

On Wed, Apr 15, 2020 at 11:15 PM Henry Cope <henrydaviscope at gmail.com>
wrote:

> I'm unsure if this is an ITK or RTK forum question so I've posted it to
> both.
> I'm attempting to build ITK with the RTK module selected. I am attempting
> this on Windows, with RTK 2.1.0 and ITK 5.1.0. I was able to successfully
> build ITK without the RTK module. I was also able to successfully build RTK
> as an external library.
> When I attempt to build ITK with the RTK module selected with either
> Release x64 or Build x64, I am met with these errors:
>
> fatal error C1083: Cannot open include file: 'gdcmImageReader.h' : No such
> file or directory
> fatal error C1083: Cannot open include file: 'gdcmAttribute.h' : No such
> file or directory
> fatal error C1083: Cannot open include file: 'gdcmDataSet.h' : No such
> file or directory
> LINK: fatal error LNK1181: cannot open input file:
> '../../../../lib/Release/itkRTK-5.1.lib'
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200415/4eb0cf92/attachment.html>

From henrydaviscope at gmail.com  Wed Apr 15 17:29:07 2020
From: henrydaviscope at gmail.com (Henry Cope)
Date: Wed, 15 Apr 2020 17:29:07 -0400
Subject: [Rtk-users] fatal error LNK1104 and C1083
In-Reply-To: <CAF0oig0LtpVCY4Sm607UmvkM7=TOn0M=rB6c2WQGZ1xD84uduA@mail.gmail.com>
References: <CAG9ZuF-7Yk0jfN-ut19dHGf8+54naOY4VViUy5BO3JRwDaj+Xw@mail.gmail.com>
 <CAF0oig0LtpVCY4Sm607UmvkM7=TOn0M=rB6c2WQGZ1xD84uduA@mail.gmail.com>
Message-ID: <CAG9ZuF__WinOqoOCbuN-Wvs5D-+Einj5TT7Ei0zfPMsu8PrcFw@mail.gmail.com>

Simon,

Ah that was a typo, I meant to post 5.0.1., but i'm not even sure that's
the version I'm using.
Yes, I have been cloning from head of the master branch. Should I
just download and use the 5.0.1 stable release from itk.org/download?

Henry

On Wed, Apr 15, 2020 at 5:18 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> So ITK 5.1 has not been released yet. It seems that you're using the HEAD
> of the master branch? Because this has been fixed today (I hope), it's a
> change from ITK impacting RTK:
>
> https://github.com/SimonRit/RTK/commit/957d049eff68011723e9c6ff0e63fc404343f8fb
> Simon
>
> On Wed, Apr 15, 2020 at 11:15 PM Henry Cope <henrydaviscope at gmail.com>
> wrote:
>
>> I'm unsure if this is an ITK or RTK forum question so I've posted it to
>> both.
>> I'm attempting to build ITK with the RTK module selected. I am attempting
>> this on Windows, with RTK 2.1.0 and ITK 5.1.0. I was able to successfully
>> build ITK without the RTK module. I was also able to successfully build RTK
>> as an external library.
>> When I attempt to build ITK with the RTK module selected with either
>> Release x64 or Build x64, I am met with these errors:
>>
>> fatal error C1083: Cannot open include file: 'gdcmImageReader.h' : No
>> such file or directory
>> fatal error C1083: Cannot open include file: 'gdcmAttribute.h' : No such
>> file or directory
>> fatal error C1083: Cannot open include file: 'gdcmDataSet.h' : No such
>> file or directory
>> LINK: fatal error LNK1181: cannot open input file:
>> '../../../../lib/Release/itkRTK-5.1.lib'
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200415/8bef52c6/attachment-0001.html>

From simon.rit at creatis.insa-lyon.fr  Wed Apr 15 17:53:15 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 15 Apr 2020 23:53:15 +0200
Subject: [Rtk-users] fatal error LNK1104 and C1083
In-Reply-To: <CAG9ZuF__WinOqoOCbuN-Wvs5D-+Einj5TT7Ei0zfPMsu8PrcFw@mail.gmail.com>
References: <CAG9ZuF-7Yk0jfN-ut19dHGf8+54naOY4VViUy5BO3JRwDaj+Xw@mail.gmail.com>
 <CAF0oig0LtpVCY4Sm607UmvkM7=TOn0M=rB6c2WQGZ1xD84uduA@mail.gmail.com>
 <CAG9ZuF__WinOqoOCbuN-Wvs5D-+Einj5TT7Ei0zfPMsu8PrcFw@mail.gmail.com>
Message-ID: <CAF0oig31dpnFLrkyrtN2wYgNnrAm7M0yFFNXP_YCBmt5N4Lw1A@mail.gmail.com>

You can now use the master branch of ITK and RTK.

On Wed, Apr 15, 2020, 23:29 Henry Cope <henrydaviscope at gmail.com> wrote:

> Simon,
>
> Ah that was a typo, I meant to post 5.0.1., but i'm not even sure that's
> the version I'm using.
> Yes, I have been cloning from head of the master branch. Should I
> just download and use the 5.0.1 stable release from itk.org/download?
>
> Henry
>
> On Wed, Apr 15, 2020 at 5:18 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
>
>> Hi,
>> So ITK 5.1 has not been released yet. It seems that you're using the HEAD
>> of the master branch? Because this has been fixed today (I hope), it's a
>> change from ITK impacting RTK:
>>
>> https://github.com/SimonRit/RTK/commit/957d049eff68011723e9c6ff0e63fc404343f8fb
>> Simon
>>
>> On Wed, Apr 15, 2020 at 11:15 PM Henry Cope <henrydaviscope at gmail.com>
>> wrote:
>>
>>> I'm unsure if this is an ITK or RTK forum question so I've posted it to
>>> both.
>>> I'm attempting to build ITK with the RTK module selected. I am
>>> attempting this on Windows, with RTK 2.1.0 and ITK 5.1.0. I was able to
>>> successfully build ITK without the RTK module. I was also able to
>>> successfully build RTK as an external library.
>>> When I attempt to build ITK with the RTK module selected with either
>>> Release x64 or Build x64, I am met with these errors:
>>>
>>> fatal error C1083: Cannot open include file: 'gdcmImageReader.h' : No
>>> such file or directory
>>> fatal error C1083: Cannot open include file: 'gdcmAttribute.h' : No such
>>> file or directory
>>> fatal error C1083: Cannot open include file: 'gdcmDataSet.h' : No such
>>> file or directory
>>> LINK: fatal error LNK1181: cannot open input file:
>>> '../../../../lib/Release/itkRTK-5.1.lib'
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200415/672e62aa/attachment.html>

From vl at xris.eu  Thu Apr 16 03:33:00 2020
From: vl at xris.eu (vincent)
Date: Thu, 16 Apr 2020 09:33:00 +0200
Subject: [Rtk-users] Rotation before and during rktprojections
In-Reply-To: <CAF0oig1H=yihYbGNKCLxjJPx0GtCXH5sW-9GzQiSbROos50Bhg@mail.gmail.com>
References: <b3c31f1b-0a7c-67da-d8b2-b63f3fb5a5b6@xris.eu>
 <CAF0oig1H=yihYbGNKCLxjJPx0GtCXH5sW-9GzQiSbROos50Bhg@mail.gmail.com>
Message-ID: <f041feae-bd61-7194-2176-a63a98d7484a@xris.eu>

Hi Simon,

thank you for your reply !

I'll have a look at the code to try and adapt and let you know if I succeed.

Best regards,

Vincent

On 15.04.20 20:13, Simon Rit wrote:
> Hi Vincent,
> Everything you did is correct but rtkfdk always applies the ramp 
> filter along the first dimension and does not check if this 
> corresponds to the direction orthogonal to the rotation axis. For your 
> case, it is probably not so difficult to adapt the code. When there is 
> a small rotation, it is debatable whether one should ignore the 
> rotation for the ramp filter, resample the image, or recalculate the 
> filter in 2D (see our recent publication here 
> <https://doi.org/10.1088/1361-6560/ab7875> which has not been 
> implemented in RTK). I have opened an issue on github 
> <https://github.com/SimonRit/RTK/issues/335>, hopefully we'll find 
> time to fix this in the future (at least raise an exception above a 
> parametrable rotation threshold).
> Best regards,
> Simon
>
> On Wed, Apr 15, 2020 at 7:00 PM vincent <vl at xris.eu 
> <mailto:vl at xris.eu>> wrote:
>
>     Hi RTK community,
>
>     I hope everyone is doing well in those hard times.
>
>     I have a panel that is rotated by 90? on the CT system.? I used to
>     rotate the images back in the right orientation before building the
>     sinogram with rtkprojections, but then I thought I might give a
>     try at
>     the "newdirection" option.? Using the matrix [0 1 0 ; 1 0 0 ; 0 0 1]
>     gives the expected results.? So far so good. But when I try to
>     reconstruct the latter with the same geometric parameters than for
>     the
>     pre-rotated projections, I obtain a very blurry result (vs a sharp
>     one
>     in the first case).? I am obviously missing something, and I would
>     suspect I am not giving the right information to the rtkfdk
>     application.? So far, here is what I have tried:
>
>     -keep the projections in the initial orientation, but give the
>     "newdirection" option to the rtkfdk application,
>
>     -specify the "newdirection" in both rtkprojections and rtkfdk,
>
>     -turn to you for advice !
>
>     I thank you very much in advance for any help you might be able to
>     give.
>
>     Best regards,
>
>     Vincent
>
>     _______________________________________________
>     Rtk-users mailing list
>     Rtk-users at public.kitware.com <mailto:Rtk-users at public.kitware.com>
>     https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200416/64961c2b/attachment.html>

From isurusuranga.wijesinghe at gmail.com  Sat Apr 18 14:20:55 2020
From: isurusuranga.wijesinghe at gmail.com (Isuru Suranga Wijesinghe)
Date: Sat, 18 Apr 2020 19:20:55 +0100
Subject: [Rtk-users] How to configure beam characteristics such as filtration
Message-ID: <CAMy-KaXAMSrztWFc2f6cNmzToySW5QPDcX3GeVxzFndOAp49OQ@mail.gmail.com>

Hi,

I?m currently working on generating DRR image from 3D CT volumes.
Is there a way to configure beam characteristics such as filtration ?
That is for an example we use a 120kVp beam, and the filtration is given as
16.25mmAl at 120kVp. Does RTK versions has two parameters to keep these two
values (120 kVp and 16.25mmAl)

Thanks and Best Regards,
Isuru
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200418/0961777a/attachment.html>

From simon.rit at creatis.insa-lyon.fr  Mon Apr 20 08:07:21 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 20 Apr 2020 14:07:21 +0200
Subject: [Rtk-users] How to configure beam characteristics such as
 filtration
In-Reply-To: <CAMy-KaXAMSrztWFc2f6cNmzToySW5QPDcX3GeVxzFndOAp49OQ@mail.gmail.com>
References: <CAMy-KaXAMSrztWFc2f6cNmzToySW5QPDcX3GeVxzFndOAp49OQ@mail.gmail.com>
Message-ID: <CAF0oig01tPQt6wfinpNC1gCmZvGQn3RAikRCQXMDQUvoTbsd7g@mail.gmail.com>

Hi,
This is not possible in RTK, the forward projections are just the line
integral of a given voxelized volume. In the Joseph forward projection
<https://github.com/SimonRit/RTK/blob/master/include/rtkJosephForwardProjectionImageFilter.h#L170>,
there is a number of templated functors that can be changed to use a
spectrum. They have been developed for Gate, see here
<https://opengate.readthedocs.io/en/latest/tools_to_interact_with_the_simulation_actors.html#fixed-forced-detection-ct>.
There, you can pass a full source spectrum to compute DRRs.
Simon

On Sat, Apr 18, 2020 at 8:21 PM Isuru Suranga Wijesinghe <
isurusuranga.wijesinghe at gmail.com> wrote:

> Hi,
>
> I?m currently working on generating DRR image from 3D CT volumes.
> Is there a way to configure beam characteristics such as filtration ?
> That is for an example we use a 120kVp beam, and the filtration is given
> as 16.25mmAl at 120kVp. Does RTK versions has two parameters to keep these
> two values (120 kVp and 16.25mmAl)
>
> Thanks and Best Regards,
> Isuru
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200420/2cacb12d/attachment.html>

From isurusuranga.wijesinghe at gmail.com  Mon Apr 20 15:30:52 2020
From: isurusuranga.wijesinghe at gmail.com (Isuru Suranga Wijesinghe)
Date: Mon, 20 Apr 2020 20:30:52 +0100
Subject: [Rtk-users] DRR image generation from 3D CT
Message-ID: <CAMy-KaWv6sT5AtsL8mo_rynMTXqbQbEZ_=peuaJk-=B3nqSA8A@mail.gmail.com>

Hi,

I'm currently looking rtkforwardprojections example [1] to generate DRR
images from 3D-CT volumes. My question is  how can I set custom geometric
configurations as in the sample attached image ?

Can you please help with a relevant example of this. ?

[1]
https://github.com/SimonRit/RTK/blob/b32cffdc6f9d7a432c50023c370ed996a7985b69/applications/rtkforwardprojections/rtkforwardprojections.cxx

Thanks and Best Regards,
Isuru
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200420/cf35c46d/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: xray_config.png
Type: image/png
Size: 151984 bytes
Desc: not available
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200420/cf35c46d/attachment-0001.png>

From simon.rit at creatis.insa-lyon.fr  Mon Apr 20 15:46:57 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 20 Apr 2020 21:46:57 +0200
Subject: [Rtk-users] DRR image generation from 3D CT
In-Reply-To: <CAMy-KaWv6sT5AtsL8mo_rynMTXqbQbEZ_=peuaJk-=B3nqSA8A@mail.gmail.com>
References: <CAMy-KaWv6sT5AtsL8mo_rynMTXqbQbEZ_=peuaJk-=B3nqSA8A@mail.gmail.com>
Message-ID: <CAF0oig0_CpL2vsJSD9NxUy1DOpvEF8_dWUc+A3RC7DKb_zP7sw@mail.gmail.com>

Hi,
Look at the doc on the geometry file
<http://www.openrtk.org/Doxygen/DocGeo3D.html> and rtksimulatedgeometry
<https://github.com/SimonRit/RTK/tree/master/applications/rtksimulatedgeometry>
for creating one file. AddProjection
<http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
takes several parameters. Given your scheme, it should look like
AddProjection(1000, 1536, angle, +/-190 etc)
It looks like an Elekta geometry given the distances, check the example here
<http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction> if
you can get access to the database.
Simon

On Mon, Apr 20, 2020 at 9:31 PM Isuru Suranga Wijesinghe <
isurusuranga.wijesinghe at gmail.com> wrote:

> Hi,
>
> I'm currently looking rtkforwardprojections example [1] to generate DRR
> images from 3D-CT volumes. My question is  how can I set custom geometric
> configurations as in the sample attached image ?
>
> Can you please help with a relevant example of this. ?
>
> [1]
> https://github.com/SimonRit/RTK/blob/b32cffdc6f9d7a432c50023c370ed996a7985b69/applications/rtkforwardprojections/rtkforwardprojections.cxx
>
> Thanks and Best Regards,
> Isuru
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200420/d3b8803f/attachment.html>

From yoonho94.na at gmail.com  Mon Apr 20 23:06:43 2020
From: yoonho94.na at gmail.com (=?UTF-8?B?64KY7Jyk7Zi4?=)
Date: Tue, 21 Apr 2020 12:06:43 +0900
Subject: [Rtk-users] using RTK with python
Message-ID: <CAPZFa=e83TWZxVA8PV36kTtjC6ASsO7yUy=9f1KhFT6GVMo0uQ@mail.gmail.com>

Hi.
I'm a newbie to ITK and RTK.
I'm currently using python not C++

so I installed ITK package and RTK package using

pip install itk
pip install itk-rtk

using ITK seems OK,  but I'm having difficulties with RTK.

When I run the ITK example code, It worked well.
but when I tried to run the FirstReconstruction.py in the github,
error occurrs.

---------------------------------------------------------------------------AttributeError
                           Traceback (most recent call
last)<ipython-input-1-be2ee9c70d3d> in <module>     19 for x in
range(0,numberOfProjections):     20   angle = firstAngle + x *
angularArc / numberOfProjections---> 21
geometry.AddProjection(sid,sdd,angle)     22      23 # Writing the
geometry to disk
> AttributeError: 'rtkFDKConeBeamReconstructionFilterIF3' object has no attribute 'AddProjection'
>
>
How can I fix this problem?

and I have another question.
I want the reconstruct the sinogram image to phantom.

usually what I did was using skimage.transform.iradon().
what should I use in RTK to do Inverse radon transform or Filtered back
projection method?
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200421/4aafc12d/attachment.html>

From yoonho94.na at gmail.com  Tue Apr 21 04:15:11 2020
From: yoonho94.na at gmail.com (=?UTF-8?B?64KY7Jyk7Zi4?=)
Date: Tue, 21 Apr 2020 17:15:11 +0900
Subject: [Rtk-users] using RTK with python
In-Reply-To: <1587455896.8916.8.camel@creatis.insa-lyon.fr>
References: <CAPZFa=e83TWZxVA8PV36kTtjC6ASsO7yUy=9f1KhFT6GVMo0uQ@mail.gmail.com>
 <1587455896.8916.8.camel@creatis.insa-lyon.fr>
Message-ID: <CAPZFa=dKOa1U8DZQDbEZ062sq2Q3uvFOEx8JuG_gV+dpoEg-JA@mail.gmail.com>

Thank you for replying.

I'm pretty sure that I haven't changed anything in the example script.
What I just did is copy and paste and run it.

geometry was defined like this

geometry = rtk.ThreeDCircularProjectionGeometry.New()

and could you explain me how to translate(?) does documents into pythonic
way?
(I don't know much about Clang)

for example, in the link you gave me it says

*rtk::FDKConeBeamReconstructionFilter< TInputImage, TOutputImage,
TFFTPrecision > Class Template Reference  *

I empirically know that in python I have to type something like

*rtk.FDKConeBeamReconstructionFilter[InputImage, OutputImage, FFTPrecision]*

Am I right??

2020? 4? 21? (?) ?? 4:58, Aur?lien Coussat <
aurelien.coussat at creatis.insa-lyon.fr>?? ??:

> Hi,
>
> Your first error is really strange. The "geometry" variable is supposed to
> be typed as rtkThreeDCircularProjectionGeometry (defined line 14), while
> according to your error message it is of type
> rtkFDKConeBeamReconstructionFilter. Are you sure you haven't somehow
> altered the example script?
>
> About your second question, you can use rtkFDKConeBeamReconstructionFilter
> and provide it a parallel geometry. See the documentation for more details
> :
> http://www.openrtk.org/Doxygen/classrtk_1_1FDKConeBeamReconstructionFilter.html
> .
>
> Don't hesitate if something remains unclear!
>
> Aur?lien.
>
> On Tue, 2020-04-21 at 12:06 +0900, ??? wrote:
>
> Hi.
> I'm a newbie to ITK and RTK.
> I'm currently using python not C++
>
> so I installed ITK package and RTK package using
>
> pip install itk
> pip install itk-rtk
>
> using ITK seems OK,  but I'm having difficulties with RTK.
>
> When I run the ITK example code, It worked well.
> but when I tried to run the FirstReconstruction.py in the github,
> error occurrs.
>
> ---------------------------------------------------------------------------AttributeError                            Traceback (most recent call last)<ipython-input-1-be2ee9c70d3d> in <module>     19 for x in range(0,numberOfProjections):     20   angle = firstAngle + x * angularArc / numberOfProjections---> 21   geometry.AddProjection(sid,sdd,angle)     22      23 # Writing the geometry to disk
> AttributeError: 'rtkFDKConeBeamReconstructionFilterIF3' object has no attribute 'AddProjection'
>
>
>
> How can I fix this problem?
>
> and I have another question.
> I want the reconstruct the sinogram image to phantom.
>
> usually what I did was using skimage.transform.iradon().
> what should I use in RTK to do Inverse radon transform or Filtered back
> projection method?
>
>
> _______________________________________________
> Rtk-users mailing listRtk-users at public.kitware.comhttps://public.kitware.com/mailman/listinfo/rtk-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200421/acaaaac7/attachment-0001.html>

From aurelien.coussat at creatis.insa-lyon.fr  Tue Apr 21 04:27:45 2020
From: aurelien.coussat at creatis.insa-lyon.fr (=?ISO-8859-1?Q?Aur=E9lien?= Coussat)
Date: Tue, 21 Apr 2020 10:27:45 +0200
Subject: [Rtk-users] using RTK with python
In-Reply-To: <CAPZFa=dKOa1U8DZQDbEZ062sq2Q3uvFOEx8JuG_gV+dpoEg-JA@mail.gmail.com>
References: <CAPZFa=e83TWZxVA8PV36kTtjC6ASsO7yUy=9f1KhFT6GVMo0uQ@mail.gmail.com>
 <1587455896.8916.8.camel@creatis.insa-lyon.fr>
 <CAPZFa=dKOa1U8DZQDbEZ062sq2Q3uvFOEx8JuG_gV+dpoEg-JA@mail.gmail.com>
Message-ID: <1587457665.8916.16.camel@creatis.insa-lyon.fr>

On Tue, 2020-04-21 at 17:15 +0900, ??? wrote:
> Thank you for replying.
> I'm pretty sure that I haven't changed anything in the example
> script.
> What I just did is copy and paste and run it.

What process did you follow in order to run it? Are you running it from
a shell command line (as in "python FirstReconstruction.py") or from a
Python command line (running "python" then copy-pasting everything) ?
Could you provide the exact steps you followed in order to reproduce
the problem?
> and could you explain me how to translate(?) does documents into
> pythonic way?
> (I don't know much about Clang)
> 
> for example, in the link you gave me it says 
> 
> rtk::FDKConeBeamReconstructionFilter< TInputImage, TOutputImage,
> TFFTPrecision > Class Template Reference  
> 
> 
> I empirically know that in python I have to type something like
> 
> rtk.FDKConeBeamReconstructionFilter[InputImage, OutputImage,
> FFTPrecision]
> 
> 
> Am I right??

Almost, but your intuition is correct! From
rtkFDKConeBeamReconstructionFilter header file (http://www.openrtk.org/
Doxygen/rtkFDKConeBeamReconstructionFilter_8h_source.html), you can see
that default values are already provided for TOutputImage and
TFFTPrecision. From Python's point of view only a single argument is
therefore required (TInputImage). You can see an example of
FDKConeBeamReconstructionFilter starting from the 65th line of
FirstReconstruction.py.
Good luck!
Aur?lien.
> 2020? 4? 21? (?) ?? 4:58, Aur?lien Coussat <aurelien.coussat at creatis.
> insa-lyon.fr>?? ??:
> > Hi,
> > Your first error is really strange. The "geometry" variable is
> > supposed to be typed as rtkThreeDCircularProjectionGeometry
> > (defined line 14), while according to your error message it is of
> > type rtkFDKConeBeamReconstructionFilter. Are you sure you haven't
> > somehow altered the example script?
> > About your second question, you can use
> > rtkFDKConeBeamReconstructionFilter and provide it a parallel
> > geometry. See the documentation for more details : http://www.openr
> > tk.org/Doxygen/classrtk_1_1FDKConeBeamReconstructionFilter.html.
> > Don't hesitate if something remains unclear!
> > Aur?lien.
> > On Tue, 2020-04-21 at 12:06 +0900, ??? wrote:
> > > Hi.I'm a newbie to ITK and RTK.
> > > I'm currently using python not C++
> > > 
> > > 
> > > so I installed ITK package and RTK package using
> > > 
> > > pip install itk
> > > pip install itk-rtk
> > > 
> > > using ITK seems OK,  but I'm having difficulties with RTK.
> > > 
> > > When I run the ITK example code, It worked well. 
> > > but when I tried to run the FirstReconstruction.py in the github,
> > > error occurrs.
> > > 
> > > > -------------------------------------------------------------
> > > > --------------
> > > > AttributeError                            Traceback (most
> > > > recent call last)
> > > > <ipython-input-1-be2ee9c70d3d> in <module>
> > > >      19 for x in range(0,numberOfProjections):
> > > >      20   angle = firstAngle + x * angularArc /
> > > > numberOfProjections
> > > > ---> 21   geometry.AddProjection(sid,sdd,angle)
> > > >      22 
> > > >      23 # Writing the geometry to disk
> > > > 
> > > > AttributeError: 'rtkFDKConeBeamReconstructionFilterIF3' object
> > > > has no attribute 'AddProjection'
> > >  
> > > How can I fix this problem?
> > > 
> > > and I have another question.
> > > I want the reconstruct the sinogram image to phantom.
> > > 
> > > usually what I did was using skimage.transform.iradon().
> > > what should I use in RTK to do Inverse radon transform or
> > > Filtered back projection method?
> > >  
> > > 
> > > _______________________________________________
> > > Rtk-users mailing list
> > > Rtk-users at public.kitware.com
> > > https://public.kitware.com/mailman/listinfo/rtk-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200421/676f69d4/attachment.html>

From aurelien.coussat at creatis.insa-lyon.fr  Tue Apr 21 03:58:16 2020
From: aurelien.coussat at creatis.insa-lyon.fr (=?ISO-8859-1?Q?Aur=E9lien?= Coussat)
Date: Tue, 21 Apr 2020 09:58:16 +0200
Subject: [Rtk-users] using RTK with python
In-Reply-To: <CAPZFa=e83TWZxVA8PV36kTtjC6ASsO7yUy=9f1KhFT6GVMo0uQ@mail.gmail.com>
References: <CAPZFa=e83TWZxVA8PV36kTtjC6ASsO7yUy=9f1KhFT6GVMo0uQ@mail.gmail.com>
Message-ID: <1587455896.8916.8.camel@creatis.insa-lyon.fr>

Hi,
Your first error is really strange. The "geometry" variable is supposed
to be typed as rtkThreeDCircularProjectionGeometry (defined line 14),
while according to your error message it is of type
rtkFDKConeBeamReconstructionFilter. Are you sure you haven't somehow
altered the example script?
About your second question, you can use
rtkFDKConeBeamReconstructionFilter and provide it a parallel geometry.
See the documentation for more details : http://www.openrtk.org/Doxygen
/classrtk_1_1FDKConeBeamReconstructionFilter.html.
Don't hesitate if something remains unclear!
Aur?lien.
On Tue, 2020-04-21 at 12:06 +0900, ??? wrote:
> Hi.I'm a newbie to ITK and RTK.
> I'm currently using python not C++
> 
> 
> so I installed ITK package and RTK package using
> 
> pip install itk
> pip install itk-rtk
> 
> using ITK seems OK,  but I'm having difficulties with RTK.
> 
> When I run the ITK example code, It worked well. 
> but when I tried to run the FirstReconstruction.py in the github,
> error occurrs.
> 
> > -----------------------------------------------------------------
> > ----------
> > AttributeError                            Traceback (most recent
> > call last)
> > <ipython-input-1-be2ee9c70d3d> in <module>
> >      19 for x in range(0,numberOfProjections):
> >      20   angle = firstAngle + x * angularArc / numberOfProjections
> > ---> 21   geometry.AddProjection(sid,sdd,angle)
> >      22 
> >      23 # Writing the geometry to disk
> > 
> > AttributeError: 'rtkFDKConeBeamReconstructionFilterIF3' object has
> > no attribute 'AddProjection'
>  
> How can I fix this problem?
> 
> and I have another question.
> I want the reconstruct the sinogram image to phantom.
> 
> usually what I did was using skimage.transform.iradon().
> what should I use in RTK to do Inverse radon transform or Filtered
> back projection method?
>  
> 
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200421/b1c27046/attachment.html>

From yoonho94.na at gmail.com  Tue Apr 21 04:40:52 2020
From: yoonho94.na at gmail.com (=?UTF-8?B?64KY7Jyk7Zi4?=)
Date: Tue, 21 Apr 2020 17:40:52 +0900
Subject: [Rtk-users] using RTK with python
In-Reply-To: <1587457665.8916.16.camel@creatis.insa-lyon.fr>
References: <CAPZFa=e83TWZxVA8PV36kTtjC6ASsO7yUy=9f1KhFT6GVMo0uQ@mail.gmail.com>
 <1587455896.8916.8.camel@creatis.insa-lyon.fr>
 <CAPZFa=dKOa1U8DZQDbEZ062sq2Q3uvFOEx8JuG_gV+dpoEg-JA@mail.gmail.com>
 <1587457665.8916.16.camel@creatis.insa-lyon.fr>
Message-ID: <CAPZFa=f0XOdkAqxMrQFR4Pwg9MesrW-8roxc+Gwxzp3cS_87nA@mail.gmail.com>

Before I run the script, I installed itk and itk-rtk using pip.
and then I copied and pasted the whole script in FirstReconstruction.py
in a jupyter notebook cell.
Do I need any additional installation to use rtk?

Thank you for your answer of second question.

2020? 4? 21? (?) ?? 5:27, Aur?lien Coussat <
aurelien.coussat at creatis.insa-lyon.fr>?? ??:

> On Tue, 2020-04-21 at 17:15 +0900, ??? wrote:
>
> Thank you for replying.
>
> I'm pretty sure that I haven't changed anything in the example script.
> What I just did is copy and paste and run it.
>
>
> What process did you follow in order to run it? Are you running it from a
> shell command line (as in "python FirstReconstruction.py") or from a Python
> command line (running "python" then copy-pasting everything) ? Could you
> provide the exact steps you followed in order to reproduce the problem?
>
> and could you explain me how to translate(?) does documents into pythonic
> way?
> (I don't know much about Clang)
>
> for example, in the link you gave me it says
>
> *rtk::FDKConeBeamReconstructionFilter< TInputImage, TOutputImage,
> TFFTPrecision > Class Template Reference  *
>
> I empirically know that in python I have to type something like
>
> *rtk.FDKConeBeamReconstructionFilter[InputImage, OutputImage,
> FFTPrecision]*
>
> Am I right??
>
>
> Almost, but your intuition is correct! From
> rtkFDKConeBeamReconstructionFilter header file (
> http://www.openrtk.org/Doxygen/rtkFDKConeBeamReconstructionFilter_8h_source.html),
> you can see that default values are already provided for TOutputImage and
> TFFTPrecision. From Python's point of view only a single argument is
> therefore required (TInputImage). You can see an example of
> FDKConeBeamReconstructionFilter starting from the 65th line of
> FirstReconstruction.py.
>
> Good luck!
>
> Aur?lien.
>
>
> 2020? 4? 21? (?) ?? 4:58, Aur?lien Coussat <
> aurelien.coussat at creatis.insa-lyon.fr>?? ??:
>
> Hi,
>
> Your first error is really strange. The "geometry" variable is supposed to
> be typed as rtkThreeDCircularProjectionGeometry (defined line 14), while
> according to your error message it is of type
> rtkFDKConeBeamReconstructionFilter. Are you sure you haven't somehow
> altered the example script?
>
> About your second question, you can use rtkFDKConeBeamReconstructionFilter
> and provide it a parallel geometry. See the documentation for more details
> :
> http://www.openrtk.org/Doxygen/classrtk_1_1FDKConeBeamReconstructionFilter.html
> .
>
> Don't hesitate if something remains unclear!
>
> Aur?lien.
>
> On Tue, 2020-04-21 at 12:06 +0900, ??? wrote:
>
> Hi.
> I'm a newbie to ITK and RTK.
> I'm currently using python not C++
>
> so I installed ITK package and RTK package using
>
> pip install itk
> pip install itk-rtk
>
> using ITK seems OK,  but I'm having difficulties with RTK.
>
> When I run the ITK example code, It worked well.
> but when I tried to run the FirstReconstruction.py in the github,
> error occurrs.
>
> ---------------------------------------------------------------------------AttributeError                            Traceback (most recent call last)<ipython-input-1-be2ee9c70d3d> in <module>     19 for x in range(0,numberOfProjections):     20   angle = firstAngle + x * angularArc / numberOfProjections---> 21   geometry.AddProjection(sid,sdd,angle)     22      23 # Writing the geometry to disk
> AttributeError: 'rtkFDKConeBeamReconstructionFilterIF3' object has no attribute 'AddProjection'
>
>
>
> How can I fix this problem?
>
> and I have another question.
> I want the reconstruct the sinogram image to phantom.
>
> usually what I did was using skimage.transform.iradon().
> what should I use in RTK to do Inverse radon transform or Filtered back
> projection method?
>
>
> _______________________________________________
> Rtk-users mailing listRtk-users at public.kitware.comhttps://public.kitware.com/mailman/listinfo/rtk-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200421/415b882f/attachment-0001.html>

From simon.rit at creatis.insa-lyon.fr  Tue Apr 21 09:24:18 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 21 Apr 2020 15:24:18 +0200
Subject: [Rtk-users] using RTK with python
In-Reply-To: <CAPZFa=f0XOdkAqxMrQFR4Pwg9MesrW-8roxc+Gwxzp3cS_87nA@mail.gmail.com>
References: <CAPZFa=e83TWZxVA8PV36kTtjC6ASsO7yUy=9f1KhFT6GVMo0uQ@mail.gmail.com>
 <1587455896.8916.8.camel@creatis.insa-lyon.fr>
 <CAPZFa=dKOa1U8DZQDbEZ062sq2Q3uvFOEx8JuG_gV+dpoEg-JA@mail.gmail.com>
 <1587457665.8916.16.camel@creatis.insa-lyon.fr>
 <CAPZFa=f0XOdkAqxMrQFR4Pwg9MesrW-8roxc+Gwxzp3cS_87nA@mail.gmail.com>
Message-ID: <CAF0oig1r7G-4o0AXdfccFEgovjFfAZS6kCJy477c64PvWj4ktw@mail.gmail.com>

Please share your ipynb jupyter notebook file because I did the test with a
new conda environment right now and it works for me... Thanks,
Simon

On Tue, Apr 21, 2020 at 10:41 AM ??? <yoonho94.na at gmail.com> wrote:

> Before I run the script, I installed itk and itk-rtk using pip.
> and then I copied and pasted the whole script in FirstReconstruction.py
> in a jupyter notebook cell.
> Do I need any additional installation to use rtk?
>
> Thank you for your answer of second question.
>
> 2020? 4? 21? (?) ?? 5:27, Aur?lien Coussat <
> aurelien.coussat at creatis.insa-lyon.fr>?? ??:
>
>> On Tue, 2020-04-21 at 17:15 +0900, ??? wrote:
>>
>> Thank you for replying.
>>
>> I'm pretty sure that I haven't changed anything in the example script.
>> What I just did is copy and paste and run it.
>>
>>
>> What process did you follow in order to run it? Are you running it from a
>> shell command line (as in "python FirstReconstruction.py") or from a Python
>> command line (running "python" then copy-pasting everything) ? Could you
>> provide the exact steps you followed in order to reproduce the problem?
>>
>> and could you explain me how to translate(?) does documents into pythonic
>> way?
>> (I don't know much about Clang)
>>
>> for example, in the link you gave me it says
>>
>> *rtk::FDKConeBeamReconstructionFilter< TInputImage, TOutputImage,
>> TFFTPrecision > Class Template Reference  *
>>
>> I empirically know that in python I have to type something like
>>
>> *rtk.FDKConeBeamReconstructionFilter[InputImage, OutputImage,
>> FFTPrecision]*
>>
>> Am I right??
>>
>>
>> Almost, but your intuition is correct! From
>> rtkFDKConeBeamReconstructionFilter header file (
>> http://www.openrtk.org/Doxygen/rtkFDKConeBeamReconstructionFilter_8h_source.html),
>> you can see that default values are already provided for TOutputImage and
>> TFFTPrecision. From Python's point of view only a single argument is
>> therefore required (TInputImage). You can see an example of
>> FDKConeBeamReconstructionFilter starting from the 65th line of
>> FirstReconstruction.py.
>>
>> Good luck!
>>
>> Aur?lien.
>>
>>
>> 2020? 4? 21? (?) ?? 4:58, Aur?lien Coussat <
>> aurelien.coussat at creatis.insa-lyon.fr>?? ??:
>>
>> Hi,
>>
>> Your first error is really strange. The "geometry" variable is supposed
>> to be typed as rtkThreeDCircularProjectionGeometry (defined line 14), while
>> according to your error message it is of type
>> rtkFDKConeBeamReconstructionFilter. Are you sure you haven't somehow
>> altered the example script?
>>
>> About your second question, you can use
>> rtkFDKConeBeamReconstructionFilter and provide it a parallel geometry. See
>> the documentation for more details :
>> http://www.openrtk.org/Doxygen/classrtk_1_1FDKConeBeamReconstructionFilter.html
>> .
>>
>> Don't hesitate if something remains unclear!
>>
>> Aur?lien.
>>
>> On Tue, 2020-04-21 at 12:06 +0900, ??? wrote:
>>
>> Hi.
>> I'm a newbie to ITK and RTK.
>> I'm currently using python not C++
>>
>> so I installed ITK package and RTK package using
>>
>> pip install itk
>> pip install itk-rtk
>>
>> using ITK seems OK,  but I'm having difficulties with RTK.
>>
>> When I run the ITK example code, It worked well.
>> but when I tried to run the FirstReconstruction.py in the github,
>> error occurrs.
>>
>> ---------------------------------------------------------------------------AttributeError                            Traceback (most recent call last)<ipython-input-1-be2ee9c70d3d> in <module>     19 for x in range(0,numberOfProjections):     20   angle = firstAngle + x * angularArc / numberOfProjections---> 21   geometry.AddProjection(sid,sdd,angle)     22      23 # Writing the geometry to disk
>> AttributeError: 'rtkFDKConeBeamReconstructionFilterIF3' object has no attribute 'AddProjection'
>>
>>
>>
>> How can I fix this problem?
>>
>> and I have another question.
>> I want the reconstruct the sinogram image to phantom.
>>
>> usually what I did was using skimage.transform.iradon().
>> what should I use in RTK to do Inverse radon transform or Filtered back
>> projection method?
>>
>>
>> _______________________________________________
>> Rtk-users mailing listRtk-users at public.kitware.comhttps://public.kitware.com/mailman/listinfo/rtk-users
>>
>> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200421/c8aed092/attachment.html>

From isurusuranga.wijesinghe at gmail.com  Tue Apr 21 11:36:03 2020
From: isurusuranga.wijesinghe at gmail.com (Isuru Suranga Wijesinghe)
Date: Tue, 21 Apr 2020 16:36:03 +0100
Subject: [Rtk-users] DRR image generation from 3D CT
In-Reply-To: <CAF0oig0_CpL2vsJSD9NxUy1DOpvEF8_dWUc+A3RC7DKb_zP7sw@mail.gmail.com>
References: <CAMy-KaWv6sT5AtsL8mo_rynMTXqbQbEZ_=peuaJk-=B3nqSA8A@mail.gmail.com>
 <CAF0oig0_CpL2vsJSD9NxUy1DOpvEF8_dWUc+A3RC7DKb_zP7sw@mail.gmail.com>
Message-ID: <CAMy-KaV5TqhNzHdT8DbkVnAaks1OXd2xptxPenXXTXiCBHtFkg@mail.gmail.com>

Hi,

I have built rtkforwardprojections code. And pass the appropriate
parameters to the generated exe from the command line as below.
But there is nothing in the output location. I have attached herewith my
geomtry.xml as well.

D:/RTK/Build/bin/Release>rtkforwardprojections -g D:/geomtry.xml -i
D:\\Subject_01\\CT\\PhaseImage_01.mha -o D:/_rtk_output.png

On Mon, Apr 20, 2020 at 8:45 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Look at the doc on the geometry file
> <http://www.openrtk.org/Doxygen/DocGeo3D.html> and rtksimulatedgeometry
> <https://github.com/SimonRit/RTK/tree/master/applications/rtksimulatedgeometry>
> for creating one file. AddProjection
> <http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
> takes several parameters. Given your scheme, it should look like
> AddProjection(1000, 1536, angle, +/-190 etc)
> It looks like an Elekta geometry given the distances, check the example
> here <http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction>
> if you can get access to the database.
> Simon
>
> On Mon, Apr 20, 2020 at 9:31 PM Isuru Suranga Wijesinghe <
> isurusuranga.wijesinghe at gmail.com> wrote:
>
>> Hi,
>>
>> I'm currently looking rtkforwardprojections example [1] to generate DRR
>> images from 3D-CT volumes. My question is  how can I set custom geometric
>> configurations as in the sample attached image ?
>>
>> Can you please help with a relevant example of this. ?
>>
>> [1]
>> https://github.com/SimonRit/RTK/blob/b32cffdc6f9d7a432c50023c370ed996a7985b69/applications/rtkforwardprojections/rtkforwardprojections.cxx
>>
>> Thanks and Best Regards,
>> Isuru
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200421/478710bf/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: geomtry.xml
Type: text/xml
Size: 651 bytes
Desc: not available
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200421/478710bf/attachment.xml>

From simon.rit at creatis.insa-lyon.fr  Tue Apr 21 11:45:15 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 21 Apr 2020 17:45:15 +0200
Subject: [Rtk-users] DRR image generation from 3D CT
In-Reply-To: <CAMy-KaV5TqhNzHdT8DbkVnAaks1OXd2xptxPenXXTXiCBHtFkg@mail.gmail.com>
References: <CAMy-KaWv6sT5AtsL8mo_rynMTXqbQbEZ_=peuaJk-=B3nqSA8A@mail.gmail.com>
 <CAF0oig0_CpL2vsJSD9NxUy1DOpvEF8_dWUc+A3RC7DKb_zP7sw@mail.gmail.com>
 <CAMy-KaV5TqhNzHdT8DbkVnAaks1OXd2xptxPenXXTXiCBHtFkg@mail.gmail.com>
Message-ID: <CAF0oig0LL6g=pByeT+ABTAGkHZst9E52FcL9Fxz3ChCS9GswDQ@mail.gmail.com>

Projection is centered on point (0,0,0) mm in your input
(PhaseImage_01.mha) (as described in the doc). Check where this point is in
your input. If it's outside, then you need to modify its origin (in the ITK
sense, check ITK doc).

On Tue, Apr 21, 2020 at 5:36 PM Isuru Suranga Wijesinghe <
isurusuranga.wijesinghe at gmail.com> wrote:

> Hi,
>
> I have built rtkforwardprojections code. And pass the appropriate
> parameters to the generated exe from the command line as below.
> But there is nothing in the output location. I have attached herewith my
> geomtry.xml as well.
>
> D:/RTK/Build/bin/Release>rtkforwardprojections -g D:/geomtry.xml -i
> D:\\Subject_01\\CT\\PhaseImage_01.mha -o D:/_rtk_output.png
>
> On Mon, Apr 20, 2020 at 8:45 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
>
>> Hi,
>> Look at the doc on the geometry file
>> <http://www.openrtk.org/Doxygen/DocGeo3D.html> and rtksimulatedgeometry
>> <https://github.com/SimonRit/RTK/tree/master/applications/rtksimulatedgeometry>
>> for creating one file. AddProjection
>> <http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
>> takes several parameters. Given your scheme, it should look like
>> AddProjection(1000, 1536, angle, +/-190 etc)
>> It looks like an Elekta geometry given the distances, check the example
>> here
>> <http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction> if
>> you can get access to the database.
>> Simon
>>
>> On Mon, Apr 20, 2020 at 9:31 PM Isuru Suranga Wijesinghe <
>> isurusuranga.wijesinghe at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I'm currently looking rtkforwardprojections example [1] to generate DRR
>>> images from 3D-CT volumes. My question is  how can I set custom geometric
>>> configurations as in the sample attached image ?
>>>
>>> Can you please help with a relevant example of this. ?
>>>
>>> [1]
>>> https://github.com/SimonRit/RTK/blob/b32cffdc6f9d7a432c50023c370ed996a7985b69/applications/rtkforwardprojections/rtkforwardprojections.cxx
>>>
>>> Thanks and Best Regards,
>>> Isuru
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200421/8bead471/attachment-0001.html>

From Yannick.Grondin at surgiqual-institute.com  Tue Apr 21 10:53:16 2020
From: Yannick.Grondin at surgiqual-institute.com (Yannick Grondin)
Date: Tue, 21 Apr 2020 16:53:16 +0200
Subject: [Rtk-users] problem with installing RTK and Python
Message-ID: <005801d617ec$9cf85750$d6e905f0$@surgiqual-institute.com>

Hi all,

I have a problem with installing ITK / RTK with Python

 

I have done:

pip install itk

pip install itk-rtk

(Python 3.8, sys 64 bits)

 

I got the following output or error:

 

pip list

Package          Version

---------------- -------

itk              5.0.1

itk-core         5.0.1

itk-filtering    5.0.1

itk-io           5.0.1

itk-numerics     5.0.1

itk-registration 5.0.1

itk-segmentation 5.0.1

numpy            1.18.3

packaging        20.3

pip              20.0.2

pyparsing        2.4.7

scikit-build     0.10.0

setuptools       41.2.0

six              1.14.0

wheel            0.34.2

 

PS C:\WINDOWS\system32> python -m pip install itk-rtk

Collecting itk-rtk

  Using cached itk-rtk-2.0.1.zip (2.1 MB)

    ERROR: Command errored out with exit status 1:

     command: 'C:\Python38-x64\python.exe' -c 'import sys, setuptools,
tokenize; sys.argv[0] =
'"'"'C:\\Users\\myUser\\AppData\\Local\\Temp\\pip-install-9fmwt65s\\itk-rtk\
\setup.py'"'"';
__file__='"'"'C:\\Users\\myUser\\AppData\\Local\\Temp\\pip-install-9fmwt65s\
\itk-rtk\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"',
open)(__file__);code=f.read().replace('"'"'\r\n'"'"',
'"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))'
egg_info --egg-base
'C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-inf
o'

         cwd:
C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\

    Complete output (8 lines):

    running egg_info

    creating
C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info
\itk_rtk.egg-info

    writing
C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info
\itk_rtk.egg-info\PKG-INFO

    writing dependency_links to
C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info
\itk_rtk.egg-info\dependency_links.txt

    writing requirements to
C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info
\itk_rtk.egg-info\requires.txt

    writing top-level names to
C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info
\itk_rtk.egg-info\top_level.txt

    writing manifest file
'C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-inf
o\itk_rtk.egg-info\SOURCES.txt'

    error: package directory 'itk' does not exist

    ----------------------------------------

ERROR: Command errored out with exit status 1: python setup.py egg_info
Check the logs for full command output.

 

Can you see something wrong?

Thanks,

Y

____________________________

 <http://www.surgiqual-institute.com/> SQI_Logo_Mail

Yannick Grondin, PhD

Radiation Physics R&D Engineer

 <http://www.surgiqual-institute.com/> http://www.surgiqual-institute.com/

+33 (0) 4 58 00 38 08

 

 

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200421/495e68b0/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image003.png
Type: image/png
Size: 22222 bytes
Desc: not available
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200421/495e68b0/attachment-0001.png>

From yoonho94.na at gmail.com  Tue Apr 21 22:33:44 2020
From: yoonho94.na at gmail.com (=?UTF-8?B?64KY7Jyk7Zi4?=)
Date: Wed, 22 Apr 2020 11:33:44 +0900
Subject: [Rtk-users] using RTK with python
In-Reply-To: <CAF0oig1r7G-4o0AXdfccFEgovjFfAZS6kCJy477c64PvWj4ktw@mail.gmail.com>
References: <CAPZFa=e83TWZxVA8PV36kTtjC6ASsO7yUy=9f1KhFT6GVMo0uQ@mail.gmail.com>
 <1587455896.8916.8.camel@creatis.insa-lyon.fr>
 <CAPZFa=dKOa1U8DZQDbEZ062sq2Q3uvFOEx8JuG_gV+dpoEg-JA@mail.gmail.com>
 <1587457665.8916.16.camel@creatis.insa-lyon.fr>
 <CAPZFa=f0XOdkAqxMrQFR4Pwg9MesrW-8roxc+Gwxzp3cS_87nA@mail.gmail.com>
 <CAF0oig1r7G-4o0AXdfccFEgovjFfAZS6kCJy477c64PvWj4ktw@mail.gmail.com>
Message-ID: <CAPZFa=cEgH-RFp4QkYh+WmzvNJ8nyL-hRc8v9M==v44QZ0Kz+g@mail.gmail.com>

Here's my jupyter file.

I just found something strange.

I'll send you two files.

they both have same script in it but having different error.

FirstReconstruction.ipynb is exactly same as the one in the github example.

and the other one is same except for the plotting of sinogram data for
practicing itk.

I have no idea why they have different error


2020? 4? 21? (?) ?? 10:22, Simon Rit <simon.rit at creatis.insa-lyon.fr>?? ??:

> Please share your ipynb jupyter notebook file because I did the test with
> a new conda environment right now and it works for me... Thanks,
> Simon
>
> On Tue, Apr 21, 2020 at 10:41 AM ??? <yoonho94.na at gmail.com> wrote:
>
>> Before I run the script, I installed itk and itk-rtk using pip.
>> and then I copied and pasted the whole script in FirstReconstruction.py
>> in a jupyter notebook cell.
>> Do I need any additional installation to use rtk?
>>
>> Thank you for your answer of second question.
>>
>> 2020? 4? 21? (?) ?? 5:27, Aur?lien Coussat <
>> aurelien.coussat at creatis.insa-lyon.fr>?? ??:
>>
>>> On Tue, 2020-04-21 at 17:15 +0900, ??? wrote:
>>>
>>> Thank you for replying.
>>>
>>> I'm pretty sure that I haven't changed anything in the example script.
>>> What I just did is copy and paste and run it.
>>>
>>>
>>> What process did you follow in order to run it? Are you running it from
>>> a shell command line (as in "python FirstReconstruction.py") or from a
>>> Python command line (running "python" then copy-pasting everything) ? Could
>>> you provide the exact steps you followed in order to reproduce the problem?
>>>
>>> and could you explain me how to translate(?) does documents into
>>> pythonic way?
>>> (I don't know much about Clang)
>>>
>>> for example, in the link you gave me it says
>>>
>>> *rtk::FDKConeBeamReconstructionFilter< TInputImage, TOutputImage,
>>> TFFTPrecision > Class Template Reference  *
>>>
>>> I empirically know that in python I have to type something like
>>>
>>> *rtk.FDKConeBeamReconstructionFilter[InputImage, OutputImage,
>>> FFTPrecision]*
>>>
>>> Am I right??
>>>
>>>
>>> Almost, but your intuition is correct! From
>>> rtkFDKConeBeamReconstructionFilter header file (
>>> http://www.openrtk.org/Doxygen/rtkFDKConeBeamReconstructionFilter_8h_source.html),
>>> you can see that default values are already provided for TOutputImage and
>>> TFFTPrecision. From Python's point of view only a single argument is
>>> therefore required (TInputImage). You can see an example of
>>> FDKConeBeamReconstructionFilter starting from the 65th line of
>>> FirstReconstruction.py.
>>>
>>> Good luck!
>>>
>>> Aur?lien.
>>>
>>>
>>> 2020? 4? 21? (?) ?? 4:58, Aur?lien Coussat <
>>> aurelien.coussat at creatis.insa-lyon.fr>?? ??:
>>>
>>> Hi,
>>>
>>> Your first error is really strange. The "geometry" variable is supposed
>>> to be typed as rtkThreeDCircularProjectionGeometry (defined line 14), while
>>> according to your error message it is of type
>>> rtkFDKConeBeamReconstructionFilter. Are you sure you haven't somehow
>>> altered the example script?
>>>
>>> About your second question, you can use
>>> rtkFDKConeBeamReconstructionFilter and provide it a parallel geometry. See
>>> the documentation for more details :
>>> http://www.openrtk.org/Doxygen/classrtk_1_1FDKConeBeamReconstructionFilter.html
>>> .
>>>
>>> Don't hesitate if something remains unclear!
>>>
>>> Aur?lien.
>>>
>>> On Tue, 2020-04-21 at 12:06 +0900, ??? wrote:
>>>
>>> Hi.
>>> I'm a newbie to ITK and RTK.
>>> I'm currently using python not C++
>>>
>>> so I installed ITK package and RTK package using
>>>
>>> pip install itk
>>> pip install itk-rtk
>>>
>>> using ITK seems OK,  but I'm having difficulties with RTK.
>>>
>>> When I run the ITK example code, It worked well.
>>> but when I tried to run the FirstReconstruction.py in the github,
>>> error occurrs.
>>>
>>> ---------------------------------------------------------------------------AttributeError                            Traceback (most recent call last)<ipython-input-1-be2ee9c70d3d> in <module>     19 for x in range(0,numberOfProjections):     20   angle = firstAngle + x * angularArc / numberOfProjections---> 21   geometry.AddProjection(sid,sdd,angle)     22      23 # Writing the geometry to disk
>>> AttributeError: 'rtkFDKConeBeamReconstructionFilterIF3' object has no attribute 'AddProjection'
>>>
>>>
>>>
>>> How can I fix this problem?
>>>
>>> and I have another question.
>>> I want the reconstruct the sinogram image to phantom.
>>>
>>> usually what I did was using skimage.transform.iradon().
>>> what should I use in RTK to do Inverse radon transform or Filtered back
>>> projection method?
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing listRtk-users at public.kitware.comhttps://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200422/bbd076aa/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: FirstReconstruction.ipynb
Type: application/octet-stream
Size: 7216 bytes
Desc: not available
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200422/bbd076aa/attachment-0002.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: RTK.ipynb
Type: application/octet-stream
Size: 29421 bytes
Desc: not available
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200422/bbd076aa/attachment-0003.obj>

From aurelien.coussat at creatis.insa-lyon.fr  Wed Apr 22 03:22:37 2020
From: aurelien.coussat at creatis.insa-lyon.fr (=?ISO-8859-1?Q?Aur=E9lien?= Coussat)
Date: Wed, 22 Apr 2020 09:22:37 +0200
Subject: [Rtk-users] using RTK with python
In-Reply-To: <CAPZFa=cEgH-RFp4QkYh+WmzvNJ8nyL-hRc8v9M==v44QZ0Kz+g@mail.gmail.com>
References: <CAPZFa=e83TWZxVA8PV36kTtjC6ASsO7yUy=9f1KhFT6GVMo0uQ@mail.gmail.com>
 <1587455896.8916.8.camel@creatis.insa-lyon.fr>
 <CAPZFa=dKOa1U8DZQDbEZ062sq2Q3uvFOEx8JuG_gV+dpoEg-JA@mail.gmail.com>
 <1587457665.8916.16.camel@creatis.insa-lyon.fr>
 <CAPZFa=f0XOdkAqxMrQFR4Pwg9MesrW-8roxc+Gwxzp3cS_87nA@mail.gmail.com>
 <CAF0oig1r7G-4o0AXdfccFEgovjFfAZS6kCJy477c64PvWj4ktw@mail.gmail.com>
 <CAPZFa=cEgH-RFp4QkYh+WmzvNJ8nyL-hRc8v9M==v44QZ0Kz+g@mail.gmail.com>
Message-ID: <1587540157.3465.5.camel@creatis.insa-lyon.fr>

Hi!
FirstReconstruction.py is initially meant to be called from the command
line as it expects two command-line arguments (specified on line 7).
When ran from a Jupyter Notebook (as in FirstReconstruction.ipynb), you
need to manually provide values for sys.argv[1] (the output image) and
sys.argv[2] (the geometry). Here, you script tries to write the image
to an undefined place, producing the error.
In RTK.ipynb, you did specify the "geometry" variable as a
rtkFDKConeBeamReconstructionFilter, hence the error. It needs to be of
type rtkThreeDCircularProjectionGeometry.
Hope it helps!
Aur?lien.
On Wed, 2020-04-22 at 11:33 +0900, ??? wrote:
> Here's my jupyter file.
> I just found something strange.
> 
> I'll send you two files.
> 
> they both have same script in it but having different error.
> 
> FirstReconstruction.ipynb is exactly same as the one in the github
> example.
> 
> and the other one is same except for the plotting of sinogram data
> for practicing itk.
> 
> I have no idea why they have different error
> 
> 
> 
> 2020? 4? 21? (?) ?? 10:22, Simon Rit <simon.rit at creatis.insa-lyon.fr>
> ?? ??:
> > Please share your ipynb jupyter notebook file because I did the
> > test with a new conda environment right now and it works for me...
> > Thanks,
> > Simon
> > 
> > On Tue, Apr 21, 2020 at 10:41 AM ??? <yoonho94.na at gmail.com> wrote:
> > > Before I run the script, I installed itk and itk-rtk using
> > > pip.and then I copied
> > > 
> > > and pasted
> > > 
> > >  the whole script in FirstReconstruction.py in a jupyter notebook
> > > cell.
> > > Do I need any additional installation to use rtk?
> > > 
> > > Thank you for your answer of second question.
> > > 
> > > 2020? 4? 21? (?) ?? 5:27, Aur?lien Coussat <aurelien.coussat at crea
> > > tis.insa-lyon.fr>?? ??:
> > > > On Tue, 2020-04-21 at 17:15 +0900, ??? wrote:
> > > > > Thank you for replying.
> > > > > I'm pretty sure that I haven't changed anything in the
> > > > > example script.
> > > > > What I just did is copy and paste and run it.
> > > > 
> > > > What process did you follow in order to run it? Are you running
> > > > it from a shell command line (as in "python
> > > > FirstReconstruction.py") or from a Python command line (running
> > > > "python" then copy-pasting everything) ? Could you provide the
> > > > exact steps you followed in order to reproduce the problem?
> > > > > and could you explain me how to translate(?) does documents
> > > > > into pythonic way?
> > > > > (I don't know much about Clang)
> > > > > 
> > > > > for example, in the link you gave me it says 
> > > > > 
> > > > > rtk::FDKConeBeamReconstructionFilter< TInputImage,
> > > > > TOutputImage, TFFTPrecision > Class Template Reference  
> > > > > 
> > > > > 
> > > > > I empirically know that in python I have to type something
> > > > > like
> > > > > 
> > > > > rtk.FDKConeBeamReconstructionFilter[InputImage, OutputImage,
> > > > > FFTPrecision]
> > > > > 
> > > > > 
> > > > > Am I right??
> > > > 
> > > > Almost, but your intuition is correct! From
> > > > rtkFDKConeBeamReconstructionFilter header file (http://www.open
> > > > rtk.org/Doxygen/rtkFDKConeBeamReconstructionFilter_8h_source.ht
> > > > ml), you can see that default values are already provided for
> > > > TOutputImage and TFFTPrecision. From Python's point of view
> > > > only a single argument is therefore required (TInputImage). You
> > > > can see an example of FDKConeBeamReconstructionFilter starting
> > > > from the 65th line of FirstReconstruction.py.
> > > > Good luck!
> > > > Aur?lien.
> > > > > 2020? 4? 21? (?) ?? 4:58, Aur?lien Coussat <aurelien.coussat@
> > > > > creatis.insa-lyon.fr>?? ??:
> > > > > > Hi,
> > > > > > Your first error is really strange. The "geometry" variable
> > > > > > is supposed to be typed as
> > > > > > rtkThreeDCircularProjectionGeometry (defined line 14),
> > > > > > while according to your error message it is of type
> > > > > > rtkFDKConeBeamReconstructionFilter. Are you sure you
> > > > > > haven't somehow altered the example script?
> > > > > > About your second question, you can use
> > > > > > rtkFDKConeBeamReconstructionFilter and provide it a
> > > > > > parallel geometry. See the documentation for more details :
> > > > > > http://www.openrtk.org/Doxygen/classrtk_1_1FDKConeBeamRecon
> > > > > > structionFilter.html.
> > > > > > Don't hesitate if something remains unclear!
> > > > > > Aur?lien.
> > > > > > On Tue, 2020-04-21 at 12:06 +0900, ??? wrote:
> > > > > > > Hi.I'm a newbie to ITK and RTK.
> > > > > > > I'm currently using python not C++
> > > > > > > 
> > > > > > > 
> > > > > > > so I installed ITK package and RTK package using
> > > > > > > 
> > > > > > > pip install itk
> > > > > > > pip install itk-rtk
> > > > > > > 
> > > > > > > using ITK seems OK,  but I'm having difficulties with
> > > > > > > RTK.
> > > > > > > 
> > > > > > > When I run the ITK example code, It worked well. 
> > > > > > > but when I tried to run the FirstReconstruction.py in the
> > > > > > > github,
> > > > > > > error occurrs.
> > > > > > > 
> > > > > > > > -----------------------------------------------------
> > > > > > > > ----------------------
> > > > > > > > AttributeError                            Traceback
> > > > > > > > (most recent call last)
> > > > > > > > <ipython-input-1-be2ee9c70d3d> in <module>
> > > > > > > >      19 for x in range(0,numberOfProjections):
> > > > > > > >      20   angle = firstAngle + x * angularArc /
> > > > > > > > numberOfProjections
> > > > > > > > ---> 21   geometry.AddProjection(sid,sdd,angle)
> > > > > > > >      22 
> > > > > > > >      23 # Writing the geometry to disk
> > > > > > > > 
> > > > > > > > AttributeError: 'rtkFDKConeBeamReconstructionFilterIF3'
> > > > > > > > object has no attribute 'AddProjection'
> > > > > > >  
> > > > > > > How can I fix this problem?
> > > > > > > 
> > > > > > > and I have another question.
> > > > > > > I want the reconstruct the sinogram image to phantom.
> > > > > > > 
> > > > > > > usually what I did was using skimage.transform.iradon().
> > > > > > > what should I use in RTK to do Inverse radon transform or
> > > > > > > Filtered back projection method?
> > > > > > >  
> > > > > > > 
> > > > > > > _______________________________________________
> > > > > > > Rtk-users mailing list
> > > > > > > Rtk-users at public.kitware.com
> > > > > > > https://public.kitware.com/mailman/listinfo/rtk-users
> > > 
> > > _______________________________________________
> > > 
> > > Rtk-users mailing list
> > > 
> > > Rtk-users at public.kitware.com
> > > 
> > > https://public.kitware.com/mailman/listinfo/rtk-users
> > > 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200422/6f95606e/attachment.html>

From isurusuranga.wijesinghe at gmail.com  Wed Apr 22 10:09:53 2020
From: isurusuranga.wijesinghe at gmail.com (Isuru Suranga Wijesinghe)
Date: Wed, 22 Apr 2020 15:09:53 +0100
Subject: [Rtk-users] DRR image generation from 3D CT
In-Reply-To: <CAF0oig0LL6g=pByeT+ABTAGkHZst9E52FcL9Fxz3ChCS9GswDQ@mail.gmail.com>
References: <CAMy-KaWv6sT5AtsL8mo_rynMTXqbQbEZ_=peuaJk-=B3nqSA8A@mail.gmail.com>
 <CAF0oig0_CpL2vsJSD9NxUy1DOpvEF8_dWUc+A3RC7DKb_zP7sw@mail.gmail.com>
 <CAMy-KaV5TqhNzHdT8DbkVnAaks1OXd2xptxPenXXTXiCBHtFkg@mail.gmail.com>
 <CAF0oig0LL6g=pByeT+ABTAGkHZst9E52FcL9Fxz3ChCS9GswDQ@mail.gmail.com>
Message-ID: <CAMy-KaVEmf073nVrhC-9-wsVfDsZtQsM-vTAHSXqUC-gsmKmoA@mail.gmail.com>

Hi,

I have tried to save the out image as .png and it gave an error as below.

itk::ImageFileWriterException (0000003E08EFFCC0)   Location: "unknown"
File: D:\ITK\Source\Modules\IO\ImageBase\include\itkImageFileWriter.hxx
Line: 128   Description:  Could not create IO object for writing file
E:/DRRGeneratedDataset/one_CT/DRR_RTK/first.png
Tried to create one of the following:
GDCMImageIO
MetaImageIO
TIFFImageIO
You probably failed to set a file suffix, or  set the suffix to an
unsupported type.

And when changing the output extension to .mha it gives below error.
'FirstReconstruction.exe' (Win32): Loaded
'C:\Windows\System32\kernel.appcore.dll'.
Exception thrown at 0x00007FF68D387919 in FirstReconstruction.exe:
0xC0000005: Access violation reading location 0xFFFFFFFFFFFFFFFF.

I have attached the source code (.cpp) file for your further reference.
Please let me know if I have done any mistake.


On Tue, Apr 21, 2020 at 4:43 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Projection is centered on point (0,0,0) mm in your input
> (PhaseImage_01.mha) (as described in the doc). Check where this point is in
> your input. If it's outside, then you need to modify its origin (in the ITK
> sense, check ITK doc).
>
> On Tue, Apr 21, 2020 at 5:36 PM Isuru Suranga Wijesinghe <
> isurusuranga.wijesinghe at gmail.com> wrote:
>
>> Hi,
>>
>> I have built rtkforwardprojections code. And pass the appropriate
>> parameters to the generated exe from the command line as below.
>> But there is nothing in the output location. I have attached herewith my
>> geomtry.xml as well.
>>
>> D:/RTK/Build/bin/Release>rtkforwardprojections -g D:/geomtry.xml -i
>> D:\\Subject_01\\CT\\PhaseImage_01.mha -o D:/_rtk_output.png
>>
>> On Mon, Apr 20, 2020 at 8:45 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
>> wrote:
>>
>>> Hi,
>>> Look at the doc on the geometry file
>>> <http://www.openrtk.org/Doxygen/DocGeo3D.html> and rtksimulatedgeometry
>>> <https://github.com/SimonRit/RTK/tree/master/applications/rtksimulatedgeometry>
>>> for creating one file. AddProjection
>>> <http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
>>> takes several parameters. Given your scheme, it should look like
>>> AddProjection(1000, 1536, angle, +/-190 etc)
>>> It looks like an Elekta geometry given the distances, check the example
>>> here
>>> <http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction>
>>> if you can get access to the database.
>>> Simon
>>>
>>> On Mon, Apr 20, 2020 at 9:31 PM Isuru Suranga Wijesinghe <
>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm currently looking rtkforwardprojections example [1] to generate DRR
>>>> images from 3D-CT volumes. My question is  how can I set custom geometric
>>>> configurations as in the sample attached image ?
>>>>
>>>> Can you please help with a relevant example of this. ?
>>>>
>>>> [1]
>>>> https://github.com/SimonRit/RTK/blob/b32cffdc6f9d7a432c50023c370ed996a7985b69/applications/rtkforwardprojections/rtkforwardprojections.cxx
>>>>
>>>> Thanks and Best Regards,
>>>> Isuru
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200422/070ba182/attachment-0001.html>
-------------- next part --------------
// RTK includes
#include <rtkConstantImageSource.h>
#include <rtkThreeDCircularProjectionGeometryXMLFileWriter.h>
#include <rtkRayEllipsoidIntersectionImageFilter.h>
#include <rtkFDKConeBeamReconstructionFilter.h>
#include <rtkFieldOfViewImageFilter.h>

#include "rtkJosephForwardProjectionImageFilter.h"
#include "rtkJosephForwardAttenuatedProjectionImageFilter.h"

// ITK includes
#include <itkImageFileWriter.h>

int main(int argc, char **argv)
{
  using OutputPixelType = float;
  constexpr unsigned int Dimension = 3;

  // Defines the image type
  using ImageType = itk::Image< float, Dimension >;
  using OutputImageType = itk::Image<OutputPixelType, Dimension>;
  bool attenuationmap_given = false;
  // Defines the RTK geometry object
  using GeometryType = rtk::ThreeDCircularProjectionGeometry;
  GeometryType::Pointer geometry = GeometryType::New();
  unsigned int numberOfProjections = 1;
  double firstAngle = 0;
  double angularArc = 360;
  unsigned int sid = 1000; // source to isocenter distance
  unsigned int sdd = 1560; // source to detector distance
  //double projectionOffset = 190;
  for(unsigned int noProj=0; noProj<numberOfProjections; noProj++)
    {
    double angle = firstAngle + noProj * angularArc / numberOfProjections;
    geometry->AddProjection(sid, sdd, angle);
    }
  
  // Write the geometry to disk
  rtk::ThreeDCircularProjectionGeometryXMLFileWriter::Pointer xmlWriter;
  xmlWriter = rtk::ThreeDCircularProjectionGeometryXMLFileWriter::New();
  xmlWriter->SetFilename("E:/DRRGeneratedDataset/one_CT/geometry/geometry.xml");
  //xmlWriter->SetObject(geometry);
  xmlWriter->SetObject(&(*geometry));
  try
  {
      std::cout << "XML writer image" << std::endl;
      xmlWriter->WriteFile();
  }
  catch (itk::ExceptionObject& err)
  {
      std::cerr << "ERROR: ExceptionObject caught !" << std::endl;
      std::cerr << err << std::endl;
  }

  // Create a stack of empty projection images
  using ConstantImageSourceType = rtk::ConstantImageSource< ImageType >;
  ConstantImageSourceType::Pointer constantImageSource = ConstantImageSourceType::New();
  ConstantImageSourceType::PointType origin;
  ConstantImageSourceType::SpacingType spacing;
  ConstantImageSourceType::SizeType sizeOutput;
  
  origin[0] = -127;
  origin[1] = -127;
  origin[2] = 0.;

  sizeOutput[0] = 128;
  sizeOutput[1] = 128;
  //numberOfProjections = gantryangles
  sizeOutput[2] = numberOfProjections;

  spacing.Fill(2.);

  constantImageSource->SetOrigin(origin);
  constantImageSource->SetSpacing(spacing);
  constantImageSource->SetSize(sizeOutput);
  constantImageSource->SetConstant(0.);
  
  using ReaderType = itk::ImageFileReader<OutputImageType>;
  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName("E:/DRRGeneratedDataset/one_CT/PhaseImage_01.mha");
  //TRY_AND_EXIT_ON_ITK_EXCEPTION(reader->Update())
  try
  {
      std::cout << "reading image" << std::endl;
      reader->Update();
  }
  catch (itk::ExceptionObject& err)
  {
      std::cerr << "ERROR: ExceptionObject caught !" << std::endl;
      std::cerr << err << std::endl;
  }
  
  itk::ImageSource<OutputImageType>::Pointer attenuationFilter;
  if (attenuationmap_given)
  {
      // Read an existing image to initialize the attenuation map
      using AttenuationReaderType = itk::ImageFileReader<OutputImageType>;
      AttenuationReaderType::Pointer attenuationReader = AttenuationReaderType::New();
      attenuationReader->SetFileName("");
      attenuationFilter = attenuationReader;
  }

    
  rtk::ForwardProjectionImageFilter<OutputImageType, OutputImageType>::Pointer forwardProjection;
  forwardProjection = rtk::JosephForwardProjectionImageFilter<OutputImageType, OutputImageType>::New();
  forwardProjection->SetInput(constantImageSource->GetOutput());
  forwardProjection->SetInput(1, reader->GetOutput());
  if (attenuationmap_given) 
  {
      forwardProjection->SetInput(2, attenuationFilter->GetOutput());
  }
  forwardProjection->SetGeometry(geometry);

  // Write
  using WriterType = itk::ImageFileWriter<OutputImageType>;
  WriterType::Pointer writer = WriterType::New();
  writer->SetFileName("E:/DRRGeneratedDataset/one_CT/DRR_RTK/first.png");
  writer->SetInput(forwardProjection->GetOutput());
  
  //TRY_AND_EXIT_ON_ITK_EXCEPTION(writer->Update())
  try
  {
      std::cout << "Writing image " << std::endl;
      writer->Update();
  }
  catch (itk::ExceptionObject& err)
  {
      std::cerr << "ERROR: ExceptionObject caught !" << std::endl;
      std::cerr << err << std::endl;
  }
  

  return EXIT_SUCCESS;
}


From andreasga22 at gmail.com  Wed Apr 22 10:37:31 2020
From: andreasga22 at gmail.com (Andreas Andersen)
Date: Wed, 22 Apr 2020 16:37:31 +0200
Subject: [Rtk-users] DRR image generation from 3D CT
In-Reply-To: <CAMy-KaVEmf073nVrhC-9-wsVfDsZtQsM-vTAHSXqUC-gsmKmoA@mail.gmail.com>
References: <CAMy-KaWv6sT5AtsL8mo_rynMTXqbQbEZ_=peuaJk-=B3nqSA8A@mail.gmail.com>
 <CAF0oig0_CpL2vsJSD9NxUy1DOpvEF8_dWUc+A3RC7DKb_zP7sw@mail.gmail.com>
 <CAMy-KaV5TqhNzHdT8DbkVnAaks1OXd2xptxPenXXTXiCBHtFkg@mail.gmail.com>
 <CAF0oig0LL6g=pByeT+ABTAGkHZst9E52FcL9Fxz3ChCS9GswDQ@mail.gmail.com>
 <CAMy-KaVEmf073nVrhC-9-wsVfDsZtQsM-vTAHSXqUC-gsmKmoA@mail.gmail.com>
Message-ID: <CAE0aawF-v4iphHNBzYfqkz54j1gRDF8c6+m3wdmjCrRyLJ_VJQ@mail.gmail.com>

It actually tells you the problem, you set the suffix of an unsupported
type.
However, it doesn't tell you that ITK can support PNG if you configure and
compile with the CMake option Module_ITKIOPNG=ON (unless they changed it)
I think the type should automatically register after a successful rebuild.

/Andreas

On Wed, 22 Apr 2020, 16:10 Isuru Suranga Wijesinghe, <
isurusuranga.wijesinghe at gmail.com> wrote:

> Hi,
>
> I have tried to save the out image as .png and it gave an error as below.
>
> itk::ImageFileWriterException (0000003E08EFFCC0)   Location: "unknown"
> File: D:\ITK\Source\Modules\IO\ImageBase\include\itkImageFileWriter.hxx
> Line: 128   Description:  Could not create IO object for writing file
> E:/DRRGeneratedDataset/one_CT/DRR_RTK/first.png
> Tried to create one of the following:
> GDCMImageIO
> MetaImageIO
> TIFFImageIO
> You probably failed to set a file suffix, or  set the suffix to an
> unsupported type.
>
> And when changing the output extension to .mha it gives below error.
> 'FirstReconstruction.exe' (Win32): Loaded
> 'C:\Windows\System32\kernel.appcore.dll'.
> Exception thrown at 0x00007FF68D387919 in FirstReconstruction.exe:
> 0xC0000005: Access violation reading location 0xFFFFFFFFFFFFFFFF.
>
> I have attached the source code (.cpp) file for your further reference.
> Please let me know if I have done any mistake.
>
>
> On Tue, Apr 21, 2020 at 4:43 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
>
>> Projection is centered on point (0,0,0) mm in your input
>> (PhaseImage_01.mha) (as described in the doc). Check where this point is in
>> your input. If it's outside, then you need to modify its origin (in the ITK
>> sense, check ITK doc).
>>
>> On Tue, Apr 21, 2020 at 5:36 PM Isuru Suranga Wijesinghe <
>> isurusuranga.wijesinghe at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I have built rtkforwardprojections code. And pass the appropriate
>>> parameters to the generated exe from the command line as below.
>>> But there is nothing in the output location. I have attached herewith my
>>> geomtry.xml as well.
>>>
>>> D:/RTK/Build/bin/Release>rtkforwardprojections -g D:/geomtry.xml -i
>>> D:\\Subject_01\\CT\\PhaseImage_01.mha -o D:/_rtk_output.png
>>>
>>> On Mon, Apr 20, 2020 at 8:45 PM Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Hi,
>>>> Look at the doc on the geometry file
>>>> <http://www.openrtk.org/Doxygen/DocGeo3D.html> and rtksimulatedgeometry
>>>> <https://github.com/SimonRit/RTK/tree/master/applications/rtksimulatedgeometry>
>>>> for creating one file. AddProjection
>>>> <http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
>>>> takes several parameters. Given your scheme, it should look like
>>>> AddProjection(1000, 1536, angle, +/-190 etc)
>>>> It looks like an Elekta geometry given the distances, check the example
>>>> here
>>>> <http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction>
>>>> if you can get access to the database.
>>>> Simon
>>>>
>>>> On Mon, Apr 20, 2020 at 9:31 PM Isuru Suranga Wijesinghe <
>>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm currently looking rtkforwardprojections example [1] to generate
>>>>> DRR images from 3D-CT volumes. My question is  how can I set custom
>>>>> geometric configurations as in the sample attached image ?
>>>>>
>>>>> Can you please help with a relevant example of this. ?
>>>>>
>>>>> [1]
>>>>> https://github.com/SimonRit/RTK/blob/b32cffdc6f9d7a432c50023c370ed996a7985b69/applications/rtkforwardprojections/rtkforwardprojections.cxx
>>>>>
>>>>> Thanks and Best Regards,
>>>>> Isuru
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200422/44062100/attachment.html>

From isurusuranga.wijesinghe at gmail.com  Wed Apr 22 10:59:27 2020
From: isurusuranga.wijesinghe at gmail.com (Isuru Suranga Wijesinghe)
Date: Wed, 22 Apr 2020 15:59:27 +0100
Subject: [Rtk-users] DRR image generation from 3D CT
In-Reply-To: <CAE0aawF-v4iphHNBzYfqkz54j1gRDF8c6+m3wdmjCrRyLJ_VJQ@mail.gmail.com>
References: <CAMy-KaWv6sT5AtsL8mo_rynMTXqbQbEZ_=peuaJk-=B3nqSA8A@mail.gmail.com>
 <CAF0oig0_CpL2vsJSD9NxUy1DOpvEF8_dWUc+A3RC7DKb_zP7sw@mail.gmail.com>
 <CAMy-KaV5TqhNzHdT8DbkVnAaks1OXd2xptxPenXXTXiCBHtFkg@mail.gmail.com>
 <CAF0oig0LL6g=pByeT+ABTAGkHZst9E52FcL9Fxz3ChCS9GswDQ@mail.gmail.com>
 <CAMy-KaVEmf073nVrhC-9-wsVfDsZtQsM-vTAHSXqUC-gsmKmoA@mail.gmail.com>
 <CAE0aawF-v4iphHNBzYfqkz54j1gRDF8c6+m3wdmjCrRyLJ_VJQ@mail.gmail.com>
Message-ID: <CAMy-KaWt85j-WKMWSq_p1t_BJoF+ERW3tpmjRKSuKpcfp9QRsQ@mail.gmail.com>

The problem is in the RTK I think. I was able to successfully save the
output image as the .png extension with an ITK eample.
I just checked  with CMake GUI and it doesn't contain a such module.
Please see the attachment. Any alternative approach is there ?

On Wed, Apr 22, 2020 at 3:37 PM Andreas Andersen <andreasga22 at gmail.com>
wrote:

> It actually tells you the problem, you set the suffix of an unsupported
> type.
> However, it doesn't tell you that ITK can support PNG if you configure and
> compile with the CMake option Module_ITKIOPNG=ON (unless they changed it)
> I think the type should automatically register after a successful rebuild.
>
> /Andreas
>
> On Wed, 22 Apr 2020, 16:10 Isuru Suranga Wijesinghe, <
> isurusuranga.wijesinghe at gmail.com> wrote:
>
>> Hi,
>>
>> I have tried to save the out image as .png and it gave an error as below.
>>
>> itk::ImageFileWriterException (0000003E08EFFCC0)   Location: "unknown"
>> File: D:\ITK\Source\Modules\IO\ImageBase\include\itkImageFileWriter.hxx
>> Line: 128   Description:  Could not create IO object for writing file
>> E:/DRRGeneratedDataset/one_CT/DRR_RTK/first.png
>> Tried to create one of the following:
>> GDCMImageIO
>> MetaImageIO
>> TIFFImageIO
>> You probably failed to set a file suffix, or  set the suffix to an
>> unsupported type.
>>
>> And when changing the output extension to .mha it gives below error.
>> 'FirstReconstruction.exe' (Win32): Loaded
>> 'C:\Windows\System32\kernel.appcore.dll'.
>> Exception thrown at 0x00007FF68D387919 in FirstReconstruction.exe:
>> 0xC0000005: Access violation reading location 0xFFFFFFFFFFFFFFFF.
>>
>> I have attached the source code (.cpp) file for your further reference.
>> Please let me know if I have done any mistake.
>>
>>
>> On Tue, Apr 21, 2020 at 4:43 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
>> wrote:
>>
>>> Projection is centered on point (0,0,0) mm in your input
>>> (PhaseImage_01.mha) (as described in the doc). Check where this point is in
>>> your input. If it's outside, then you need to modify its origin (in the ITK
>>> sense, check ITK doc).
>>>
>>> On Tue, Apr 21, 2020 at 5:36 PM Isuru Suranga Wijesinghe <
>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have built rtkforwardprojections code. And pass the appropriate
>>>> parameters to the generated exe from the command line as below.
>>>> But there is nothing in the output location. I have attached herewith
>>>> my geomtry.xml as well.
>>>>
>>>> D:/RTK/Build/bin/Release>rtkforwardprojections -g D:/geomtry.xml -i
>>>> D:\\Subject_01\\CT\\PhaseImage_01.mha -o D:/_rtk_output.png
>>>>
>>>> On Mon, Apr 20, 2020 at 8:45 PM Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> Hi,
>>>>> Look at the doc on the geometry file
>>>>> <http://www.openrtk.org/Doxygen/DocGeo3D.html> and
>>>>> rtksimulatedgeometry
>>>>> <https://github.com/SimonRit/RTK/tree/master/applications/rtksimulatedgeometry>
>>>>> for creating one file. AddProjection
>>>>> <http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
>>>>> takes several parameters. Given your scheme, it should look like
>>>>> AddProjection(1000, 1536, angle, +/-190 etc)
>>>>> It looks like an Elekta geometry given the distances, check the
>>>>> example here
>>>>> <http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction>
>>>>> if you can get access to the database.
>>>>> Simon
>>>>>
>>>>> On Mon, Apr 20, 2020 at 9:31 PM Isuru Suranga Wijesinghe <
>>>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm currently looking rtkforwardprojections example [1] to generate
>>>>>> DRR images from 3D-CT volumes. My question is  how can I set custom
>>>>>> geometric configurations as in the sample attached image ?
>>>>>>
>>>>>> Can you please help with a relevant example of this. ?
>>>>>>
>>>>>> [1]
>>>>>> https://github.com/SimonRit/RTK/blob/b32cffdc6f9d7a432c50023c370ed996a7985b69/applications/rtkforwardprojections/rtkforwardprojections.cxx
>>>>>>
>>>>>> Thanks and Best Regards,
>>>>>> Isuru
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200422/d79d9505/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: CMake_config.png
Type: image/png
Size: 37880 bytes
Desc: not available
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200422/d79d9505/attachment-0001.png>

From simon.rit at creatis.insa-lyon.fr  Wed Apr 22 11:04:55 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 22 Apr 2020 17:04:55 +0200
Subject: [Rtk-users] DRR image generation from 3D CT
In-Reply-To: <CAMy-KaWt85j-WKMWSq_p1t_BJoF+ERW3tpmjRKSuKpcfp9QRsQ@mail.gmail.com>
References: <CAMy-KaWv6sT5AtsL8mo_rynMTXqbQbEZ_=peuaJk-=B3nqSA8A@mail.gmail.com>
 <CAF0oig0_CpL2vsJSD9NxUy1DOpvEF8_dWUc+A3RC7DKb_zP7sw@mail.gmail.com>
 <CAMy-KaV5TqhNzHdT8DbkVnAaks1OXd2xptxPenXXTXiCBHtFkg@mail.gmail.com>
 <CAF0oig0LL6g=pByeT+ABTAGkHZst9E52FcL9Fxz3ChCS9GswDQ@mail.gmail.com>
 <CAMy-KaVEmf073nVrhC-9-wsVfDsZtQsM-vTAHSXqUC-gsmKmoA@mail.gmail.com>
 <CAE0aawF-v4iphHNBzYfqkz54j1gRDF8c6+m3wdmjCrRyLJ_VJQ@mail.gmail.com>
 <CAMy-KaWt85j-WKMWSq_p1t_BJoF+ERW3tpmjRKSuKpcfp9QRsQ@mail.gmail.com>
Message-ID: <CAF0oig0HMFskb1QoECEeEj8ooZ1ZZRctkqXCvmgE2K5Prj96+Q@mail.gmail.com>

Hi,
Can you check this thread
<https://discourse.itk.org/t/is-png-no-longer-supported/2893/16>? A similar
problem was solved there. Note that I don't think that PNG can support
float types.
Simon

On Wed, Apr 22, 2020 at 4:59 PM Isuru Suranga Wijesinghe <
isurusuranga.wijesinghe at gmail.com> wrote:

> The problem is in the RTK I think. I was able to successfully save the
> output image as the .png extension with an ITK eample.
> I just checked  with CMake GUI and it doesn't contain a such module.
> Please see the attachment. Any alternative approach is there ?
>
> On Wed, Apr 22, 2020 at 3:37 PM Andreas Andersen <andreasga22 at gmail.com>
> wrote:
>
>> It actually tells you the problem, you set the suffix of an unsupported
>> type.
>> However, it doesn't tell you that ITK can support PNG if you configure
>> and compile with the CMake option Module_ITKIOPNG=ON (unless they changed
>> it)
>> I think the type should automatically register after a successful rebuild.
>>
>> /Andreas
>>
>> On Wed, 22 Apr 2020, 16:10 Isuru Suranga Wijesinghe, <
>> isurusuranga.wijesinghe at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I have tried to save the out image as .png and it gave an error as below.
>>>
>>> itk::ImageFileWriterException (0000003E08EFFCC0)   Location: "unknown"
>>> File: D:\ITK\Source\Modules\IO\ImageBase\include\itkImageFileWriter.hxx
>>> Line: 128   Description:  Could not create IO object for writing file
>>> E:/DRRGeneratedDataset/one_CT/DRR_RTK/first.png
>>> Tried to create one of the following:
>>> GDCMImageIO
>>> MetaImageIO
>>> TIFFImageIO
>>> You probably failed to set a file suffix, or  set the suffix to an
>>> unsupported type.
>>>
>>> And when changing the output extension to .mha it gives below error.
>>> 'FirstReconstruction.exe' (Win32): Loaded
>>> 'C:\Windows\System32\kernel.appcore.dll'.
>>> Exception thrown at 0x00007FF68D387919 in FirstReconstruction.exe:
>>> 0xC0000005: Access violation reading location 0xFFFFFFFFFFFFFFFF.
>>>
>>> I have attached the source code (.cpp) file for your further reference.
>>> Please let me know if I have done any mistake.
>>>
>>>
>>> On Tue, Apr 21, 2020 at 4:43 PM Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Projection is centered on point (0,0,0) mm in your input
>>>> (PhaseImage_01.mha) (as described in the doc). Check where this point is in
>>>> your input. If it's outside, then you need to modify its origin (in the ITK
>>>> sense, check ITK doc).
>>>>
>>>> On Tue, Apr 21, 2020 at 5:36 PM Isuru Suranga Wijesinghe <
>>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have built rtkforwardprojections code. And pass the appropriate
>>>>> parameters to the generated exe from the command line as below.
>>>>> But there is nothing in the output location. I have attached herewith
>>>>> my geomtry.xml as well.
>>>>>
>>>>> D:/RTK/Build/bin/Release>rtkforwardprojections -g D:/geomtry.xml -i
>>>>> D:\\Subject_01\\CT\\PhaseImage_01.mha -o D:/_rtk_output.png
>>>>>
>>>>> On Mon, Apr 20, 2020 at 8:45 PM Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Hi,
>>>>>> Look at the doc on the geometry file
>>>>>> <http://www.openrtk.org/Doxygen/DocGeo3D.html> and
>>>>>> rtksimulatedgeometry
>>>>>> <https://github.com/SimonRit/RTK/tree/master/applications/rtksimulatedgeometry>
>>>>>> for creating one file. AddProjection
>>>>>> <http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
>>>>>> takes several parameters. Given your scheme, it should look like
>>>>>> AddProjection(1000, 1536, angle, +/-190 etc)
>>>>>> It looks like an Elekta geometry given the distances, check the
>>>>>> example here
>>>>>> <http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction>
>>>>>> if you can get access to the database.
>>>>>> Simon
>>>>>>
>>>>>> On Mon, Apr 20, 2020 at 9:31 PM Isuru Suranga Wijesinghe <
>>>>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I'm currently looking rtkforwardprojections example [1] to generate
>>>>>>> DRR images from 3D-CT volumes. My question is  how can I set custom
>>>>>>> geometric configurations as in the sample attached image ?
>>>>>>>
>>>>>>> Can you please help with a relevant example of this. ?
>>>>>>>
>>>>>>> [1]
>>>>>>> https://github.com/SimonRit/RTK/blob/b32cffdc6f9d7a432c50023c370ed996a7985b69/applications/rtkforwardprojections/rtkforwardprojections.cxx
>>>>>>>
>>>>>>> Thanks and Best Regards,
>>>>>>> Isuru
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200422/0fb3add6/attachment.html>

From isurusuranga.wijesinghe at gmail.com  Wed Apr 22 12:16:42 2020
From: isurusuranga.wijesinghe at gmail.com (Isuru Suranga Wijesinghe)
Date: Wed, 22 Apr 2020 17:16:42 +0100
Subject: [Rtk-users] DRR image generation from 3D CT
In-Reply-To: <CAF0oig0HMFskb1QoECEeEj8ooZ1ZZRctkqXCvmgE2K5Prj96+Q@mail.gmail.com>
References: <CAMy-KaWv6sT5AtsL8mo_rynMTXqbQbEZ_=peuaJk-=B3nqSA8A@mail.gmail.com>
 <CAF0oig0_CpL2vsJSD9NxUy1DOpvEF8_dWUc+A3RC7DKb_zP7sw@mail.gmail.com>
 <CAMy-KaV5TqhNzHdT8DbkVnAaks1OXd2xptxPenXXTXiCBHtFkg@mail.gmail.com>
 <CAF0oig0LL6g=pByeT+ABTAGkHZst9E52FcL9Fxz3ChCS9GswDQ@mail.gmail.com>
 <CAMy-KaVEmf073nVrhC-9-wsVfDsZtQsM-vTAHSXqUC-gsmKmoA@mail.gmail.com>
 <CAE0aawF-v4iphHNBzYfqkz54j1gRDF8c6+m3wdmjCrRyLJ_VJQ@mail.gmail.com>
 <CAMy-KaWt85j-WKMWSq_p1t_BJoF+ERW3tpmjRKSuKpcfp9QRsQ@mail.gmail.com>
 <CAF0oig0HMFskb1QoECEeEj8ooZ1ZZRctkqXCvmgE2K5Prj96+Q@mail.gmail.com>
Message-ID: <CAMy-KaXURWiNBPYk95ixc-bhyz+QucN-c5=0Xdbgrrv7=xHpGA@mail.gmail.com>

*I have tried to change my CMake configuration as in the given asnwers but
I have got an error as below.*


*Severity Code Description Project File Line Suppression StateError LNK2001
unresolved external symbol "void __cdecl
itk::JPEG2000ImageIOFactoryRegister__Private(void)"
(?JPEG2000ImageIOFactoryRegister__Private at itk@@YAXXZ) FirstReconstruction
D:\RTKExample\Build\FirstReconstruction.obj 1 *

*For your further reference I have copied my CMKaeLsits file as well.*














*cmake_minimum_required(VERSION 3.9.5 FATAL_ERROR)# This project is
designed to be built outside the RTK source
tree.project(FirstReconstruction)# Find ITK with RTKfind_package(ITK
REQUIRED COMPONENTS RTK ITKImageIO)include(${ITK_USE_FILE})#
Executable(s)add_executable(FirstReconstruction FirstReconstruction.cpp
)#target_link_libraries(FirstReconstruction
${RTK_LIBRARIES})target_link_libraries(FirstReconstruction
${ITK_LIBRARIES})*

On Wed, Apr 22, 2020 at 4:03 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Can you check this thread
> <https://discourse.itk.org/t/is-png-no-longer-supported/2893/16>? A
> similar problem was solved there. Note that I don't think that PNG can
> support float types.
> Simon
>
> On Wed, Apr 22, 2020 at 4:59 PM Isuru Suranga Wijesinghe <
> isurusuranga.wijesinghe at gmail.com> wrote:
>
>> The problem is in the RTK I think. I was able to successfully save the
>> output image as the .png extension with an ITK eample.
>> I just checked  with CMake GUI and it doesn't contain a such module.
>> Please see the attachment. Any alternative approach is there ?
>>
>> On Wed, Apr 22, 2020 at 3:37 PM Andreas Andersen <andreasga22 at gmail.com>
>> wrote:
>>
>>> It actually tells you the problem, you set the suffix of an unsupported
>>> type.
>>> However, it doesn't tell you that ITK can support PNG if you configure
>>> and compile with the CMake option Module_ITKIOPNG=ON (unless they changed
>>> it)
>>> I think the type should automatically register after a successful
>>> rebuild.
>>>
>>> /Andreas
>>>
>>> On Wed, 22 Apr 2020, 16:10 Isuru Suranga Wijesinghe, <
>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have tried to save the out image as .png and it gave an error as
>>>> below.
>>>>
>>>> itk::ImageFileWriterException (0000003E08EFFCC0)   Location: "unknown"
>>>> File: D:\ITK\Source\Modules\IO\ImageBase\include\itkImageFileWriter.hxx
>>>> Line: 128   Description:  Could not create IO object for writing file
>>>> E:/DRRGeneratedDataset/one_CT/DRR_RTK/first.png
>>>> Tried to create one of the following:
>>>> GDCMImageIO
>>>> MetaImageIO
>>>> TIFFImageIO
>>>> You probably failed to set a file suffix, or  set the suffix to an
>>>> unsupported type.
>>>>
>>>> And when changing the output extension to .mha it gives below error.
>>>> 'FirstReconstruction.exe' (Win32): Loaded
>>>> 'C:\Windows\System32\kernel.appcore.dll'.
>>>> Exception thrown at 0x00007FF68D387919 in FirstReconstruction.exe:
>>>> 0xC0000005: Access violation reading location 0xFFFFFFFFFFFFFFFF.
>>>>
>>>> I have attached the source code (.cpp) file for your further reference.
>>>> Please let me know if I have done any mistake.
>>>>
>>>>
>>>> On Tue, Apr 21, 2020 at 4:43 PM Simon Rit <
>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>
>>>>> Projection is centered on point (0,0,0) mm in your input
>>>>> (PhaseImage_01.mha) (as described in the doc). Check where this point is in
>>>>> your input. If it's outside, then you need to modify its origin (in the ITK
>>>>> sense, check ITK doc).
>>>>>
>>>>> On Tue, Apr 21, 2020 at 5:36 PM Isuru Suranga Wijesinghe <
>>>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I have built rtkforwardprojections code. And pass the appropriate
>>>>>> parameters to the generated exe from the command line as below.
>>>>>> But there is nothing in the output location. I have attached herewith
>>>>>> my geomtry.xml as well.
>>>>>>
>>>>>> D:/RTK/Build/bin/Release>rtkforwardprojections -g D:/geomtry.xml -i
>>>>>> D:\\Subject_01\\CT\\PhaseImage_01.mha -o D:/_rtk_output.png
>>>>>>
>>>>>> On Mon, Apr 20, 2020 at 8:45 PM Simon Rit <
>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>> Look at the doc on the geometry file
>>>>>>> <http://www.openrtk.org/Doxygen/DocGeo3D.html> and
>>>>>>> rtksimulatedgeometry
>>>>>>> <https://github.com/SimonRit/RTK/tree/master/applications/rtksimulatedgeometry>
>>>>>>> for creating one file. AddProjection
>>>>>>> <http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
>>>>>>> takes several parameters. Given your scheme, it should look like
>>>>>>> AddProjection(1000, 1536, angle, +/-190 etc)
>>>>>>> It looks like an Elekta geometry given the distances, check the
>>>>>>> example here
>>>>>>> <http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction>
>>>>>>> if you can get access to the database.
>>>>>>> Simon
>>>>>>>
>>>>>>> On Mon, Apr 20, 2020 at 9:31 PM Isuru Suranga Wijesinghe <
>>>>>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I'm currently looking rtkforwardprojections example [1] to generate
>>>>>>>> DRR images from 3D-CT volumes. My question is  how can I set custom
>>>>>>>> geometric configurations as in the sample attached image ?
>>>>>>>>
>>>>>>>> Can you please help with a relevant example of this. ?
>>>>>>>>
>>>>>>>> [1]
>>>>>>>> https://github.com/SimonRit/RTK/blob/b32cffdc6f9d7a432c50023c370ed996a7985b69/applications/rtkforwardprojections/rtkforwardprojections.cxx
>>>>>>>>
>>>>>>>> Thanks and Best Regards,
>>>>>>>> Isuru
>>>>>>>> _______________________________________________
>>>>>>>> Rtk-users mailing list
>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200422/2f4c369e/attachment.html>

From simon.rit at creatis.insa-lyon.fr  Wed Apr 22 15:33:57 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 22 Apr 2020 21:33:57 +0200
Subject: [Rtk-users] DRR image generation from 3D CT
In-Reply-To: <CAMy-KaXURWiNBPYk95ixc-bhyz+QucN-c5=0Xdbgrrv7=xHpGA@mail.gmail.com>
References: <CAMy-KaWv6sT5AtsL8mo_rynMTXqbQbEZ_=peuaJk-=B3nqSA8A@mail.gmail.com>
 <CAF0oig0_CpL2vsJSD9NxUy1DOpvEF8_dWUc+A3RC7DKb_zP7sw@mail.gmail.com>
 <CAMy-KaV5TqhNzHdT8DbkVnAaks1OXd2xptxPenXXTXiCBHtFkg@mail.gmail.com>
 <CAF0oig0LL6g=pByeT+ABTAGkHZst9E52FcL9Fxz3ChCS9GswDQ@mail.gmail.com>
 <CAMy-KaVEmf073nVrhC-9-wsVfDsZtQsM-vTAHSXqUC-gsmKmoA@mail.gmail.com>
 <CAE0aawF-v4iphHNBzYfqkz54j1gRDF8c6+m3wdmjCrRyLJ_VJQ@mail.gmail.com>
 <CAMy-KaWt85j-WKMWSq_p1t_BJoF+ERW3tpmjRKSuKpcfp9QRsQ@mail.gmail.com>
 <CAF0oig0HMFskb1QoECEeEj8ooZ1ZZRctkqXCvmgE2K5Prj96+Q@mail.gmail.com>
 <CAMy-KaXURWiNBPYk95ixc-bhyz+QucN-c5=0Xdbgrrv7=xHpGA@mail.gmail.com>
Message-ID: <CAF0oig2cNNPBUpo4gtZ+DO2ZMEWWpoG5GvtA4kkPPOzOGOpsuw@mail.gmail.com>

Have you tried without ITKImageIO? I think png is present by default
anyway. I would also check if you are using the same configuration between
ITK and your code (shared vs static libraries).

On Wed, Apr 22, 2020 at 6:17 PM Isuru Suranga Wijesinghe <
isurusuranga.wijesinghe at gmail.com> wrote:

> *I have tried to change my CMake configuration as in the given asnwers but
> I have got an error as below.*
>
>
> *Severity Code Description Project File Line Suppression StateError
> LNK2001 unresolved external symbol "void __cdecl
> itk::JPEG2000ImageIOFactoryRegister__Private(void)"
> (?JPEG2000ImageIOFactoryRegister__Private at itk@@YAXXZ) FirstReconstruction
> D:\RTKExample\Build\FirstReconstruction.obj 1 *
>
> *For your further reference I have copied my CMKaeLsits file as well.*
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *cmake_minimum_required(VERSION 3.9.5 FATAL_ERROR)# This project is
> designed to be built outside the RTK source
> tree.project(FirstReconstruction)# Find ITK with RTKfind_package(ITK
> REQUIRED COMPONENTS RTK ITKImageIO)include(${ITK_USE_FILE})#
> Executable(s)add_executable(FirstReconstruction FirstReconstruction.cpp
> )#target_link_libraries(FirstReconstruction
> ${RTK_LIBRARIES})target_link_libraries(FirstReconstruction
> ${ITK_LIBRARIES})*
>
> On Wed, Apr 22, 2020 at 4:03 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
>
>> Hi,
>> Can you check this thread
>> <https://discourse.itk.org/t/is-png-no-longer-supported/2893/16>? A
>> similar problem was solved there. Note that I don't think that PNG can
>> support float types.
>> Simon
>>
>> On Wed, Apr 22, 2020 at 4:59 PM Isuru Suranga Wijesinghe <
>> isurusuranga.wijesinghe at gmail.com> wrote:
>>
>>> The problem is in the RTK I think. I was able to successfully save the
>>> output image as the .png extension with an ITK eample.
>>> I just checked  with CMake GUI and it doesn't contain a such module.
>>> Please see the attachment. Any alternative approach is there ?
>>>
>>> On Wed, Apr 22, 2020 at 3:37 PM Andreas Andersen <andreasga22 at gmail.com>
>>> wrote:
>>>
>>>> It actually tells you the problem, you set the suffix of an unsupported
>>>> type.
>>>> However, it doesn't tell you that ITK can support PNG if you configure
>>>> and compile with the CMake option Module_ITKIOPNG=ON (unless they changed
>>>> it)
>>>> I think the type should automatically register after a successful
>>>> rebuild.
>>>>
>>>> /Andreas
>>>>
>>>> On Wed, 22 Apr 2020, 16:10 Isuru Suranga Wijesinghe, <
>>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have tried to save the out image as .png and it gave an error as
>>>>> below.
>>>>>
>>>>> itk::ImageFileWriterException (0000003E08EFFCC0)   Location: "unknown"
>>>>> File: D:\ITK\Source\Modules\IO\ImageBase\include\itkImageFileWriter.hxx
>>>>> Line: 128   Description:  Could not create IO object for writing file
>>>>> E:/DRRGeneratedDataset/one_CT/DRR_RTK/first.png
>>>>> Tried to create one of the following:
>>>>> GDCMImageIO
>>>>> MetaImageIO
>>>>> TIFFImageIO
>>>>> You probably failed to set a file suffix, or  set the suffix to an
>>>>> unsupported type.
>>>>>
>>>>> And when changing the output extension to .mha it gives below error.
>>>>> 'FirstReconstruction.exe' (Win32): Loaded
>>>>> 'C:\Windows\System32\kernel.appcore.dll'.
>>>>> Exception thrown at 0x00007FF68D387919 in FirstReconstruction.exe:
>>>>> 0xC0000005: Access violation reading location 0xFFFFFFFFFFFFFFFF.
>>>>>
>>>>> I have attached the source code (.cpp) file for your further
>>>>> reference. Please let me know if I have done any mistake.
>>>>>
>>>>>
>>>>> On Tue, Apr 21, 2020 at 4:43 PM Simon Rit <
>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>
>>>>>> Projection is centered on point (0,0,0) mm in your input
>>>>>> (PhaseImage_01.mha) (as described in the doc). Check where this point is in
>>>>>> your input. If it's outside, then you need to modify its origin (in the ITK
>>>>>> sense, check ITK doc).
>>>>>>
>>>>>> On Tue, Apr 21, 2020 at 5:36 PM Isuru Suranga Wijesinghe <
>>>>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I have built rtkforwardprojections code. And pass the appropriate
>>>>>>> parameters to the generated exe from the command line as below.
>>>>>>> But there is nothing in the output location. I have attached
>>>>>>> herewith my geomtry.xml as well.
>>>>>>>
>>>>>>> D:/RTK/Build/bin/Release>rtkforwardprojections -g D:/geomtry.xml -i
>>>>>>> D:\\Subject_01\\CT\\PhaseImage_01.mha -o D:/_rtk_output.png
>>>>>>>
>>>>>>> On Mon, Apr 20, 2020 at 8:45 PM Simon Rit <
>>>>>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>> Look at the doc on the geometry file
>>>>>>>> <http://www.openrtk.org/Doxygen/DocGeo3D.html> and
>>>>>>>> rtksimulatedgeometry
>>>>>>>> <https://github.com/SimonRit/RTK/tree/master/applications/rtksimulatedgeometry>
>>>>>>>> for creating one file. AddProjection
>>>>>>>> <http://www.openrtk.org/Doxygen/classrtk_1_1ThreeDCircularProjectionGeometry.html#a39d6a67147cac1f2b5d75f5958a48f9a>
>>>>>>>> takes several parameters. Given your scheme, it should look like
>>>>>>>> AddProjection(1000, 1536, angle, +/-190 etc)
>>>>>>>> It looks like an Elekta geometry given the distances, check the
>>>>>>>> example here
>>>>>>>> <http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction>
>>>>>>>> if you can get access to the database.
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> On Mon, Apr 20, 2020 at 9:31 PM Isuru Suranga Wijesinghe <
>>>>>>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I'm currently looking rtkforwardprojections example [1] to
>>>>>>>>> generate DRR images from 3D-CT volumes. My question is  how can I set
>>>>>>>>> custom geometric configurations as in the sample attached image ?
>>>>>>>>>
>>>>>>>>> Can you please help with a relevant example of this. ?
>>>>>>>>>
>>>>>>>>> [1]
>>>>>>>>> https://github.com/SimonRit/RTK/blob/b32cffdc6f9d7a432c50023c370ed996a7985b69/applications/rtkforwardprojections/rtkforwardprojections.cxx
>>>>>>>>>
>>>>>>>>> Thanks and Best Regards,
>>>>>>>>> Isuru
>>>>>>>>> _______________________________________________
>>>>>>>>> Rtk-users mailing list
>>>>>>>>> Rtk-users at public.kitware.com
>>>>>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200422/4b8f60dc/attachment-0001.html>

From vl at xris.eu  Thu Apr 23 09:56:35 2020
From: vl at xris.eu (vincent)
Date: Thu, 23 Apr 2020 15:56:35 +0200
Subject: [Rtk-users] Rotation before and during rktprojections
In-Reply-To: <CAF0oig1H=yihYbGNKCLxjJPx0GtCXH5sW-9GzQiSbROos50Bhg@mail.gmail.com>
References: <b3c31f1b-0a7c-67da-d8b2-b63f3fb5a5b6@xris.eu>
 <CAF0oig1H=yihYbGNKCLxjJPx0GtCXH5sW-9GzQiSbROos50Bhg@mail.gmail.com>
Message-ID: <7929e541-b9af-ca45-e81c-e9e6b5bebf6f@xris.eu>

Hi,

just to bring some closure to that problem..

I didn't manage to adapt the ramp filter, so I instead modified 
rtkProjectionsReader to include an Orientation parameter that sets the 
right coefficients for an itkPermuteAxis filter.

I don't think it is worthy to be included in the official source, but I 
am happy to share if someone requires it.

Best regards,

Vincent

On 15.04.20 20:13, Simon Rit wrote:
> Hi Vincent,
> Everything you did is correct but rtkfdk always applies the ramp 
> filter along the first dimension and does not check if this 
> corresponds to the direction orthogonal to the rotation axis. For your 
> case, it is probably not so difficult to adapt the code. When there is 
> a small rotation, it is debatable whether one should ignore the 
> rotation for the ramp filter, resample the image, or recalculate the 
> filter in 2D (see our recent publication here 
> <https://doi.org/10.1088/1361-6560/ab7875> which has not been 
> implemented in RTK). I have opened an issue on github 
> <https://github.com/SimonRit/RTK/issues/335>, hopefully we'll find 
> time to fix this in the future (at least raise an exception above a 
> parametrable rotation threshold).
> Best regards,
> Simon
>
> On Wed, Apr 15, 2020 at 7:00 PM vincent <vl at xris.eu 
> <mailto:vl at xris.eu>> wrote:
>
>     Hi RTK community,
>
>     I hope everyone is doing well in those hard times.
>
>     I have a panel that is rotated by 90? on the CT system.? I used to
>     rotate the images back in the right orientation before building the
>     sinogram with rtkprojections, but then I thought I might give a
>     try at
>     the "newdirection" option.? Using the matrix [0 1 0 ; 1 0 0 ; 0 0 1]
>     gives the expected results.? So far so good. But when I try to
>     reconstruct the latter with the same geometric parameters than for
>     the
>     pre-rotated projections, I obtain a very blurry result (vs a sharp
>     one
>     in the first case).? I am obviously missing something, and I would
>     suspect I am not giving the right information to the rtkfdk
>     application.? So far, here is what I have tried:
>
>     -keep the projections in the initial orientation, but give the
>     "newdirection" option to the rtkfdk application,
>
>     -specify the "newdirection" in both rtkprojections and rtkfdk,
>
>     -turn to you for advice !
>
>     I thank you very much in advance for any help you might be able to
>     give.
>
>     Best regards,
>
>     Vincent
>
>     _______________________________________________
>     Rtk-users mailing list
>     Rtk-users at public.kitware.com <mailto:Rtk-users at public.kitware.com>
>     https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200423/5f796a4b/attachment.html>

From simon.rit at creatis.insa-lyon.fr  Thu Apr 23 12:13:24 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 23 Apr 2020 18:13:24 +0200
Subject: [Rtk-users] Rotation before and during rktprojections
In-Reply-To: <7929e541-b9af-ca45-e81c-e9e6b5bebf6f@xris.eu>
References: <b3c31f1b-0a7c-67da-d8b2-b63f3fb5a5b6@xris.eu>
 <CAF0oig1H=yihYbGNKCLxjJPx0GtCXH5sW-9GzQiSbROos50Bhg@mail.gmail.com>
 <7929e541-b9af-ca45-e81c-e9e6b5bebf6f@xris.eu>
Message-ID: <CAF0oig2UM9hHbZeT3_wqfuE6poyqFpnyxMyxQ4-qrEEKi9dQHA@mail.gmail.com>

Thanks for the update. It's not a bad idea to include this in the
projections reader but ideally, it should calculate the permutation
parameter automatically from the geometry. If it's optional, it's not a bad
idea to have it in the projections reader pipeline, don't hesitate to
submit if you have a clean PR.

On Thu, Apr 23, 2020 at 3:56 PM vincent <vl at xris.eu> wrote:

> Hi,
>
> just to bring some closure to that problem..
>
> I didn't manage to adapt the ramp filter, so I instead modified
> rtkProjectionsReader to include an Orientation parameter that sets the
> right coefficients for an itkPermuteAxis filter.
>
> I don't think it is worthy to be included in the official source, but I am
> happy to share if someone requires it.
>
> Best regards,
>
> Vincent
> On 15.04.20 20:13, Simon Rit wrote:
>
> Hi Vincent,
> Everything you did is correct but rtkfdk always applies the ramp filter
> along the first dimension and does not check if this corresponds to the
> direction orthogonal to the rotation axis. For your case, it is probably
> not so difficult to adapt the code. When there is a small rotation, it is
> debatable whether one should ignore the rotation for the ramp filter,
> resample the image, or recalculate the filter in 2D (see our recent
> publication here <https://doi.org/10.1088/1361-6560/ab7875> which has not
> been implemented in RTK). I have opened an issue on github
> <https://github.com/SimonRit/RTK/issues/335>, hopefully we'll find time
> to fix this in the future (at least raise an exception above a parametrable
> rotation threshold).
> Best regards,
> Simon
>
> On Wed, Apr 15, 2020 at 7:00 PM vincent <vl at xris.eu> wrote:
>
>> Hi RTK community,
>>
>> I hope everyone is doing well in those hard times.
>>
>> I have a panel that is rotated by 90? on the CT system.  I used to
>> rotate the images back in the right orientation before building the
>> sinogram with rtkprojections, but then I thought I might give a try at
>> the "newdirection" option.  Using the matrix [0 1 0 ; 1 0 0 ; 0 0 1]
>> gives the expected results.  So far so good. But when I try to
>> reconstruct the latter with the same geometric parameters than for the
>> pre-rotated projections, I obtain a very blurry result (vs a sharp one
>> in the first case).  I am obviously missing something, and I would
>> suspect I am not giving the right information to the rtkfdk
>> application.  So far, here is what I have tried:
>>
>> -keep the projections in the initial orientation, but give the
>> "newdirection" option to the rtkfdk application,
>>
>> -specify the "newdirection" in both rtkprojections and rtkfdk,
>>
>> -turn to you for advice !
>>
>> I thank you very much in advance for any help you might be able to give.
>>
>> Best regards,
>>
>> Vincent
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200423/4b516f72/attachment.html>

From vl at xris.eu  Fri Apr 24 03:10:03 2020
From: vl at xris.eu (vincent)
Date: Fri, 24 Apr 2020 09:10:03 +0200
Subject: [Rtk-users] Rotation before and during rktprojections
In-Reply-To: <CAF0oig2UM9hHbZeT3_wqfuE6poyqFpnyxMyxQ4-qrEEKi9dQHA@mail.gmail.com>
References: <b3c31f1b-0a7c-67da-d8b2-b63f3fb5a5b6@xris.eu>
 <CAF0oig1H=yihYbGNKCLxjJPx0GtCXH5sW-9GzQiSbROos50Bhg@mail.gmail.com>
 <7929e541-b9af-ca45-e81c-e9e6b5bebf6f@xris.eu>
 <CAF0oig2UM9hHbZeT3_wqfuE6poyqFpnyxMyxQ4-qrEEKi9dQHA@mail.gmail.com>
Message-ID: <5c0aee4a-ba36-f59b-867e-47e99ed1a014@xris.eu>

Hi Simon,

I will clean my code and submit today or Monday then.

best regards,

V.

On 23.04.20 18:13, Simon Rit wrote:
> Thanks for the update. It's not a bad idea to include this in the 
> projections reader but ideally, it should calculate the permutation 
> parameter automatically from the geometry. If it's optional, it's not 
> a bad idea to have it in the projections reader pipeline, don't 
> hesitate to submit if you have a clean PR.
>
> On Thu, Apr 23, 2020 at 3:56 PM vincent <vl at xris.eu 
> <mailto:vl at xris.eu>> wrote:
>
>     Hi,
>
>     just to bring some closure to that problem..
>
>     I didn't manage to adapt the ramp filter, so I instead modified
>     rtkProjectionsReader to include an Orientation parameter that sets
>     the right coefficients for an itkPermuteAxis filter.
>
>     I don't think it is worthy to be included in the official source,
>     but I am happy to share if someone requires it.
>
>     Best regards,
>
>     Vincent
>
>     On 15.04.20 20:13, Simon Rit wrote:
>>     Hi Vincent,
>>     Everything you did is correct but rtkfdk always applies the ramp
>>     filter along the first dimension and does not check if this
>>     corresponds to the direction orthogonal to the rotation axis. For
>>     your case, it is probably not so difficult to adapt the code.
>>     When there is a small rotation, it is debatable whether one
>>     should ignore the rotation for the ramp filter, resample the
>>     image, or recalculate the filter in 2D (see our recent
>>     publication here <https://doi.org/10.1088/1361-6560/ab7875> which
>>     has not been implemented in RTK). I have opened an issue on
>>     github <https://github.com/SimonRit/RTK/issues/335>, hopefully
>>     we'll find time to fix this in the future (at least raise an
>>     exception above a parametrable rotation threshold).
>>     Best regards,
>>     Simon
>>
>>     On Wed, Apr 15, 2020 at 7:00 PM vincent <vl at xris.eu
>>     <mailto:vl at xris.eu>> wrote:
>>
>>         Hi RTK community,
>>
>>         I hope everyone is doing well in those hard times.
>>
>>         I have a panel that is rotated by 90? on the CT system.? I
>>         used to
>>         rotate the images back in the right orientation before
>>         building the
>>         sinogram with rtkprojections, but then I thought I might give
>>         a try at
>>         the "newdirection" option.? Using the matrix [0 1 0 ; 1 0 0 ;
>>         0 0 1]
>>         gives the expected results.? So far so good. But when I try to
>>         reconstruct the latter with the same geometric parameters
>>         than for the
>>         pre-rotated projections, I obtain a very blurry result (vs a
>>         sharp one
>>         in the first case).? I am obviously missing something, and I
>>         would
>>         suspect I am not giving the right information to the rtkfdk
>>         application.? So far, here is what I have tried:
>>
>>         -keep the projections in the initial orientation, but give the
>>         "newdirection" option to the rtkfdk application,
>>
>>         -specify the "newdirection" in both rtkprojections and rtkfdk,
>>
>>         -turn to you for advice !
>>
>>         I thank you very much in advance for any help you might be
>>         able to give.
>>
>>         Best regards,
>>
>>         Vincent
>>
>>         _______________________________________________
>>         Rtk-users mailing list
>>         Rtk-users at public.kitware.com
>>         <mailto:Rtk-users at public.kitware.com>
>>         https://public.kitware.com/mailman/listinfo/rtk-users
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200424/8d1f928b/attachment.html>

From yoonho94.na at gmail.com  Mon Apr 27 03:59:13 2020
From: yoonho94.na at gmail.com (=?UTF-8?B?64KY7Jyk7Zi4?=)
Date: Mon, 27 Apr 2020 16:59:13 +0900
Subject: [Rtk-users] Forward Projection
Message-ID: <CAPZFa=eVN2T9VDOq-29NkNX3ihTrVUf_9sbtry9mkNHRNFBm4Q@mail.gmail.com>

Hi I'm trying to make an sinogram of shepp logan phantom.

But I don't know how to do it using RTK...

Do I need to define geometry for this?

Here's what I did so far


image = itk.imread('C:\\Users\\USER\\Jupyter
Notebook\\ITK-RTK\\shepp_logan_phantom.png', itk.F)
array = itk.array_from_image(image)
expand = np.expand_dims(array, axis=2)   # just to make it into 3 dimension
( ForwardProjectionImageFilter only supports 3D )
expand = itk.image_from_array(expand)

ImageType = itk.Image[itk.F,3]

FWDType = rtk.ForwardProjectionImageFilter[ImageType, ImageType]
fwd = FWDType.New()


For the last line I have tried both

fwd = FWDType.New(expand)   --->   AttributeError: No method found to set
the input.
and
fwd = FWDType.New(Input = expand)    --->    AttributeError: 'itkObject'
object has no attribute 'SetInput'

they both had error like this.

How can I make an sinogram of shepp logan phantom?


Yoonho.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200427/944682eb/attachment.html>

From vl at xris.eu  Mon Apr 27 10:08:35 2020
From: vl at xris.eu (vincent)
Date: Mon, 27 Apr 2020 16:08:35 +0200
Subject: [Rtk-users] Forward Projection
In-Reply-To: <CAPZFa=eVN2T9VDOq-29NkNX3ihTrVUf_9sbtry9mkNHRNFBm4Q@mail.gmail.com>
References: <CAPZFa=eVN2T9VDOq-29NkNX3ihTrVUf_9sbtry9mkNHRNFBm4Q@mail.gmail.com>
Message-ID: <15a0ae7e-2b7e-d44a-a64d-55135587dc92@xris.eu>

Hi Yoonho,

my guess would be that FWDType possesses a SetInput method, from what? I 
understand from the inheritance diagram.

Also make sure to define a geometry using an instance 
ofrtk.ThreeDCircularProjectionGeometry.

I encourage you to have a look at the class documentation: 
http://www.openrtk.org/Doxygen/classrtk_1_1ForwardProjectionImageFilter.html

Hope it helps,

best regards,

Vincent

On 27.04.20 09:59, ??? wrote:
> Hi I'm trying to make an sinogram of shepp logan phantom.
>
> But I don't know how to do it using RTK...
>
> Do I need to define geometry for this?
>
> Here's what I did so far
>
>
> image = itk.imread('C:\\Users\\USER\\Jupyter 
> Notebook\\ITK-RTK\\shepp_logan_phantom.png', itk.F)
> array = itk.array_from_image(image)
> expand = np.expand_dims(array, axis=2)? ?# just to make it into 3 
> dimension ( ForwardProjectionImageFilter only supports 3D )
> expand = itk.image_from_array(expand)
>
> ImageType = itk.Image[itk.F,3]
>
> FWDType = rtk.ForwardProjectionImageFilter[ImageType, ImageType]
> fwd = FWDType.New()
>
>
> For the last line I have tried both
>
> fwd = FWDType.New(expand)? ?---> AttributeError: No method found to 
> set the input.
> and
> fwd = FWDType.New(Input = expand)? ? ---> AttributeError: 'itkObject' 
> object has no attribute 'SetInput'
>
> they both had error like this.
>
> How can I make an sinogram of shepp logan phantom?
>
>
> Yoonho.
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200427/38932e3c/attachment.html>

From simon.rit at creatis.insa-lyon.fr  Mon Apr 27 10:42:07 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 27 Apr 2020 16:42:07 +0200
Subject: [Rtk-users] Forward Projection
In-Reply-To: <15a0ae7e-2b7e-d44a-a64d-55135587dc92@xris.eu>
References: <CAPZFa=eVN2T9VDOq-29NkNX3ihTrVUf_9sbtry9mkNHRNFBm4Q@mail.gmail.com>
 <15a0ae7e-2b7e-d44a-a64d-55135587dc92@xris.eu>
Message-ID: <CAF0oig3AnNjHbHZx_ECSK7uaG5Vb9NVRmf41AhzOOYkZWJkbaQ@mail.gmail.com>

Hi,
ForwardProjectionImageFilter is a purely virtual class. Try for
example Joseph's
projector
<http://www.openrtk.org/Doxygen/classrtk_1_1JosephForwardProjectionImageFilter.html>
.
The forward projectors in RTK need two inputs : empty projections in which
to project (input 0) and the volume to project (input 1).
Check the c++ code of rtkforwarprojection
<https://github.com/SimonRit/RTK/blob/master/applications/rtkforwardprojections/rtkforwardprojections.cxx>
for a complete example, it's really not too hard to translate it to python.
Simon

On Mon, Apr 27, 2020 at 4:15 PM vincent via Rtk-users <
rtk-users at public.kitware.com> wrote:

> Hi Yoonho,
>
> my guess would be that FWDType possesses a SetInput method, from what  I
> understand from the inheritance diagram.
>
> Also make sure to define a geometry using an instance of
> rtk.ThreeDCircularProjectionGeometry.
>
> I encourage you to have a look at the class documentation:
> http://www.openrtk.org/Doxygen/classrtk_1_1ForwardProjectionImageFilter.html
>
> Hope it helps,
>
> best regards,
>
> Vincent
> On 27.04.20 09:59, ??? wrote:
>
> Hi I'm trying to make an sinogram of shepp logan phantom.
>
> But I don't know how to do it using RTK...
>
> Do I need to define geometry for this?
>
> Here's what I did so far
>
>
> image = itk.imread('C:\\Users\\USER\\Jupyter
> Notebook\\ITK-RTK\\shepp_logan_phantom.png', itk.F)
> array = itk.array_from_image(image)
> expand = np.expand_dims(array, axis=2)   # just to make it into 3
> dimension ( ForwardProjectionImageFilter only supports 3D )
> expand = itk.image_from_array(expand)
>
> ImageType = itk.Image[itk.F,3]
>
> FWDType = rtk.ForwardProjectionImageFilter[ImageType, ImageType]
> fwd = FWDType.New()
>
>
> For the last line I have tried both
>
> fwd = FWDType.New(expand)   --->   AttributeError: No method found to set
> the input.
> and
> fwd = FWDType.New(Input = expand)    --->    AttributeError: 'itkObject'
> object has no attribute 'SetInput'
>
> they both had error like this.
>
> How can I make an sinogram of shepp logan phantom?
>
>
> Yoonho.
>
> _______________________________________________
> Rtk-users mailing listRtk-users at public.kitware.comhttps://public.kitware.com/mailman/listinfo/rtk-users
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200427/1b735738/attachment.html>

From simon.rit at creatis.insa-lyon.fr  Tue Apr 28 11:17:14 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Tue, 28 Apr 2020 17:17:14 +0200
Subject: [Rtk-users] problem with installing RTK and Python
In-Reply-To: <005801d617ec$9cf85750$d6e905f0$@surgiqual-institute.com>
References: <005801d617ec$9cf85750$d6e905f0$@surgiqual-institute.com>
Message-ID: <CAF0oig3Nm0yVm67eKG0TGAxhO1cP+WzVHzh4=g=x_t3wOLyFaQ@mail.gmail.com>

Hi Yannick,
Sorry for the late reply. Actually, we do not have a python 3.8 itk-rtk
release yet. That's probably the problem here...
We'll try to provide one asap!
Simon

On Tue, Apr 21, 2020 at 6:09 PM Yannick Grondin <
Yannick.Grondin at surgiqual-institute.com> wrote:

> Hi all,
>
> I have a problem with installing ITK / RTK with Python
>
>
>
> I have done:
>
> pip install itk
>
> pip install itk-rtk
>
> (Python 3.8, sys 64 bits)
>
>
>
> I got the following output or error:
>
>
>
> pip list
>
> Package          Version
>
> ---------------- -------
>
> itk              5.0.1
>
> itk-core         5.0.1
>
> itk-filtering    5.0.1
>
> itk-io           5.0.1
>
> itk-numerics     5.0.1
>
> itk-registration 5.0.1
>
> itk-segmentation 5.0.1
>
> numpy            1.18.3
>
> packaging        20.3
>
> pip              20.0.2
>
> pyparsing        2.4.7
>
> scikit-build     0.10.0
>
> setuptools       41.2.0
>
> six              1.14.0
>
> wheel            0.34.2
>
>
>
> PS C:\WINDOWS\system32> python -m pip install itk-rtk
>
> Collecting itk-rtk
>
>   Using cached itk-rtk-2.0.1.zip (2.1 MB)
>
>     ERROR: Command errored out with exit status 1:
>
>      command: 'C:\Python38-x64\python.exe' -c 'import sys, setuptools,
> tokenize; sys.argv[0] =
> '"'"'C:\\Users\\myUser\\AppData\\Local\\Temp\\pip-install-9fmwt65s\\itk-rtk\\setup.py'"'"';
> __file__='"'"'C:\\Users\\myUser\\AppData\\Local\\Temp\\pip-install-9fmwt65s\\itk-rtk\\setup.py'"'"';f=getattr(tokenize,
> '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"',
> '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))'
> egg_info --egg-base
> 'C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info'
>
>          cwd:
> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\
>
>     Complete output (8 lines):
>
>     running egg_info
>
>     creating
> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info
>
>     writing
> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info\PKG-INFO
>
>     writing dependency_links to
> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info\dependency_links.txt
>
>     writing requirements to
> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info\requires.txt
>
>     writing top-level names to
> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info\top_level.txt
>
>     writing manifest file
> 'C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info\SOURCES.txt'
>
>     error: package directory 'itk' does not exist
>
>     ----------------------------------------
>
> ERROR: Command errored out with exit status 1: python setup.py egg_info
> Check the logs for full command output.
>
>
>
> Can you see something wrong?
>
> Thanks,
>
> Y
>
> ____________________________
>
> [image: SQI_Logo_Mail] <http://www.surgiqual-institute.com/>
>
> *Yannick Grondin, PhD*
>
> *Radiation Physics R&D Engineer*
>
> http://www.surgiqual-institute.com/
>
> +33 (0) 4 58 00 38 08
>
>
>
>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200428/0adcfefe/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image003.png
Type: image/png
Size: 22222 bytes
Desc: not available
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200428/0adcfefe/attachment-0001.png>

From simon.rit at creatis.insa-lyon.fr  Tue Apr 28 18:38:27 2020
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 29 Apr 2020 00:38:27 +0200
Subject: [Rtk-users] problem with installing RTK and Python
In-Reply-To: <CAF0oig3Nm0yVm67eKG0TGAxhO1cP+WzVHzh4=g=x_t3wOLyFaQ@mail.gmail.com>
References: <005801d617ec$9cf85750$d6e905f0$@surgiqual-institute.com>
 <CAF0oig3Nm0yVm67eKG0TGAxhO1cP+WzVHzh4=g=x_t3wOLyFaQ@mail.gmail.com>
Message-ID: <CAF0oig3mWNHhQmH1uJQ5gjwdaCLgyU0oZhr82C9CSbc-BAw_ig@mail.gmail.com>

Hi Yannick,
I have added 3.8 in a new PR <https://github.com/SimonRit/RTK/pull/341>.
Our continuous integration has produced a python package which is available
here
<https://dev.azure.com/simonrit/RTK/_build/results?buildId=429&view=artifacts&type=publishedArtifacts>.
It seems to work and it depends on the new ITK 5.1 python package (which
has not even been announced yet!).
I hope this helps,
Simon

On Tue, Apr 28, 2020 at 5:17 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi Yannick,
> Sorry for the late reply. Actually, we do not have a python 3.8 itk-rtk
> release yet. That's probably the problem here...
> We'll try to provide one asap!
> Simon
>
> On Tue, Apr 21, 2020 at 6:09 PM Yannick Grondin <
> Yannick.Grondin at surgiqual-institute.com> wrote:
>
>> Hi all,
>>
>> I have a problem with installing ITK / RTK with Python
>>
>>
>>
>> I have done:
>>
>> pip install itk
>>
>> pip install itk-rtk
>>
>> (Python 3.8, sys 64 bits)
>>
>>
>>
>> I got the following output or error:
>>
>>
>>
>> pip list
>>
>> Package          Version
>>
>> ---------------- -------
>>
>> itk              5.0.1
>>
>> itk-core         5.0.1
>>
>> itk-filtering    5.0.1
>>
>> itk-io           5.0.1
>>
>> itk-numerics     5.0.1
>>
>> itk-registration 5.0.1
>>
>> itk-segmentation 5.0.1
>>
>> numpy            1.18.3
>>
>> packaging        20.3
>>
>> pip              20.0.2
>>
>> pyparsing        2.4.7
>>
>> scikit-build     0.10.0
>>
>> setuptools       41.2.0
>>
>> six              1.14.0
>>
>> wheel            0.34.2
>>
>>
>>
>> PS C:\WINDOWS\system32> python -m pip install itk-rtk
>>
>> Collecting itk-rtk
>>
>>   Using cached itk-rtk-2.0.1.zip (2.1 MB)
>>
>>     ERROR: Command errored out with exit status 1:
>>
>>      command: 'C:\Python38-x64\python.exe' -c 'import sys, setuptools,
>> tokenize; sys.argv[0] =
>> '"'"'C:\\Users\\myUser\\AppData\\Local\\Temp\\pip-install-9fmwt65s\\itk-rtk\\setup.py'"'"';
>> __file__='"'"'C:\\Users\\myUser\\AppData\\Local\\Temp\\pip-install-9fmwt65s\\itk-rtk\\setup.py'"'"';f=getattr(tokenize,
>> '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"',
>> '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))'
>> egg_info --egg-base
>> 'C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info'
>>
>>          cwd:
>> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\
>>
>>     Complete output (8 lines):
>>
>>     running egg_info
>>
>>     creating
>> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info
>>
>>     writing
>> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info\PKG-INFO
>>
>>     writing dependency_links to
>> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info\dependency_links.txt
>>
>>     writing requirements to
>> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info\requires.txt
>>
>>     writing top-level names to
>> C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info\top_level.txt
>>
>>     writing manifest file
>> 'C:\Users\myUser\AppData\Local\Temp\pip-install-9fmwt65s\itk-rtk\pip-egg-info\itk_rtk.egg-info\SOURCES.txt'
>>
>>     error: package directory 'itk' does not exist
>>
>>     ----------------------------------------
>>
>> ERROR: Command errored out with exit status 1: python setup.py egg_info
>> Check the logs for full command output.
>>
>>
>>
>> Can you see something wrong?
>>
>> Thanks,
>>
>> Y
>>
>> ____________________________
>>
>> [image: SQI_Logo_Mail] <http://www.surgiqual-institute.com/>
>>
>> *Yannick Grondin, PhD*
>>
>> *Radiation Physics R&D Engineer*
>>
>> http://www.surgiqual-institute.com/
>>
>> +33 (0) 4 58 00 38 08
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200429/1e159ead/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image003.png
Type: image/png
Size: 22222 bytes
Desc: not available
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200429/1e159ead/attachment-0001.png>