From bakkari.abdelkhalek at hotmail.fr  Sat Dec  3 17:39:08 2016
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Sat, 3 Dec 2016 22:39:08 +0000
Subject: [ITK] [ITK-users] 3D Binary Mask to Point Set - 3D Image
	Registration -
Message-ID: <AM2PR09MB0562A437E9B769C2BA1261E983810@AM2PR09MB0562.eurprd09.prod.outlook.com>

Hi,

I am a little familiar with ITK.
I just need to know how can I apply the model to Image registration 2 to a dicom image  series.


https://itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ModelToImageRegistration2_8cxx-example.html#_a13


Thank you inadvance.

Kind regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland


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From bakkari.abdelkhalek at hotmail.fr  Sat Dec  3 18:08:26 2016
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Sat, 3 Dec 2016 23:08:26 +0000
Subject: [ITK] [ITK-users] 3D Binary Mask to Point Set -
	3D	Image	Registration -
In-Reply-To: <DM2PR07MB3500699E69CC50CB201BB74D8810@DM2PR07MB350.namprd07.prod.outlook.com>
References: <AM2PR09MB0562A437E9B769C2BA1261E983810@AM2PR09MB0562.eurprd09.prod.outlook.com>,
 <DM2PR07MB3500699E69CC50CB201BB74D8810@DM2PR07MB350.namprd07.prod.outlook.com>
Message-ID: <AM2PR09MB056200D9576E64EB5ECC14D083810@AM2PR09MB0562.eurprd09.prod.outlook.com>


Hi Andras,


I am not using just using examples. But, I am creating my own application from existing examples in ITK.




________________________________
From: Andras Lasso <lasso at queensu.ca>
Sent: 03 December 2016 23:57
To: Abdelkhalek Bakkari
Subject: RE: [ITK] [ITK-users] 3D Binary Mask to Point Set - 3D Image Registration -

Hi Abdelkhalek,

ITK is a only for algorithm developers or advanced users (who can figure out how to perform simple operations such as applying a transform from the plenty of examples and tests that are included in ITK). If you want to just use algorithms then it's much more efficient to use applications that ITK is integrated into.

For example, applying a transform to a DICOM series is a trivial operation in 3D Slicer (drag-and-drop DICOM directory to import your DICOM data, use DICOM module to load DICOM series, drag-and-drop transform file to load transform, using Transforms module apply transform to image). You can also perform all kinds of analysis, segmentation, quantification, and visualization tasks in Slicer (you can visualize the original and transformed volume, original and transformed landmark points, segmented surfaces; or the transformation itself). You can also fully script all operations if you need to process a large number of sequences in batch mode.

Andras

From: Abdelkhalek Bakkari<mailto:bakkari.abdelkhalek at hotmail.fr>
Sent: Saturday, December 3, 2016 17:39
To: insight-users<mailto:insight-users at itk.org>
Subject: [ITK] [ITK-users] 3D Binary Mask to Point Set - 3D Image Registration -


Hi,

I am a little familiar with ITK.
I just need to know how can I apply the model to Image registration 2 to a dicom image  series.


https://itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ModelToImageRegistration2_8cxx-example.html#_a13


Thank you inadvance.

Kind regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland


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From lasso at queensu.ca  Sat Dec  3 20:15:56 2016
From: lasso at queensu.ca (Andras Lasso)
Date: Sun, 4 Dec 2016 01:15:56 +0000
Subject: [ITK] [ITK-users] 3D Binary Mask to Point Set -
	3D	Image	Registration -
In-Reply-To: <AM2PR09MB056200D9576E64EB5ECC14D083810@AM2PR09MB0562.eurprd09.prod.outlook.com>
References: <AM2PR09MB0562A437E9B769C2BA1261E983810@AM2PR09MB0562.eurprd09.prod.outlook.com>,
 <DM2PR07MB3500699E69CC50CB201BB74D8810@DM2PR07MB350.namprd07.prod.outlook.com>
 <AM2PR09MB056200D9576E64EB5ECC14D083810@AM2PR09MB0562.eurprd09.prod.outlook.com>
Message-ID: <DM2PR07MB350EEE84EFAD04AC5B2D269D8800@DM2PR07MB350.namprd07.prod.outlook.com>

The point I'm trying to make is that you should not start developing a custom application from scratch before you have a complete, proven, and tested solution.

You can develop and test solutions very quickly by using existing application frameworks (3D Slicer, MITK, Paraview, etc). They all allow writing plugins to add custom algorithms or streamlined user interface.

Andras

From: Abdelkhalek Bakkari [mailto:bakkari.abdelkhalek at hotmail.fr]
Sent: December 3, 2016 18:08
To: Andras Lasso <lasso at queensu.ca>; insight-users <insight-users at itk.org>
Subject: Re: [ITK] [ITK-users] 3D Binary Mask to Point Set - 3D Image Registration -




Hi Andras,



I am not using just using examples. But, I am creating my own application from existing examples in ITK.





________________________________
From: Andras Lasso <lasso at queensu.ca<mailto:lasso at queensu.ca>>
Sent: 03 December 2016 23:57
To: Abdelkhalek Bakkari
Subject: RE: [ITK] [ITK-users] 3D Binary Mask to Point Set - 3D Image Registration -

Hi Abdelkhalek,

ITK is a only for algorithm developers or advanced users (who can figure out how to perform simple operations such as applying a transform from the plenty of examples and tests that are included in ITK). If you want to just use algorithms then it's much more efficient to use applications that ITK is integrated into.

For example, applying a transform to a DICOM series is a trivial operation in 3D Slicer (drag-and-drop DICOM directory to import your DICOM data, use DICOM module to load DICOM series, drag-and-drop transform file to load transform, using Transforms module apply transform to image). You can also perform all kinds of analysis, segmentation, quantification, and visualization tasks in Slicer (you can visualize the original and transformed volume, original and transformed landmark points, segmented surfaces; or the transformation itself). You can also fully script all operations if you need to process a large number of sequences in batch mode.

Andras

From: Abdelkhalek Bakkari<mailto:bakkari.abdelkhalek at hotmail.fr>
Sent: Saturday, December 3, 2016 17:39
To: insight-users<mailto:insight-users at itk.org>
Subject: [ITK] [ITK-users] 3D Binary Mask to Point Set - 3D Image Registration -

Hi,

I am a little familiar with ITK.
I just need to know how can I apply the model to Image registration 2 to a dicom image  series.


https://itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ModelToImageRegistration2_8cxx-example.html#_a13


Thank you inadvance.

Kind regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland


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From cgo_2113 at hotmail.com  Sun Dec  4 09:15:29 2016
From: cgo_2113 at hotmail.com (CocoM)
Date: Sun, 4 Dec 2016 07:15:29 -0700 (MST)
Subject: [ITK] [ITK-users] Optimization in deformable registration
Message-ID: <1480860929243-7589502.post@n2.nabble.com>

Hi everyone,

Being fairly new in ITK, I have kind of a general question about deformable
registration. I'm working with the LevelSetMotionRegistrationFilter/Function
classes and the example DeformableRegistration5, which is using them. I
noticed this example doesn't use any optimizer class. It seems to be the
same for the other PDEDeformable methods. So my question is : why? Is that
because it's non parametric registration? And I guess there isn't any
possibility to use an optimizer class in that kind of problem?

Thanks a lot in advance,

Marie



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Optimization-in-deformable-registration-tp7589502.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
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From dzenanz at gmail.com  Sun Dec  4 13:04:28 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sun, 4 Dec 2016 13:04:28 -0500
Subject: [ITK] [ITK-users] Optimization in deformable registration
In-Reply-To: <1480860929243-7589502.post@n2.nabble.com>
References: <1480860929243-7589502.post@n2.nabble.com>
Message-ID: <CAPf2UMTMPPLWh=b-8--y20c9puGzJ+skDZ_CcQJ-zW32_SY-QQ@mail.gmail.com>

Hi Marie,

by looking at the documentation of Level-Set Motion Registration Filter
<https://itk.org/Doxygen/html/classitk_1_1LevelSetMotionRegistrationFilter.html>,
optimizer is not needed. The whole registration is set up as an iterative
process, executing motion equations at each iteration. You need to
experiment with it to see which number of iterations produces good results
for your case.

Regards,
D?enan

On Sun, Dec 4, 2016 at 9:15 AM, CocoM <cgo_2113 at hotmail.com> wrote:

> Hi everyone,
>
> Being fairly new in ITK, I have kind of a general question about deformable
> registration. I'm working with the LevelSetMotionRegistrationFilt
> er/Function
> classes and the example DeformableRegistration5, which is using them. I
> noticed this example doesn't use any optimizer class. It seems to be the
> same for the other PDEDeformable methods. So my question is : why? Is that
> because it's non parametric registration? And I guess there isn't any
> possibility to use an optimizer class in that kind of problem?
>
> Thanks a lot in advance,
>
> Marie
>
>
>
> --
> View this message in context: http://itk-insight-users.
> 2283740.n2.nabble.com/Optimization-in-deformable-
> registration-tp7589502.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
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From steve at sumost.ca  Sun Dec  4 13:43:37 2016
From: steve at sumost.ca (Steve M. Robbins)
Date: Sun, 04 Dec 2016 12:43:37 -0600
Subject: [ITK] [ITK-users] Picking corresponding anatomical points --
	best	software for a clinician?
Message-ID: <2164522.aeE28Xrt1B@riemann>

Hi,

I have an urgent need to acquire some data to validate (medical) image 
registration in a clinical context.  To that end, I plan to sit with several 
clinicians and have them identify salient points in two datasets that will be 
registered.  Then I plan to use the residual errors of these points after 
registration -- e.g. the median distance -- as a quality metric.

What I'm after right now is a really easy-to-use tool with which the clinician 
can pick the points.  So that one can judge the points are indeed 
corresponding: my present thought is to have an MPR view of each image volume 
side-by-side; e.g. axial/sagittal/coronal of volume 1 on top of the same 
slices of volume 2.  Or similar.  My main requirement is that a clinician who 
is familar with PACS viewers can learn to use it in a minute or so.  

The other requirement is that the point coordinates can be saved to a file for 
later analysis.  Despite posting to the ITK list: ITK is not a requirement.

My question, briefly, is: what software would you recommend for this scenario?

I have briefly looked at 3D Slicer, MITK, Amide, and RegistrationShop.  So far, 
3D Slicer is the only one that I can even find the functionality I want -- 
using the LandmarkRegistration module.   I realize this next part may come 
across as whining so let me say up front I mean no denigration of the many fine 
folks who put hard work into 3D Slicer!  If I were the one picking the points, 
I think the Landmark Registration of 3D Slicer would be fine.  However, the 
clinician will be driving and will typically have limited time and patience -- 
so I want something reasonably familiar.   For example: in navigating through 
the stacks: I can use the scrool wheel or slider to choose a slice.  But then 
I have to manipulate all three slices to find a point.  In other software, one 
can grab the slice intersection lines and update the other two slices -- e.g. 
move the coronal and sagittal to intersect a point of interest located on the 
axial.    I can turn on slice intersection lines, but it shows intersections 
for BOTH volumes, which I don't want as they are not registered.  And when I 
use SHIFT to drag around the lines, both volumes are updated.  I need to do 
one volume at a time.  

Maybe there is a way to tune the Slicer GUI to my needs?  Or maybe a more 
appropriate module I have overlooked?

For any thoughts: thanks in advance,
-Steve
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From fepegar at gmail.com  Sun Dec  4 13:59:52 2016
From: fepegar at gmail.com (=?UTF-8?B?RmVybmFuZG8gUMOpcmV6LUdhcmPDrWE=?=)
Date: Sun, 4 Dec 2016 19:59:52 +0100
Subject: [ITK] [ITK-users] Picking corresponding anatomical points --
 best software for a clinician?
In-Reply-To: <2164522.aeE28Xrt1B@riemann>
References: <2164522.aeE28Xrt1B@riemann>
Message-ID: <CAC6GVWgO+pD_Kq9vU+H7MvE8tm20Z6Mqjv6DG+uqShJnH3gPkA@mail.gmail.com>

?Hi Steve,

I think you should ask in Slicer mailing list:
http://slicer-users.65878.n3.nabble.com/

You should be able to do what you want with some Python scripting.


Best,

Fernando?

2016-12-04 19:43 GMT+01:00 Steve M. Robbins <steve at sumost.ca>:

> Hi,
>
> I have an urgent need to acquire some data to validate (medical) image
> registration in a clinical context.  To that end, I plan to sit with
> several
> clinicians and have them identify salient points in two datasets that will
> be
> registered.  Then I plan to use the residual errors of these points after
> registration -- e.g. the median distance -- as a quality metric.
>
> What I'm after right now is a really easy-to-use tool with which the
> clinician
> can pick the points.  So that one can judge the points are indeed
> corresponding: my present thought is to have an MPR view of each image
> volume
> side-by-side; e.g. axial/sagittal/coronal of volume 1 on top of the same
> slices of volume 2.  Or similar.  My main requirement is that a clinician
> who
> is familar with PACS viewers can learn to use it in a minute or so.
>
> The other requirement is that the point coordinates can be saved to a file
> for
> later analysis.  Despite posting to the ITK list: ITK is not a requirement.
>
> My question, briefly, is: what software would you recommend for this
> scenario?
>
> I have briefly looked at 3D Slicer, MITK, Amide, and RegistrationShop.  So
> far,
> 3D Slicer is the only one that I can even find the functionality I want --
> using the LandmarkRegistration module.   I realize this next part may come
> across as whining so let me say up front I mean no denigration of the many
> fine
> folks who put hard work into 3D Slicer!  If I were the one picking the
> points,
> I think the Landmark Registration of 3D Slicer would be fine.  However, the
> clinician will be driving and will typically have limited time and
> patience --
> so I want something reasonably familiar.   For example: in navigating
> through
> the stacks: I can use the scrool wheel or slider to choose a slice.  But
> then
> I have to manipulate all three slices to find a point.  In other software,
> one
> can grab the slice intersection lines and update the other two slices --
> e.g.
> move the coronal and sagittal to intersect a point of interest located on
> the
> axial.    I can turn on slice intersection lines, but it shows
> intersections
> for BOTH volumes, which I don't want as they are not registered.  And when
> I
> use SHIFT to drag around the lines, both volumes are updated.  I need to do
> one volume at a time.
>
> Maybe there is a way to tune the Slicer GUI to my needs?  Or maybe a more
> appropriate module I have overlooked?
>
> For any thoughts: thanks in advance,
> -Steve
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From dzenanz at gmail.com  Sun Dec  4 19:04:06 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sun, 4 Dec 2016 19:04:06 -0500
Subject: [ITK] [ITK-users] Picking corresponding anatomical points --
 best software for a clinician?
In-Reply-To: <2164522.aeE28Xrt1B@riemann>
References: <2164522.aeE28Xrt1B@riemann>
Message-ID: <CAPf2UMTTUo+o3iaVetvUOogeeEtCQ-5mKJb_iiXDmtNTNXffWA@mail.gmail.com>

Hi Steve,

in 3DSlicer, pressing shift key (Windows, could be different on Mac) and
moving mouse will select other 2 slices corresponding to mouse position.
Slicer can also save fiducial points list into a file (comma separated
values format).

Regards,
D?enan

On Sun, Dec 4, 2016 at 1:43 PM, Steve M. Robbins <steve at sumost.ca> wrote:

> Hi,
>
> I have an urgent need to acquire some data to validate (medical) image
> registration in a clinical context.  To that end, I plan to sit with
> several
> clinicians and have them identify salient points in two datasets that will
> be
> registered.  Then I plan to use the residual errors of these points after
> registration -- e.g. the median distance -- as a quality metric.
>
> What I'm after right now is a really easy-to-use tool with which the
> clinician
> can pick the points.  So that one can judge the points are indeed
> corresponding: my present thought is to have an MPR view of each image
> volume
> side-by-side; e.g. axial/sagittal/coronal of volume 1 on top of the same
> slices of volume 2.  Or similar.  My main requirement is that a clinician
> who
> is familar with PACS viewers can learn to use it in a minute or so.
>
> The other requirement is that the point coordinates can be saved to a file
> for
> later analysis.  Despite posting to the ITK list: ITK is not a requirement.
>
> My question, briefly, is: what software would you recommend for this
> scenario?
>
> I have briefly looked at 3D Slicer, MITK, Amide, and RegistrationShop.  So
> far,
> 3D Slicer is the only one that I can even find the functionality I want --
> using the LandmarkRegistration module.   I realize this next part may come
> across as whining so let me say up front I mean no denigration of the many
> fine
> folks who put hard work into 3D Slicer!  If I were the one picking the
> points,
> I think the Landmark Registration of 3D Slicer would be fine.  However, the
> clinician will be driving and will typically have limited time and
> patience --
> so I want something reasonably familiar.   For example: in navigating
> through
> the stacks: I can use the scrool wheel or slider to choose a slice.  But
> then
> I have to manipulate all three slices to find a point.  In other software,
> one
> can grab the slice intersection lines and update the other two slices --
> e.g.
> move the coronal and sagittal to intersect a point of interest located on
> the
> axial.    I can turn on slice intersection lines, but it shows
> intersections
> for BOTH volumes, which I don't want as they are not registered.  And when
> I
> use SHIFT to drag around the lines, both volumes are updated.  I need to do
> one volume at a time.
>
> Maybe there is a way to tune the Slicer GUI to my needs?  Or maybe a more
> appropriate module I have overlooked?
>
> For any thoughts: thanks in advance,
> -Steve
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From steve at sumost.ca  Sun Dec  4 22:40:18 2016
From: steve at sumost.ca (Steve M. Robbins)
Date: Sun, 04 Dec 2016 21:40:18 -0600
Subject: [ITK] [ITK-users] Picking corresponding anatomical points --
	best	software for a clinician?
In-Reply-To: <CAPf2UMTTUo+o3iaVetvUOogeeEtCQ-5mKJb_iiXDmtNTNXffWA@mail.gmail.com>
References: <2164522.aeE28Xrt1B@riemann>
 <CAPf2UMTTUo+o3iaVetvUOogeeEtCQ-5mKJb_iiXDmtNTNXffWA@mail.gmail.com>
Message-ID: <296184501.RM8fqRJEb6@riemann>

Dear slicer-users: I originally asked a question in insight-users but it 
touches on slicer, so I'm cross-posting.


On Sunday, December 4, 2016 7:04:06 PM CST D?enan Zuki? wrote:
> Hi Steve,
> 
> in 3DSlicer, pressing shift key (Windows, could be different on Mac) and
> moving mouse will select other 2 slices corresponding to mouse position.

Yes, but when I have two volumes displayed using Landmark Registration module, 
the shift-mouse-move operation on axial updates the sagital and coronal of 
BOTH volumes, not just the one I'm operating on.  This seems wrong to me when 
the two volumes are not registered.

> Slicer can also save fiducial points list into a file (comma separated
> values format).

Yes, that is great.


> 
> Regards,
> D?enan
> 
> On Sun, Dec 4, 2016 at 1:43 PM, Steve M. Robbins <steve at sumost.ca> wrote:
> > Hi,
> > 
> > I have an urgent need to acquire some data to validate (medical) image
> > registration in a clinical context.  To that end, I plan to sit with
> > several
> > clinicians and have them identify salient points in two datasets that will
> > be
> > registered.  Then I plan to use the residual errors of these points after
> > registration -- e.g. the median distance -- as a quality metric.
> > 
> > What I'm after right now is a really easy-to-use tool with which the
> > clinician
> > can pick the points.  So that one can judge the points are indeed
> > corresponding: my present thought is to have an MPR view of each image
> > volume
> > side-by-side; e.g. axial/sagittal/coronal of volume 1 on top of the same
> > slices of volume 2.  Or similar.  My main requirement is that a clinician
> > who
> > is familar with PACS viewers can learn to use it in a minute or so.
> > 
> > The other requirement is that the point coordinates can be saved to a file
> > for
> > later analysis.  Despite posting to the ITK list: ITK is not a
> > requirement.
> > 
> > My question, briefly, is: what software would you recommend for this
> > scenario?
> > 
> > I have briefly looked at 3D Slicer, MITK, Amide, and RegistrationShop.  So
> > far,
> > 3D Slicer is the only one that I can even find the functionality I want --
> > using the LandmarkRegistration module.   I realize this next part may come
> > across as whining so let me say up front I mean no denigration of the many
> > fine
> > folks who put hard work into 3D Slicer!  If I were the one picking the
> > points,
> > I think the Landmark Registration of 3D Slicer would be fine.  However,
> > the
> > clinician will be driving and will typically have limited time and
> > patience --
> > so I want something reasonably familiar.   For example: in navigating
> > through
> > the stacks: I can use the scrool wheel or slider to choose a slice.  But
> > then
> > I have to manipulate all three slices to find a point.  In other software,
> > one
> > can grab the slice intersection lines and update the other two slices --
> > e.g.
> > move the coronal and sagittal to intersect a point of interest located on
> > the
> > axial.    I can turn on slice intersection lines, but it shows
> > intersections
> > for BOTH volumes, which I don't want as they are not registered.  And when
> > I
> > use SHIFT to drag around the lines, both volumes are updated.  I need to
> > do
> > one volume at a time.
> > 
> > Maybe there is a way to tune the Slicer GUI to my needs?  Or maybe a more
> > appropriate module I have overlooked?
> > 
> > For any thoughts: thanks in advance,
> > -Steve
> > 
> > _____________________________________
> > Powered by www.kitware.com
> > 
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> > 
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> > 
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> > 
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users

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From blowekamp at mail.nih.gov  Mon Dec  5 13:17:59 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 5 Dec 2016 18:17:59 +0000
Subject: [ITK] [ITK-dev] Visual Studio 2017 RC
Message-ID: <40570EE4-3979-4125-9A81-39FFDBCDBF12@mail.nih.gov>

Hello,

Has anyone tried out the new MS Visual Studio 2017 RC with ITK?

Thanks,
Brad
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From dzenanz at gmail.com  Tue Dec  6 10:20:18 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 6 Dec 2016 10:20:18 -0500
Subject: [ITK] [ITK-dev] Visual Studio 2017 RC
In-Reply-To: <40570EE4-3979-4125-9A81-39FFDBCDBF12@mail.nih.gov>
References: <40570EE4-3979-4125-9A81-39FFDBCDBF12@mail.nih.gov>
Message-ID: <CAPf2UMQ_NHgP_3FQ=SdozWvCY9B_TnC5RVZWLQP59gVOw40F9A@mail.gmail.com>

I have. It has internal compiler error a few hundred times when compiling
ITK. I submitted the issue to Microsoft. Beta 3 or 4 (I don't remember
which one I tried) compiled ITK without issues - but that version was still
using the old compiler toolchain (v140). 2017 RC uses toolset v141.

Regards,
D?enan

On Mon, Dec 5, 2016 at 1:17 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Hello,
>
> Has anyone tried out the new MS Visual Studio 2017 RC with ITK?
>
> Thanks,
> Brad
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>
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From blowekamp at mail.nih.gov  Tue Dec  6 13:14:29 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 6 Dec 2016 18:14:29 +0000
Subject: [ITK] [ITK-dev] Visual Studio 2017 RC
In-Reply-To: <CAPf2UMQ_NHgP_3FQ=SdozWvCY9B_TnC5RVZWLQP59gVOw40F9A@mail.gmail.com>
References: <40570EE4-3979-4125-9A81-39FFDBCDBF12@mail.nih.gov>
 <CAPf2UMQ_NHgP_3FQ=SdozWvCY9B_TnC5RVZWLQP59gVOw40F9A@mail.gmail.com>
Message-ID: <89356520-B449-420C-A87F-9BB1C65F8AD1@mail.nih.gov>

I am not were where to get that ?toolset? version number from. I just downloaded the VS 2017 RC this morning.

I am getting this info from the compiler:

/c/Program\ Files\ \(x86\)/Microsoft\ Visual\ Studio\ 14.0/VC/bin/cl.exe
Microsoft (R) C/C++ Optimizing Compiler Version 19.00.24215.1 for x86
Copyright (C) Microsoft Corporation.  All rights reserved.

Here is the build on CDash:
https://open.cdash.org/buildSummary.php?buildid=4673579

It looks like the internal compiler errors have been resolved. Just one relevant failing test.

Brad

On Dec 6, 2016, at 10:20 AM, D?enan Zuki? <dzenanz at gmail.com<mailto:dzenanz at gmail.com>> wrote:

I have. It has internal compiler error a few hundred times when compiling ITK. I submitted the issue to Microsoft. Beta 3 or 4 (I don't remember which one I tried) compiled ITK without issues - but that version was still using the old compiler toolchain (v140). 2017 RC uses toolset v141.

Regards,
D?enan

On Mon, Dec 5, 2016 at 1:17 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:
Hello,

Has anyone tried out the new MS Visual Studio 2017 RC with ITK?

Thanks,
Brad
_______________________________________________
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From blowekamp at mail.nih.gov  Tue Dec  6 13:23:00 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 6 Dec 2016 18:23:00 +0000
Subject: [ITK] [ITK-dev] Visual Studio 2017 RC
In-Reply-To: <89356520-B449-420C-A87F-9BB1C65F8AD1@mail.nih.gov>
References: <40570EE4-3979-4125-9A81-39FFDBCDBF12@mail.nih.gov>
 <CAPf2UMQ_NHgP_3FQ=SdozWvCY9B_TnC5RVZWLQP59gVOw40F9A@mail.gmail.com>
 <89356520-B449-420C-A87F-9BB1C65F8AD1@mail.nih.gov>
Message-ID: <3BFB9F03-677F-4E1C-9913-F0FB6996B626@mail.nih.gov>

Correction: I am not aware of where to get that ?toolset? version number from.

On Dec 6, 2016, at 1:14 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:

I am not were where to get that ?toolset? version number from. I just downloaded the VS 2017 RC this morning.

I am getting this info from the compiler:

/c/Program\ Files\ \(x86\)/Microsoft\ Visual\ Studio\ 14.0/VC/bin/cl.exe
Microsoft (R) C/C++ Optimizing Compiler Version 19.00.24215.1 for x86
Copyright (C) Microsoft Corporation.  All rights reserved.

Here is the build on CDash:
https://open.cdash.org/buildSummary.php?buildid=4673579

It looks like the internal compiler errors have been resolved. Just one relevant failing test.

Brad

On Dec 6, 2016, at 10:20 AM, D?enan Zuki? <dzenanz at gmail.com<mailto:dzenanz at gmail.com>> wrote:

I have. It has internal compiler error a few hundred times when compiling ITK. I submitted the issue to Microsoft. Beta 3 or 4 (I don't remember which one I tried) compiled ITK without issues - but that version was still using the old compiler toolchain (v140). 2017 RC uses toolset v141.

Regards,
D?enan

On Mon, Dec 5, 2016 at 1:17 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:
Hello,

Has anyone tried out the new MS Visual Studio 2017 RC with ITK?

Thanks,
Brad
_______________________________________________
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Visit other Kitware open-source projects at
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http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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_______________________________________________
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From brad.king at kitware.com  Tue Dec  6 13:50:16 2016
From: brad.king at kitware.com (Brad King)
Date: Tue, 6 Dec 2016 13:50:16 -0500
Subject: [ITK] [ITK-dev] Visual Studio 2017 RC
In-Reply-To: <3BFB9F03-677F-4E1C-9913-F0FB6996B626@mail.nih.gov>
References: <40570EE4-3979-4125-9A81-39FFDBCDBF12@mail.nih.gov>
 <CAPf2UMQ_NHgP_3FQ=SdozWvCY9B_TnC5RVZWLQP59gVOw40F9A@mail.gmail.com>
 <89356520-B449-420C-A87F-9BB1C65F8AD1@mail.nih.gov>
 <3BFB9F03-677F-4E1C-9913-F0FB6996B626@mail.nih.gov>
Message-ID: <5f78ba87-bc03-59a9-e0fa-d7c42d9e6284@kitware.com>

On 12/06/2016 01:23 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
> Correction: I am not aware of where to get that ?toolset? version number from.
> 
>> I am getting this info from the compiler:
>>
>> /c/Program\ Files\ \(x86\)/Microsoft\ Visual\ Studio\ 14.0/VC/bin/cl.exe 
>> Microsoft (R) C/C++ Optimizing Compiler Version 19.00.24215.1 for x86
>> Copyright (C) Microsoft Corporation.  All rights reserved.

You need to use CMake 3.7.1 or above to get proper VS 2017 RC toolset
selection.

-Brad K

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From blowekamp at mail.nih.gov  Tue Dec  6 15:11:54 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 6 Dec 2016 20:11:54 +0000
Subject: [ITK] [ITK-dev] Visual Studio 2017 RC
In-Reply-To: <5f78ba87-bc03-59a9-e0fa-d7c42d9e6284@kitware.com>
References: <40570EE4-3979-4125-9A81-39FFDBCDBF12@mail.nih.gov>
 <CAPf2UMQ_NHgP_3FQ=SdozWvCY9B_TnC5RVZWLQP59gVOw40F9A@mail.gmail.com>
 <89356520-B449-420C-A87F-9BB1C65F8AD1@mail.nih.gov>
 <3BFB9F03-677F-4E1C-9913-F0FB6996B626@mail.nih.gov>
 <5f78ba87-bc03-59a9-e0fa-d7c42d9e6284@kitware.com>
Message-ID: <7A225D29-56DD-4867-935A-7695588C8535@mail.nih.gov>

Thanks!

I was using CMake 3.7.0 and specified ?Visual Studio 15 Win64?. It looks like it used the VS14 compiler.

I upgraded to CMake 3.7.1, specified ?Visual Studio 15 2017 Win64?, verified it was using the correct cl.exe, and now we have a CDash entry:

https://open.cdash.org/buildSummary.php?buildid=4673682

which now contains some internal compiler errors?.

Brad

> On Dec 6, 2016, at 1:50 PM, Brad King <brad.king at kitware.com> wrote:
> 
> On 12/06/2016 01:23 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
>> Correction: I am not aware of where to get that ?toolset? version number from.
>> 
>>> I am getting this info from the compiler:
>>> 
>>> /c/Program\ Files\ \(x86\)/Microsoft\ Visual\ Studio\ 14.0/VC/bin/cl.exe 
>>> Microsoft (R) C/C++ Optimizing Compiler Version 19.00.24215.1 for x86
>>> Copyright (C) Microsoft Corporation.  All rights reserved.
> 
> You need to use CMake 3.7.1 or above to get proper VS 2017 RC toolset
> selection.
> 
> -Brad K
> 

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From tobias.wood at kcl.ac.uk  Tue Dec  6 04:51:09 2016
From: tobias.wood at kcl.ac.uk (Wood, Tobias)
Date: Tue, 6 Dec 2016 09:51:09 +0000
Subject: [ITK] Volume of one voxel
Message-ID: <91933950-5139-479B-B1F1-A7D797333AA9@kcl.ac.uk>

Hello,

Is there a more elegant way to calculate the volume of a single voxel in an image than:

    double vox_volume = img->GetSpacing()[0];
    for (int v = 1; v < 3; v++)
        vox_volume *= img->GetSpacing()[v];

(With appropriate dimensionality)

It feels like I?m missing something cleaner.

Toby


From blowekamp at mail.nih.gov  Wed Dec  7 08:34:41 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 7 Dec 2016 13:34:41 +0000
Subject: [ITK] Volume of one voxel
In-Reply-To: <91933950-5139-479B-B1F1-A7D797333AA9@kcl.ac.uk>
References: <91933950-5139-479B-B1F1-A7D797333AA9@kcl.ac.uk>
Message-ID: <C9426856-C07B-4CD0-AFCE-71B840184E8B@mail.nih.gov>


Your code looks fine. You just may want to use ImageType::ImageDimension instead of 3 to be more generic.

In C++ some may call this more elegant:

const ImageType::SpacingType &spacing = img->GetSpacing();
double vox_volume = std::accumulate( spacing.Begin(), Spacing.End(), 1.0, std::multiplies<double>() );

However, I think you'll find your initial approach is more common throughout ITK code.

HTH,
Brad

> On Dec 6, 2016, at 4:51 AM, Wood, Tobias <tobias.wood at kcl.ac.uk> wrote:
> 
> Hello,
> 
> Is there a more elegant way to calculate the volume of a single voxel in an image than:
> 
>    double vox_volume = img->GetSpacing()[0];
>    for (int v = 1; v < 3; v++)
>        vox_volume *= img->GetSpacing()[v];
> 
> (With appropriate dimensionality)
> 
> It feels like I?m missing something cleaner.
> 
> Toby
> 
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From dzenanz at gmail.com  Wed Dec  7 18:37:13 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 7 Dec 2016 18:37:13 -0500
Subject: [ITK] [ITK-users] Fwd: [Developer Community] Ulzii Luvsanbat posted
 a new comment on "Compiling ITK triggers internal error"
In-Reply-To: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com>
References: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com>
Message-ID: <CAPf2UMQPBfxHmzGyh8538NJF9ii26hiwsmcvv=B3sKEX+Ry0Kg@mail.gmail.com>

---------- Forwarded message ----------
From: <vscommun at microsoft.com>
Date: Wed, Dec 7, 2016 at 6:17 PM
Subject: [Developer Community] Ulzii Luvsanbat posted a new comment on
"Compiling ITK triggers internal error"
To: dzenanz at gmail.com


<http://www.visualstudio.com>

Hi d?enan-zuki?,

A new comment on a *Compiling ITK triggers internal error*
<https://developercommunity.visualstudio.com/comments/6266/view.html> was
posted by Ulzii Luvsanbat on Developer Community:

* Hello, Thanks for this report. We'll look into fixing this for VS2017.
We're also going to add this open source project to our compiler validation
test suites to ensure we don't ship future VS releases that don't compile
ITK sources. Thanks, Ulzii Luvsanbat Visual C++ Team *

View Ulzii Luvsanbat's new comment
<https://developercommunity.visualstudio.com/comments/6266/view.html>

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Notification
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From dzenanz at gmail.com  Wed Dec  7 18:37:13 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 7 Dec 2016 18:37:13 -0500
Subject: [ITK] [ITK-dev] Fwd: [Developer Community] Ulzii Luvsanbat posted a
 new comment on "Compiling ITK triggers internal error"
In-Reply-To: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com>
References: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com>
Message-ID: <CAPf2UMQPBfxHmzGyh8538NJF9ii26hiwsmcvv=B3sKEX+Ry0Kg@mail.gmail.com>

---------- Forwarded message ----------
From: <vscommun at microsoft.com>
Date: Wed, Dec 7, 2016 at 6:17 PM
Subject: [Developer Community] Ulzii Luvsanbat posted a new comment on
"Compiling ITK triggers internal error"
To: dzenanz at gmail.com


<http://www.visualstudio.com>

Hi d?enan-zuki?,

A new comment on a *Compiling ITK triggers internal error*
<https://developercommunity.visualstudio.com/comments/6266/view.html> was
posted by Ulzii Luvsanbat on Developer Community:

* Hello, Thanks for this report. We'll look into fixing this for VS2017.
We're also going to add this open source project to our compiler validation
test suites to ensure we don't ship future VS releases that don't compile
ITK sources. Thanks, Ulzii Luvsanbat Visual C++ Team *

View Ulzii Luvsanbat's new comment
<https://developercommunity.visualstudio.com/comments/6266/view.html>

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Settings
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From tobias.wood at kcl.ac.uk  Wed Dec  7 10:19:59 2016
From: tobias.wood at kcl.ac.uk (Wood, Tobias)
Date: Wed, 7 Dec 2016 15:19:59 +0000
Subject: [ITK] Volume of one voxel
In-Reply-To: <C9426856-C07B-4CD0-AFCE-71B840184E8B@mail.nih.gov>
References: <91933950-5139-479B-B1F1-A7D797333AA9@kcl.ac.uk>
 <C9426856-C07B-4CD0-AFCE-71B840184E8B@mail.nih.gov>
Message-ID: <1FA09C7D-C9BD-4F5F-90C1-9668183BBC3C@kcl.ac.uk>

Thanks Brad. I guess I was wondering whether this was wrapped into function call on the Image class that I had missed. I will wrap it up in my own function now.

Best wishes,
Toby 


From blowekamp at mail.nih.gov  Thu Dec  8 10:34:22 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 8 Dec 2016 15:34:22 +0000
Subject: [ITK] [ITK-dev] [ITK-users] Fwd: [Developer Community] Ulzii
 Luvsanbat posted a new comment on "Compiling ITK triggers internal error"
In-Reply-To: <CAPf2UMQPBfxHmzGyh8538NJF9ii26hiwsmcvv=B3sKEX+Ry0Kg@mail.gmail.com>
References: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com>
 <CAPf2UMQPBfxHmzGyh8538NJF9ii26hiwsmcvv=B3sKEX+Ry0Kg@mail.gmail.com>
Message-ID: <303FFB15-F51A-48A3-AD3A-01CEEA30059F@mail.nih.gov>

Thanks for reporting and forwarding that reported issue. That sounds outstanding that they will try to fix the issue for the VS release, and are also consider adding ITK into their compiler validation tests.

Based on the Experimental build I did:
https://open.cdash.org/viewBuildError.php?buildid=4673717

This looks like the only internal compiler error (ICE) encountered. I hope there are not more ICE encounter after this one.

One thing to note is that with this ICE no tests were able to run, so we don?t know if the code generated has any differences or problems. I wonder if there is a little hack that could be done to work around this ICE issue in itkPrometeType.h, to see if there are any other issues later one?

Brad

On Dec 7, 2016, at 6:37 PM, D?enan Zuki? <dzenanz at gmail.com<mailto:dzenanz at gmail.com>> wrote:


---------- Forwarded message ----------
From: <vscommun at microsoft.com<mailto:vscommun at microsoft.com>>
Date: Wed, Dec 7, 2016 at 6:17 PM
Subject: [Developer Community] Ulzii Luvsanbat posted a new comment on "Compiling ITK triggers internal error"
To: dzenanz at gmail.com<mailto:dzenanz at gmail.com>


[https://developercommunity.visualstudio.com/themes/microsoft/images/visual_studio_logo_small.png] <http://www.visualstudio.com/>

Hi d?enan-zuki?,


A new comment on a Compiling ITK triggers internal error<https://developercommunity.visualstudio.com/comments/6266/view.html> was posted by Ulzii Luvsanbat on Developer Community:


Hello,

Thanks for this report. We'll look into fixing this for VS2017. We're also going to add this open source project to our compiler validation test suites to ensure we don't ship future VS releases that don't compile ITK sources.

Thanks,

Ulzii Luvsanbat

Visual C++ Team


View Ulzii Luvsanbat's new comment<https://developercommunity.visualstudio.com/comments/6266/view.html>



If you do not wish to receive these notifications you can update your Notification Settings<https://developercommunity.visualstudio.com/users/572/c029694a-14cf-4127-b809-54d1678fe43a/preferences.html#/notifyTab>.

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Microsoft respects your privacy. Please read our Privacy Statement<https://www.visualstudio.com/en-us/dn948229>.




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_____________________________________
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From blowekamp at mail.nih.gov  Thu Dec  8 10:34:22 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 8 Dec 2016 15:34:22 +0000
Subject: [ITK] [ITK-users] Fwd: [Developer Community] Ulzii Luvsanbat
 posted a new comment on "Compiling ITK triggers internal error"
In-Reply-To: <CAPf2UMQPBfxHmzGyh8538NJF9ii26hiwsmcvv=B3sKEX+Ry0Kg@mail.gmail.com>
References: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com>
 <CAPf2UMQPBfxHmzGyh8538NJF9ii26hiwsmcvv=B3sKEX+Ry0Kg@mail.gmail.com>
Message-ID: <303FFB15-F51A-48A3-AD3A-01CEEA30059F@mail.nih.gov>

Thanks for reporting and forwarding that reported issue. That sounds outstanding that they will try to fix the issue for the VS release, and are also consider adding ITK into their compiler validation tests.

Based on the Experimental build I did:
https://open.cdash.org/viewBuildError.php?buildid=4673717

This looks like the only internal compiler error (ICE) encountered. I hope there are not more ICE encounter after this one.

One thing to note is that with this ICE no tests were able to run, so we don?t know if the code generated has any differences or problems. I wonder if there is a little hack that could be done to work around this ICE issue in itkPrometeType.h, to see if there are any other issues later one?

Brad

On Dec 7, 2016, at 6:37 PM, D?enan Zuki? <dzenanz at gmail.com<mailto:dzenanz at gmail.com>> wrote:


---------- Forwarded message ----------
From: <vscommun at microsoft.com<mailto:vscommun at microsoft.com>>
Date: Wed, Dec 7, 2016 at 6:17 PM
Subject: [Developer Community] Ulzii Luvsanbat posted a new comment on "Compiling ITK triggers internal error"
To: dzenanz at gmail.com<mailto:dzenanz at gmail.com>


[https://developercommunity.visualstudio.com/themes/microsoft/images/visual_studio_logo_small.png] <http://www.visualstudio.com/>

Hi d?enan-zuki?,


A new comment on a Compiling ITK triggers internal error<https://developercommunity.visualstudio.com/comments/6266/view.html> was posted by Ulzii Luvsanbat on Developer Community:


Hello,

Thanks for this report. We'll look into fixing this for VS2017. We're also going to add this open source project to our compiler validation test suites to ensure we don't ship future VS releases that don't compile ITK sources.

Thanks,

Ulzii Luvsanbat

Visual C++ Team


View Ulzii Luvsanbat's new comment<https://developercommunity.visualstudio.com/comments/6266/view.html>



If you do not wish to receive these notifications you can update your Notification Settings<https://developercommunity.visualstudio.com/users/572/c029694a-14cf-4127-b809-54d1678fe43a/preferences.html#/notifyTab>.

This message from Microsoft is an important part of a program, service, or product that you or your company purchased or participate in.
Microsoft respects your privacy. Please read our Privacy Statement<https://www.visualstudio.com/en-us/dn948229>.




[https://developercommunity.visualstudio.com/themes/microsoft/images/Microsoft-logo_rgb_c-gray4.png]

_____________________________________
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From dzenanz at gmail.com  Thu Dec  8 10:37:58 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 8 Dec 2016 10:37:58 -0500
Subject: [ITK] [ITK-dev] [ITK-users] Fwd: [Developer Community] Ulzii
 Luvsanbat posted a new comment on "Compiling ITK triggers internal error"
In-Reply-To: <303FFB15-F51A-48A3-AD3A-01CEEA30059F@mail.nih.gov>
References: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com>
 <CAPf2UMQPBfxHmzGyh8538NJF9ii26hiwsmcvv=B3sKEX+Ry0Kg@mail.gmail.com>
 <303FFB15-F51A-48A3-AD3A-01CEEA30059F@mail.nih.gov>
Message-ID: <CAPf2UMSEu7H6U-WhDs98S5pCrgB8-BVHsggWdPTstZ5ix+9GRA@mail.gmail.com>

Hopefully they will give me a chance to thoroughly test the fix, in case
they don't do it themselves. There will probably be another update to the
RC release - there was one already.

Regards,
D?enan

On Thu, Dec 8, 2016 at 10:34 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Thanks for reporting and forwarding that reported issue. That sounds
> outstanding that they will try to fix the issue for the VS release, and are
> also consider adding ITK into their compiler validation tests.
>
> Based on the Experimental build I did:
> https://open.cdash.org/viewBuildError.php?buildid=4673717
>
> This looks like the only internal compiler error (ICE) encountered. I hope
> there are not more ICE encounter after this one.
>
> One thing to note is that with this ICE no tests were able to run, so we
> don?t know if the code generated has any differences or problems. I wonder
> if there is a little hack that could be done to work around this ICE issue
> in itkPrometeType.h, to see if there are any other issues later one?
>
> Brad
>
> On Dec 7, 2016, at 6:37 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>
> ---------- Forwarded message ----------
> From: <vscommun at microsoft.com>
> Date: Wed, Dec 7, 2016 at 6:17 PM
> Subject: [Developer Community] Ulzii Luvsanbat posted a new comment on
> "Compiling ITK triggers internal error"
> To: dzenanz at gmail.com
>
>
> <http://www.visualstudio.com/>
>
> Hi d?enan-zuki?,
>
> A new comment on a *Compiling ITK triggers internal error*
> <https://developercommunity.visualstudio.com/comments/6266/view.html> was
> posted by Ulzii Luvsanbat on Developer Community:
>
>
>
> * Hello, Thanks for this report. We'll look into fixing this for VS2017.
> We're also going to add this open source project to our compiler validation
> test suites to ensure we don't ship future VS releases that don't compile
> ITK sources. Thanks, Ulzii Luvsanbat Visual C++ Team *
>
> View Ulzii Luvsanbat's new comment
> <https://developercommunity.visualstudio.com/comments/6266/view.html>
>
> If you do not wish to receive these notifications you can update your Notification
> Settings
> <https://developercommunity.visualstudio.com/users/572/c029694a-14cf-4127-b809-54d1678fe43a/preferences.html#/notifyTab>
> .
>
> This message from Microsoft is an important part of a program, service, or
> product that you or your company purchased or participate in.
> Microsoft respects your privacy. Please read our Privacy Statement
> <https://www.visualstudio.com/en-us/dn948229>.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
>
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Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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From dzenanz at gmail.com  Thu Dec  8 10:37:58 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 8 Dec 2016 10:37:58 -0500
Subject: [ITK] [ITK-users] Fwd: [Developer Community] Ulzii Luvsanbat
 posted a new comment on "Compiling ITK triggers internal error"
In-Reply-To: <303FFB15-F51A-48A3-AD3A-01CEEA30059F@mail.nih.gov>
References: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com>
 <CAPf2UMQPBfxHmzGyh8538NJF9ii26hiwsmcvv=B3sKEX+Ry0Kg@mail.gmail.com>
 <303FFB15-F51A-48A3-AD3A-01CEEA30059F@mail.nih.gov>
Message-ID: <CAPf2UMSEu7H6U-WhDs98S5pCrgB8-BVHsggWdPTstZ5ix+9GRA@mail.gmail.com>

Hopefully they will give me a chance to thoroughly test the fix, in case
they don't do it themselves. There will probably be another update to the
RC release - there was one already.

Regards,
D?enan

On Thu, Dec 8, 2016 at 10:34 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Thanks for reporting and forwarding that reported issue. That sounds
> outstanding that they will try to fix the issue for the VS release, and are
> also consider adding ITK into their compiler validation tests.
>
> Based on the Experimental build I did:
> https://open.cdash.org/viewBuildError.php?buildid=4673717
>
> This looks like the only internal compiler error (ICE) encountered. I hope
> there are not more ICE encounter after this one.
>
> One thing to note is that with this ICE no tests were able to run, so we
> don?t know if the code generated has any differences or problems. I wonder
> if there is a little hack that could be done to work around this ICE issue
> in itkPrometeType.h, to see if there are any other issues later one?
>
> Brad
>
> On Dec 7, 2016, at 6:37 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>
> ---------- Forwarded message ----------
> From: <vscommun at microsoft.com>
> Date: Wed, Dec 7, 2016 at 6:17 PM
> Subject: [Developer Community] Ulzii Luvsanbat posted a new comment on
> "Compiling ITK triggers internal error"
> To: dzenanz at gmail.com
>
>
> <http://www.visualstudio.com/>
>
> Hi d?enan-zuki?,
>
> A new comment on a *Compiling ITK triggers internal error*
> <https://developercommunity.visualstudio.com/comments/6266/view.html> was
> posted by Ulzii Luvsanbat on Developer Community:
>
>
>
> * Hello, Thanks for this report. We'll look into fixing this for VS2017.
> We're also going to add this open source project to our compiler validation
> test suites to ensure we don't ship future VS releases that don't compile
> ITK sources. Thanks, Ulzii Luvsanbat Visual C++ Team *
>
> View Ulzii Luvsanbat's new comment
> <https://developercommunity.visualstudio.com/comments/6266/view.html>
>
> If you do not wish to receive these notifications you can update your Notification
> Settings
> <https://developercommunity.visualstudio.com/users/572/c029694a-14cf-4127-b809-54d1678fe43a/preferences.html#/notifyTab>
> .
>
> This message from Microsoft is an important part of a program, service, or
> product that you or your company purchased or participate in.
> Microsoft respects your privacy. Please read our Privacy Statement
> <https://www.visualstudio.com/en-us/dn948229>.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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> _______________________________________________
> Community mailing list
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>
>
>
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From dzenanz at gmail.com  Thu Dec  8 14:05:42 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 8 Dec 2016 14:05:42 -0500
Subject: [ITK] [ITK-users] Fwd: [Developer Community] Ulzii Luvsanbat posted
 a new solution to "Compiling ITK triggers internal error"
In-Reply-To: <6.7.37951.572.SOLUTION.ca0f8282a528bda939595b4871560509@microsoft.com>
References: <6.7.37951.572.SOLUTION.ca0f8282a528bda939595b4871560509@microsoft.com>
Message-ID: <CAPf2UMQ03W-nSUCMbvnmCCOjBgepQmiJTeMy_JOSEqhcTVxNZg@mail.gmail.com>

I guess they are nearing release.
---------- Forwarded message ----------
From: <vscommun at microsoft.com>
Date: Dec 8, 2016 13:23
Subject: [Developer Community] Ulzii Luvsanbat posted a new solution to
"Compiling ITK triggers internal error"
To: <dzenanz at gmail.com>
Cc:

<http://www.visualstudio.com>
>
> Hi d?enan-zuki?,
>
> A new solution to the problem "Compiling ITK triggers internal error" was
> posted by Ulzii Luvsanbat on Developer Community:
>
> * Hello, We've validated that with /Od and /O2 compilations with our
> latest compiler for VS2017 final release, this bug doesn't exist. As I've
> mentioned we'll add ITK and VTK projects into our compiler validation test
> suites going forward. Thanks, Ulzii Luvsanbat Visual C++ Team *
>
> View Ulzii Luvsanbat's new solution
> <https://developercommunity.visualstudio.com/content/problem/4679/compiling-itk-triggers-internal-error.html>
>
> If you do not wish to receive these notifications you can update your Notification
> Settings
> <https://developercommunity.visualstudio.com/users/572/c029694a-14cf-4127-b809-54d1678fe43a/preferences.html#/notifyTab>
> .
>
> This message from Microsoft is an important part of a program, service, or
> product that you or your company purchased or participate in.
> Microsoft respects your privacy. Please read our Privacy Statement
> <https://www.visualstudio.com/en-us/dn948229>.
>
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From dzenanz at gmail.com  Thu Dec  8 14:05:42 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 8 Dec 2016 14:05:42 -0500
Subject: [ITK] [ITK-dev] Fwd: [Developer Community] Ulzii Luvsanbat posted a
 new solution to "Compiling ITK triggers internal error"
In-Reply-To: <6.7.37951.572.SOLUTION.ca0f8282a528bda939595b4871560509@microsoft.com>
References: <6.7.37951.572.SOLUTION.ca0f8282a528bda939595b4871560509@microsoft.com>
Message-ID: <CAPf2UMQ03W-nSUCMbvnmCCOjBgepQmiJTeMy_JOSEqhcTVxNZg@mail.gmail.com>

I guess they are nearing release.
---------- Forwarded message ----------
From: <vscommun at microsoft.com>
Date: Dec 8, 2016 13:23
Subject: [Developer Community] Ulzii Luvsanbat posted a new solution to
"Compiling ITK triggers internal error"
To: <dzenanz at gmail.com>
Cc:

<http://www.visualstudio.com>
>
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From blowekamp at mail.nih.gov  Mon Dec 12 11:17:35 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 12 Dec 2016 16:17:35 +0000
Subject: [ITK] [ITK-dev] ITK Link errors: Template parent not exported
Message-ID: <85C190AF-D1C5-48E7-B9E4-0CEC59493D79@mail.nih.gov>

Hello,

I just wanted to report what I see is going on in two simular cases of link errors in ITK and SimpleITK.


The first is ITK with VS12 and shared libraries and CMAKE_WINDOWS_ALL_SYMBOLS:BOOL=ON. It is here on the ITK dashboard [1] and here is the error:

itkPolylineMask2DImageFilterTest.cxx.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) const itk::Path,2>::`vftable'" (__imp_??_7?$Path at NV?$ContinuousIndex at N$01 at itk@@$01 at itk@@6B@) referenced in function "protected: virtual __cdecl itk::PolyLineParametricPath<2>::~PolyLineParametricPath<2>(void)" (??1?$PolyLineParametricPath@$01 at itk@@MEAA at XZ)

This error began occurring after explicit exporting of the explicitly instantiated of PolyLineParametericPath<2> was merged ( to fix other linking error )[3]. The missing symbol?s class that class's parent itk::Path<2> class, which does not get explicitly instantiated or explicitly exported.


The second linking error seems very similar. It is on the SimpleITK dashboard also with VS12 and shared libraries. This configuration does not have the CMAKE_WINDOWS_ALL_SYMBOLS enabled, just the default explicit export for VS. The errors are here [2]:

ITKOptimizersv4-4.11.lib(ITKOptimizersv4-4.11.dll) : error LNK2005: "public: virtual void __cdecl itk::ObjectToObjectOptimizerBaseTemplate::StartOptimization(bool)" (?StartOptimization@?$ObjectToObjectOptimizerBaseTemplate at N@itk@@UEAAX_N at Z) already defined in sitkImageRegistrationMethod.obj [C:\d\vs11\SimpleITK-build\SimpleITK-build\Code\Registration\src\SimpleITKRegistration.vcxproj] [C:\d\vs11\SimpleITK-build\SimpleITK.vcxproj]

This is similar because the itk::ObjectToObjectOptimiserBaseTemplate class is a parent of the explicitly exported and instantiated itk::SingleValuedNonLinearVnlOptimizerv4.

I recall a couple comments related to exporting parent template classes here:
http://review.source.kitware.com/#/c/20020/2/Modules/Numerics/Optimizersv4/include/itkLBFGSOptimizerBasev4.h
http://review.source.kitware.com/#/c/20020/6/Modules/Numerics/Optimizersv4/include/itkLBFGSOptimizerBasev4.h


My hypothesis with these error is: VS12 requires all parents in a exported explicitly instantiated template class to be exported for correct linking.

Anyone have any experience to confirm this or additional information?

Thanks,
Brad

[1] https://open.cdash.org/viewBuildError.php?buildid=4681054
[2] https://open.cdash.org/viewBuildError.php?buildid=4680972
[3] https://github.com/InsightSoftwareConsortium/ITK/commit/a94bc525c0f5911b71fcacb647245efd8306990c
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From bele195 at yahoo.com  Tue Dec 13 11:12:15 2016
From: bele195 at yahoo.com (Belen Martin)
Date: Tue, 13 Dec 2016 16:12:15 +0000 (UTC)
Subject: [ITK] Curve2DExtraction ITApp Spatial Function Parameters vs
 Parametric Space
References: <1113838137.3641069.1481645535692.ref@mail.yahoo.com>
Message-ID: <1113838137.3641069.1481645535692@mail.yahoo.com>

Dear ITK list,
I am using Curve2DExtraction application to extract center lines in X-ray or DSA images previous to calculate stenosis.Although the results of modulus, Gradient || EigenVector, Laplacian, etc looks good, when plotting Curve2D Points I get poor results.1) According to which criteria should we adjust the Spatial Function Parameters???? 2) Whats the relation between the parametric space and the spatial function parameters?
Thanks in advance
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From bele195 at yahoo.com  Wed Dec 14 02:53:18 2016
From: bele195 at yahoo.com (Belen Martin)
Date: Wed, 14 Dec 2016 07:53:18 +0000 (UTC)
Subject: [ITK] Curve2DExtraction parametemer
References: <104762312.4242714.1481701998477.ref@mail.yahoo.com>
Message-ID: <104762312.4242714.1481701998477@mail.yahoo.com>

Dear ITK list,
Is there anyway in Curve2DExtraction (or with further implementation) to automate the result as much as possible, meaning tuning all parameters, sigma, and Spatial Function parameters?
If not can you recommend me a different module in ITK? I am using Curve2DExtraction application to extract center lines in X-ray or DSA images previous to the calculation stenosis. I do not want the physician have to know about pyramid or spatial function to tune results.

Thanks in advance


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From ndel314 at gmail.com  Wed Dec 14 08:56:15 2016
From: ndel314 at gmail.com (Nico Del Piano)
Date: Wed, 14 Dec 2016 10:56:15 -0300
Subject: [ITK] [ITK-users] Error conversion from
Message-ID: <CAAq9_B7fox6AL_mc-1s5CdqfNnj7zBkH0tZcXJXZTZ72se+3Ww@mail.gmail.com>

Hello ITK community,

I'm struggling with an error and I don't understand why it's happening:


/usr/local/include/ITK-4.11/itkConceptChecking.h:796:28: error:
conversion from ?itk::Concept::IsFloatingPoint<short
int>::Constraints::FalseT {aka
itk::Concept::Detail::UniqueType_bool<false>}? to non-scalar type
?itk::Concept::IsFloatingPoint<short int>::Constraints::IntegralT {aka
itk::Concept::Detail::UniqueType_bool<true>}? requested
      IntegralT a = FalseT();
                           ^
/usr/local/include/ITK-4.11/itkConceptChecking.h:797:28: error:
conversion from ?itk::Concept::IsFloatingPoint<short
int>::Constraints::FalseT {aka
itk::Concept::Detail::UniqueType_bool<false>}? to non-scalar type
?itk::Concept::IsFloatingPoint<short int>::Constraints::ExactT {aka
itk::Concept::Detail::UniqueType_bool<true>}? requested
      ExactT    b = FalseT();


Any hint of what could be causing this? If you need the whole error I
can paste it.

Thanks,

Nico.
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From blowekamp at mail.nih.gov  Wed Dec 14 09:03:26 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 14 Dec 2016 14:03:26 +0000
Subject: [ITK] [ITK-users] Error conversion from
In-Reply-To: <CAAq9_B7fox6AL_mc-1s5CdqfNnj7zBkH0tZcXJXZTZ72se+3Ww@mail.gmail.com>
References: <CAAq9_B7fox6AL_mc-1s5CdqfNnj7zBkH0tZcXJXZTZ72se+3Ww@mail.gmail.com>
Message-ID: <3ACA34EA-C664-4D0C-BB46-5010BBE0EF71@mail.nih.gov>

This error message is suppose to be an improvement from the default to indicate why the code/filter does not work with the template parameters you selected. 

Here is the key part:
> itk::Concept::IsFloatingPoint<short int>::Constraints::False


This a a concept check to verify the template parameter is a floating point type which is required by the algorithm/filter/code. The type ?short int? is not a floating point type, so it generates a compilation error.

I have no clue what is causing it, as you didn?t include any code :)

If you look at the all error messages it should indicate the origin of the error. Most likely the cause is: you provided a "short" type for a template parameter (or image type) to a filter or algorithm which requires a floating point type.

HTH,
Brad

> On Dec 14, 2016, at 8:56 AM, Nico Del Piano <ndel314 at gmail.com> wrote:
> 
> Hello ITK community,
> 
> I'm struggling with an error and I don't understand why it's happening:
> 
> 
> /usr/local/include/ITK-4.11/itkConceptChecking.h:796:28: error:
> conversion from ?itk::Concept::IsFloatingPoint<short
> int>::Constraints::FalseT {aka
> itk::Concept::Detail::UniqueType_bool<false>}? to non-scalar type
> ?itk::Concept::IsFloatingPoint<short int>::Constraints::IntegralT {aka
> itk::Concept::Detail::UniqueType_bool<true>}? requested
>      IntegralT a = FalseT();
>                           ^
> /usr/local/include/ITK-4.11/itkConceptChecking.h:797:28: error:
> conversion from ?itk::Concept::IsFloatingPoint<short
> int>::Constraints::FalseT {aka
> itk::Concept::Detail::UniqueType_bool<false>}? to non-scalar type
> ?itk::Concept::IsFloatingPoint<short int>::Constraints::ExactT {aka
> itk::Concept::Detail::UniqueType_bool<true>}? requested
>      ExactT    b = FalseT();
> 
> 
> Any hint of what could be causing this? If you need the whole error I
> can paste it.
> 
> Thanks,
> 
> Nico.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

_____________________________________
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From blowekamp at mail.nih.gov  Wed Dec 14 09:03:26 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 14 Dec 2016 14:03:26 +0000
Subject: [ITK] [ITK-dev] [ITK-users] Error conversion from
In-Reply-To: <CAAq9_B7fox6AL_mc-1s5CdqfNnj7zBkH0tZcXJXZTZ72se+3Ww@mail.gmail.com>
References: <CAAq9_B7fox6AL_mc-1s5CdqfNnj7zBkH0tZcXJXZTZ72se+3Ww@mail.gmail.com>
Message-ID: <3ACA34EA-C664-4D0C-BB46-5010BBE0EF71@mail.nih.gov>

This error message is suppose to be an improvement from the default to indicate why the code/filter does not work with the template parameters you selected. 

Here is the key part:
> itk::Concept::IsFloatingPoint<short int>::Constraints::False


This a a concept check to verify the template parameter is a floating point type which is required by the algorithm/filter/code. The type ?short int? is not a floating point type, so it generates a compilation error.

I have no clue what is causing it, as you didn?t include any code :)

If you look at the all error messages it should indicate the origin of the error. Most likely the cause is: you provided a "short" type for a template parameter (or image type) to a filter or algorithm which requires a floating point type.

HTH,
Brad

> On Dec 14, 2016, at 8:56 AM, Nico Del Piano <ndel314 at gmail.com> wrote:
> 
> Hello ITK community,
> 
> I'm struggling with an error and I don't understand why it's happening:
> 
> 
> /usr/local/include/ITK-4.11/itkConceptChecking.h:796:28: error:
> conversion from ?itk::Concept::IsFloatingPoint<short
> int>::Constraints::FalseT {aka
> itk::Concept::Detail::UniqueType_bool<false>}? to non-scalar type
> ?itk::Concept::IsFloatingPoint<short int>::Constraints::IntegralT {aka
> itk::Concept::Detail::UniqueType_bool<true>}? requested
>      IntegralT a = FalseT();
>                           ^
> /usr/local/include/ITK-4.11/itkConceptChecking.h:797:28: error:
> conversion from ?itk::Concept::IsFloatingPoint<short
> int>::Constraints::FalseT {aka
> itk::Concept::Detail::UniqueType_bool<false>}? to non-scalar type
> ?itk::Concept::IsFloatingPoint<short int>::Constraints::ExactT {aka
> itk::Concept::Detail::UniqueType_bool<true>}? requested
>      ExactT    b = FalseT();
> 
> 
> Any hint of what could be causing this? If you need the whole error I
> can paste it.
> 
> Thanks,
> 
> Nico.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

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From aharr8 at uwo.ca  Wed Dec 14 10:21:01 2016
From: aharr8 at uwo.ca (Andrew Harris)
Date: Wed, 14 Dec 2016 10:21:01 -0500
Subject: [ITK] [ITK-users]  LBFGSBOptimizerv4 step size
Message-ID: <CAJ0LxQLsphbmyikfCaaTeOXWG-Gxu4kArEC=HGaC+440jnyOYQ@mail.gmail.com>

Hello, hopefully someone can point me in the right direction.  I have been
trying to use a LBFGSBOptimizerv4 with some ultrasound images to do a rigid
3D versor transform registration, but can't find anywhere that either
allows me to set the step size for the optimizer or documents what the step
size is. Does anyone have a reference for this?

--

AH


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

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
thereto.*
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From dzenanz at gmail.com  Wed Dec 14 14:32:36 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 14 Dec 2016 14:32:36 -0500
Subject: [ITK] [ITK-users]  LBFGSBOptimizerv4 step size
In-Reply-To: <CAJ0LxQLsphbmyikfCaaTeOXWG-Gxu4kArEC=HGaC+440jnyOYQ@mail.gmail.com>
References: <CAJ0LxQLsphbmyikfCaaTeOXWG-Gxu4kArEC=HGaC+440jnyOYQ@mail.gmail.com>
Message-ID: <CAPf2UMTyO+BUubNvzjojb+1uachvbENpZ_YVLh83vvZnMDHA-A@mail.gmail.com>

There is no mention of step size in source code of this optimizer. It
probably does not use fixed step size.

Regards

On Wed, Dec 14, 2016 at 10:21 AM, Andrew Harris <aharr8 at uwo.ca> wrote:

> Hello, hopefully someone can point me in the right direction.  I have been
> trying to use a LBFGSBOptimizerv4 with some ultrasound images to do a rigid
> 3D versor transform registration, but can't find anywhere that either
> allows me to set the step size for the optimizer or documents what the step
> size is. Does anyone have a reference for this?
>
> --
>
> AH
>
>
> ------------------------------------------------------------
> -----------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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>
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From dzenanz at gmail.com  Wed Dec 14 14:45:32 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 14 Dec 2016 14:45:32 -0500
Subject: [ITK] [ITK-users]  LBFGSBOptimizerv4 step size
In-Reply-To: <CAJ0LxQJGsk_0atJMAEKMtupeShinesz5kjZ-pQHWdsT=87fGjg@mail.gmail.com>
References: <CAJ0LxQLsphbmyikfCaaTeOXWG-Gxu4kArEC=HGaC+440jnyOYQ@mail.gmail.com>
 <CAPf2UMTyO+BUubNvzjojb+1uachvbENpZ_YVLh83vvZnMDHA-A@mail.gmail.com>
 <CAJ0LxQJGsk_0atJMAEKMtupeShinesz5kjZ-pQHWdsT=87fGjg@mail.gmail.com>
Message-ID: <CAPf2UMSGRwCFm+DFfjUaZ8Aw=KRPRTjQuwFH6XtyQ7z7VGzEug@mail.gmail.com>

I guess there are a few stopping criteria, by looking at the public
functions <https://itk.org/Doxygen/html/classitk_1_1LBFGSBOptimizerv4.html>:
SetCostFunctionConvergenceFactor - probably examines changes in cost
function value
SetMaximumNumberOfCorrections - sounds like iteration count
There is probably also some implicit epsilon-like criterion on position
changes.

Regards,
D?enan


On Wed, Dec 14, 2016 at 2:38 PM, Andrew Harris <aharr8 at uwo.ca> wrote:

> Thanks for getting back to me.  Do you have any idea what the stopping
> criteria is for the Broyden-Fletcher implementation?
>
> --
>
> AH
>
>
> ------------------------------------------------------------
> -----------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> On Wed, Dec 14, 2016 at 2:32 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> There is no mention of step size in source code of this optimizer. It
>> probably does not use fixed step size.
>>
>> Regards
>>
>> On Wed, Dec 14, 2016 at 10:21 AM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>
>>> Hello, hopefully someone can point me in the right direction.  I have
>>> been trying to use a LBFGSBOptimizerv4 with some ultrasound images to do a
>>> rigid 3D versor transform registration, but can't find anywhere that either
>>> allows me to set the step size for the optimizer or documents what the step
>>> size is. Does anyone have a reference for this?
>>>
>>> --
>>>
>>> AH
>>>
>>>
>>> ------------------------------------------------------------
>>> -----------------------------------
>>>
>>> *This email and any attachments thereto may contain private,
>>> confidential, and privileged materials for the sole use of the intended
>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>> attachments thereto) by other than the intended recipient is strictly
>>> prohibited. If you are not the intended recipient, please contact the
>>> sender immediately and permanently destroy this email and any attachments
>>> thereto.*
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>
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From aharr8 at uwo.ca  Wed Dec 14 14:38:27 2016
From: aharr8 at uwo.ca (Andrew Harris)
Date: Wed, 14 Dec 2016 14:38:27 -0500
Subject: [ITK] [ITK-users]  LBFGSBOptimizerv4 step size
In-Reply-To: <CAPf2UMTyO+BUubNvzjojb+1uachvbENpZ_YVLh83vvZnMDHA-A@mail.gmail.com>
References: <CAJ0LxQLsphbmyikfCaaTeOXWG-Gxu4kArEC=HGaC+440jnyOYQ@mail.gmail.com>
 <CAPf2UMTyO+BUubNvzjojb+1uachvbENpZ_YVLh83vvZnMDHA-A@mail.gmail.com>
Message-ID: <CAJ0LxQJGsk_0atJMAEKMtupeShinesz5kjZ-pQHWdsT=87fGjg@mail.gmail.com>

Thanks for getting back to me.  Do you have any idea what the stopping
criteria is for the Broyden-Fletcher implementation?

--

AH


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

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
thereto.*

On Wed, Dec 14, 2016 at 2:32 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> There is no mention of step size in source code of this optimizer. It
> probably does not use fixed step size.
>
> Regards
>
> On Wed, Dec 14, 2016 at 10:21 AM, Andrew Harris <aharr8 at uwo.ca> wrote:
>
>> Hello, hopefully someone can point me in the right direction.  I have
>> been trying to use a LBFGSBOptimizerv4 with some ultrasound images to do a
>> rigid 3D versor transform registration, but can't find anywhere that either
>> allows me to set the step size for the optimizer or documents what the step
>> size is. Does anyone have a reference for this?
>>
>> --
>>
>> AH
>>
>>
>> ------------------------------------------------------------
>> -----------------------------------
>>
>> *This email and any attachments thereto may contain private,
>> confidential, and privileged materials for the sole use of the intended
>> recipient. Any reviewing, copying, or distribution of this email (or any
>> attachments thereto) by other than the intended recipient is strictly
>> prohibited. If you are not the intended recipient, please contact the
>> sender immediately and permanently destroy this email and any attachments
>> thereto.*
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
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From cr at neuro.ma.uni-heidelberg.de  Fri Dec 16 05:26:54 2016
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Fri, 16 Dec 2016 11:26:54 +0100
Subject: [ITK] [ITK-users] Example with wrong name
Message-ID: <aed4cd4f-c26d-243c-229a-3a5f9f7b29b8@neuro.ma.uni-heidelberg.de>

Hi,

I guess WikiExamples/Statistics/HistogramToImageFilterGrayscale.cxx 
<https://itk.org/Doxygen/html/WikiExamples_2Statistics_2HistogramToImageFilterGrayscale_8cxx-example.html#_a1> 
should be renamed to .../ImageToHistogramFilterGrayscale.cxx

Regards,

Christina


<https://itk.org/Doxygen/html/WikiExamples_2Statistics_2HistogramToImageFilterGrayscale_8cxx-example.html#_a1>

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From bill.lorensen at gmail.com  Fri Dec 16 07:51:07 2016
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 16 Dec 2016 07:51:07 -0500
Subject: [ITK] [ITK-users] Example with wrong name
In-Reply-To: <aed4cd4f-c26d-243c-229a-3a5f9f7b29b8@neuro.ma.uni-heidelberg.de>
References: <aed4cd4f-c26d-243c-229a-3a5f9f7b29b8@neuro.ma.uni-heidelberg.de>
Message-ID: <CADZJ4hOVEWm1jsTDY5GBfpL_ULTZNrRDe0O-yYEbE6dx23-YYg@mail.gmail.com>

Thanks. I'll take care of it.

On Dec 16, 2016 5:39 AM, "Chr. Rossmanith" <cr at neuro.ma.uni-heidelberg.de>
wrote:

> Hi,
>
> I guess WikiExamples/Statistics/HistogramToImageFilterGrayscale.cxx
> <https://itk.org/Doxygen/html/WikiExamples_2Statistics_2HistogramToImageFilterGrayscale_8cxx-example.html#_a1>
> should be renamed to .../ImageToHistogramFilterGrayscale.cxx
>
> Regards,
>
> Christina
>
>
>
> <https://itk.org/Doxygen/html/WikiExamples_2Statistics_2HistogramToImageFilterGrayscale_8cxx-example.html#_a1>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
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>
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From isaiah.norton at gmail.com  Fri Dec 16 16:24:43 2016
From: isaiah.norton at gmail.com (Isaiah Norton)
Date: Fri, 16 Dec 2016 16:24:43 -0500
Subject: [ITK] [ITK-dev] ITK+static+wrapping [ref: 21857 "Enable singleton
	program	global timestamp"]
Message-ID: <CADFtqoq+0kvvBPKKOCL9Tz_hPbjC8=uD6vY7DAK5JsOnwLiymA@mail.gmail.com>

I was added as a reviewer on #21857 [1], but my comment is more general, so
I don't think gerrit is the best place for it.

The background of that merge request is [2], where a user demonstrated
inconsistent modification times when objects are modified by functions from
different modules, via Python, with ITK compiled in static library mode.
The underlying cause is that each module has a separate, private instance
of the GlobalTimeStamp, so the operations increment different counter
variables.

The proposed solution in [1] is to provide a singleton-like object with a
settable internal pointer, initialized by the Python loader to point to a
single instance in ITKCommon.

The technical implementation looks ok, but the original situation in [2] is
strange:

What is the rationale behind creating so many separate, statically-linked
Python modules? (78 `_ITK*Python.so` files on my machine). Creating a
single bundle instead should resolve the original issue, and might also
reduce the size of the final library [3].

Additionally, I am wondering if cross-module `dynamic_cast` works correctly
in the current situation -- because the typeinfos in each static module .so
have different addresses [4]. (I'm not sure how to create a situation to
test this from Python)

Best,
Isaiah

[1] http://review.source.kitware.com/#/c/21857/4
[2] https://issues.itk.org/jira/browse/ITK-3456

[3] As a point of reference, the total size of the static `_ITK*Python.so`
files on my mac is about 670MB. If I manually link everything into a single
file, the size drops to about 430MB, presumably due to deduplication of
symbols. Further reduction might be possible: there are still many
duplicate symbols which may not be merged due to differing offsets.

[4] https://gist.github.com/ihnorton/6691645ede869d6bc6c25b143fbf3003
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From kris.f.thielemans at gmail.com  Sat Dec 17 10:14:37 2016
From: kris.f.thielemans at gmail.com (Kris Thielemans)
Date: Sat, 17 Dec 2016 16:14:37 +0100
Subject: [ITK] link problems to library that uses ITK as external project
Message-ID: <00ea01d25878$48946410$d9bd2c30$@gmail.com>

Hi all

 

I'm trying to add CMake export facilities to our open source library
http://github.com/UCL/STIR. This uses ITK for IO. I succeeded in modifying
my CMake files to "export" that when you link to my STIR-library, you also
needs to link to the ITK libraries. However, as I have installed ITK in a
non-standard location (I build STIR by setting ITK_DIR), so the ITK
libraries are not automatically found by the linker. I am now getting
linking errors in my final application (that uses STIR, and hence ITK). More
detail below. So, what am I missing in my CMake files to "export" the
location of the ITK libraries that were used when building STIR? 

 

I am using CMake 3.7.0 on CentOS 7 if that matters.

 

Thanks for your help

 

Kris Thielemans

 

Detail:

Our CMakeLists.txt files contain stuff like

 

find_package(ITK QUIET)

add_library(IO some_sources)

if (ITK_FOUND) 

  target_link_libraries(IO ${ITK_LIBRARIES})

endif()

 

This works nicely. Now I'm putting in the necessary stuff for an external
project to be able to link to our IO library. I'm following a scheme similar
to

https://rix0r.nl/blog/2015/08/13/cmake-guide/ (sorry, firefox claims that
this web-site uses an invalided certificate at the moment).

 

So I've added for instance

 

install(TARGETS IO EXPORT STIRTargets DESTINATION lib)

 

Checking the generated STIRTargets-release.cmake I see indeed that it
contains

 

set_target_properties(IO PROPERTIES

  IMPORTED_LINK_INTERFACE_LANGUAGES_RELEASE "CXX"

  IMPORTED_LINK_INTERFACE_LIBRARIES_RELEASE
"ITKCommon;lots-of-others-itk-libraries"

)

 

So, now in my final STIR application that uses STIR, I have a simple
CMakeLists.txt with

 

find_package(STIR 3.0.0 REQUIRED)

include_directories(${STIR_INCLUDE_DIRS})

add_executable(testfile testfile.cxx )

target_link_libraries(testfile ${STIR_LIBRARIES})

 

However, when building this (on Lubuntu with gcc etc) I get lots of messages
like this

 

/usr/bin/ld: cannot find -lITKCommon

 

Indeed, in the generated link.txt I do not see anything that tells gcc/ld
where the ITK libraries would be.

 

 

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From matt.mccormick at kitware.com  Sat Dec 17 10:41:06 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 17 Dec 2016 10:41:06 -0500
Subject: [ITK] [ITK-dev] ITK+static+wrapping [ref: 21857 "Enable
	singleton	program global timestamp"]
In-Reply-To: <CADFtqoq+0kvvBPKKOCL9Tz_hPbjC8=uD6vY7DAK5JsOnwLiymA@mail.gmail.com>
References: <CADFtqoq+0kvvBPKKOCL9Tz_hPbjC8=uD6vY7DAK5JsOnwLiymA@mail.gmail.com>
Message-ID: <CALzTN-Q_RpKMEekQ-cgzHQaF8eV7R_VpE+QaNKxn-d-9t0ZuGw@mail.gmail.com>

Hi Isaiah,

Here is some more information and background.


> What is the rationale behind creating so many separate, statically-linked
> Python modules? (78 `_ITK*Python.so` files on my machine). Creating a single
> bundle instead should resolve the original issue, and might also reduce the
> size of the final library [3].

For background, the GlobalTimeStamp, is a very important variable in
ITK (and VTK). This is an atomic integer that gets incremented when
any itk::Object (most classes in ITK) is "Modified", i.e. changed to
note that it should be updated in a processing pipeline. So, almost
all ITK-based code needs it, and it needs to be global across the
entire program.

The GlobalTimeStamp lives in and is used my itk::TimeStamp.cxx, and it
is incremented on every call to ::Modified(). The itk::TimeStamp class
is linked into libITKCommon.

When ITK is built with shared libraries, libITKCommon is shared, and
everything shares the GlobalTimeStamp. When ITK is built with static
libraries, every binary that links in libITKCommon will get its own
GlobalTimeStamp.

Unfortunately, a shared libITKCommon is not always possible. For the
official Python packaging format, wheels, native libraries are not yet
officially supported [1].

The advantages of not linking everything into one, giant, monolithic
`_ITK*Python.so` are that 1) we can lazily load only the parts of the
library that we need, and 2) the brilliant ITK community members can
extend ITK to create their own ITK Python module. For example, see the
awesome ITKMinimalPathExtraction [2] or ITKIsotropicWavelets [3]
modules.

While I also investigated, for example, using CMake object libraries
to make itk::TimeStamp an exported symbol in _ITKCommonPython.so and
only linked there [4], this is a more complex build configuration.
Additionally, according to the Python documentation, exporting extra
symbols in a CPython extension module is officially not supported [5].
In practice, I have found that extra symbols can segfault the process
on module import with Python 3.5 on Windows. So, the sharing is done
the officially supported way, via PyCapsule.


> Additionally, I am wondering if cross-module `dynamic_cast` works correctly
> in the current situation -- because the typeinfos in each static module .so
> have different addresses [4]. (I'm not sure how to create a situation to
> test this from Python)

Yes, since the Python wrapping covers the entire toolkit, it is an
excellent stress test for the dynamic_cast issue. When we developed
the dynamic_cast patch, we used Python wrapping with static libraries
and experimentally enabled hidden symbols by default [6]. Without the
dynamic_cast fix, the Python tests failed, and with the fix, they
pass. It turns out that we missed some mark-up on a few classes as
indicated by warnings in the Python wrapping and non-wrapping test
failures, but we are working on resolving those now.

Thanks,
Matt


[1] https://mail.python.org/pipermail/wheel-builders/2016-April/000090.html

[2] https://github.com/InsightSoftwareConsortium/ITKMinimalPathExtraction

[3] https://github.com/phcerdan/ITKIsotropicWavelets

[4] https://github.com/thewtex/ITK/commits/thewtex-PythonModifiedTime55

[5] https://docs.python.org/3.5/extending/extending.html#providing-a-c-api-for-an-extension-module

[6] http://review.source.kitware.com/#/c/21766/
_______________________________________________
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From matt.mccormick at kitware.com  Sat Dec 17 11:38:28 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 17 Dec 2016 11:38:28 -0500
Subject: [ITK] link problems to library that uses ITK as external project
In-Reply-To: <00ea01d25878$48946410$d9bd2c30$@gmail.com>
References: <00ea01d25878$48946410$d9bd2c30$@gmail.com>
Message-ID: <CALzTN-Q4-jvvFdLnMGj9O6+Ej+1JpN6n09+7hZKp=9Cf1NSo0g@mail.gmail.com>

Hi Kris,

In the STIR CMake Config-file package [1], include code like:

  set(ITK_DIR "@ITK_DIR@")
  find_package(ITK REQUIRED)

where @ITK_DIR@ is set to the ITK Config-file location for the ITK
used to build STIR using the CMake configure_file command. This will
help client libraries or executables of STIR to find where ITK was
located and load the location of ITK libraries like ITKCommon.

HTH,
Matt

[1] https://cmake.org/cmake/help/v3.7/manual/cmake-packages.7.html#id1

On Sat, Dec 17, 2016 at 10:14 AM, Kris Thielemans
<kris.f.thielemans at gmail.com> wrote:
> Hi all
>
>
>
> I?m trying to add CMake export facilities to our open source library
> http://github.com/UCL/STIR. This uses ITK for IO. I succeeded in modifying
> my CMake files to ?export? that when you link to my STIR-library, you also
> needs to link to the ITK libraries. However, as I have installed ITK in a
> non-standard location (I build STIR by setting ITK_DIR), so the ITK
> libraries are not automatically found by the linker. I am now getting
> linking errors in my final application (that uses STIR, and hence ITK). More
> detail below. So, what am I missing in my CMake files to ?export? the
> location of the ITK libraries that were used when building STIR?
>
>
>
> I am using CMake 3.7.0 on CentOS 7 if that matters.
>
>
>
> Thanks for your help
>
>
>
> Kris Thielemans
>
>
>
> Detail:
>
> Our CMakeLists.txt files contain stuff like
>
>
>
> find_package(ITK QUIET)
>
> add_library(IO some_sources)
>
> if (ITK_FOUND)
>
>   target_link_libraries(IO ${ITK_LIBRARIES})
>
> endif()
>
>
>
> This works nicely. Now I?m putting in the necessary stuff for an external
> project to be able to link to our IO library. I?m following a scheme similar
> to
>
> https://rix0r.nl/blog/2015/08/13/cmake-guide/ (sorry, firefox claims that
> this web-site uses an invalided certificate at the moment).
>
>
>
> So I?ve added for instance
>
>
>
> install(TARGETS IO EXPORT STIRTargets DESTINATION lib)
>
>
>
> Checking the generated STIRTargets-release.cmake I see indeed that it
> contains
>
>
>
> set_target_properties(IO PROPERTIES
>
>   IMPORTED_LINK_INTERFACE_LANGUAGES_RELEASE "CXX"
>
>   IMPORTED_LINK_INTERFACE_LIBRARIES_RELEASE
> "ITKCommon;lots-of-others-itk-libraries?
>
> )
>
>
>
> So, now in my final STIR application that uses STIR, I have a simple
> CMakeLists.txt with
>
>
>
> find_package(STIR 3.0.0 REQUIRED)
>
> include_directories(${STIR_INCLUDE_DIRS})
>
> add_executable(testfile testfile.cxx )
>
> target_link_libraries(testfile ${STIR_LIBRARIES})
>
>
>
> However, when building this (on Lubuntu with gcc etc) I get lots of messages
> like this
>
>
>
> /usr/bin/ld: cannot find -lITKCommon
>
>
>
> Indeed, in the generated link.txt I do not see anything that tells gcc/ld
> where the ITK libraries would be.
>
>
>
>
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From matt.mccormick at kitware.com  Sat Dec 17 12:01:10 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 17 Dec 2016 12:01:10 -0500
Subject: [ITK] RFI on the NLM Strategic Plan
Message-ID: <CALzTN-R8ucssgasu-LWiUfBADfGFC1X15iV423LjHad_w9hRww@mail.gmail.com>

Hi,

The National Library of Medicine (NLM) has driven open science and
reproducible research long before the recent surge in popularity of
the movement. Not only did the NLM start the Insight Toolkit (ITK)
project in 1999, but it has continuously enabled it to thrive by
supporting community development, maintenance, and algorithmic and
technological advances to this day [1] [2].

Open science needs active communities, supported communities,
standards, open-source tools, strong ties will commercial / clinical
efforts, high-quality practices, transparency, and more - and those
are exactly the strengths of our community's toolkits, applications,
and projects. We should to encourage the NLM (NIH, DHHS, US
Government) to continue to prioritize these efforts via their funding.

The NLM has called for Request for Information (RFI) on the strategic
plan for the institute:

  https://grants.nih.gov/grants/guide/notice-files/NOT-LM-17-002.html

that is due by January 9th. Please consider letting the NLM know how
important their role is in open science and open source.


Thanks,
Matt

[1] https://itk.org/ITK/project/about.html

[2] http://journal.frontiersin.org/article/10.3389/fninf.2014.00013/full

From kris.f.thielemans at gmail.com  Sat Dec 17 17:26:49 2016
From: kris.f.thielemans at gmail.com (Kris Thielemans)
Date: Sat, 17 Dec 2016 23:26:49 +0100
Subject: [ITK] link problems to library that uses ITK as external project
In-Reply-To: <CALzTN-Q4-jvvFdLnMGj9O6+Ej+1JpN6n09+7hZKp=9Cf1NSo0g@mail.gmail.com>
References: <00ea01d25878$48946410$d9bd2c30$@gmail.com>
 <CALzTN-Q4-jvvFdLnMGj9O6+Ej+1JpN6n09+7hZKp=9Cf1NSo0g@mail.gmail.com>
Message-ID: <012001d258b4$a9601690$fc2043b0$@gmail.com>

Thanks Matt

This works great. I like it better than using CMakeFindDependencyMacro's find_dependency that I stumbled on, as I believe that find_dependency could lead the user to link with a different ITK version, while your version forces usage of the same ITK version, which seems like a good thing to me!

So I'll be using 

if (@ITK_FOUND@)
  set(ITK_DIR "@ITK_DIR@")
  find_package(ITK REQUIRED)
endif()

as ITK is optional in my case.

By the way, this might be worth adding to the tutorial you mentioned (it's somewhat cryptic, but I'm getting there).

Thanks!
Kris

-----Original Message-----
From: Matt McCormick 
Sent: 17 December 2016 17:38
To: Kris Thielemans 
Cc: community at itk.org
Subject: Re: [ITK] link problems to library that uses ITK as external project

Hi Kris,

In the STIR CMake Config-file package [1], include code like:

  set(ITK_DIR "@ITK_DIR@")
  find_package(ITK REQUIRED)

where @ITK_DIR@ is set to the ITK Config-file location for the ITK used to build STIR using the CMake configure_file command. This will help client libraries or executables of STIR to find where ITK was located and load the location of ITK libraries like ITKCommon.

HTH,
Matt

[1] https://cmake.org/cmake/help/v3.7/manual/cmake-packages.7.html#id1

On Sat, Dec 17, 2016 at 10:14 AM, Kris Thielemans wrote:
> Hi all
>
>
>
> I?m trying to add CMake export facilities to our open source library 
> http://github.com/UCL/STIR. This uses ITK for IO. I succeeded in 
> modifying my CMake files to ?export? that when you link to my 
> STIR-library, you also needs to link to the ITK libraries. However, as 
> I have installed ITK in a non-standard location (I build STIR by 
> setting ITK_DIR), so the ITK libraries are not automatically found by 
> the linker. I am now getting linking errors in my final application 
> (that uses STIR, and hence ITK). More detail below. So, what am I 
> missing in my CMake files to ?export? the location of the ITK libraries that were used when building STIR?
>
>
>
> I am using CMake 3.7.0 on CentOS 7 if that matters.
>
>
>
> Thanks for your help
>
>
>
> Kris Thielemans
>
>
>
> Detail:
>
> Our CMakeLists.txt files contain stuff like
>
>
>
> find_package(ITK QUIET)
>
> add_library(IO some_sources)
>
> if (ITK_FOUND)
>
>   target_link_libraries(IO ${ITK_LIBRARIES})
>
> endif()
>
>
>
> This works nicely. Now I?m putting in the necessary stuff for an 
> external project to be able to link to our IO library. I?m following a 
> scheme similar to
>
> https://rix0r.nl/blog/2015/08/13/cmake-guide/ (sorry, firefox claims 
> that this web-site uses an invalided certificate at the moment).
>
>
>
> So I?ve added for instance
>
>
>
> install(TARGETS IO EXPORT STIRTargets DESTINATION lib)
>
>
>
> Checking the generated STIRTargets-release.cmake I see indeed that it 
> contains
>
>
>
> set_target_properties(IO PROPERTIES
>
>   IMPORTED_LINK_INTERFACE_LANGUAGES_RELEASE "CXX"
>
>   IMPORTED_LINK_INTERFACE_LIBRARIES_RELEASE
> "ITKCommon;lots-of-others-itk-libraries?
>
> )
>
>
>
> So, now in my final STIR application that uses STIR, I have a simple 
> CMakeLists.txt with
>
>
>
> find_package(STIR 3.0.0 REQUIRED)
>
> include_directories(${STIR_INCLUDE_DIRS})
>
> add_executable(testfile testfile.cxx )
>
> target_link_libraries(testfile ${STIR_LIBRARIES})
>
>
>
> However, when building this (on Lubuntu with gcc etc) I get lots of 
> messages like this
>
>
>
> /usr/bin/ld: cannot find -lITKCommon
>
>
>
> Indeed, in the generated link.txt I do not see anything that tells 
> gcc/ld where the ITK libraries would be.
>
>
>
>
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>


From mohammedrashadkm at gmail.com  Tue Dec 20 04:48:43 2016
From: mohammedrashadkm at gmail.com (Rashad Kanavath)
Date: Tue, 20 Dec 2016 10:48:43 +0100
Subject: [ITK] [ITK-dev] installed ITK cannot be moved due to absolute
	path
In-Reply-To: <CALzTN-Q-Q9Ho4fmG99B4RUSwrpYCiihA3fiD_7WpKe5Kt24gtg@mail.gmail.com>
References: <CANNqv9eKZygjeSgdauFADK6jev2V9Q4Bhk8gfP=GkR5ngLfoGA@mail.gmail.com>
 <CAPf2UMTo6LY09u1gKxa+MPjOgyQjMh25ADHSdpv4wTc3GRzbZA@mail.gmail.com>
 <CANNqv9dC9F6PHSyrLfnqY2NbA8dSDxnD-kzEKTdUqwhW_Mea8A@mail.gmail.com>
 <CALzTN-Q-Q9Ho4fmG99B4RUSwrpYCiihA3fiD_7WpKe5Kt24gtg@mail.gmail.com>
Message-ID: <CANNqv9fSqBF0vdQQTa5An5xh8NPBd+cAuo=MvoR5UPDTr-cdOA@mail.gmail.com>

Hello all,

Is there a simple FindITK.cmake which can be used instead of config and
targets cmake files?

in my install tree, in ITKTargets-release.Cmake there exists absolute path
for include and lib file.

My install tree of ITK does not work on a different machine unless I copy
them too exact same directory where I installed on machine.

This goes against portability and it is cmake who is doing this work.

Here is code in ITKTargets-release.cmake

set_property(TARGET ITKMetaIO APPEND PROPERTY IMPORTED_CONFIGURATIONS
RELEASE)
set_target_properties(ITKMetaIO PROPERTIES
  IMPORTED_IMPLIB_RELEASE "${_IMPORT_PREFIX}/lib/ITKMetaIO-4.10.lib"
  IMPORTED_LINK_INTERFACE_LIBRARIES_RELEASE
"C:/dashboard/otb/install_sb_x86/lib/zdll.lib;comctl32;wsock32"
  IMPORTED_LOCATION_RELEASE "${_IMPORT_PREFIX}/bin/ITKMetaIO-4.10.dll"
  )

see the absolute path to C:/dashboard/otb/install_sb_x86/lib/zdll.lib

so if on a different machine no matter where I copy these cmake files for
ITK, I must have zdll.lib in C:/dashboard/otb/install_sb_x86/lib/
and same goes for fftw, expat etc.. if enabled.

A simple find_package searching for for include and headers is portable
than config files. Right now even copying the files on same compiler won't
work.
But in reality there is no technical issues.

Is anyone aware of a better way other than manually updating those absolute
path to zdll.lib

On Tue, May 24, 2016 at 1:21 AM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Rashad,
>
> It looks like MXE is configured to use system versions of EXPAT, HDF5,
> JPEG, PNG, TIFF, and ZLIB:
>
>   https://github.com/mxe/mxe/blob/4135f9b1227ba56b92ceb8a9820163
> 70ad5c8894/src/itk.mk#L28-L33
>
> USE_SYSTEM could be disabled for these libraries.
>
> Or, it may be possible for the module system to learn relative
> locations of these libraries with ITK_USE_SYSTEM*. But, it would work
> best if these projects were configured with CMake, create a
> <project>Config.cmake or <project>-config.cmake file, and use relative
> paths internally.
>
> HTH,
> Matt
>
> On Tue, May 10, 2016 at 5:25 PM, Rashad Kanavath
> <mohammedrashadkm at gmail.com> wrote:
> >
> >
> > On Tue, May 10, 2016 at 10:50 PM, D?enan Zuki? <dzenanz at gmail.com>
> wrote:
> >>
> >> Hi Rashad,
> >>
> >> a few months ago relative paths were completely removed from CMake,
> >> because they were never fully implemented. Have you followed
> recommendations
> >> from here for cross-compiling?
> >
> >
> > Yes. indeed. I had updated the mxe/src/itk.mk for several versions of
> ITK!
> >
> > Regarding relative path in cmake, I don't understand.  I didn't use cmake
> > specific REL_PATH.
> >>
> >>
> >> As for integrating your changes into ITK, you should submit a patch
> >> following the instructions here. If your changes don't break anything,
> they
> >> are likely to be integrated.
> >
> >
> > issue here is a bit different. For all libitk* stuff the story ends well.
> > For thirdparties, zlib, expat etc.. it is good idea to put the full path
> > because we don't know if they are in same install directory as ITK or
> not.
> > But this make the installed cmake modules non-portable even to a
> different
> > location on the same disk.
> >
> > Now if anyone want to provide a distributable setup of ITK. patch the
> > generated cmake files with sed and then copy it. This is what I am doing
> > right now!
> > A simple not perfect solution is to have all thirdparties make
> > <LIBRARY>_PREFIX variable inside the ITKConfig.cmake
> >
> > and for each library we use <LIBRARY>_PREFIX/include and
> > <LIBRARY>_PREFIX/lib
> >
> >
> > Another option is to avoid full path directly inside cmake module files
> and
> > put find_package() calls in the install tree.
> >
> > As these files are autogenerated by cmake, don't know what is possible.
> >
> >
> >
> >
> >
> >>
> >> Regards,
> >> D?enan
> >>
> >> On Mon, May 9, 2016 at 4:27 PM, Rashad Kanavath
> >> <mohammedrashadkm at gmail.com> wrote:
> >>>
> >>> Hello all,
> >>>
> >>> I have some issue when copying ITK install directory to a different
> >>> system. I agree this is not usual and may not appear on a linux distro
> or
> >>> windows.
> >>>
> >>> My requirement is bit different. I cross-compile ITK and then use the
> >>> binaries on Windows. Using dll and headers are fine. But the installed
> cmake
> >>> files are a problem. They have absolute path in ITK-4.8/Modules/*.cmake
> >>> files. It is not in all .cmake files even though I put a wildcard
> there..
> >>>
> >>> For a easy and quick workaround. I rely on mighty sed command to insert
> >>> something into installed cmake file.
> >>>
> >>> For example see this;
> >>> lib/cmake/ITK-4.8/ITKTargets-release.cmake
> >>>
> >>> set(CMAKE_IMPORT_FILE_VERSION 1)
> >>> set(LIB_INSTALL_PREFIX)
> >>> get_filename_component(CURRENT_FILE_DIR "${CMAKE_CURRENT_LIST_FILE}"
> >>> PATH)
> >>> get_filename_component(LIB_INSTALL_PREFIX "${CURRENT_FILE_DIR}" PATH)
> >>> get_filename_component(LIB_INSTALL_PREFIX "${LIB_INSTALL_PREFIX}"
> PATH)
> >>> get_filename_component(LIB_INSTALL_PREFIX "${LIB_INSTALL_PREFIX}"
> PATH)
> >>>
> >>> and at last:
> >>>
> >>> $(SED) -i 's,$(PREFIX)/$(TARGET),\${LIB_INSTALL_PREFIX},g'
> >>> 'lib/cmake/ITK-$(ITK_VER)/ITKTargets-release.cmake'
> >>>
> >>> I would like to have this patch inside the other .cmake files in the
> >>> installation and avoid the sed commands during post-installation
> >>>
> >>> Here is the list of cmake files that needs this change.
> >>> lib/cmake/ITK-4.8/ITKTargets-release.cmake
> >>> lib/cmake/ITK-4.8/Modules/ITKZLIB.cmake
> >>> lib/cmake/ITK-4.8/Modules/ITKExpat.cmake
> >>> lib/cmake/ITK-4.8/Modules/ITKHDF5.cmake
> >>> lib/cmake/ITK-4.8/Modules/ITKJPEG.cmake
> >>> lib/cmake/ITK-4.8/Modules/ITKTIFF.cmake
> >>> lib/cmake/ITK-4.8/Modules/ITKPNG.cmake
> >>>
> >>> So is it possible to make the change into future version of ITK?
> >>>
> >>> The major issue here is those cmake files are generated by cmake. Is
> >>> there a way cmake could use relative path ?
> >>>
> >>>
> >>> --
> >>> Regards,
> >>>    Rashad
> >>>
> >>> _______________________________________________
> >>> Powered by www.kitware.com
> >>>
> >>> Visit other Kitware open-source projects at
> >>> http://www.kitware.com/opensource/opensource.html
> >>>
> >>> Kitware offers ITK Training Courses, for more information visit:
> >>> http://kitware.com/products/protraining.php
> >>>
> >>> Please keep messages on-topic and check the ITK FAQ at:
> >>> http://www.itk.org/Wiki/ITK_FAQ
> >>>
> >>> Follow this link to subscribe/unsubscribe:
> >>> http://public.kitware.com/mailman/listinfo/insight-developers
> >>>
> >>
> >
> >
> >
> > --
> > Regards,
> >    Rashad
> >
> > _______________________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-developers
> >
>



-- 
Regards,
   Rashad
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_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-developers

From dzenanz at gmail.com  Tue Dec 20 10:15:03 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 20 Dec 2016 10:15:03 -0500
Subject: [ITK] [ITK-dev] installed ITK cannot be moved due to absolute
	path
In-Reply-To: <CANNqv9fSqBF0vdQQTa5An5xh8NPBd+cAuo=MvoR5UPDTr-cdOA@mail.gmail.com>
References: <CANNqv9eKZygjeSgdauFADK6jev2V9Q4Bhk8gfP=GkR5ngLfoGA@mail.gmail.com>
 <CAPf2UMTo6LY09u1gKxa+MPjOgyQjMh25ADHSdpv4wTc3GRzbZA@mail.gmail.com>
 <CANNqv9dC9F6PHSyrLfnqY2NbA8dSDxnD-kzEKTdUqwhW_Mea8A@mail.gmail.com>
 <CALzTN-Q-Q9Ho4fmG99B4RUSwrpYCiihA3fiD_7WpKe5Kt24gtg@mail.gmail.com>
 <CANNqv9fSqBF0vdQQTa5An5xh8NPBd+cAuo=MvoR5UPDTr-cdOA@mail.gmail.com>
Message-ID: <CAPf2UMRTmOMG9CON1w1X+-GUYzmcNGch5bu0dxq31_WVpT-O8g@mail.gmail.com>

Hi Rashad,

one way to generate install tree in a different location is by
changing CMAKE_INSTALL_PREFIX in CMake, reconfiguring, regenerating
project, the building the INSTALL target. That should generate the install
tree in your desired location.

Regards,
D?enan

On Tue, Dec 20, 2016 at 4:48 AM, Rashad Kanavath <mohammedrashadkm at gmail.com
> wrote:

> Hello all,
>
> Is there a simple FindITK.cmake which can be used instead of config and
> targets cmake files?
>
> in my install tree, in ITKTargets-release.Cmake there exists absolute path
> for include and lib file.
>
> My install tree of ITK does not work on a different machine unless I copy
> them too exact same directory where I installed on machine.
>
> This goes against portability and it is cmake who is doing this work.
>
> Here is code in ITKTargets-release.cmake
>
> set_property(TARGET ITKMetaIO APPEND PROPERTY IMPORTED_CONFIGURATIONS
> RELEASE)
> set_target_properties(ITKMetaIO PROPERTIES
>   IMPORTED_IMPLIB_RELEASE "${_IMPORT_PREFIX}/lib/ITKMetaIO-4.10.lib"
>   IMPORTED_LINK_INTERFACE_LIBRARIES_RELEASE "C:/dashboard/otb/install_sb_
> x86/lib/zdll.lib;comctl32;wsock32"
>   IMPORTED_LOCATION_RELEASE "${_IMPORT_PREFIX}/bin/ITKMetaIO-4.10.dll"
>   )
>
> see the absolute path to C:/dashboard/otb/install_sb_x86/lib/zdll.lib
>
> so if on a different machine no matter where I copy these cmake files for
> ITK, I must have zdll.lib in C:/dashboard/otb/install_sb_x86/lib/
> and same goes for fftw, expat etc.. if enabled.
>
> A simple find_package searching for for include and headers is portable
> than config files. Right now even copying the files on same compiler won't
> work.
> But in reality there is no technical issues.
>
> Is anyone aware of a better way other than manually updating those
> absolute path to zdll.lib
>
> On Tue, May 24, 2016 at 1:21 AM, Matt McCormick <
> matt.mccormick at kitware.com> wrote:
>
>> Hi Rashad,
>>
>> It looks like MXE is configured to use system versions of EXPAT, HDF5,
>> JPEG, PNG, TIFF, and ZLIB:
>>
>>   https://github.com/mxe/mxe/blob/4135f9b1227ba56b92ceb8a98201
>> 6370ad5c8894/src/itk.mk#L28-L33
>>
>> USE_SYSTEM could be disabled for these libraries.
>>
>> Or, it may be possible for the module system to learn relative
>> locations of these libraries with ITK_USE_SYSTEM*. But, it would work
>> best if these projects were configured with CMake, create a
>> <project>Config.cmake or <project>-config.cmake file, and use relative
>> paths internally.
>>
>> HTH,
>> Matt
>>
>> On Tue, May 10, 2016 at 5:25 PM, Rashad Kanavath
>> <mohammedrashadkm at gmail.com> wrote:
>> >
>> >
>> > On Tue, May 10, 2016 at 10:50 PM, D?enan Zuki? <dzenanz at gmail.com>
>> wrote:
>> >>
>> >> Hi Rashad,
>> >>
>> >> a few months ago relative paths were completely removed from CMake,
>> >> because they were never fully implemented. Have you followed
>> recommendations
>> >> from here for cross-compiling?
>> >
>> >
>> > Yes. indeed. I had updated the mxe/src/itk.mk for several versions of
>> ITK!
>> >
>> > Regarding relative path in cmake, I don't understand.  I didn't use
>> cmake
>> > specific REL_PATH.
>> >>
>> >>
>> >> As for integrating your changes into ITK, you should submit a patch
>> >> following the instructions here. If your changes don't break anything,
>> they
>> >> are likely to be integrated.
>> >
>> >
>> > issue here is a bit different. For all libitk* stuff the story ends
>> well.
>> > For thirdparties, zlib, expat etc.. it is good idea to put the full path
>> > because we don't know if they are in same install directory as ITK or
>> not.
>> > But this make the installed cmake modules non-portable even to a
>> different
>> > location on the same disk.
>> >
>> > Now if anyone want to provide a distributable setup of ITK. patch the
>> > generated cmake files with sed and then copy it. This is what I am doing
>> > right now!
>> > A simple not perfect solution is to have all thirdparties make
>> > <LIBRARY>_PREFIX variable inside the ITKConfig.cmake
>> >
>> > and for each library we use <LIBRARY>_PREFIX/include and
>> > <LIBRARY>_PREFIX/lib
>> >
>> >
>> > Another option is to avoid full path directly inside cmake module files
>> and
>> > put find_package() calls in the install tree.
>> >
>> > As these files are autogenerated by cmake, don't know what is possible.
>> >
>> >
>> >
>> >
>> >
>> >>
>> >> Regards,
>> >> D?enan
>> >>
>> >> On Mon, May 9, 2016 at 4:27 PM, Rashad Kanavath
>> >> <mohammedrashadkm at gmail.com> wrote:
>> >>>
>> >>> Hello all,
>> >>>
>> >>> I have some issue when copying ITK install directory to a different
>> >>> system. I agree this is not usual and may not appear on a linux
>> distro or
>> >>> windows.
>> >>>
>> >>> My requirement is bit different. I cross-compile ITK and then use the
>> >>> binaries on Windows. Using dll and headers are fine. But the
>> installed cmake
>> >>> files are a problem. They have absolute path in
>> ITK-4.8/Modules/*.cmake
>> >>> files. It is not in all .cmake files even though I put a wildcard
>> there..
>> >>>
>> >>> For a easy and quick workaround. I rely on mighty sed command to
>> insert
>> >>> something into installed cmake file.
>> >>>
>> >>> For example see this;
>> >>> lib/cmake/ITK-4.8/ITKTargets-release.cmake
>> >>>
>> >>> set(CMAKE_IMPORT_FILE_VERSION 1)
>> >>> set(LIB_INSTALL_PREFIX)
>> >>> get_filename_component(CURRENT_FILE_DIR "${CMAKE_CURRENT_LIST_FILE}"
>> >>> PATH)
>> >>> get_filename_component(LIB_INSTALL_PREFIX "${CURRENT_FILE_DIR}" PATH)
>> >>> get_filename_component(LIB_INSTALL_PREFIX "${LIB_INSTALL_PREFIX}"
>> PATH)
>> >>> get_filename_component(LIB_INSTALL_PREFIX "${LIB_INSTALL_PREFIX}"
>> PATH)
>> >>>
>> >>> and at last:
>> >>>
>> >>> $(SED) -i 's,$(PREFIX)/$(TARGET),\${LIB_INSTALL_PREFIX},g'
>> >>> 'lib/cmake/ITK-$(ITK_VER)/ITKTargets-release.cmake'
>> >>>
>> >>> I would like to have this patch inside the other .cmake files in the
>> >>> installation and avoid the sed commands during post-installation
>> >>>
>> >>> Here is the list of cmake files that needs this change.
>> >>> lib/cmake/ITK-4.8/ITKTargets-release.cmake
>> >>> lib/cmake/ITK-4.8/Modules/ITKZLIB.cmake
>> >>> lib/cmake/ITK-4.8/Modules/ITKExpat.cmake
>> >>> lib/cmake/ITK-4.8/Modules/ITKHDF5.cmake
>> >>> lib/cmake/ITK-4.8/Modules/ITKJPEG.cmake
>> >>> lib/cmake/ITK-4.8/Modules/ITKTIFF.cmake
>> >>> lib/cmake/ITK-4.8/Modules/ITKPNG.cmake
>> >>>
>> >>> So is it possible to make the change into future version of ITK?
>> >>>
>> >>> The major issue here is those cmake files are generated by cmake. Is
>> >>> there a way cmake could use relative path ?
>> >>>
>> >>>
>> >>> --
>> >>> Regards,
>> >>>    Rashad
>> >>>
>> >>> _______________________________________________
>> >>> Powered by www.kitware.com
>> >>>
>> >>> Visit other Kitware open-source projects at
>> >>> http://www.kitware.com/opensource/opensource.html
>> >>>
>> >>> Kitware offers ITK Training Courses, for more information visit:
>> >>> http://kitware.com/products/protraining.php
>> >>>
>> >>> Please keep messages on-topic and check the ITK FAQ at:
>> >>> http://www.itk.org/Wiki/ITK_FAQ
>> >>>
>> >>> Follow this link to subscribe/unsubscribe:
>> >>> http://public.kitware.com/mailman/listinfo/insight-developers
>> >>>
>> >>
>> >
>> >
>> >
>> > --
>> > Regards,
>> >    Rashad
>> >
>> > _______________________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-developers
>> >
>>
>
>
>
> --
> Regards,
>    Rashad
>
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_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-developers

From mohammedrashadkm at gmail.com  Wed Dec 21 09:03:00 2016
From: mohammedrashadkm at gmail.com (Rashad Kanavath)
Date: Wed, 21 Dec 2016 15:03:00 +0100
Subject: [ITK] [ITK-dev] installed ITK cannot be moved due to absolute
	path
In-Reply-To: <CAPf2UMRTmOMG9CON1w1X+-GUYzmcNGch5bu0dxq31_WVpT-O8g@mail.gmail.com>
References: <CANNqv9eKZygjeSgdauFADK6jev2V9Q4Bhk8gfP=GkR5ngLfoGA@mail.gmail.com>
 <CAPf2UMTo6LY09u1gKxa+MPjOgyQjMh25ADHSdpv4wTc3GRzbZA@mail.gmail.com>
 <CANNqv9dC9F6PHSyrLfnqY2NbA8dSDxnD-kzEKTdUqwhW_Mea8A@mail.gmail.com>
 <CALzTN-Q-Q9Ho4fmG99B4RUSwrpYCiihA3fiD_7WpKe5Kt24gtg@mail.gmail.com>
 <CANNqv9fSqBF0vdQQTa5An5xh8NPBd+cAuo=MvoR5UPDTr-cdOA@mail.gmail.com>
 <CAPf2UMRTmOMG9CON1w1X+-GUYzmcNGch5bu0dxq31_WVpT-O8g@mail.gmail.com>
Message-ID: <CANNqv9fFF4ukPPy8KSTDe+WWuCdqZDUz5=MLQN81V1Sf8j9Rpw@mail.gmail.com>

Hello D?enan,

Thanks for your reply.  Unfortunately, this won't work in my case. I will
try to explain it.

I have installed itk in my system say: c:/projects/itk_install

now I copy itk_install directory to another system of my colleague. If
he/she is copying my "itk_install" folder into any directory other than
c:/projects/, itk build is useless.
cmake says it cannot find file c:/projects/itk_install/lib/ITKxxxxx.dll
etc..

This error is coming from
c:/projects/itk_install/lib/cmake/ITK-4.10/ITKTargets-release.cmake. Note
that this file is generated by cmake.

So I have two options:
1. ask to copy "itk_install" directory to c:/projects/itk_install (easy, )
2. copy "itk_install" directory anywhere but search in
<your-install-prefix>/lib/cmake/ITK-4.10 and replace all occurrence of
c:/projects/itk_install with <your-install-prefix>

Second solution is more awful compared to first. So for now, I insist on
first option. But after a couple of such installation of "itk_install", it
seems bad to me.
Like I mentioned in last thread, technically my itk_install could be reused
if cmake does not have absolute path in the install tree for ZLIB, fftw
etc..

FYI, there are other projects which does same thing and for them I have a
custom Find<Package>.cmake in source tree. So don't care what ever they
have in their lib/cmake/<Package> files

If ITK devs can provide FindITK.cmake , then we could reuse that. Instead
of ITKConfig.cmake stuff.

Hope I explained case well. Let me know if you need any more information.

Appreciate your help in solving this.


On Tue, Dec 20, 2016 at 4:15 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Rashad,
>
> one way to generate install tree in a different location is by
> changing CMAKE_INSTALL_PREFIX in CMake, reconfiguring, regenerating
> project, the building the INSTALL target. That should generate the install
> tree in your desired location.
>
> Regards,
> D?enan
>
> On Tue, Dec 20, 2016 at 4:48 AM, Rashad Kanavath <
> mohammedrashadkm at gmail.com> wrote:
>
>> Hello all,
>>
>> Is there a simple FindITK.cmake which can be used instead of config and
>> targets cmake files?
>>
>> in my install tree, in ITKTargets-release.Cmake there exists absolute
>> path for include and lib file.
>>
>> My install tree of ITK does not work on a different machine unless I copy
>> them too exact same directory where I installed on machine.
>>
>> This goes against portability and it is cmake who is doing this work.
>>
>> Here is code in ITKTargets-release.cmake
>>
>> set_property(TARGET ITKMetaIO APPEND PROPERTY IMPORTED_CONFIGURATIONS
>> RELEASE)
>> set_target_properties(ITKMetaIO PROPERTIES
>>   IMPORTED_IMPLIB_RELEASE "${_IMPORT_PREFIX}/lib/ITKMetaIO-4.10.lib"
>>   IMPORTED_LINK_INTERFACE_LIBRARIES_RELEASE
>> "C:/dashboard/otb/install_sb_x86/lib/zdll.lib;comctl32;wsock32"
>>   IMPORTED_LOCATION_RELEASE "${_IMPORT_PREFIX}/bin/ITKMetaIO-4.10.dll"
>>   )
>>
>> see the absolute path to C:/dashboard/otb/install_sb_x86/lib/zdll.lib
>>
>> so if on a different machine no matter where I copy these cmake files for
>> ITK, I must have zdll.lib in C:/dashboard/otb/install_sb_x86/lib/
>> and same goes for fftw, expat etc.. if enabled.
>>
>> A simple find_package searching for for include and headers is portable
>> than config files. Right now even copying the files on same compiler won't
>> work.
>> But in reality there is no technical issues.
>>
>> Is anyone aware of a better way other than manually updating those
>> absolute path to zdll.lib
>>
>> On Tue, May 24, 2016 at 1:21 AM, Matt McCormick <
>> matt.mccormick at kitware.com> wrote:
>>
>>> Hi Rashad,
>>>
>>> It looks like MXE is configured to use system versions of EXPAT, HDF5,
>>> JPEG, PNG, TIFF, and ZLIB:
>>>
>>>   https://github.com/mxe/mxe/blob/4135f9b1227ba56b92ceb8a98201
>>> 6370ad5c8894/src/itk.mk#L28-L33
>>>
>>> USE_SYSTEM could be disabled for these libraries.
>>>
>>> Or, it may be possible for the module system to learn relative
>>> locations of these libraries with ITK_USE_SYSTEM*. But, it would work
>>> best if these projects were configured with CMake, create a
>>> <project>Config.cmake or <project>-config.cmake file, and use relative
>>> paths internally.
>>>
>>> HTH,
>>> Matt
>>>
>>> On Tue, May 10, 2016 at 5:25 PM, Rashad Kanavath
>>> <mohammedrashadkm at gmail.com> wrote:
>>> >
>>> >
>>> > On Tue, May 10, 2016 at 10:50 PM, D?enan Zuki? <dzenanz at gmail.com>
>>> wrote:
>>> >>
>>> >> Hi Rashad,
>>> >>
>>> >> a few months ago relative paths were completely removed from CMake,
>>> >> because they were never fully implemented. Have you followed
>>> recommendations
>>> >> from here for cross-compiling?
>>> >
>>> >
>>> > Yes. indeed. I had updated the mxe/src/itk.mk for several versions of
>>> ITK!
>>> >
>>> > Regarding relative path in cmake, I don't understand.  I didn't use
>>> cmake
>>> > specific REL_PATH.
>>> >>
>>> >>
>>> >> As for integrating your changes into ITK, you should submit a patch
>>> >> following the instructions here. If your changes don't break
>>> anything, they
>>> >> are likely to be integrated.
>>> >
>>> >
>>> > issue here is a bit different. For all libitk* stuff the story ends
>>> well.
>>> > For thirdparties, zlib, expat etc.. it is good idea to put the full
>>> path
>>> > because we don't know if they are in same install directory as ITK or
>>> not.
>>> > But this make the installed cmake modules non-portable even to a
>>> different
>>> > location on the same disk.
>>> >
>>> > Now if anyone want to provide a distributable setup of ITK. patch the
>>> > generated cmake files with sed and then copy it. This is what I am
>>> doing
>>> > right now!
>>> > A simple not perfect solution is to have all thirdparties make
>>> > <LIBRARY>_PREFIX variable inside the ITKConfig.cmake
>>> >
>>> > and for each library we use <LIBRARY>_PREFIX/include and
>>> > <LIBRARY>_PREFIX/lib
>>> >
>>> >
>>> > Another option is to avoid full path directly inside cmake module
>>> files and
>>> > put find_package() calls in the install tree.
>>> >
>>> > As these files are autogenerated by cmake, don't know what is possible.
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >>
>>> >> Regards,
>>> >> D?enan
>>> >>
>>> >> On Mon, May 9, 2016 at 4:27 PM, Rashad Kanavath
>>> >> <mohammedrashadkm at gmail.com> wrote:
>>> >>>
>>> >>> Hello all,
>>> >>>
>>> >>> I have some issue when copying ITK install directory to a different
>>> >>> system. I agree this is not usual and may not appear on a linux
>>> distro or
>>> >>> windows.
>>> >>>
>>> >>> My requirement is bit different. I cross-compile ITK and then use the
>>> >>> binaries on Windows. Using dll and headers are fine. But the
>>> installed cmake
>>> >>> files are a problem. They have absolute path in
>>> ITK-4.8/Modules/*.cmake
>>> >>> files. It is not in all .cmake files even though I put a wildcard
>>> there..
>>> >>>
>>> >>> For a easy and quick workaround. I rely on mighty sed command to
>>> insert
>>> >>> something into installed cmake file.
>>> >>>
>>> >>> For example see this;
>>> >>> lib/cmake/ITK-4.8/ITKTargets-release.cmake
>>> >>>
>>> >>> set(CMAKE_IMPORT_FILE_VERSION 1)
>>> >>> set(LIB_INSTALL_PREFIX)
>>> >>> get_filename_component(CURRENT_FILE_DIR "${CMAKE_CURRENT_LIST_FILE}"
>>> >>> PATH)
>>> >>> get_filename_component(LIB_INSTALL_PREFIX "${CURRENT_FILE_DIR}"
>>> PATH)
>>> >>> get_filename_component(LIB_INSTALL_PREFIX "${LIB_INSTALL_PREFIX}"
>>> PATH)
>>> >>> get_filename_component(LIB_INSTALL_PREFIX "${LIB_INSTALL_PREFIX}"
>>> PATH)
>>> >>>
>>> >>> and at last:
>>> >>>
>>> >>> $(SED) -i 's,$(PREFIX)/$(TARGET),\${LIB_INSTALL_PREFIX},g'
>>> >>> 'lib/cmake/ITK-$(ITK_VER)/ITKTargets-release.cmake'
>>> >>>
>>> >>> I would like to have this patch inside the other .cmake files in the
>>> >>> installation and avoid the sed commands during post-installation
>>> >>>
>>> >>> Here is the list of cmake files that needs this change.
>>> >>> lib/cmake/ITK-4.8/ITKTargets-release.cmake
>>> >>> lib/cmake/ITK-4.8/Modules/ITKZLIB.cmake
>>> >>> lib/cmake/ITK-4.8/Modules/ITKExpat.cmake
>>> >>> lib/cmake/ITK-4.8/Modules/ITKHDF5.cmake
>>> >>> lib/cmake/ITK-4.8/Modules/ITKJPEG.cmake
>>> >>> lib/cmake/ITK-4.8/Modules/ITKTIFF.cmake
>>> >>> lib/cmake/ITK-4.8/Modules/ITKPNG.cmake
>>> >>>
>>> >>> So is it possible to make the change into future version of ITK?
>>> >>>
>>> >>> The major issue here is those cmake files are generated by cmake. Is
>>> >>> there a way cmake could use relative path ?
>>> >>>
>>> >>>
>>> >>> --
>>> >>> Regards,
>>> >>>    Rashad
>>> >>>
>>> >>> _______________________________________________
>>> >>> Powered by www.kitware.com
>>> >>>
>>> >>> Visit other Kitware open-source projects at
>>> >>> http://www.kitware.com/opensource/opensource.html
>>> >>>
>>> >>> Kitware offers ITK Training Courses, for more information visit:
>>> >>> http://kitware.com/products/protraining.php
>>> >>>
>>> >>> Please keep messages on-topic and check the ITK FAQ at:
>>> >>> http://www.itk.org/Wiki/ITK_FAQ
>>> >>>
>>> >>> Follow this link to subscribe/unsubscribe:
>>> >>> http://public.kitware.com/mailman/listinfo/insight-developers
>>> >>>
>>> >>
>>> >
>>> >
>>> >
>>> > --
>>> > Regards,
>>> >    Rashad
>>> >
>>> > _______________________________________________
>>> > Powered by www.kitware.com
>>> >
>>> > Visit other Kitware open-source projects at
>>> > http://www.kitware.com/opensource/opensource.html
>>> >
>>> > Kitware offers ITK Training Courses, for more information visit:
>>> > http://kitware.com/products/protraining.php
>>> >
>>> > Please keep messages on-topic and check the ITK FAQ at:
>>> > http://www.itk.org/Wiki/ITK_FAQ
>>> >
>>> > Follow this link to subscribe/unsubscribe:
>>> > http://public.kitware.com/mailman/listinfo/insight-developers
>>> >
>>>
>>
>>
>>
>> --
>> Regards,
>>    Rashad
>>
>
>


-- 
Regards,
   Rashad
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From matt.mccormick at kitware.com  Wed Dec 21 11:06:23 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 21 Dec 2016 11:06:23 -0500
Subject: [ITK] [ITK-dev] installed ITK cannot be moved due to absolute
	path
In-Reply-To: <CANNqv9fFF4ukPPy8KSTDe+WWuCdqZDUz5=MLQN81V1Sf8j9Rpw@mail.gmail.com>
References: <CANNqv9eKZygjeSgdauFADK6jev2V9Q4Bhk8gfP=GkR5ngLfoGA@mail.gmail.com>
 <CAPf2UMTo6LY09u1gKxa+MPjOgyQjMh25ADHSdpv4wTc3GRzbZA@mail.gmail.com>
 <CANNqv9dC9F6PHSyrLfnqY2NbA8dSDxnD-kzEKTdUqwhW_Mea8A@mail.gmail.com>
 <CALzTN-Q-Q9Ho4fmG99B4RUSwrpYCiihA3fiD_7WpKe5Kt24gtg@mail.gmail.com>
 <CANNqv9fSqBF0vdQQTa5An5xh8NPBd+cAuo=MvoR5UPDTr-cdOA@mail.gmail.com>
 <CAPf2UMRTmOMG9CON1w1X+-GUYzmcNGch5bu0dxq31_WVpT-O8g@mail.gmail.com>
 <CANNqv9fFF4ukPPy8KSTDe+WWuCdqZDUz5=MLQN81V1Sf8j9Rpw@mail.gmail.com>
Message-ID: <CALzTN-RDpB_gRY1L_fvFfyke2Jyhk=h2OAAMuy4hY1TJoy4KZQ@mail.gmail.com>

Hi Rashad,

The Find<Package>.cmake are purposely not provided because it is not
reliable and does not provide all the information required. The CMake
package configuration file allows ITK to declare what is required to
build it instead of requiring CMake to guess (and get it wrong).

For this case, it is recommended to turn off ITK_USE_SYSTEM_ZLIB,
which will make the ITK installation portable.

HTH,
Matt

On Wed, Dec 21, 2016 at 9:03 AM, Rashad Kanavath
<mohammedrashadkm at gmail.com> wrote:
> Hello D?enan,
>
> Thanks for your reply.  Unfortunately, this won't work in my case. I will
> try to explain it.
>
> I have installed itk in my system say: c:/projects/itk_install
>
> now I copy itk_install directory to another system of my colleague. If
> he/she is copying my "itk_install" folder into any directory other than
> c:/projects/, itk build is useless.
> cmake says it cannot find file c:/projects/itk_install/lib/ITKxxxxx.dll
> etc..
>
> This error is coming from
> c:/projects/itk_install/lib/cmake/ITK-4.10/ITKTargets-release.cmake. Note
> that this file is generated by cmake.
>
> So I have two options:
> 1. ask to copy "itk_install" directory to c:/projects/itk_install (easy, )
> 2. copy "itk_install" directory anywhere but search in
> <your-install-prefix>/lib/cmake/ITK-4.10 and replace all occurrence of
> c:/projects/itk_install with <your-install-prefix>
>
> Second solution is more awful compared to first. So for now, I insist on
> first option. But after a couple of such installation of "itk_install", it
> seems bad to me.
> Like I mentioned in last thread, technically my itk_install could be reused
> if cmake does not have absolute path in the install tree for ZLIB, fftw
> etc..
>
> FYI, there are other projects which does same thing and for them I have a
> custom Find<Package>.cmake in source tree. So don't care what ever they have
> in their lib/cmake/<Package> files
>
> If ITK devs can provide FindITK.cmake , then we could reuse that. Instead of
> ITKConfig.cmake stuff.
>
> Hope I explained case well. Let me know if you need any more information.
>
> Appreciate your help in solving this.
>
>
> On Tue, Dec 20, 2016 at 4:15 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>
>> Hi Rashad,
>>
>> one way to generate install tree in a different location is by changing
>> CMAKE_INSTALL_PREFIX in CMake, reconfiguring, regenerating project, the
>> building the INSTALL target. That should generate the install tree in your
>> desired location.
>>
>> Regards,
>> D?enan
>>
>> On Tue, Dec 20, 2016 at 4:48 AM, Rashad Kanavath
>> <mohammedrashadkm at gmail.com> wrote:
>>>
>>> Hello all,
>>>
>>> Is there a simple FindITK.cmake which can be used instead of config and
>>> targets cmake files?
>>>
>>> in my install tree, in ITKTargets-release.Cmake there exists absolute
>>> path for include and lib file.
>>>
>>> My install tree of ITK does not work on a different machine unless I copy
>>> them too exact same directory where I installed on machine.
>>>
>>> This goes against portability and it is cmake who is doing this work.
>>>
>>> Here is code in ITKTargets-release.cmake
>>>
>>> set_property(TARGET ITKMetaIO APPEND PROPERTY IMPORTED_CONFIGURATIONS
>>> RELEASE)
>>> set_target_properties(ITKMetaIO PROPERTIES
>>>   IMPORTED_IMPLIB_RELEASE "${_IMPORT_PREFIX}/lib/ITKMetaIO-4.10.lib"
>>>   IMPORTED_LINK_INTERFACE_LIBRARIES_RELEASE
>>> "C:/dashboard/otb/install_sb_x86/lib/zdll.lib;comctl32;wsock32"
>>>   IMPORTED_LOCATION_RELEASE "${_IMPORT_PREFIX}/bin/ITKMetaIO-4.10.dll"
>>>   )
>>>
>>> see the absolute path to C:/dashboard/otb/install_sb_x86/lib/zdll.lib
>>>
>>> so if on a different machine no matter where I copy these cmake files for
>>> ITK, I must have zdll.lib in C:/dashboard/otb/install_sb_x86/lib/
>>> and same goes for fftw, expat etc.. if enabled.
>>>
>>> A simple find_package searching for for include and headers is portable
>>> than config files. Right now even copying the files on same compiler won't
>>> work.
>>> But in reality there is no technical issues.
>>>
>>> Is anyone aware of a better way other than manually updating those
>>> absolute path to zdll.lib
>>>
>>> On Tue, May 24, 2016 at 1:21 AM, Matt McCormick
>>> <matt.mccormick at kitware.com> wrote:
>>>>
>>>> Hi Rashad,
>>>>
>>>> It looks like MXE is configured to use system versions of EXPAT, HDF5,
>>>> JPEG, PNG, TIFF, and ZLIB:
>>>>
>>>>
>>>> https://github.com/mxe/mxe/blob/4135f9b1227ba56b92ceb8a982016370ad5c8894/src/itk.mk#L28-L33
>>>>
>>>> USE_SYSTEM could be disabled for these libraries.
>>>>
>>>> Or, it may be possible for the module system to learn relative
>>>> locations of these libraries with ITK_USE_SYSTEM*. But, it would work
>>>> best if these projects were configured with CMake, create a
>>>> <project>Config.cmake or <project>-config.cmake file, and use relative
>>>> paths internally.
>>>>
>>>> HTH,
>>>> Matt
>>>>
>>>> On Tue, May 10, 2016 at 5:25 PM, Rashad Kanavath
>>>> <mohammedrashadkm at gmail.com> wrote:
>>>> >
>>>> >
>>>> > On Tue, May 10, 2016 at 10:50 PM, D?enan Zuki? <dzenanz at gmail.com>
>>>> > wrote:
>>>> >>
>>>> >> Hi Rashad,
>>>> >>
>>>> >> a few months ago relative paths were completely removed from CMake,
>>>> >> because they were never fully implemented. Have you followed
>>>> >> recommendations
>>>> >> from here for cross-compiling?
>>>> >
>>>> >
>>>> > Yes. indeed. I had updated the mxe/src/itk.mk for several versions of
>>>> > ITK!
>>>> >
>>>> > Regarding relative path in cmake, I don't understand.  I didn't use
>>>> > cmake
>>>> > specific REL_PATH.
>>>> >>
>>>> >>
>>>> >> As for integrating your changes into ITK, you should submit a patch
>>>> >> following the instructions here. If your changes don't break
>>>> >> anything, they
>>>> >> are likely to be integrated.
>>>> >
>>>> >
>>>> > issue here is a bit different. For all libitk* stuff the story ends
>>>> > well.
>>>> > For thirdparties, zlib, expat etc.. it is good idea to put the full
>>>> > path
>>>> > because we don't know if they are in same install directory as ITK or
>>>> > not.
>>>> > But this make the installed cmake modules non-portable even to a
>>>> > different
>>>> > location on the same disk.
>>>> >
>>>> > Now if anyone want to provide a distributable setup of ITK. patch the
>>>> > generated cmake files with sed and then copy it. This is what I am
>>>> > doing
>>>> > right now!
>>>> > A simple not perfect solution is to have all thirdparties make
>>>> > <LIBRARY>_PREFIX variable inside the ITKConfig.cmake
>>>> >
>>>> > and for each library we use <LIBRARY>_PREFIX/include and
>>>> > <LIBRARY>_PREFIX/lib
>>>> >
>>>> >
>>>> > Another option is to avoid full path directly inside cmake module
>>>> > files and
>>>> > put find_package() calls in the install tree.
>>>> >
>>>> > As these files are autogenerated by cmake, don't know what is
>>>> > possible.
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >>
>>>> >> Regards,
>>>> >> D?enan
>>>> >>
>>>> >> On Mon, May 9, 2016 at 4:27 PM, Rashad Kanavath
>>>> >> <mohammedrashadkm at gmail.com> wrote:
>>>> >>>
>>>> >>> Hello all,
>>>> >>>
>>>> >>> I have some issue when copying ITK install directory to a different
>>>> >>> system. I agree this is not usual and may not appear on a linux
>>>> >>> distro or
>>>> >>> windows.
>>>> >>>
>>>> >>> My requirement is bit different. I cross-compile ITK and then use
>>>> >>> the
>>>> >>> binaries on Windows. Using dll and headers are fine. But the
>>>> >>> installed cmake
>>>> >>> files are a problem. They have absolute path in
>>>> >>> ITK-4.8/Modules/*.cmake
>>>> >>> files. It is not in all .cmake files even though I put a wildcard
>>>> >>> there..
>>>> >>>
>>>> >>> For a easy and quick workaround. I rely on mighty sed command to
>>>> >>> insert
>>>> >>> something into installed cmake file.
>>>> >>>
>>>> >>> For example see this;
>>>> >>> lib/cmake/ITK-4.8/ITKTargets-release.cmake
>>>> >>>
>>>> >>> set(CMAKE_IMPORT_FILE_VERSION 1)
>>>> >>> set(LIB_INSTALL_PREFIX)
>>>> >>> get_filename_component(CURRENT_FILE_DIR "${CMAKE_CURRENT_LIST_FILE}"
>>>> >>> PATH)
>>>> >>> get_filename_component(LIB_INSTALL_PREFIX "${CURRENT_FILE_DIR}"
>>>> >>> PATH)
>>>> >>> get_filename_component(LIB_INSTALL_PREFIX "${LIB_INSTALL_PREFIX}"
>>>> >>> PATH)
>>>> >>> get_filename_component(LIB_INSTALL_PREFIX "${LIB_INSTALL_PREFIX}"
>>>> >>> PATH)
>>>> >>>
>>>> >>> and at last:
>>>> >>>
>>>> >>> $(SED) -i 's,$(PREFIX)/$(TARGET),\${LIB_INSTALL_PREFIX},g'
>>>> >>> 'lib/cmake/ITK-$(ITK_VER)/ITKTargets-release.cmake'
>>>> >>>
>>>> >>> I would like to have this patch inside the other .cmake files in the
>>>> >>> installation and avoid the sed commands during post-installation
>>>> >>>
>>>> >>> Here is the list of cmake files that needs this change.
>>>> >>> lib/cmake/ITK-4.8/ITKTargets-release.cmake
>>>> >>> lib/cmake/ITK-4.8/Modules/ITKZLIB.cmake
>>>> >>> lib/cmake/ITK-4.8/Modules/ITKExpat.cmake
>>>> >>> lib/cmake/ITK-4.8/Modules/ITKHDF5.cmake
>>>> >>> lib/cmake/ITK-4.8/Modules/ITKJPEG.cmake
>>>> >>> lib/cmake/ITK-4.8/Modules/ITKTIFF.cmake
>>>> >>> lib/cmake/ITK-4.8/Modules/ITKPNG.cmake
>>>> >>>
>>>> >>> So is it possible to make the change into future version of ITK?
>>>> >>>
>>>> >>> The major issue here is those cmake files are generated by cmake. Is
>>>> >>> there a way cmake could use relative path ?
>>>> >>>
>>>> >>>
>>>> >>> --
>>>> >>> Regards,
>>>> >>>    Rashad
>>>> >>>
>>>> >>> _______________________________________________
>>>> >>> Powered by www.kitware.com
>>>> >>>
>>>> >>> Visit other Kitware open-source projects at
>>>> >>> http://www.kitware.com/opensource/opensource.html
>>>> >>>
>>>> >>> Kitware offers ITK Training Courses, for more information visit:
>>>> >>> http://kitware.com/products/protraining.php
>>>> >>>
>>>> >>> Please keep messages on-topic and check the ITK FAQ at:
>>>> >>> http://www.itk.org/Wiki/ITK_FAQ
>>>> >>>
>>>> >>> Follow this link to subscribe/unsubscribe:
>>>> >>> http://public.kitware.com/mailman/listinfo/insight-developers
>>>> >>>
>>>> >>
>>>> >
>>>> >
>>>> >
>>>> > --
>>>> > Regards,
>>>> >    Rashad
>>>> >
>>>> > _______________________________________________
>>>> > Powered by www.kitware.com
>>>> >
>>>> > Visit other Kitware open-source projects at
>>>> > http://www.kitware.com/opensource/opensource.html
>>>> >
>>>> > Kitware offers ITK Training Courses, for more information visit:
>>>> > http://kitware.com/products/protraining.php
>>>> >
>>>> > Please keep messages on-topic and check the ITK FAQ at:
>>>> > http://www.itk.org/Wiki/ITK_FAQ
>>>> >
>>>> > Follow this link to subscribe/unsubscribe:
>>>> > http://public.kitware.com/mailman/listinfo/insight-developers
>>>> >
>>>
>>>
>>>
>>>
>>> --
>>> Regards,
>>>    Rashad
>>
>>
>
>
>
> --
> Regards,
>    Rashad
_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-developers

From mohammedrashadkm at gmail.com  Wed Dec 21 12:05:54 2016
From: mohammedrashadkm at gmail.com (Rashad Kanavath)
Date: Wed, 21 Dec 2016 18:05:54 +0100
Subject: [ITK] [ITK-dev] installed ITK cannot be moved due to absolute
	path
In-Reply-To: <CALzTN-RDpB_gRY1L_fvFfyke2Jyhk=h2OAAMuy4hY1TJoy4KZQ@mail.gmail.com>
References: <CANNqv9eKZygjeSgdauFADK6jev2V9Q4Bhk8gfP=GkR5ngLfoGA@mail.gmail.com>
 <CAPf2UMTo6LY09u1gKxa+MPjOgyQjMh25ADHSdpv4wTc3GRzbZA@mail.gmail.com>
 <CANNqv9dC9F6PHSyrLfnqY2NbA8dSDxnD-kzEKTdUqwhW_Mea8A@mail.gmail.com>
 <CALzTN-Q-Q9Ho4fmG99B4RUSwrpYCiihA3fiD_7WpKe5Kt24gtg@mail.gmail.com>
 <CANNqv9fSqBF0vdQQTa5An5xh8NPBd+cAuo=MvoR5UPDTr-cdOA@mail.gmail.com>
 <CAPf2UMRTmOMG9CON1w1X+-GUYzmcNGch5bu0dxq31_WVpT-O8g@mail.gmail.com>
 <CANNqv9fFF4ukPPy8KSTDe+WWuCdqZDUz5=MLQN81V1Sf8j9Rpw@mail.gmail.com>
 <CALzTN-RDpB_gRY1L_fvFfyke2Jyhk=h2OAAMuy4hY1TJoy4KZQ@mail.gmail.com>
Message-ID: <CANNqv9d5WoUsaGwm8o56pU_o=gTp3wacVmbmg-jnncnz7TSrNA@mail.gmail.com>

On Wed, Dec 21, 2016 at 5:06 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Rashad,
>
> The Find<Package>.cmake are purposely not provided because it is not
> reliable and does not provide all the information required. The CMake
> package configuration file allows ITK to declare what is required to
> build it instead of requiring CMake to guess (and get it wrong).
>
> For this case, it is recommended to turn off ITK_USE_SYSTEM_ZLIB,
> which will make the ITK installation portable.
>

I need to use zlib, fftw and expat in that case from ITK build/

But I have also providing a different build of zlib for my other projects.

What are the missing information when using FindITK.cmake as opposed to itk
cmake configuration files?

I understand that saving absolute path of libraries which link with project
is easy to avoid any issues in linking or at runtime.
 And that is one type of solution and IMHO does not solve the problem.

Apart from that I would like to find out what are real issues with
Find<Package>.cmake



> HTH,
> Matt
>
> On Wed, Dec 21, 2016 at 9:03 AM, Rashad Kanavath
> <mohammedrashadkm at gmail.com> wrote:
> > Hello D?enan,
> >
> > Thanks for your reply.  Unfortunately, this won't work in my case. I will
> > try to explain it.
> >
> > I have installed itk in my system say: c:/projects/itk_install
> >
> > now I copy itk_install directory to another system of my colleague. If
> > he/she is copying my "itk_install" folder into any directory other than
> > c:/projects/, itk build is useless.
> > cmake says it cannot find file c:/projects/itk_install/lib/ITKxxxxx.dll
> > etc..
> >
> > This error is coming from
> > c:/projects/itk_install/lib/cmake/ITK-4.10/ITKTargets-release.cmake.
> Note
> > that this file is generated by cmake.
> >
> > So I have two options:
> > 1. ask to copy "itk_install" directory to c:/projects/itk_install (easy,
> )
> > 2. copy "itk_install" directory anywhere but search in
> > <your-install-prefix>/lib/cmake/ITK-4.10 and replace all occurrence of
> > c:/projects/itk_install with <your-install-prefix>
> >
> > Second solution is more awful compared to first. So for now, I insist on
> > first option. But after a couple of such installation of "itk_install",
> it
> > seems bad to me.
> > Like I mentioned in last thread, technically my itk_install could be
> reused
> > if cmake does not have absolute path in the install tree for ZLIB, fftw
> > etc..
> >
> > FYI, there are other projects which does same thing and for them I have a
> > custom Find<Package>.cmake in source tree. So don't care what ever they
> have
> > in their lib/cmake/<Package> files
> >
> > If ITK devs can provide FindITK.cmake , then we could reuse that.
> Instead of
> > ITKConfig.cmake stuff.
> >
> > Hope I explained case well. Let me know if you need any more information.
> >
> > Appreciate your help in solving this.
> >
> >
> > On Tue, Dec 20, 2016 at 4:15 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> >>
> >> Hi Rashad,
> >>
> >> one way to generate install tree in a different location is by changing
> >> CMAKE_INSTALL_PREFIX in CMake, reconfiguring, regenerating project, the
> >> building the INSTALL target. That should generate the install tree in
> your
> >> desired location.
> >>
> >> Regards,
> >> D?enan
> >>
> >> On Tue, Dec 20, 2016 at 4:48 AM, Rashad Kanavath
> >> <mohammedrashadkm at gmail.com> wrote:
> >>>
> >>> Hello all,
> >>>
> >>> Is there a simple FindITK.cmake which can be used instead of config and
> >>> targets cmake files?
> >>>
> >>> in my install tree, in ITKTargets-release.Cmake there exists absolute
> >>> path for include and lib file.
> >>>
> >>> My install tree of ITK does not work on a different machine unless I
> copy
> >>> them too exact same directory where I installed on machine.
> >>>
> >>> This goes against portability and it is cmake who is doing this work.
> >>>
> >>> Here is code in ITKTargets-release.cmake
> >>>
> >>> set_property(TARGET ITKMetaIO APPEND PROPERTY IMPORTED_CONFIGURATIONS
> >>> RELEASE)
> >>> set_target_properties(ITKMetaIO PROPERTIES
> >>>   IMPORTED_IMPLIB_RELEASE "${_IMPORT_PREFIX}/lib/ITKMetaIO-4.10.lib"
> >>>   IMPORTED_LINK_INTERFACE_LIBRARIES_RELEASE
> >>> "C:/dashboard/otb/install_sb_x86/lib/zdll.lib;comctl32;wsock32"
> >>>   IMPORTED_LOCATION_RELEASE "${_IMPORT_PREFIX}/bin/ITKMetaIO-4.10.dll"
> >>>   )
> >>>
> >>> see the absolute path to C:/dashboard/otb/install_sb_x86/lib/zdll.lib
> >>>
> >>> so if on a different machine no matter where I copy these cmake files
> for
> >>> ITK, I must have zdll.lib in C:/dashboard/otb/install_sb_x86/lib/
> >>> and same goes for fftw, expat etc.. if enabled.
> >>>
> >>> A simple find_package searching for for include and headers is portable
> >>> than config files. Right now even copying the files on same compiler
> won't
> >>> work.
> >>> But in reality there is no technical issues.
> >>>
> >>> Is anyone aware of a better way other than manually updating those
> >>> absolute path to zdll.lib
> >>>
> >>> On Tue, May 24, 2016 at 1:21 AM, Matt McCormick
> >>> <matt.mccormick at kitware.com> wrote:
> >>>>
> >>>> Hi Rashad,
> >>>>
> >>>> It looks like MXE is configured to use system versions of EXPAT, HDF5,
> >>>> JPEG, PNG, TIFF, and ZLIB:
> >>>>
> >>>>
> >>>> https://github.com/mxe/mxe/blob/4135f9b1227ba56b92ceb8a9820163
> 70ad5c8894/src/itk.mk#L28-L33
> >>>>
> >>>> USE_SYSTEM could be disabled for these libraries.
> >>>>
> >>>> Or, it may be possible for the module system to learn relative
> >>>> locations of these libraries with ITK_USE_SYSTEM*. But, it would work
> >>>> best if these projects were configured with CMake, create a
> >>>> <project>Config.cmake or <project>-config.cmake file, and use relative
> >>>> paths internally.
> >>>>
> >>>> HTH,
> >>>> Matt
> >>>>
> >>>> On Tue, May 10, 2016 at 5:25 PM, Rashad Kanavath
> >>>> <mohammedrashadkm at gmail.com> wrote:
> >>>> >
> >>>> >
> >>>> > On Tue, May 10, 2016 at 10:50 PM, D?enan Zuki? <dzenanz at gmail.com>
> >>>> > wrote:
> >>>> >>
> >>>> >> Hi Rashad,
> >>>> >>
> >>>> >> a few months ago relative paths were completely removed from CMake,
> >>>> >> because they were never fully implemented. Have you followed
> >>>> >> recommendations
> >>>> >> from here for cross-compiling?
> >>>> >
> >>>> >
> >>>> > Yes. indeed. I had updated the mxe/src/itk.mk for several versions
> of
> >>>> > ITK!
> >>>> >
> >>>> > Regarding relative path in cmake, I don't understand.  I didn't use
> >>>> > cmake
> >>>> > specific REL_PATH.
> >>>> >>
> >>>> >>
> >>>> >> As for integrating your changes into ITK, you should submit a patch
> >>>> >> following the instructions here. If your changes don't break
> >>>> >> anything, they
> >>>> >> are likely to be integrated.
> >>>> >
> >>>> >
> >>>> > issue here is a bit different. For all libitk* stuff the story ends
> >>>> > well.
> >>>> > For thirdparties, zlib, expat etc.. it is good idea to put the full
> >>>> > path
> >>>> > because we don't know if they are in same install directory as ITK
> or
> >>>> > not.
> >>>> > But this make the installed cmake modules non-portable even to a
> >>>> > different
> >>>> > location on the same disk.
> >>>> >
> >>>> > Now if anyone want to provide a distributable setup of ITK. patch
> the
> >>>> > generated cmake files with sed and then copy it. This is what I am
> >>>> > doing
> >>>> > right now!
> >>>> > A simple not perfect solution is to have all thirdparties make
> >>>> > <LIBRARY>_PREFIX variable inside the ITKConfig.cmake
> >>>> >
> >>>> > and for each library we use <LIBRARY>_PREFIX/include and
> >>>> > <LIBRARY>_PREFIX/lib
> >>>> >
> >>>> >
> >>>> > Another option is to avoid full path directly inside cmake module
> >>>> > files and
> >>>> > put find_package() calls in the install tree.
> >>>> >
> >>>> > As these files are autogenerated by cmake, don't know what is
> >>>> > possible.
> >>>> >
> >>>> >
> >>>> >
> >>>> >
> >>>> >
> >>>> >>
> >>>> >> Regards,
> >>>> >> D?enan
> >>>> >>
> >>>> >> On Mon, May 9, 2016 at 4:27 PM, Rashad Kanavath
> >>>> >> <mohammedrashadkm at gmail.com> wrote:
> >>>> >>>
> >>>> >>> Hello all,
> >>>> >>>
> >>>> >>> I have some issue when copying ITK install directory to a
> different
> >>>> >>> system. I agree this is not usual and may not appear on a linux
> >>>> >>> distro or
> >>>> >>> windows.
> >>>> >>>
> >>>> >>> My requirement is bit different. I cross-compile ITK and then use
> >>>> >>> the
> >>>> >>> binaries on Windows. Using dll and headers are fine. But the
> >>>> >>> installed cmake
> >>>> >>> files are a problem. They have absolute path in
> >>>> >>> ITK-4.8/Modules/*.cmake
> >>>> >>> files. It is not in all .cmake files even though I put a wildcard
> >>>> >>> there..
> >>>> >>>
> >>>> >>> For a easy and quick workaround. I rely on mighty sed command to
> >>>> >>> insert
> >>>> >>> something into installed cmake file.
> >>>> >>>
> >>>> >>> For example see this;
> >>>> >>> lib/cmake/ITK-4.8/ITKTargets-release.cmake
> >>>> >>>
> >>>> >>> set(CMAKE_IMPORT_FILE_VERSION 1)
> >>>> >>> set(LIB_INSTALL_PREFIX)
> >>>> >>> get_filename_component(CURRENT_FILE_DIR
> "${CMAKE_CURRENT_LIST_FILE}"
> >>>> >>> PATH)
> >>>> >>> get_filename_component(LIB_INSTALL_PREFIX "${CURRENT_FILE_DIR}"
> >>>> >>> PATH)
> >>>> >>> get_filename_component(LIB_INSTALL_PREFIX "${LIB_INSTALL_PREFIX}"
> >>>> >>> PATH)
> >>>> >>> get_filename_component(LIB_INSTALL_PREFIX "${LIB_INSTALL_PREFIX}"
> >>>> >>> PATH)
> >>>> >>>
> >>>> >>> and at last:
> >>>> >>>
> >>>> >>> $(SED) -i 's,$(PREFIX)/$(TARGET),\${LIB_INSTALL_PREFIX},g'
> >>>> >>> 'lib/cmake/ITK-$(ITK_VER)/ITKTargets-release.cmake'
> >>>> >>>
> >>>> >>> I would like to have this patch inside the other .cmake files in
> the
> >>>> >>> installation and avoid the sed commands during post-installation
> >>>> >>>
> >>>> >>> Here is the list of cmake files that needs this change.
> >>>> >>> lib/cmake/ITK-4.8/ITKTargets-release.cmake
> >>>> >>> lib/cmake/ITK-4.8/Modules/ITKZLIB.cmake
> >>>> >>> lib/cmake/ITK-4.8/Modules/ITKExpat.cmake
> >>>> >>> lib/cmake/ITK-4.8/Modules/ITKHDF5.cmake
> >>>> >>> lib/cmake/ITK-4.8/Modules/ITKJPEG.cmake
> >>>> >>> lib/cmake/ITK-4.8/Modules/ITKTIFF.cmake
> >>>> >>> lib/cmake/ITK-4.8/Modules/ITKPNG.cmake
> >>>> >>>
> >>>> >>> So is it possible to make the change into future version of ITK?
> >>>> >>>
> >>>> >>> The major issue here is those cmake files are generated by cmake.
> Is
> >>>> >>> there a way cmake could use relative path ?
> >>>> >>>
> >>>> >>>
> >>>> >>> --
> >>>> >>> Regards,
> >>>> >>>    Rashad
> >>>> >>>
> >>>> >>> _______________________________________________
> >>>> >>> Powered by www.kitware.com
> >>>> >>>
> >>>> >>> Visit other Kitware open-source projects at
> >>>> >>> http://www.kitware.com/opensource/opensource.html
> >>>> >>>
> >>>> >>> Kitware offers ITK Training Courses, for more information visit:
> >>>> >>> http://kitware.com/products/protraining.php
> >>>> >>>
> >>>> >>> Please keep messages on-topic and check the ITK FAQ at:
> >>>> >>> http://www.itk.org/Wiki/ITK_FAQ
> >>>> >>>
> >>>> >>> Follow this link to subscribe/unsubscribe:
> >>>> >>> http://public.kitware.com/mailman/listinfo/insight-developers
> >>>> >>>
> >>>> >>
> >>>> >
> >>>> >
> >>>> >
> >>>> > --
> >>>> > Regards,
> >>>> >    Rashad
> >>>> >
> >>>> > _______________________________________________
> >>>> > Powered by www.kitware.com
> >>>> >
> >>>> > Visit other Kitware open-source projects at
> >>>> > http://www.kitware.com/opensource/opensource.html
> >>>> >
> >>>> > Kitware offers ITK Training Courses, for more information visit:
> >>>> > http://kitware.com/products/protraining.php
> >>>> >
> >>>> > Please keep messages on-topic and check the ITK FAQ at:
> >>>> > http://www.itk.org/Wiki/ITK_FAQ
> >>>> >
> >>>> > Follow this link to subscribe/unsubscribe:
> >>>> > http://public.kitware.com/mailman/listinfo/insight-developers
> >>>> >
> >>>
> >>>
> >>>
> >>>
> >>> --
> >>> Regards,
> >>>    Rashad
> >>
> >>
> >
> >
> >
> > --
> > Regards,
> >    Rashad
>



-- 
Regards,
   Rashad
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From matt.mccormick at kitware.com  Wed Dec 21 19:07:03 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 21 Dec 2016 19:07:03 -0500
Subject: [ITK] [ITK-dev] installed ITK cannot be moved due to absolute
	path
In-Reply-To: <CANNqv9d5WoUsaGwm8o56pU_o=gTp3wacVmbmg-jnncnz7TSrNA@mail.gmail.com>
References: <CANNqv9eKZygjeSgdauFADK6jev2V9Q4Bhk8gfP=GkR5ngLfoGA@mail.gmail.com>
 <CAPf2UMTo6LY09u1gKxa+MPjOgyQjMh25ADHSdpv4wTc3GRzbZA@mail.gmail.com>
 <CANNqv9dC9F6PHSyrLfnqY2NbA8dSDxnD-kzEKTdUqwhW_Mea8A@mail.gmail.com>
 <CALzTN-Q-Q9Ho4fmG99B4RUSwrpYCiihA3fiD_7WpKe5Kt24gtg@mail.gmail.com>
 <CANNqv9fSqBF0vdQQTa5An5xh8NPBd+cAuo=MvoR5UPDTr-cdOA@mail.gmail.com>
 <CAPf2UMRTmOMG9CON1w1X+-GUYzmcNGch5bu0dxq31_WVpT-O8g@mail.gmail.com>
 <CANNqv9fFF4ukPPy8KSTDe+WWuCdqZDUz5=MLQN81V1Sf8j9Rpw@mail.gmail.com>
 <CALzTN-RDpB_gRY1L_fvFfyke2Jyhk=h2OAAMuy4hY1TJoy4KZQ@mail.gmail.com>
 <CANNqv9d5WoUsaGwm8o56pU_o=gTp3wacVmbmg-jnncnz7TSrNA@mail.gmail.com>
Message-ID: <CALzTN-RChiSwPcs0f7r1Lpd4Myg_M7zM8f7DAA=TMSrNWecxOQ@mail.gmail.com>

On Wed, Dec 21, 2016 at 12:05 PM, Rashad Kanavath
<mohammedrashadkm at gmail.com> wrote:
>
>
> On Wed, Dec 21, 2016 at 5:06 PM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> Hi Rashad,
>>
>> The Find<Package>.cmake are purposely not provided because it is not
>> reliable and does not provide all the information required. The CMake
>> package configuration file allows ITK to declare what is required to
>> build it instead of requiring CMake to guess (and get it wrong).
>>
>> For this case, it is recommended to turn off ITK_USE_SYSTEM_ZLIB,
>> which will make the ITK installation portable.
>
>
> I need to use zlib, fftw and expat in that case from ITK build/
>
> But I have also providing a different build of zlib for my other projects.

ITK's zlib will play nicely with the other zlibs -- it is name mangled.

Another path forward is to use a zlib that has a CMake package
configuration file and teach ITK to use that.


> What are the missing information when using FindITK.cmake as opposed to itk
> cmake configuration files?

ITK has required build flags, configuration options, and build include
directories, third party library requirements, linking library
requirements that depend on its modular configuration and differ based
on whether it is a build tree or an install tree. This would be
difficult if not impossible to try to recreate in a FindITK.cmake
module.


> I understand that saving absolute path of libraries which link with project
> is easy to avoid any issues in linking or at runtime.
>  And that is one type of solution and IMHO does not solve the problem.
>
> Apart from that I would like to find out what are real issues with
> Find<Package>.cmake

For example, if there are multiple zlib's on your system or if they
are installed in non-standard locations, the build system will be
lucky if it finds the one ITK was built against.

Another fundamental issue: for CMake to use a Find<Package>.cmake to
find <Package>, Find<Package>.cmake must exist and be used before
<Package> is found. That is, Find<Package>.cmake must be shipped with
CMake or a library that is trying to use <Package>. The version of
Find<Package>.cmake that comes with CMake or another library does not
necessarily correspond to the configuration required by the version of
<Package> that is available.

CMake Config-file modules should be used instead of Find-file modules
as a general best practice. The package can declare its build
requirements instead of making CMake try to guess them.

HTH,
Matt
_______________________________________________
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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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From blowekamp at mail.nih.gov  Thu Dec 22 12:02:03 2016
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 22 Dec 2016 17:02:03 +0000
Subject: [ITK] [ITK-dev] ParameterScalesEstimator,
	EulerTransform and Randomness
Message-ID: <88501962-795D-4560-BC0F-9805B44E7F42@mail.nih.gov>

Hello,

After a recent change to ITK some random sampling is now being seeded by the wall clock instead of a fixed integer[1]. While one can globally set the seed to a fixed value. I am thinking it would be best to allow the user to control which components are ?fixed? random verses ?wall clock? random, to aid in reproducibility and what not.

In SimpleITK I have a test for the Optimizer?s scales estimator that began failing to my surprise[1] with the ITK updated locally. I expected some registration related to random sampling of the virtual domain to change but I was surprised about the Optimizer?s scales. So what is interesting:

1) The Euler2DTransform is not being classified as an Affine transform by the parameter estimator.
2) The random sampling strategy is used for the parameter scale estimator.
3) There is no way to set the specific seed used for this random image iteration. The further oddity is that the ImageRandomIterators use a global singleton, so if you did set a seed for the iterator, it modified the global singleton, there by having global side effects.

The parameters estimator is an interesting case for ?wall clock? randomness. The small differences in the parameter scales due to randomness get amplified over the optimization process of registration.

What to do? How can we provide control of the scales estimator?s randomness?

Thanks,
Brad





[1] https://github.com/InsightSoftwareConsortium/ITK/commit/4e6c5bd69a8c24181fee18901ea232084f6ab785
[2] https://github.com/SimpleITK/SimpleITK/blob/69bb27bde3250a0db591bfa111a5bd2f44de0ef5/Testing/Unit/sitkImageRegistrationMethodTests.cxx#L844-L873
[3] https://github.com/InsightSoftwareConsortium/ITK/blob/6b8108dd6a05cd32dee20e5f1fd29e47d7f31a77/Modules/Numerics/Optimizersv4/include/itkRegistrationParameterScalesEstimator.hxx#L397
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From isaiah.norton at gmail.com  Thu Dec 22 12:55:03 2016
From: isaiah.norton at gmail.com (Isaiah Norton)
Date: Thu, 22 Dec 2016 12:55:03 -0500
Subject: [ITK] [ITK-dev] ITK+static+wrapping [ref: 21857 "Enable
	singleton	program global timestamp"]
In-Reply-To: <CALzTN-Q_RpKMEekQ-cgzHQaF8eV7R_VpE+QaNKxn-d-9t0ZuGw@mail.gmail.com>
References: <CADFtqoq+0kvvBPKKOCL9Tz_hPbjC8=uD6vY7DAK5JsOnwLiymA@mail.gmail.com>
 <CALzTN-Q_RpKMEekQ-cgzHQaF8eV7R_VpE+QaNKxn-d-9t0ZuGw@mail.gmail.com>
Message-ID: <CADFtqootJKmcY3fGb2WDk9VU+5D3RZnfBHXVShNuU0guZMG60g@mail.gmail.com>

Hi Matt,

There is one potential technical issue with the scheme added by 21857. I
think that users who embed Python in a native application, with the app
statically linked to ITK, will need to manually ensure that the
application-side timestamp is initialized to point to the variable from
_ITKCommonPython. Otherwise, any objects initialized from application-side
ITK code would face the same desynchronization issue. Also, as mentioned in
the comments on the merge request, fully supporting the
(ITK_WRAP_PYTHON=ON, BUILD_SHARED_LIBS=OFF) multi-object configuration will
require moving other globals to the new Python side-loaded singleton system.

Given the above, perhaps that build configuration should be an error by
default, for now (with override available), so people don't use it
inadvertently? The problems caused can be difficult to debug.

Best,
Isaiah


On Sat, Dec 17, 2016 at 10:41 AM, Matt McCormick <matt.mccormick at kitware.com
> wrote:

> Hi Isaiah,
>
> Here is some more information and background.
>
>
> > What is the rationale behind creating so many separate, statically-linked
> > Python modules? (78 `_ITK*Python.so` files on my machine). Creating a
> single
> > bundle instead should resolve the original issue, and might also reduce
> the
> > size of the final library [3].
>
> For background, the GlobalTimeStamp, is a very important variable in
> ITK (and VTK). This is an atomic integer that gets incremented when
> any itk::Object (most classes in ITK) is "Modified", i.e. changed to
> note that it should be updated in a processing pipeline. So, almost
> all ITK-based code needs it, and it needs to be global across the
> entire program.
>
> The GlobalTimeStamp lives in and is used my itk::TimeStamp.cxx, and it
> is incremented on every call to ::Modified(). The itk::TimeStamp class
> is linked into libITKCommon.
>
> When ITK is built with shared libraries, libITKCommon is shared, and
> everything shares the GlobalTimeStamp. When ITK is built with static
> libraries, every binary that links in libITKCommon will get its own
> GlobalTimeStamp.
>
> Unfortunately, a shared libITKCommon is not always possible. For the
> official Python packaging format, wheels, native libraries are not yet
> officially supported [1].
>
> The advantages of not linking everything into one, giant, monolithic
> `_ITK*Python.so` are that 1) we can lazily load only the parts of the
> library that we need, and 2) the brilliant ITK community members can
> extend ITK to create their own ITK Python module. For example, see the
> awesome ITKMinimalPathExtraction [2] or ITKIsotropicWavelets [3]
> modules.
>
> While I also investigated, for example, using CMake object libraries
> to make itk::TimeStamp an exported symbol in _ITKCommonPython.so and
> only linked there [4], this is a more complex build configuration.
> Additionally, according to the Python documentation, exporting extra
> symbols in a CPython extension module is officially not supported [5].
> In practice, I have found that extra symbols can segfault the process
> on module import with Python 3.5 on Windows. So, the sharing is done
> the officially supported way, via PyCapsule.
>
>
> > Additionally, I am wondering if cross-module `dynamic_cast` works
> correctly
> > in the current situation -- because the typeinfos in each static module
> .so
> > have different addresses [4]. (I'm not sure how to create a situation to
> > test this from Python)
>
> Yes, since the Python wrapping covers the entire toolkit, it is an
> excellent stress test for the dynamic_cast issue. When we developed
> the dynamic_cast patch, we used Python wrapping with static libraries
> and experimentally enabled hidden symbols by default [6]. Without the
> dynamic_cast fix, the Python tests failed, and with the fix, they
> pass. It turns out that we missed some mark-up on a few classes as
> indicated by warnings in the Python wrapping and non-wrapping test
> failures, but we are working on resolving those now.
>
> Thanks,
> Matt
>
>
> [1] https://mail.python.org/pipermail/wheel-builders/2016-April/
> 000090.html
>
> [2] https://github.com/InsightSoftwareConsortium/ITKMinimalPathExtraction
>
> [3] https://github.com/phcerdan/ITKIsotropicWavelets
>
> [4] https://github.com/thewtex/ITK/commits/thewtex-PythonModifiedTime55
>
> [5] https://docs.python.org/3.5/extending/extending.html#providi
> ng-a-c-api-for-an-extension-module
>
> [6] http://review.source.kitware.com/#/c/21766/
>
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From fisidoro at ethz.ch  Sat Dec 31 05:13:44 2016
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Sat, 31 Dec 2016 10:13:44 +0000
Subject: [ITK] [ITK-users] Itk Python GetParameters
Message-ID: <50B858FB5F53124F9E32314E5C1B40943A18A889@MBX112.d.ethz.ch>

Hallo,

within the context of exploring the domain of an image metric (MeanSquaresImageMetric1.cxx), I want to check the current parameters used for the translation transform:

parameters = transform.GetParameters()
parameters[0] = dx
parameters[1] = dy
metric.SetParameters( parameters )


If I then code:


print(metric.GetParameters())


I get the proxy of Swig Object, from which I can't see the parameters.

[cid:image001.png at 01D26356.608C9950]

I have tried in many ways:


print(metric.GetParameters()[0])
print(metric.GetParameters()[1])

print(metric.GetTransform().GetParameters())

print(metric.GetTransform().GetParameters().GetElement(0))

but none of them works.

How can I get the elements from the Swig Object?

Thank you!

Fabio

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