From vl at xris.eu  Mon Oct  1 10:34:51 2018
From: vl at xris.eu (vincent)
Date: Mon, 1 Oct 2018 16:34:51 +0200
Subject: [Rtk-users] Error message: cannot account for detector displacement
 larger than 50% of panel size
Message-ID: <a543c0c1-7610-2ef6-45a9-0c5d324428cd@xris.eu>

Hi everyone,

I am facing a problem when I try to reconstruct an object. I'll try to 
be as complete as possible in the description.

I acquired 18000 views from a custom-made ct scanner, of which I 
extracted 360 for the sake of reconstruction speed for my tests. The 
images are cropped to 1001*1761 pixels.? An external calibration program 
estimated that the x and y detector offsets where 5.2mm and -8mm 
respectively.? The sdd and sid are 983mm and 483mm.? I used those value 
to generate a simulated geometry.

I then created a projection volume with the command

rtkprojections -v? -o rec1Proj.mha -p . -r cropped.*.tif --i0 7000 where 
I estimated the i0 value on the images background (for the sake of 
completeness, I also tested with the automatic value which resulted in 
the same problem)

Finally, I wanted to reconstruct the volume with the command

rtkfdk? -g geoCT.xml -p . -r rec1Proj.mha? --spacing 0.2 --dimension 
1761,1761,1761 -v -o recFDK.mha? --hardware cuda


The exact error message is:

Reconstructing and writing... ExceptionObject caught with 
writer->Update() in file 
~/IPTools/RTK/RTK/applications/rtkfdk/rtkfdk.cxx line 218

itk::ExceptionObject (0x1cf4b90)
Location: "unknown"
File: ~/IPTools/RTK/RTK/code/rtkDisplacedDetectorImageFilter.hxx
Line: 155
Description: itk::ERROR: Cannot account for detector displacement larger 
than 50% of panel size. Corner inf=2.55504 and corner sup=100.826

I had a look at the aforementionned line in the 
rtkDisplacedDetectorImageFilter.hxx file but I didn't really understand 
how the corners are computed in the 
inputPtr->TransformIndexToPhysicalPoint(inputPtr->GetLargestPossibleRegion().GetIndex(), 
corner function.

I have no problem sharing the projections if needed, but they weight 1.3 
Go altogether.


I thank you very much in advance for any kind of help you can provide.

Best regards,

Vincent



From simon.rit at creatis.insa-lyon.fr  Mon Oct  1 14:43:30 2018
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 1 Oct 2018 20:43:30 +0200
Subject: [Rtk-users] Error message: cannot account for detector
 displacement larger than 50% of panel size
In-Reply-To: <a543c0c1-7610-2ef6-45a9-0c5d324428cd@xris.eu>
References: <a543c0c1-7610-2ef6-45a9-0c5d324428cd@xris.eu>
Message-ID: <CAF0oig2yFh5+J_5YwJu2s3=DZDGWX_otdHE_YZ_3vUYN-QM+kQ@mail.gmail.com>

Hi Vincent,
This generally occurs when your detector offset is not adequately passed to
the geometry. When you say that you have "5.2mm and -8mm" offsets, I guess
it is with respect to a centered geometry, where the central ray hits the
detector. For this to be the case in RTK, you must check that the
coordinate (0,0) mm corresponds to the center of the detector. By default,
I guess that tif puts it in the corner. So you probably need to add to
rtkprojections an option like --neworigin xorig,yorig,0 where xorig and
yorig is something like -0.5*(npixels-1)*spacing.
If that doesn't help, you don't need to share the data, the mhd headers are
sufficient to test the geometry.
Good luck!
Simon

On Mon, Oct 1, 2018 at 5:13 PM vincent <vl at xris.eu> wrote:

> Hi everyone,
>
> I am facing a problem when I try to reconstruct an object. I'll try to
> be as complete as possible in the description.
>
> I acquired 18000 views from a custom-made ct scanner, of which I
> extracted 360 for the sake of reconstruction speed for my tests. The
> images are cropped to 1001*1761 pixels.  An external calibration program
> estimated that the x and y detector offsets where 5.2mm and -8mm
> respectively.  The sdd and sid are 983mm and 483mm.  I used those value
> to generate a simulated geometry.
>
> I then created a projection volume with the command
>
> rtkprojections -v  -o rec1Proj.mha -p . -r cropped.*.tif --i0 7000 where
> I estimated the i0 value on the images background (for the sake of
> completeness, I also tested with the automatic value which resulted in
> the same problem)
>
> Finally, I wanted to reconstruct the volume with the command
>
> rtkfdk  -g geoCT.xml -p . -r rec1Proj.mha  --spacing 0.2 --dimension
> 1761,1761,1761 -v -o recFDK.mha  --hardware cuda
>
>
> The exact error message is:
>
> Reconstructing and writing... ExceptionObject caught with
> writer->Update() in file
> ~/IPTools/RTK/RTK/applications/rtkfdk/rtkfdk.cxx line 218
>
> itk::ExceptionObject (0x1cf4b90)
> Location: "unknown"
> File: ~/IPTools/RTK/RTK/code/rtkDisplacedDetectorImageFilter.hxx
> Line: 155
> Description: itk::ERROR: Cannot account for detector displacement larger
> than 50% of panel size. Corner inf=2.55504 and corner sup=100.826
>
> I had a look at the aforementionned line in the
> rtkDisplacedDetectorImageFilter.hxx file but I didn't really understand
> how the corners are computed in the
> inputPtr->TransformIndexToPhysicalPoint(inputPtr->GetLargestPossibleRegion().GetIndex(),
>
> corner function.
>
> I have no problem sharing the projections if needed, but they weight 1.3
> Go altogether.
>
>
> I thank you very much in advance for any kind of help you can provide.
>
> Best regards,
>
> Vincent
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From vl at xris.eu  Tue Oct  2 03:42:28 2018
From: vl at xris.eu (vincent)
Date: Tue, 2 Oct 2018 09:42:28 +0200
Subject: [Rtk-users] Error message: cannot account for detector
 displacement larger than 50% of panel size
In-Reply-To: <CAF0oig2yFh5+J_5YwJu2s3=DZDGWX_otdHE_YZ_3vUYN-QM+kQ@mail.gmail.com>
References: <a543c0c1-7610-2ef6-45a9-0c5d324428cd@xris.eu>
 <CAF0oig2yFh5+J_5YwJu2s3=DZDGWX_otdHE_YZ_3vUYN-QM+kQ@mail.gmail.com>
Message-ID: <27fa04f7-ff6f-f842-b41d-e65a86269d06@xris.eu>

Hi Simon,

thank you very much for your quick reply.? Your analysis was correct, I 
needed to redefine the center.

I wish you a very nice day,

best regards,

Vincent



On 2018-10-01 20:43, Simon Rit wrote:
> Hi Vincent,
> This generally occurs when your detector offset is not adequately 
> passed to the geometry. When you say that you have "5.2mm and -8mm" 
> offsets, I guess it is with respect to a centered geometry, where the 
> central ray hits the detector. For this to be the case in RTK, you 
> must check that the coordinate (0,0) mm corresponds to the center of 
> the detector. By default, I guess that tif puts it in the corner. So 
> you probably need to add to rtkprojections an option like --neworigin 
> xorig,yorig,0 where xorig and yorig is something like 
> -0.5*(npixels-1)*spacing.
> If that doesn't help, you don't need to share the data, the mhd 
> headers are sufficient to test the geometry.
> Good luck!
> Simon
>
> On Mon, Oct 1, 2018 at 5:13 PM vincent <vl at xris.eu 
> <mailto:vl at xris.eu>> wrote:
>
>     Hi everyone,
>
>     I am facing a problem when I try to reconstruct an object. I'll
>     try to
>     be as complete as possible in the description.
>
>     I acquired 18000 views from a custom-made ct scanner, of which I
>     extracted 360 for the sake of reconstruction speed for my tests. The
>     images are cropped to 1001*1761 pixels.? An external calibration
>     program
>     estimated that the x and y detector offsets where 5.2mm and -8mm
>     respectively.? The sdd and sid are 983mm and 483mm.? I used those
>     value
>     to generate a simulated geometry.
>
>     I then created a projection volume with the command
>
>     rtkprojections -v? -o rec1Proj.mha -p . -r cropped.*.tif --i0 7000
>     where
>     I estimated the i0 value on the images background (for the sake of
>     completeness, I also tested with the automatic value which
>     resulted in
>     the same problem)
>
>     Finally, I wanted to reconstruct the volume with the command
>
>     rtkfdk? -g geoCT.xml -p . -r rec1Proj.mha? --spacing 0.2 --dimension
>     1761,1761,1761 -v -o recFDK.mha? --hardware cuda
>
>
>     The exact error message is:
>
>     Reconstructing and writing... ExceptionObject caught with
>     writer->Update() in file
>     ~/IPTools/RTK/RTK/applications/rtkfdk/rtkfdk.cxx line 218
>
>     itk::ExceptionObject (0x1cf4b90)
>     Location: "unknown"
>     File: ~/IPTools/RTK/RTK/code/rtkDisplacedDetectorImageFilter.hxx
>     Line: 155
>     Description: itk::ERROR: Cannot account for detector displacement
>     larger
>     than 50% of panel size. Corner inf=2.55504 and corner sup=100.826
>
>     I had a look at the aforementionned line in the
>     rtkDisplacedDetectorImageFilter.hxx file but I didn't really
>     understand
>     how the corners are computed in the
>     inputPtr->TransformIndexToPhysicalPoint(inputPtr->GetLargestPossibleRegion().GetIndex(),
>
>     corner function.
>
>     I have no problem sharing the projections if needed, but they
>     weight 1.3
>     Go altogether.
>
>
>     I thank you very much in advance for any kind of help you can provide.
>
>     Best regards,
>
>     Vincent
>
>
>     _______________________________________________
>     Rtk-users mailing list
>     Rtk-users at public.kitware.com <mailto:Rtk-users at public.kitware.com>
>     https://public.kitware.com/mailman/listinfo/rtk-users
>

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From simon.rit at creatis.insa-lyon.fr  Mon Oct 15 05:56:48 2018
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Mon, 15 Oct 2018 11:56:48 +0200
Subject: [Rtk-users] ATTIRE summer school
In-Reply-To: <CAJ-g2_1uy8DGZRJ78p3dvt3sNAiEeimXHmRT4vuLrJ8go753yA@mail.gmail.com>
References: <CAJ-g2_2iPaJkp5F2WWpZ-sRsN04ufWC5=XeAHsHrkqQykSpovA@mail.gmail.com>
 <20181005213452.GA22140@timc-cami-65p>
 <f0127115-24e7-7747-8100-932821252a3d@hsc.utah.edu>
 <20181008180526.GA22652@timc-cami-65p>
 <CAF0oig01GFm6cpGUH-Vre+BdBWnJDwHpjMpEM2s04JtvAgB2Pg@mail.gmail.com>
 <DB7PR01MB4233511E52058A6B35A2BDE8F0E10@DB7PR01MB4233.eurprd01.prod.exchangelabs.com>
 <CAJ-g2_0DFYjAY-T1DLgQVeJpiNiqbEfDL9xxEyg3rtNRPjfVPg@mail.gmail.com>
 <CAF0oig1wBuunh9ze4CLGZ7+LLN8-HuWTm4XNOwz3CF4PrWdk5A@mail.gmail.com>
 <CAJ-g2_1uy8DGZRJ78p3dvt3sNAiEeimXHmRT4vuLrJ8go753yA@mail.gmail.com>
Message-ID: <CAF0oig2BGiquFfobWCSHRMJXzFb6cbvkCpaJHh=X_gVGBP+fcA@mail.gmail.com>

Dear RTK users,
We are proud to announce the first edition of the international summer
school
*ATTIRE*
Algorithms and Theory in Tomographic Image REconstruction.
>From Sunday June 23, 2019 to Saturday June 29, 2019
at Le Clos des Capucins, Yenne, Rhone Alpes, France.

Additional information (schedule, program, prices...) on
https://attire.sciencesconf.org. Note the (optional) hands-on sessions
using RTK.

We are looking forward to seeing you in Yenne,

The ATTIRE Team (Rolf Clackdoyle, Michel Defrise, Laurent Desbat, J?r?me
Lesaint, Fr?d?ric Noo, Simon Rit)
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From estelle.morin at thalesgroup.com  Fri Oct 19 08:13:40 2018
From: estelle.morin at thalesgroup.com (MORIN Estelle)
Date: Fri, 19 Oct 2018 12:13:40 +0000
Subject: [Rtk-users] Physical interpretation of the input and output images
 when doing a forward projection
Message-ID: <9192b4a1b3924f33b95fc9290a9528fd@thalesgroup.com>

Dear RTK users,

I would like to do projections of volumes stored in 3D images. However, I do not understand what the voxel values of my 3D images should represent physically speaking. Should they represent attenuation coefficients, densities or something else? Should they be normalized?

On the wiki page "RTK/Scripts/ForwardProjection", it is highlighted that the image used for the projection is in Hounsfield units. However, computing a projection on the image given in example gives me an output image with very high negative values which I can't interpret. Moreover, as the output values are so big and negative, I cannot compute the attenuated image with the formula: attenuatedImage = I0 * exp(-projection). Indeed, this results in an image with a lot of pixel values equal to infinity.

I also looked at the file "rtkSheppLoganPhantom.cxx" and its header in order to understand what should be my input image. It seems that the Shepp Logan Phantom is composed of 10 ellipsoids whose "densities" are included in the interval [-1,1]. Moreover, the sum of those densities is equal to one. Does this mean that the coefficients of my 3D images should be normalized between -1 et 1? What is the physical meaning of this?

I thank you in advance for your answer,
Best wishes,

Estelle Morin
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From simon.rit at creatis.insa-lyon.fr  Fri Oct 19 08:35:28 2018
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 19 Oct 2018 14:35:28 +0200
Subject: [Rtk-users] Physical interpretation of the input and output
 images when doing a forward projection
In-Reply-To: <9192b4a1b3924f33b95fc9290a9528fd@thalesgroup.com>
References: <9192b4a1b3924f33b95fc9290a9528fd@thalesgroup.com>
Message-ID: <CAF0oig2y_nix7MX1XQ_p4XTd+jxcsZVt=ffncjT--eyeZCvFcA@mail.gmail.com>

Hi Estelle,
Forward projection simply takes the line integrals of your volume. So 3D
images have to represent the physical quantity you want to integrate. For
x-ray imaging, you generally want to have linear attenuation coefficient.
But for PET or SPECT, that would be the emission map in counts per voxel.
In your case, if you want to compute I0*exp(-projection), then it seems
that you're dealing with x-rays and the projection should be the line
integral of the linear attenuation coefficient.
As we point out on the wiki page, integrating HUs makes no physical sense
so you need to convert the input volume or the output projections (since
the operation is linear) before taking the exp.
For the Shepp Logan, be aware that the densities in the text file is to be
understood in the additive sense. So if you have a -0.1 ellipsoid in a
larger 1. ellipsoid, then its density will be 0.9. Use
rtkdrawshepploganphantom to verify what are the actual densities.
Best regards,
Simon

On Fri, Oct 19, 2018 at 2:19 PM MORIN Estelle <estelle.morin at thalesgroup.com>
wrote:

> Dear RTK users,
>
>
>
> I would like to do projections of volumes stored in 3D images. However, I
> do not understand what the voxel values of my 3D images should represent
> physically speaking. Should they represent attenuation coefficients,
> densities or something else? Should they be normalized?
>
>
>
> On the wiki page ?RTK/Scripts/ForwardProjection?, it is highlighted that
> the image used for the projection is in Hounsfield units. However,
> computing a projection on the image given in example gives me an output
> image with very high negative values which I can?t interpret. Moreover, as
> the output values are so big and negative, I cannot compute the attenuated
> image with the formula: attenuatedImage = I0 * exp(-projection). Indeed,
> this results in an image with a lot of pixel values equal to infinity.
>
>
>
> I also looked at the file ?rtkSheppLoganPhantom.cxx? and its header in
> order to understand what should be my input image. It seems that the Shepp
> Logan Phantom is composed of 10 ellipsoids whose ?densities? are included
> in the interval [-1,1]. Moreover, the sum of those densities is equal to
> one. Does this mean that the coefficients of my 3D images should be
> normalized between -1 et 1? What is the physical meaning of this?
>
>
>
> I thank you in advance for your answer,
>
> Best wishes,
>
>
>
> Estelle Morin
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From infrombox at yandex.ru  Thu Oct 25 10:21:03 2018
From: infrombox at yandex.ru (1 1)
Date: Thu, 25 Oct 2018 21:21:03 +0700
Subject: [Rtk-users] compilation issues in case of outside of ITK directory
 build
Message-ID: <6759201540477263@sas2-5d23d1328f85.qloud-c.yandex.net>

Hello guys.
I can't build RTK in Linux. I've done all default steps described in wiki, but on configure i've got: 
CMake Error at utilities/lp_solve/CMakeLists.txt:9 (include):
   include could not find load file:

     ITKModuleMacros


Hm.. it tries include module that exists in src ITK dir, not install...
I mean 
"ls /usr/local/lib/cmake/ITK-4.13 | grep ITKModuleMacros" prints nothing
"ls /home/user/src/ITK/CMake | grep ITKModuleMacros" prints ITKModuleMacros.cmake

OK, i have just tried to add CMAKE_MODULE_PATH=/home/user/src/ITK/CMake and got next error:

CMake Error at CMakeLists.txt:250 (message):
  Modules can only be built against an ITK build tree; they cannot be built
  against an ITK install tree.

Let's look at the code:

if(NOT ITK_SOURCE_DIR)
  if(NOT EXISTS ${ITK_CMAKE_DIR}/ITKModuleMacros.cmake)
    message(FATAL_ERROR "Modules can only be built against an ITK build tree; they cannot be built against an ITK install tree.")
  endif()
  list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
  include(ITKModuleExternal)
else()
  itk_module_impl()
endif()

Yea, ITK_SOURCE_DIR is not set in my case, but why there is must be ITKModuleMacros.cmake at my ITK_CMAKE_DIR dir that points to ITK installation dir ?

If i set ITK_CMAKE_DIR to /home/user/src/ITK/CMake where ITKModuleMacros is, it resets back to ITK installation directory at 
# --------------------------------------------------------
# Find ITK (required)
if(NOT ITK_SOURCE_DIR)
  find_package(ITK 4.12.0 REQUIRED)
endif()


So, the only way i see is to build inside ITK, but i am not familiar with this. Could anyone help me how to build RTK inside ITK.

From prekrasnaya1985 at gmail.com  Thu Oct 25 11:16:07 2018
From: prekrasnaya1985 at gmail.com (Julia Semyakishkina)
Date: Thu, 25 Oct 2018 22:16:07 +0700
Subject: [Rtk-users] compilation issues in case of outside of ITK directory
 build
Message-ID: <CANma8tajk1rny4wAZj8gCbFUaYEV6=7OUzcBuPxW0Wsy2KsamA@mail.gmail.com>

Hello.
I can't build RTK in Linux. I've done all default steps described in wiki,
but on configure i've got:
CMake Error at utilities/lp_solve/CMakeLists.txt:9 (include):
   include could not find load file:

     ITKModuleMacros


Hm.. it tries include module that exists in src ITK dir, not install...
I mean
"ls /usr/local/lib/cmake/ITK-4.13 | grep ITKModuleMacros" prints nothing
"ls /home/user/src/ITK/CMake | grep ITKModuleMacros" prints
ITKModuleMacros.cmake

OK, i have just tried to add CMAKE_MODULE_PATH=/home/user/src/ITK/CMake and
got next error:

CMake Error at CMakeLists.txt:250 (message):
  Modules can only be built against an ITK build tree; they cannot be built
  against an ITK install tree.

Let's look at the code:

if(NOT ITK_SOURCE_DIR)
  if(NOT EXISTS ${ITK_CMAKE_DIR}/ITKModuleMacros.cmake)
    message(FATAL_ERROR "Modules can only be built against an ITK build
tree; they cannot be built against an ITK install tree.")
  endif()
  list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
  include(ITKModuleExternal)
else()
  itk_module_impl()
endif()

Yea, ITK_SOURCE_DIR is not set in my case, but why there is must be
ITKModuleMacros.cmake at my ITK_CMAKE_DIR dir that points to ITK
installation dir ?

If i set ITK_CMAKE_DIR to /home/user/src/ITK/CMake where ITKModuleMacros
is, it resets back to ITK installation directory at
# --------------------------------------------------------
# Find ITK (required)
if(NOT ITK_SOURCE_DIR)
  find_package(ITK 4.12.0 REQUIRED)
endif()


So, the only way i see is to build inside ITK, but i am not familiar with
this. Could anyone help me how to build RTK inside ITK.
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From simon.rit at creatis.insa-lyon.fr  Thu Oct 25 15:59:42 2018
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 25 Oct 2018 21:59:42 +0200
Subject: [Rtk-users] compilation issues in case of outside of ITK
 directory build
In-Reply-To: <CANma8tajk1rny4wAZj8gCbFUaYEV6=7OUzcBuPxW0Wsy2KsamA@mail.gmail.com>
References: <CANma8tajk1rny4wAZj8gCbFUaYEV6=7OUzcBuPxW0Wsy2KsamA@mail.gmail.com>
Message-ID: <CAF0oig2SZD9CzT9OydzRg9P0KdVKjgazgjDKA0EdNizoLcPN5w@mail.gmail.com>

Hi,
It seems that you are trying to compile against an installed ITK_DIR. This
is no longer possible, see this thread:
https://github.com/SimonRit/RTK/issues/207
Can you try to compile against your build directory (set ITK_DIR to the
build directory)?
Thanks,
Simon

On Thu, Oct 25, 2018 at 5:16 PM Julia Semyakishkina <
prekrasnaya1985 at gmail.com> wrote:

> Hello.
> I can't build RTK in Linux. I've done all default steps described in wiki,
> but on configure i've got:
> CMake Error at utilities/lp_solve/CMakeLists.txt:9 (include):
>    include could not find load file:
>
>      ITKModuleMacros
>
>
> Hm.. it tries include module that exists in src ITK dir, not install...
> I mean
> "ls /usr/local/lib/cmake/ITK-4.13 | grep ITKModuleMacros" prints nothing
> "ls /home/user/src/ITK/CMake | grep ITKModuleMacros" prints
> ITKModuleMacros.cmake
>
> OK, i have just tried to add CMAKE_MODULE_PATH=/home/user/src/ITK/CMake
> and got next error:
>
> CMake Error at CMakeLists.txt:250 (message):
>   Modules can only be built against an ITK build tree; they cannot be built
>   against an ITK install tree.
>
> Let's look at the code:
>
> if(NOT ITK_SOURCE_DIR)
>   if(NOT EXISTS ${ITK_CMAKE_DIR}/ITKModuleMacros.cmake)
>     message(FATAL_ERROR "Modules can only be built against an ITK build
> tree; they cannot be built against an ITK install tree.")
>   endif()
>   list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
>   include(ITKModuleExternal)
> else()
>   itk_module_impl()
> endif()
>
> Yea, ITK_SOURCE_DIR is not set in my case, but why there is must be
> ITKModuleMacros.cmake at my ITK_CMAKE_DIR dir that points to ITK
> installation dir ?
>
> If i set ITK_CMAKE_DIR to /home/user/src/ITK/CMake where ITKModuleMacros
> is, it resets back to ITK installation directory at
> # --------------------------------------------------------
> # Find ITK (required)
> if(NOT ITK_SOURCE_DIR)
>   find_package(ITK 4.12.0 REQUIRED)
> endif()
>
>
> So, the only way i see is to build inside ITK, but i am not familiar with
> this. Could anyone help me how to build RTK inside ITK.
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From prekrasnaya1985 at gmail.com  Thu Oct 25 23:16:55 2018
From: prekrasnaya1985 at gmail.com (Julia Semyakishkina)
Date: Fri, 26 Oct 2018 10:16:55 +0700
Subject: [Rtk-users] compilation issues in case of outside of ITK
 directory build
In-Reply-To: <CAF0oig2SZD9CzT9OydzRg9P0KdVKjgazgjDKA0EdNizoLcPN5w@mail.gmail.com>
References: <CANma8tajk1rny4wAZj8gCbFUaYEV6=7OUzcBuPxW0Wsy2KsamA@mail.gmail.com>
 <CAF0oig2SZD9CzT9OydzRg9P0KdVKjgazgjDKA0EdNizoLcPN5w@mail.gmail.com>
Message-ID: <CANma8tYdhOvQAUT+baJNsCV7Eri6B35x1iMv9RuAz+3FV9r7Yw@mail.gmail.com>

Ok, it works in case ITK Static -> RTK Static. When i try to build ITK
Shared -> RTK Shared, i have got:
[ 19%] Linking CXX executable ../../bin/rtkamsterdamshroud
CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
`rtk::ThreeDCircularProjectionGeometryXMLFileReader::New()':
rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0xe):
undefined reference to `typeinfo for
rtk::ThreeDCircularProjectionGeometryXMLFileReader'
rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0x41):
undefined reference to `typeinfo for
rtk::ThreeDCircularProjectionGeometryXMLFileReader'
rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0xc9):
undefined reference to
`rtk::ThreeDCircularProjectionGeometryXMLFileReader::ThreeDCircularProjectionGeometryXMLFileReader()'
CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
`std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > const
rtk::GetProjectionsFileNamesFromGgo<args_info_rtkamsterdamshroud>(args_info_rtkamsterdamshroud
const&)':
rtkamsterdamshroud.cxx:(.text._ZN3rtk30GetProjectionsFileNamesFromGgoI28args_info_rtkamsterdamshroudEEKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERKT_[_ZN3rtk30GetProjectionsFileNamesFromGgoI28args_info_rtkamsterdamshroudEEKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERKT_]+0x3c1):
undefined reference to `rtk::RegisterIOFactories()'
CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
`rtk::ProjectionsReader<itk::Image<double, 3u>
>::GenerateOutputInformation()':
rtkamsterdamshroud.cxx:(.text._ZN3rtk17ProjectionsReaderIN3itk5ImageIdLj3EEEE25GenerateOutputInformationEv[_ZN3rtk17ProjectionsReaderIN3itk5ImageIdLj3EEEE25GenerateOutputInformationEv]+0x8e1):
undefined reference to `rtk::RegisterIOFactories()'
collect2: error: ld returned 1 exit status
applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/build.make:141:
recipe for target 'bin/rtkamsterdamshroud' failed
make[2]: *** [bin/rtkamsterdamshroud] Error 1
CMakeFiles/Makefile2:512: recipe for target
'applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/all'
failed
make[1]: ***
[applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/all]
Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

On Fri, Oct 26, 2018 at 2:59 AM Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> It seems that you are trying to compile against an installed ITK_DIR. This
> is no longer possible, see this thread:
> https://github.com/SimonRit/RTK/issues/207
> Can you try to compile against your build directory (set ITK_DIR to the
> build directory)?
> Thanks,
> Simon
>
> On Thu, Oct 25, 2018 at 5:16 PM Julia Semyakishkina <
> prekrasnaya1985 at gmail.com> wrote:
>
>> Hello.
>> I can't build RTK in Linux. I've done all default steps described in
>> wiki, but on configure i've got:
>> CMake Error at utilities/lp_solve/CMakeLists.txt:9 (include):
>>    include could not find load file:
>>
>>      ITKModuleMacros
>>
>>
>> Hm.. it tries include module that exists in src ITK dir, not install...
>> I mean
>> "ls /usr/local/lib/cmake/ITK-4.13 | grep ITKModuleMacros" prints nothing
>> "ls /home/user/src/ITK/CMake | grep ITKModuleMacros" prints
>> ITKModuleMacros.cmake
>>
>> OK, i have just tried to add CMAKE_MODULE_PATH=/home/user/src/ITK/CMake
>> and got next error:
>>
>> CMake Error at CMakeLists.txt:250 (message):
>>   Modules can only be built against an ITK build tree; they cannot be
>> built
>>   against an ITK install tree.
>>
>> Let's look at the code:
>>
>> if(NOT ITK_SOURCE_DIR)
>>   if(NOT EXISTS ${ITK_CMAKE_DIR}/ITKModuleMacros.cmake)
>>     message(FATAL_ERROR "Modules can only be built against an ITK build
>> tree; they cannot be built against an ITK install tree.")
>>   endif()
>>   list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
>>   include(ITKModuleExternal)
>> else()
>>   itk_module_impl()
>> endif()
>>
>> Yea, ITK_SOURCE_DIR is not set in my case, but why there is must be
>> ITKModuleMacros.cmake at my ITK_CMAKE_DIR dir that points to ITK
>> installation dir ?
>>
>> If i set ITK_CMAKE_DIR to /home/user/src/ITK/CMake where ITKModuleMacros
>> is, it resets back to ITK installation directory at
>> # --------------------------------------------------------
>> # Find ITK (required)
>> if(NOT ITK_SOURCE_DIR)
>>   find_package(ITK 4.12.0 REQUIRED)
>> endif()
>>
>>
>> So, the only way i see is to build inside ITK, but i am not familiar with
>> this. Could anyone help me how to build RTK inside ITK.
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Oct 26 09:04:52 2018
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 26 Oct 2018 15:04:52 +0200
Subject: [Rtk-users] compilation issues in case of outside of ITK
 directory build
In-Reply-To: <CANma8tYdhOvQAUT+baJNsCV7Eri6B35x1iMv9RuAz+3FV9r7Yw@mail.gmail.com>
References: <CANma8tajk1rny4wAZj8gCbFUaYEV6=7OUzcBuPxW0Wsy2KsamA@mail.gmail.com>
 <CAF0oig2SZD9CzT9OydzRg9P0KdVKjgazgjDKA0EdNizoLcPN5w@mail.gmail.com>
 <CANma8tYdhOvQAUT+baJNsCV7Eri6B35x1iMv9RuAz+3FV9r7Yw@mail.gmail.com>
Message-ID: <CAF0oig2R-=Eo21S7sPg3ZrNSQ0WcVbHfD0BaV63WcC8dyRHxGw@mail.gmail.com>

Hi,
Are you sure it's shared with the same compilation mode (Debug or Release) ?
Simon

On Fri, Oct 26, 2018 at 5:18 AM Julia Semyakishkina <
prekrasnaya1985 at gmail.com> wrote:

> Ok, it works in case ITK Static -> RTK Static. When i try to build ITK
> Shared -> RTK Shared, i have got:
> [ 19%] Linking CXX executable ../../bin/rtkamsterdamshroud
> CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
> `rtk::ThreeDCircularProjectionGeometryXMLFileReader::New()':
> rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0xe):
> undefined reference to `typeinfo for
> rtk::ThreeDCircularProjectionGeometryXMLFileReader'
> rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0x41):
> undefined reference to `typeinfo for
> rtk::ThreeDCircularProjectionGeometryXMLFileReader'
> rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0xc9):
> undefined reference to
> `rtk::ThreeDCircularProjectionGeometryXMLFileReader::ThreeDCircularProjectionGeometryXMLFileReader()'
> CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
> `std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > > const
> rtk::GetProjectionsFileNamesFromGgo<args_info_rtkamsterdamshroud>(args_info_rtkamsterdamshroud
> const&)':
> rtkamsterdamshroud.cxx:(.text._ZN3rtk30GetProjectionsFileNamesFromGgoI28args_info_rtkamsterdamshroudEEKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERKT_[_ZN3rtk30GetProjectionsFileNamesFromGgoI28args_info_rtkamsterdamshroudEEKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERKT_]+0x3c1):
> undefined reference to `rtk::RegisterIOFactories()'
> CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
> `rtk::ProjectionsReader<itk::Image<double, 3u>
> >::GenerateOutputInformation()':
> rtkamsterdamshroud.cxx:(.text._ZN3rtk17ProjectionsReaderIN3itk5ImageIdLj3EEEE25GenerateOutputInformationEv[_ZN3rtk17ProjectionsReaderIN3itk5ImageIdLj3EEEE25GenerateOutputInformationEv]+0x8e1):
> undefined reference to `rtk::RegisterIOFactories()'
> collect2: error: ld returned 1 exit status
> applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/build.make:141:
> recipe for target 'bin/rtkamsterdamshroud' failed
> make[2]: *** [bin/rtkamsterdamshroud] Error 1
> CMakeFiles/Makefile2:512: recipe for target
> 'applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/all'
> failed
> make[1]: ***
> [applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/all]
> Error 2
> Makefile:129: recipe for target 'all' failed
> make: *** [all] Error 2
>
> On Fri, Oct 26, 2018 at 2:59 AM Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
>
>> Hi,
>> It seems that you are trying to compile against an installed ITK_DIR.
>> This is no longer possible, see this thread:
>> https://github.com/SimonRit/RTK/issues/207
>> Can you try to compile against your build directory (set ITK_DIR to the
>> build directory)?
>> Thanks,
>> Simon
>>
>> On Thu, Oct 25, 2018 at 5:16 PM Julia Semyakishkina <
>> prekrasnaya1985 at gmail.com> wrote:
>>
>>> Hello.
>>> I can't build RTK in Linux. I've done all default steps described in
>>> wiki, but on configure i've got:
>>> CMake Error at utilities/lp_solve/CMakeLists.txt:9 (include):
>>>    include could not find load file:
>>>
>>>      ITKModuleMacros
>>>
>>>
>>> Hm.. it tries include module that exists in src ITK dir, not install...
>>> I mean
>>> "ls /usr/local/lib/cmake/ITK-4.13 | grep ITKModuleMacros" prints nothing
>>> "ls /home/user/src/ITK/CMake | grep ITKModuleMacros" prints
>>> ITKModuleMacros.cmake
>>>
>>> OK, i have just tried to add CMAKE_MODULE_PATH=/home/user/src/ITK/CMake
>>> and got next error:
>>>
>>> CMake Error at CMakeLists.txt:250 (message):
>>>   Modules can only be built against an ITK build tree; they cannot be
>>> built
>>>   against an ITK install tree.
>>>
>>> Let's look at the code:
>>>
>>> if(NOT ITK_SOURCE_DIR)
>>>   if(NOT EXISTS ${ITK_CMAKE_DIR}/ITKModuleMacros.cmake)
>>>     message(FATAL_ERROR "Modules can only be built against an ITK build
>>> tree; they cannot be built against an ITK install tree.")
>>>   endif()
>>>   list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
>>>   include(ITKModuleExternal)
>>> else()
>>>   itk_module_impl()
>>> endif()
>>>
>>> Yea, ITK_SOURCE_DIR is not set in my case, but why there is must be
>>> ITKModuleMacros.cmake at my ITK_CMAKE_DIR dir that points to ITK
>>> installation dir ?
>>>
>>> If i set ITK_CMAKE_DIR to /home/user/src/ITK/CMake where ITKModuleMacros
>>> is, it resets back to ITK installation directory at
>>> # --------------------------------------------------------
>>> # Find ITK (required)
>>> if(NOT ITK_SOURCE_DIR)
>>>   find_package(ITK 4.12.0 REQUIRED)
>>> endif()
>>>
>>>
>>> So, the only way i see is to build inside ITK, but i am not familiar
>>> with this. Could anyone help me how to build RTK inside ITK.
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
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From prekrasnaya1985 at gmail.com  Sat Oct 27 00:04:47 2018
From: prekrasnaya1985 at gmail.com (Julia Semyakishkina)
Date: Sat, 27 Oct 2018 11:04:47 +0700
Subject: [Rtk-users] compilation issues in case of outside of ITK
 directory build
In-Reply-To: <CAF0oig2R-=Eo21S7sPg3ZrNSQ0WcVbHfD0BaV63WcC8dyRHxGw@mail.gmail.com>
References: <CANma8tajk1rny4wAZj8gCbFUaYEV6=7OUzcBuPxW0Wsy2KsamA@mail.gmail.com>
 <CAF0oig2SZD9CzT9OydzRg9P0KdVKjgazgjDKA0EdNizoLcPN5w@mail.gmail.com>
 <CANma8tYdhOvQAUT+baJNsCV7Eri6B35x1iMv9RuAz+3FV9r7Yw@mail.gmail.com>
 <CAF0oig2R-=Eo21S7sPg3ZrNSQ0WcVbHfD0BaV63WcC8dyRHxGw@mail.gmail.com>
Message-ID: <CANma8ta4R3mLkktkN52tvrbeJmo4z9iBazLnXn2=craartx0og@mail.gmail.com>

Hi. Yes, i am.
Could you just run this simple script in empty directory:
#!/bin/sh
wget
https://sourceforge.net/projects/itk/files/itk/4.13/InsightToolkit-4.13.1.tar.gz
tar -xvzf InsightToolkit-4.13.1.tar.gz
mkdir InsightToolkit-4.13.1/build && cd InsightToolkit-4.13.1/build
cmake -D CMAKE_BUILD_TYPE=Release -D BUILD_SHARED_LIBS:BOOL=ON .. && make
-j`grep -c processor /proc/cpuinfo`
ITK_DIR=`pwd`
cd ../../
git clone https://github.com/SimonRit/RTK
mkdir RTK/build && cd RTK/build
cmake -D CMAKE_BUILD_TYPE=Release -D BUILD_SHARED_LIBS:BOOL=ON -D
BUILD_TESTING:BOOL=OFF -D ITK_DIR:PATH=$ITK_DIR .. && make

Don't you have the same linker errors i wrote in the previous message ?

some info about my system
Ubuntu 17.04
Linux mnolro6001 4.10.0-42-generic #46-Ubuntu SMP Mon Dec 4 14:38:01 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
gcc version 6.3.0 20170406 (Ubuntu 6.3.0-12ubuntu2)
cmake version 3.13.0-rc1




On Fri, Oct 26, 2018 at 8:05 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Are you sure it's shared with the same compilation mode (Debug or Release)
> ?
> Simon
>
> On Fri, Oct 26, 2018 at 5:18 AM Julia Semyakishkina <
> prekrasnaya1985 at gmail.com> wrote:
>
>> Ok, it works in case ITK Static -> RTK Static. When i try to build ITK
>> Shared -> RTK Shared, i have got:
>> [ 19%] Linking CXX executable ../../bin/rtkamsterdamshroud
>> CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
>> `rtk::ThreeDCircularProjectionGeometryXMLFileReader::New()':
>> rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0xe):
>> undefined reference to `typeinfo for
>> rtk::ThreeDCircularProjectionGeometryXMLFileReader'
>> rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0x41):
>> undefined reference to `typeinfo for
>> rtk::ThreeDCircularProjectionGeometryXMLFileReader'
>> rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0xc9):
>> undefined reference to
>> `rtk::ThreeDCircularProjectionGeometryXMLFileReader::ThreeDCircularProjectionGeometryXMLFileReader()'
>> CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
>> `std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
>> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
>> std::char_traits<char>, std::allocator<char> > > > const
>> rtk::GetProjectionsFileNamesFromGgo<args_info_rtkamsterdamshroud>(args_info_rtkamsterdamshroud
>> const&)':
>> rtkamsterdamshroud.cxx:(.text._ZN3rtk30GetProjectionsFileNamesFromGgoI28args_info_rtkamsterdamshroudEEKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERKT_[_ZN3rtk30GetProjectionsFileNamesFromGgoI28args_info_rtkamsterdamshroudEEKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERKT_]+0x3c1):
>> undefined reference to `rtk::RegisterIOFactories()'
>> CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
>> `rtk::ProjectionsReader<itk::Image<double, 3u>
>> >::GenerateOutputInformation()':
>> rtkamsterdamshroud.cxx:(.text._ZN3rtk17ProjectionsReaderIN3itk5ImageIdLj3EEEE25GenerateOutputInformationEv[_ZN3rtk17ProjectionsReaderIN3itk5ImageIdLj3EEEE25GenerateOutputInformationEv]+0x8e1):
>> undefined reference to `rtk::RegisterIOFactories()'
>> collect2: error: ld returned 1 exit status
>> applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/build.make:141:
>> recipe for target 'bin/rtkamsterdamshroud' failed
>> make[2]: *** [bin/rtkamsterdamshroud] Error 1
>> CMakeFiles/Makefile2:512: recipe for target
>> 'applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/all'
>> failed
>> make[1]: ***
>> [applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/all]
>> Error 2
>> Makefile:129: recipe for target 'all' failed
>> make: *** [all] Error 2
>>
>> On Fri, Oct 26, 2018 at 2:59 AM Simon Rit <simon.rit at creatis.insa-lyon.fr>
>> wrote:
>>
>>> Hi,
>>> It seems that you are trying to compile against an installed ITK_DIR.
>>> This is no longer possible, see this thread:
>>> https://github.com/SimonRit/RTK/issues/207
>>> Can you try to compile against your build directory (set ITK_DIR to the
>>> build directory)?
>>> Thanks,
>>> Simon
>>>
>>> On Thu, Oct 25, 2018 at 5:16 PM Julia Semyakishkina <
>>> prekrasnaya1985 at gmail.com> wrote:
>>>
>>>> Hello.
>>>> I can't build RTK in Linux. I've done all default steps described in
>>>> wiki, but on configure i've got:
>>>> CMake Error at utilities/lp_solve/CMakeLists.txt:9 (include):
>>>>    include could not find load file:
>>>>
>>>>      ITKModuleMacros
>>>>
>>>>
>>>> Hm.. it tries include module that exists in src ITK dir, not install...
>>>> I mean
>>>> "ls /usr/local/lib/cmake/ITK-4.13 | grep ITKModuleMacros" prints nothing
>>>> "ls /home/user/src/ITK/CMake | grep ITKModuleMacros" prints
>>>> ITKModuleMacros.cmake
>>>>
>>>> OK, i have just tried to add CMAKE_MODULE_PATH=/home/user/src/ITK/CMake
>>>> and got next error:
>>>>
>>>> CMake Error at CMakeLists.txt:250 (message):
>>>>   Modules can only be built against an ITK build tree; they cannot be
>>>> built
>>>>   against an ITK install tree.
>>>>
>>>> Let's look at the code:
>>>>
>>>> if(NOT ITK_SOURCE_DIR)
>>>>   if(NOT EXISTS ${ITK_CMAKE_DIR}/ITKModuleMacros.cmake)
>>>>     message(FATAL_ERROR "Modules can only be built against an ITK build
>>>> tree; they cannot be built against an ITK install tree.")
>>>>   endif()
>>>>   list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
>>>>   include(ITKModuleExternal)
>>>> else()
>>>>   itk_module_impl()
>>>> endif()
>>>>
>>>> Yea, ITK_SOURCE_DIR is not set in my case, but why there is must be
>>>> ITKModuleMacros.cmake at my ITK_CMAKE_DIR dir that points to ITK
>>>> installation dir ?
>>>>
>>>> If i set ITK_CMAKE_DIR to /home/user/src/ITK/CMake where
>>>> ITKModuleMacros is, it resets back to ITK installation directory at
>>>> # --------------------------------------------------------
>>>> # Find ITK (required)
>>>> if(NOT ITK_SOURCE_DIR)
>>>>   find_package(ITK 4.12.0 REQUIRED)
>>>> endif()
>>>>
>>>>
>>>> So, the only way i see is to build inside ITK, but i am not familiar
>>>> with this. Could anyone help me how to build RTK inside ITK.
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
>
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From simon.rit at creatis.insa-lyon.fr  Wed Oct 31 11:55:59 2018
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Wed, 31 Oct 2018 16:55:59 +0100
Subject: [Rtk-users] compilation issues in case of outside of ITK
 directory build
In-Reply-To: <CANma8ta4R3mLkktkN52tvrbeJmo4z9iBazLnXn2=craartx0og@mail.gmail.com>
References: <CANma8tajk1rny4wAZj8gCbFUaYEV6=7OUzcBuPxW0Wsy2KsamA@mail.gmail.com>
 <CAF0oig2SZD9CzT9OydzRg9P0KdVKjgazgjDKA0EdNizoLcPN5w@mail.gmail.com>
 <CANma8tYdhOvQAUT+baJNsCV7Eri6B35x1iMv9RuAz+3FV9r7Yw@mail.gmail.com>
 <CAF0oig2R-=Eo21S7sPg3ZrNSQ0WcVbHfD0BaV63WcC8dyRHxGw@mail.gmail.com>
 <CANma8ta4R3mLkktkN52tvrbeJmo4z9iBazLnXn2=craartx0og@mail.gmail.com>
Message-ID: <CAF0oig1=ajnUFXvuzsOTGe2Sp7gG_zg+u5P+NSUhQ9=Jiq-noA@mail.gmail.com>

Hi,
I can reproduce the problem and I haven't found a solution yet. I'll let
you know when I have a fix...
Simon

On Sat, Oct 27, 2018 at 6:06 AM Julia Semyakishkina <
prekrasnaya1985 at gmail.com> wrote:

> Hi. Yes, i am.
> Could you just run this simple script in empty directory:
> #!/bin/sh
> wget
> https://sourceforge.net/projects/itk/files/itk/4.13/InsightToolkit-4.13.1.tar.gz
> tar -xvzf InsightToolkit-4.13.1.tar.gz
> mkdir InsightToolkit-4.13.1/build && cd InsightToolkit-4.13.1/build
> cmake -D CMAKE_BUILD_TYPE=Release -D BUILD_SHARED_LIBS:BOOL=ON .. && make
> -j`grep -c processor /proc/cpuinfo`
> ITK_DIR=`pwd`
> cd ../../
> git clone https://github.com/SimonRit/RTK
> mkdir RTK/build && cd RTK/build
> cmake -D CMAKE_BUILD_TYPE=Release -D BUILD_SHARED_LIBS:BOOL=ON -D
> BUILD_TESTING:BOOL=OFF -D ITK_DIR:PATH=$ITK_DIR .. && make
>
> Don't you have the same linker errors i wrote in the previous message ?
>
> some info about my system
> Ubuntu 17.04
> Linux mnolro6001 4.10.0-42-generic #46-Ubuntu SMP Mon Dec 4 14:38:01 UTC
> 2017 x86_64 x86_64 x86_64 GNU/Linux
> gcc version 6.3.0 20170406 (Ubuntu 6.3.0-12ubuntu2)
> cmake version 3.13.0-rc1
>
>
>
>
> On Fri, Oct 26, 2018 at 8:05 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
>
>> Hi,
>> Are you sure it's shared with the same compilation mode (Debug or
>> Release) ?
>> Simon
>>
>> On Fri, Oct 26, 2018 at 5:18 AM Julia Semyakishkina <
>> prekrasnaya1985 at gmail.com> wrote:
>>
>>> Ok, it works in case ITK Static -> RTK Static. When i try to build ITK
>>> Shared -> RTK Shared, i have got:
>>> [ 19%] Linking CXX executable ../../bin/rtkamsterdamshroud
>>> CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
>>> `rtk::ThreeDCircularProjectionGeometryXMLFileReader::New()':
>>> rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0xe):
>>> undefined reference to `typeinfo for
>>> rtk::ThreeDCircularProjectionGeometryXMLFileReader'
>>> rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0x41):
>>> undefined reference to `typeinfo for
>>> rtk::ThreeDCircularProjectionGeometryXMLFileReader'
>>> rtkamsterdamshroud.cxx:(.text._ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv[_ZN3rtk45ThreeDCircularProjectionGeometryXMLFileReader3NewEv]+0xc9):
>>> undefined reference to
>>> `rtk::ThreeDCircularProjectionGeometryXMLFileReader::ThreeDCircularProjectionGeometryXMLFileReader()'
>>> CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
>>> `std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
>>> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
>>> std::char_traits<char>, std::allocator<char> > > > const
>>> rtk::GetProjectionsFileNamesFromGgo<args_info_rtkamsterdamshroud>(args_info_rtkamsterdamshroud
>>> const&)':
>>> rtkamsterdamshroud.cxx:(.text._ZN3rtk30GetProjectionsFileNamesFromGgoI28args_info_rtkamsterdamshroudEEKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERKT_[_ZN3rtk30GetProjectionsFileNamesFromGgoI28args_info_rtkamsterdamshroudEEKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERKT_]+0x3c1):
>>> undefined reference to `rtk::RegisterIOFactories()'
>>> CMakeFiles/rtkamsterdamshroud.dir/rtkamsterdamshroud.cxx.o: In function
>>> `rtk::ProjectionsReader<itk::Image<double, 3u>
>>> >::GenerateOutputInformation()':
>>> rtkamsterdamshroud.cxx:(.text._ZN3rtk17ProjectionsReaderIN3itk5ImageIdLj3EEEE25GenerateOutputInformationEv[_ZN3rtk17ProjectionsReaderIN3itk5ImageIdLj3EEEE25GenerateOutputInformationEv]+0x8e1):
>>> undefined reference to `rtk::RegisterIOFactories()'
>>> collect2: error: ld returned 1 exit status
>>> applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/build.make:141:
>>> recipe for target 'bin/rtkamsterdamshroud' failed
>>> make[2]: *** [bin/rtkamsterdamshroud] Error 1
>>> CMakeFiles/Makefile2:512: recipe for target
>>> 'applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/all'
>>> failed
>>> make[1]: ***
>>> [applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/all]
>>> Error 2
>>> Makefile:129: recipe for target 'all' failed
>>> make: *** [all] Error 2
>>>
>>> On Fri, Oct 26, 2018 at 2:59 AM Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Hi,
>>>> It seems that you are trying to compile against an installed ITK_DIR.
>>>> This is no longer possible, see this thread:
>>>> https://github.com/SimonRit/RTK/issues/207
>>>> Can you try to compile against your build directory (set ITK_DIR to the
>>>> build directory)?
>>>> Thanks,
>>>> Simon
>>>>
>>>> On Thu, Oct 25, 2018 at 5:16 PM Julia Semyakishkina <
>>>> prekrasnaya1985 at gmail.com> wrote:
>>>>
>>>>> Hello.
>>>>> I can't build RTK in Linux. I've done all default steps described in
>>>>> wiki, but on configure i've got:
>>>>> CMake Error at utilities/lp_solve/CMakeLists.txt:9 (include):
>>>>>    include could not find load file:
>>>>>
>>>>>      ITKModuleMacros
>>>>>
>>>>>
>>>>> Hm.. it tries include module that exists in src ITK dir, not install...
>>>>> I mean
>>>>> "ls /usr/local/lib/cmake/ITK-4.13 | grep ITKModuleMacros" prints
>>>>> nothing
>>>>> "ls /home/user/src/ITK/CMake | grep ITKModuleMacros" prints
>>>>> ITKModuleMacros.cmake
>>>>>
>>>>> OK, i have just tried to add
>>>>> CMAKE_MODULE_PATH=/home/user/src/ITK/CMake and got next error:
>>>>>
>>>>> CMake Error at CMakeLists.txt:250 (message):
>>>>>   Modules can only be built against an ITK build tree; they cannot be
>>>>> built
>>>>>   against an ITK install tree.
>>>>>
>>>>> Let's look at the code:
>>>>>
>>>>> if(NOT ITK_SOURCE_DIR)
>>>>>   if(NOT EXISTS ${ITK_CMAKE_DIR}/ITKModuleMacros.cmake)
>>>>>     message(FATAL_ERROR "Modules can only be built against an ITK
>>>>> build tree; they cannot be built against an ITK install tree.")
>>>>>   endif()
>>>>>   list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
>>>>>   include(ITKModuleExternal)
>>>>> else()
>>>>>   itk_module_impl()
>>>>> endif()
>>>>>
>>>>> Yea, ITK_SOURCE_DIR is not set in my case, but why there is must be
>>>>> ITKModuleMacros.cmake at my ITK_CMAKE_DIR dir that points to ITK
>>>>> installation dir ?
>>>>>
>>>>> If i set ITK_CMAKE_DIR to /home/user/src/ITK/CMake where
>>>>> ITKModuleMacros is, it resets back to ITK installation directory at
>>>>> # --------------------------------------------------------
>>>>> # Find ITK (required)
>>>>> if(NOT ITK_SOURCE_DIR)
>>>>>   find_package(ITK 4.12.0 REQUIRED)
>>>>> endif()
>>>>>
>>>>>
>>>>> So, the only way i see is to build inside ITK, but i am not familiar
>>>>> with this. Could anyone help me how to build RTK inside ITK.
>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>>>
>>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>> _______________________________________________
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