From dongjbstrong at 163.com Wed Jun 5 04:46:31 2019 From: dongjbstrong at 163.com (Jianbing) Date: Wed, 5 Jun 2019 16:46:31 +0800 (CST) Subject: [Rtk-users] how to draw geometric phantom in RTK? Message-ID: <6362264f.cc59.16b26d17d98.Coremail.dongjbstrong@163.com> Hi: I want to use RTK to draw a geometric phantom. But the only thing I could find is , and there is only a simple txt file. I could not find any document about how to draw a geometric phantom with such command, what is the meaning of each parameters in the txt file? rtkdrawgeometricphantom --phantomfile GeometricPhantom.txt -o newPhantom.mha Furthermore, what documents shoud I refer to to modify these parameters in order to generate my own phantom? Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: From aurelien.coussat at creatis.insa-lyon.fr Thu Jun 6 09:16:04 2019 From: aurelien.coussat at creatis.insa-lyon.fr (=?ISO-8859-1?Q?Aur=E9lien?= Coussat) Date: Thu, 06 Jun 2019 15:16:04 +0200 Subject: [Rtk-users] how to draw geometric phantom in RTK? In-Reply-To: <6362264f.cc59.16b26d17d98.Coremail.dongjbstrong@163.com> References: <6362264f.cc59.16b26d17d98.Coremail.dongjbstrong@163.com> Message-ID: <1559826964.9199.6.camel@creatis.insa-lyon.fr> Hi, As far as I understand it, the text file accepts all geometries shown in https://en.wikipedia.org/wiki/Quadric, except parabolic cylinder and paraboloid family (as detailed in the last line of http://wiki.openrtk. org/index.php/RTK/Scripts/DrawGeometricPhantom).The parameters x, y and z refer to the position of the quadric in the space, while a, b and c refer to its size in each of the dimension, respectively. The parameter beta refers to its rotation. The parameter "gray" refers to the value of your phantom within the quadric. Note that gray values add up: for instance if you want a sphere whose value is 2 within a bigger sphere whose value is one, both of them should have the parameter "gray" set to one. Hope that this is clearer now! Aur?lien. On Wed, 2019-06-05 at 16:46 +0800, Jianbing wrote: > Hi: > I want to use RTK to draw a geometric phantom. But the only > thing I could find is , and there > is only a simple txt file. I could not find any document about how to > draw a geometric phantom with such command, what is the meaning of > each parameters in the txt file? > rtkdrawgeometricphantom --phantomfile GeometricPhantom.txt -o > newPhantom.mha > Furthermore, what documents shoud I refer to to modify these > parameters in order to generate my own phantom? > Thanks in advance. > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > https://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From dongjbstrong at 163.com Thu Jun 6 10:04:40 2019 From: dongjbstrong at 163.com (Jianbing) Date: Thu, 6 Jun 2019 22:04:40 +0800 (CST) Subject: [Rtk-users] how to draw geometric phantom in RTK? In-Reply-To: <1559826964.9199.6.camel@creatis.insa-lyon.fr> References: <6362264f.cc59.16b26d17d98.Coremail.dongjbstrong@163.com> <1559826964.9199.6.camel@creatis.insa-lyon.fr> Message-ID: <2a96786e.10010.16b2d1b1ed0.Coremail.dongjbstrong@163.com> Thanks for your reply, that is very helpful. There is anthor problem bothing me: how to determine the voxel size and the data size on mhd file? Using GeometricPhantom.txt, the mhd data has dimensions of 256 * 256 * 256, I could not figure out where the '256' is coming from? At 2019-06-06 21:16:04, "Aur?lien Coussat" wrote: Hi, As far as I understand it, the text file accepts all geometries shown in https://en.wikipedia.org/wiki/Quadric, except parabolic cylinder and paraboloid family (as detailed in the last line of http://wiki.openrtk.org/index.php/RTK/Scripts/DrawGeometricPhantom). The parameters x, y and z refer to the position of the quadric in the space, while a, b and c refer to its size in each of the dimension, respectively. The parameter beta refers to its rotation. The parameter "gray" refers to the value of your phantom within the quadric. Note that gray values add up: for instance if you want a sphere whose value is 2 within a bigger sphere whose value is one, both of them should have the parameter "gray" set to one. Hope that this is clearer now! Aur?lien. On Wed, 2019-06-05 at 16:46 +0800, Jianbing wrote: Hi: I want to use RTK to draw a geometric phantom. But the only thing I could find is , and there is only a simple txt file. I could not find any document about how to draw a geometric phantom with such command, what is the meaning of each parameters in the txt file? rtkdrawgeometricphantom --phantomfile GeometricPhantom.txt -o newPhantom.mha Furthermore, what documents shoud I refer to to modify these parameters in order to generate my own phantom? Thanks in advance. _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.comhttps://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Jun 7 01:40:02 2019 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 7 Jun 2019 07:40:02 +0200 Subject: [Rtk-users] how to draw geometric phantom in RTK? In-Reply-To: <2a96786e.10010.16b2d1b1ed0.Coremail.dongjbstrong@163.com> References: <6362264f.cc59.16b26d17d98.Coremail.dongjbstrong@163.com> <1559826964.9199.6.camel@creatis.insa-lyon.fr> <2a96786e.10010.16b2d1b1ed0.Coremail.dongjbstrong@163.com> Message-ID: Hi, The sampling grid is defined on the command line, see rtkdrawgeometricphantom -h: Output 3D image properties: --origin=DOUBLE Origin (default=centered) --dimension=INT Dimension (default=`256') --spacing=DOUBLE Spacing (default=`1') --direction=DOUBLE Direction To complete Aur?lien's answer, you can also use the forbild file format, which is well documented here , using the flag --forbild. The format that Aur?lien described still needs a proper doc. Simon On Thu, Jun 6, 2019 at 4:20 PM Jianbing wrote: > Thanks for your reply, that is very helpful. > There is anthor problem bothing me: > how to determine the voxel size and the data size on mhd file? Using > GeometricPhantom.txt, the mhd data has dimensions of 256 * 256 * 256, I > could not figure out where the '256' is coming from? > > At 2019-06-06 21:16:04, "Aur?lien Coussat" < > aurelien.coussat at creatis.insa-lyon.fr> wrote: > > Hi, > > As far as I understand it, the text file accepts all geometries shown in > https://en.wikipedia.org/wiki/Quadric, except parabolic cylinder and > paraboloid family (as detailed in the last line of > http://wiki.openrtk.org/index.php/RTK/Scripts/DrawGeometricPhantom > ). > The parameters x, y and z refer to the position of the quadric in the > space, while a, b and c refer to its size in each of the dimension, > respectively. The parameter beta refers to its rotation. The parameter > "gray" refers to the value of your phantom within the quadric. Note that > gray values add up: for instance if you want a sphere whose value is 2 > within a bigger sphere whose value is one, both of them should have the > parameter "gray" set to one. > > Hope that this is clearer now! > > Aur?lien. > > On Wed, 2019-06-05 at 16:46 +0800, Jianbing wrote: > > Hi: > I want to use RTK to draw a geometric phantom. But the only thing > I could find is >, > and there is only a simple txt file. I could not find any document about > how to draw a geometric phantom with such command, what is the meaning of > each parameters in the txt file? > > rtkdrawgeometricphantom --phantomfile GeometricPhantom.txt -o newPhantom.mha > > Furthermore, what documents shoud I refer to to modify these > parameters in order to generate my own phantom? > Thanks in advance. > > > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttps://public.kitware.com/mailman/listinfo/rtk-users > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > https://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lomahu at gmail.com Mon Jun 24 15:37:01 2019 From: lomahu at gmail.com (Howard) Date: Mon, 24 Jun 2019 15:37:01 -0400 Subject: [Rtk-users] error in ThreeDCircularProjectionGeometry GeometryType Message-ID: Hi, I was trying to play with the simple example to reconstruct a sphere from the RTK wiki page. The sample code: // Projection matrices unsigned int numberOfProjections = 360; unsigned int firstAngle = 0; unsigned int angularArc = 360; unsigned int sid = 80; // source to isocenter distance in mm unsigned int sdd = 160; // source to detector distance in mm int isox = 0; // X coordinate on the projection image of isocenter int isoy = 0; // Y coordinate on the projection image of isocenter for(unsigned int noProj=0; noProjAddProjection(sid, sdd, angle, isox, isoy); } When I compiled the code, I got an error from the line in the projection loop: geometry->AddProjection(sid, sdd, angle, isox, isoy); I am using an old version of RTK 1.1 but it should not matter. Can anyone help me out? Thanks! [chaom02 at minerva2 recon]$ make Scanning dependencies of target Test1 [ 50%] Building CXX object CMakeFiles/Test1.dir/Test1.cxx.o [100%] Linking CXX executable Test1 /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): In function `itk::MatrixOffsetTransformBase::GetFixedParameters() const': rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18GetFixedParametersEv[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18GetFixedParametersEv]+0x23): undefined reference to `vnl_vector::set_size(unsigned int)' /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): In function `itk::MatrixOffsetTransformBase::SetFixedParameters(itk::OptimizerParameters const&)': rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18SetFixedParametersERKNS_19OptimizerParametersIdEE[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18SetFixedParametersERKNS_19OptimizerParametersIdEE]+0x4f): undefined reference to `vnl_vector::set_size(unsigned int)' /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): In function `itk::CenteredEuler3DTransform::SetParameters(itk::OptimizerParameters const&)': rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk24CenteredEuler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk24CenteredEuler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x31): undefined reference to `vnl_vector::set_size(unsigned int)' /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): In function `itk::Euler3DTransform::SetParameters(itk::OptimizerParameters const&)': rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk16Euler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk16Euler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x40): undefined reference to `vnl_vector::set_size(unsigned int)' /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): In function `itk::Transform::Transform(unsigned long)': rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk9TransformIdLj3ELj3EEC2Em[_ZN3itk9TransformIdLj3ELj3EEC5Em]+0x49): undefined reference to `vnl_vector::vnl_vector(unsigned int)' rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk9TransformIdLj3ELj3EEC2Em[_ZN3itk9TransformIdLj3ELj3EEC5Em]+0xa3): undefined reference to `vnl_vector::vnl_vector(unsigned int)' /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): In function `itk::MatrixOffsetTransformBase::MatrixOffsetTransformBase()': rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EEC2Ev[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EEC5Ev]+0x21b): undefined reference to `vnl_vector::set_size(unsigned int)' /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): In function `itk::Rigid3DTransform::SetParameters(itk::OptimizerParameters const&)': rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk16Rigid3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk16Rigid3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x3e): undefined reference to `vnl_vector::set_size(unsigned int)' /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): In function `itk::MatrixOffsetTransformBase::SetParameters(itk::OptimizerParameters const&)': rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE13SetParametersERKNS_19OptimizerParametersIdEE]+0x43): undefined reference to `vnl_vector::set_size(unsigned int)' /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): In function `itk::MatrixOffsetTransformBase::TransformVector(itk::VariableLengthVector const&) const': rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE15TransformVectorERKNS_20VariableLengthVectorIdEE[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE15TransformVectorERKNS_20VariableLengthVectorIdEE]+0x2f): undefined reference to `vnl_vector::vnl_vector(unsigned int)' /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): In function `itk::MatrixOffsetTransformBase::TransformCovariantVector(itk::VariableLengthVector const&) const': rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE24TransformCovariantVectorERKNS_20VariableLengthVectorIdEE[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE24TransformCovariantVectorERKNS_20VariableLengthVectorIdEE]+0x3a): undefined reference to `vnl_vector::vnl_vector(unsigned int)' collect2: error: ld returned 1 exit status make[2]: *** [Test1] Error 1 make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 make: *** [all] Error 2 From simon.rit at creatis.insa-lyon.fr Tue Jun 25 04:50:15 2019 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 25 Jun 2019 10:50:15 +0200 Subject: [Rtk-users] error in ThreeDCircularProjectionGeometry GeometryType In-Reply-To: References: Message-ID: Hi Howard, Since it's a linking problem, maybe you should check that you have linked the RTK_libraries, see e.g., https://github.com/SimonRit/RTK/blob/master/examples/FirstReconstruction/CMakeLists.txt#L12 I can try to fix the problem if you provide a full example. Simon On Mon, Jun 24, 2019 at 9:45 PM Howard wrote: > Hi, > > I was trying to play with the simple example to reconstruct a sphere > from the RTK wiki page. The sample code: > > // Projection matrices > unsigned int numberOfProjections = 360; > unsigned int firstAngle = 0; > unsigned int angularArc = 360; > unsigned int sid = 80; // source to isocenter distance in mm > unsigned int sdd = 160; // source to detector distance in mm > int isox = 0; // X coordinate on the projection image of isocenter > int isoy = 0; // Y coordinate on the projection image of isocenter > > > for(unsigned int noProj=0; noProj double angle = (float)firstAngle + (float)noProj * angularArc / > (float)numberOfProjections; > geometry->AddProjection(sid, sdd, angle, isox, isoy); > } > > > When I compiled the code, I got an error from the line in the projection > loop: > > geometry->AddProjection(sid, sdd, angle, isox, isoy); > > I am using an old version of RTK 1.1 but it should not matter. Can > anyone help me out? Thanks! > > [chaom02 at minerva2 recon]$ make > Scanning dependencies of target Test1 > [ 50%] Building CXX object CMakeFiles/Test1.dir/Test1.cxx.o > [100%] Linking CXX executable Test1 > > /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): > In function `itk::MatrixOffsetTransformBase 3u>::GetFixedParameters() const': > > rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18GetFixedParametersEv[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18GetFixedParametersEv]+0x23): > undefined reference to `vnl_vector::set_size(unsigned int)' > > /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): > In function `itk::MatrixOffsetTransformBase 3u>::SetFixedParameters(itk::OptimizerParameters const&)': > > rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18SetFixedParametersERKNS_19OptimizerParametersIdEE[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18SetFixedParametersERKNS_19OptimizerParametersIdEE]+0x4f): > undefined reference to `vnl_vector::set_size(unsigned int)' > > /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): > In function > `itk::CenteredEuler3DTransform::SetParameters(itk::OptimizerParameters > const&)': > > rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk24CenteredEuler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk24CenteredEuler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x31): > undefined reference to `vnl_vector::set_size(unsigned int)' > > /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): > In function > `itk::Euler3DTransform::SetParameters(itk::OptimizerParameters > const&)': > > rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk16Euler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk16Euler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x40): > undefined reference to `vnl_vector::set_size(unsigned int)' > > /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): > In function `itk::Transform::Transform(unsigned > long)': > > rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk9TransformIdLj3ELj3EEC2Em[_ZN3itk9TransformIdLj3ELj3EEC5Em]+0x49): > undefined reference to `vnl_vector::vnl_vector(unsigned int)' > > rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk9TransformIdLj3ELj3EEC2Em[_ZN3itk9TransformIdLj3ELj3EEC5Em]+0xa3): > undefined reference to `vnl_vector::vnl_vector(unsigned int)' > > /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): > In function `itk::MatrixOffsetTransformBase 3u>::MatrixOffsetTransformBase()': > > rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EEC2Ev[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EEC5Ev]+0x21b): > undefined reference to `vnl_vector::set_size(unsigned int)' > > /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): > In function > `itk::Rigid3DTransform::SetParameters(itk::OptimizerParameters > const&)': > > rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk16Rigid3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk16Rigid3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x3e): > undefined reference to `vnl_vector::set_size(unsigned int)' > > /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): > In function `itk::MatrixOffsetTransformBase 3u>::SetParameters(itk::OptimizerParameters const&)': > > rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE13SetParametersERKNS_19OptimizerParametersIdEE]+0x43): > undefined reference to `vnl_vector::set_size(unsigned int)' > > /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): > In function `itk::MatrixOffsetTransformBase 3u>::TransformVector(itk::VariableLengthVector const&) const': > > rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE15TransformVectorERKNS_20VariableLengthVectorIdEE[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE15TransformVectorERKNS_20VariableLengthVectorIdEE]+0x2f): > undefined reference to `vnl_vector::vnl_vector(unsigned int)' > > /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): > In function `itk::MatrixOffsetTransformBase 3u>::TransformCovariantVector(itk::VariableLengthVector > const&) const': > > rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE24TransformCovariantVectorERKNS_20VariableLengthVectorIdEE[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE24TransformCovariantVectorERKNS_20VariableLengthVectorIdEE]+0x3a): > undefined reference to `vnl_vector::vnl_vector(unsigned int)' > collect2: error: ld returned 1 exit status > make[2]: *** [Test1] Error 1 > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 > make: *** [all] Error 2 > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > https://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lomahu at gmail.com Tue Jun 25 08:37:05 2019 From: lomahu at gmail.com (Howard) Date: Tue, 25 Jun 2019 08:37:05 -0400 Subject: [Rtk-users] error in ThreeDCircularProjectionGeometry GeometryType In-Reply-To: References: Message-ID: Hi Simon, Here is the CMakeLists.txt I used for compiling and linking. Thanks for looking into the issue. Howard =============================================== cmake_minimum_required(VERSION 3.12) PROJECT(Test1) # Find the RTK libraries and includes FIND_PACKAGE(RTK REQUIRED) INCLUDE(${RTK_USE_FILE}) # Find ITK with RTK find_package(ITK REQUIRED) include(${ITK_USE_FILE}) # Executable ADD_EXECUTABLE(Test1 Test1.cxx ) TARGET_LINK_LIBRARIES(Test1 ${RTK_LIBRARIES}) TARGET_LINK_LIBRARIES(Test1 ${ITK_LIBRARIES}) On 6/25/19, Simon Rit wrote: > Hi Howard, > Since it's a linking problem, maybe you should check that you have linked > the RTK_libraries, see e.g., > https://github.com/SimonRit/RTK/blob/master/examples/FirstReconstruction/CMakeLists.txt#L12 > I can try to fix the problem if you provide a full example. > Simon > > On Mon, Jun 24, 2019 at 9:45 PM Howard wrote: > >> Hi, >> >> I was trying to play with the simple example to reconstruct a sphere >> from the RTK wiki page. The sample code: >> >> // Projection matrices >> unsigned int numberOfProjections = 360; >> unsigned int firstAngle = 0; >> unsigned int angularArc = 360; >> unsigned int sid = 80; // source to isocenter distance in mm >> unsigned int sdd = 160; // source to detector distance in mm >> int isox = 0; // X coordinate on the projection image of isocenter >> int isoy = 0; // Y coordinate on the projection image of isocenter >> >> >> for(unsigned int noProj=0; noProj> double angle = (float)firstAngle + (float)noProj * angularArc / >> (float)numberOfProjections; >> geometry->AddProjection(sid, sdd, angle, isox, isoy); >> } >> >> >> When I compiled the code, I got an error from the line in the projection >> loop: >> >> geometry->AddProjection(sid, sdd, angle, isox, isoy); >> >> I am using an old version of RTK 1.1 but it should not matter. Can >> anyone help me out? Thanks! >> >> [chaom02 at minerva2 recon]$ make >> Scanning dependencies of target Test1 >> [ 50%] Building CXX object CMakeFiles/Test1.dir/Test1.cxx.o >> [100%] Linking CXX executable Test1 >> >> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >> In function `itk::MatrixOffsetTransformBase> 3u>::GetFixedParameters() const': >> >> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18GetFixedParametersEv[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18GetFixedParametersEv]+0x23): >> undefined reference to `vnl_vector::set_size(unsigned int)' >> >> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >> In function `itk::MatrixOffsetTransformBase> 3u>::SetFixedParameters(itk::OptimizerParameters const&)': >> >> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18SetFixedParametersERKNS_19OptimizerParametersIdEE[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18SetFixedParametersERKNS_19OptimizerParametersIdEE]+0x4f): >> undefined reference to `vnl_vector::set_size(unsigned int)' >> >> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >> In function >> `itk::CenteredEuler3DTransform::SetParameters(itk::OptimizerParameters >> const&)': >> >> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk24CenteredEuler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk24CenteredEuler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x31): >> undefined reference to `vnl_vector::set_size(unsigned int)' >> >> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >> In function >> `itk::Euler3DTransform::SetParameters(itk::OptimizerParameters >> const&)': >> >> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk16Euler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk16Euler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x40): >> undefined reference to `vnl_vector::set_size(unsigned int)' >> >> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >> In function `itk::Transform::Transform(unsigned >> long)': >> >> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk9TransformIdLj3ELj3EEC2Em[_ZN3itk9TransformIdLj3ELj3EEC5Em]+0x49): >> undefined reference to `vnl_vector::vnl_vector(unsigned int)' >> >> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk9TransformIdLj3ELj3EEC2Em[_ZN3itk9TransformIdLj3ELj3EEC5Em]+0xa3): >> undefined reference to `vnl_vector::vnl_vector(unsigned int)' >> >> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >> In function `itk::MatrixOffsetTransformBase> 3u>::MatrixOffsetTransformBase()': >> >> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EEC2Ev[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EEC5Ev]+0x21b): >> undefined reference to `vnl_vector::set_size(unsigned int)' >> >> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >> In function >> `itk::Rigid3DTransform::SetParameters(itk::OptimizerParameters >> const&)': >> >> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk16Rigid3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk16Rigid3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x3e): >> undefined reference to `vnl_vector::set_size(unsigned int)' >> >> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >> In function `itk::MatrixOffsetTransformBase> 3u>::SetParameters(itk::OptimizerParameters const&)': >> >> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE13SetParametersERKNS_19OptimizerParametersIdEE]+0x43): >> undefined reference to `vnl_vector::set_size(unsigned int)' >> >> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >> In function `itk::MatrixOffsetTransformBase> 3u>::TransformVector(itk::VariableLengthVector const&) const': >> >> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE15TransformVectorERKNS_20VariableLengthVectorIdEE[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE15TransformVectorERKNS_20VariableLengthVectorIdEE]+0x2f): >> undefined reference to `vnl_vector::vnl_vector(unsigned int)' >> >> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >> In function `itk::MatrixOffsetTransformBase> 3u>::TransformCovariantVector(itk::VariableLengthVector >> const&) const': >> >> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE24TransformCovariantVectorERKNS_20VariableLengthVectorIdEE[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE24TransformCovariantVectorERKNS_20VariableLengthVectorIdEE]+0x3a): >> undefined reference to `vnl_vector::vnl_vector(unsigned int)' >> collect2: error: ld returned 1 exit status >> make[2]: *** [Test1] Error 1 >> make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 >> make: *** [all] Error 2 >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> https://public.kitware.com/mailman/listinfo/rtk-users >> > From lomahu at gmail.com Tue Jun 25 09:03:05 2019 From: lomahu at gmail.com (Howard) Date: Tue, 25 Jun 2019 09:03:05 -0400 Subject: [Rtk-users] error in ThreeDCircularProjectionGeometry GeometryType In-Reply-To: References: Message-ID: I felt it might be useful to show the cxx code as well including the header files. ========================================= #include "rtkGgoFunctions.h" #include #include #include #include #include #include int main(int argc, char * argv[]) { typedef float OutputPixelType; const unsigned int Dimension = 3; typedef itk::Image< OutputPixelType, Dimension > OutputImageType; // Defines the RTK geometry object.....We will have to revisit this geometry typedef rtk::ThreeDCircularProjectionGeometry GeometryType; GeometryType::Pointer geometry = GeometryType::New(); // Projection matrices unsigned int numberOfProjections = 360; unsigned int firstAngle = 0; unsigned int angularArc = 360; unsigned int sid = 80; // source to isocenter distance in mm unsigned int sdd = 160; // source to detector distance in mm int isox = 0; // X coordinate on the projection image of isocenter int isoy = 0; // Y coordinate on the projection image of isocenter for(unsigned int noProj=0; noProjAddProjection(sid, sdd, angle, isox, isoy); } // Define and allocate the FDK Back Projection Filter typedef rtk::FDKBackProjectionImageFilter BPType; BPType::Pointer p = BPType::New(); std::cout << "RTK Hello World!" << std::endl; // Write //typedef itk::ImageFileWriter< OutputImageType > WriterType; //WriterType::Pointer writer = WriterType::New(); //writer->SetFileName( args_info.output_arg ); //writer->SetInput( add->GetOutput() ); //TRY_AND_EXIT_ON_ITK_EXCEPTION( writer->Update() ); return 0; } On 6/25/19, Howard wrote: > Hi Simon, > > Here is the CMakeLists.txt I used for compiling and linking. Thanks > for looking into the issue. > > Howard > > =============================================== > > cmake_minimum_required(VERSION 3.12) > > PROJECT(Test1) > > # Find the RTK libraries and includes > FIND_PACKAGE(RTK REQUIRED) > INCLUDE(${RTK_USE_FILE}) > > # Find ITK with RTK > find_package(ITK REQUIRED) > include(${ITK_USE_FILE}) > > # Executable > ADD_EXECUTABLE(Test1 Test1.cxx ) > TARGET_LINK_LIBRARIES(Test1 ${RTK_LIBRARIES}) > TARGET_LINK_LIBRARIES(Test1 ${ITK_LIBRARIES}) > > > On 6/25/19, Simon Rit wrote: >> Hi Howard, >> Since it's a linking problem, maybe you should check that you have linked >> the RTK_libraries, see e.g., >> https://github.com/SimonRit/RTK/blob/master/examples/FirstReconstruction/CMakeLists.txt#L12 >> I can try to fix the problem if you provide a full example. >> Simon >> >> On Mon, Jun 24, 2019 at 9:45 PM Howard wrote: >> >>> Hi, >>> >>> I was trying to play with the simple example to reconstruct a sphere >>> from the RTK wiki page. The sample code: >>> >>> // Projection matrices >>> unsigned int numberOfProjections = 360; >>> unsigned int firstAngle = 0; >>> unsigned int angularArc = 360; >>> unsigned int sid = 80; // source to isocenter distance in mm >>> unsigned int sdd = 160; // source to detector distance in mm >>> int isox = 0; // X coordinate on the projection image of isocenter >>> int isoy = 0; // Y coordinate on the projection image of isocenter >>> >>> >>> for(unsigned int noProj=0; noProj>> double angle = (float)firstAngle + (float)noProj * angularArc / >>> (float)numberOfProjections; >>> geometry->AddProjection(sid, sdd, angle, isox, isoy); >>> } >>> >>> >>> When I compiled the code, I got an error from the line in the projection >>> loop: >>> >>> geometry->AddProjection(sid, sdd, angle, isox, isoy); >>> >>> I am using an old version of RTK 1.1 but it should not matter. Can >>> anyone help me out? Thanks! >>> >>> [chaom02 at minerva2 recon]$ make >>> Scanning dependencies of target Test1 >>> [ 50%] Building CXX object CMakeFiles/Test1.dir/Test1.cxx.o >>> [100%] Linking CXX executable Test1 >>> >>> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >>> In function `itk::MatrixOffsetTransformBase>> 3u>::GetFixedParameters() const': >>> >>> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18GetFixedParametersEv[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18GetFixedParametersEv]+0x23): >>> undefined reference to `vnl_vector::set_size(unsigned int)' >>> >>> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >>> In function `itk::MatrixOffsetTransformBase>> 3u>::SetFixedParameters(itk::OptimizerParameters const&)': >>> >>> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18SetFixedParametersERKNS_19OptimizerParametersIdEE[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE18SetFixedParametersERKNS_19OptimizerParametersIdEE]+0x4f): >>> undefined reference to `vnl_vector::set_size(unsigned int)' >>> >>> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >>> In function >>> `itk::CenteredEuler3DTransform::SetParameters(itk::OptimizerParameters >>> const&)': >>> >>> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk24CenteredEuler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk24CenteredEuler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x31): >>> undefined reference to `vnl_vector::set_size(unsigned int)' >>> >>> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >>> In function >>> `itk::Euler3DTransform::SetParameters(itk::OptimizerParameters >>> const&)': >>> >>> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk16Euler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk16Euler3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x40): >>> undefined reference to `vnl_vector::set_size(unsigned int)' >>> >>> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >>> In function `itk::Transform::Transform(unsigned >>> long)': >>> >>> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk9TransformIdLj3ELj3EEC2Em[_ZN3itk9TransformIdLj3ELj3EEC5Em]+0x49): >>> undefined reference to `vnl_vector::vnl_vector(unsigned int)' >>> >>> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk9TransformIdLj3ELj3EEC2Em[_ZN3itk9TransformIdLj3ELj3EEC5Em]+0xa3): >>> undefined reference to `vnl_vector::vnl_vector(unsigned int)' >>> >>> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >>> In function `itk::MatrixOffsetTransformBase>> 3u>::MatrixOffsetTransformBase()': >>> >>> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EEC2Ev[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EEC5Ev]+0x21b): >>> undefined reference to `vnl_vector::set_size(unsigned int)' >>> >>> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >>> In function >>> `itk::Rigid3DTransform::SetParameters(itk::OptimizerParameters >>> const&)': >>> >>> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk16Rigid3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk16Rigid3DTransformIdE13SetParametersERKNS_19OptimizerParametersIdEE]+0x3e): >>> undefined reference to `vnl_vector::set_size(unsigned int)' >>> >>> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >>> In function `itk::MatrixOffsetTransformBase>> 3u>::SetParameters(itk::OptimizerParameters const&)': >>> >>> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE13SetParametersERKNS_19OptimizerParametersIdEE[_ZN3itk25MatrixOffsetTransformBaseIdLj3ELj3EE13SetParametersERKNS_19OptimizerParametersIdEE]+0x43): >>> undefined reference to `vnl_vector::set_size(unsigned int)' >>> >>> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >>> In function `itk::MatrixOffsetTransformBase>> 3u>::TransformVector(itk::VariableLengthVector const&) const': >>> >>> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE15TransformVectorERKNS_20VariableLengthVectorIdEE[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE15TransformVectorERKNS_20VariableLengthVectorIdEE]+0x2f): >>> undefined reference to `vnl_vector::vnl_vector(unsigned int)' >>> >>> /sc/orga/work/chaom02/usr/local/RTK/RTK-bin/bin/libRTK.a(rtkThreeDCircularProjectionGeometry.cxx.o): >>> In function `itk::MatrixOffsetTransformBase>> 3u>::TransformCovariantVector(itk::VariableLengthVector >>> const&) const': >>> >>> rtkThreeDCircularProjectionGeometry.cxx:(.text._ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE24TransformCovariantVectorERKNS_20VariableLengthVectorIdEE[_ZNK3itk25MatrixOffsetTransformBaseIdLj3ELj3EE24TransformCovariantVectorERKNS_20VariableLengthVectorIdEE]+0x3a): >>> undefined reference to `vnl_vector::vnl_vector(unsigned int)' >>> collect2: error: ld returned 1 exit status >>> make[2]: *** [Test1] Error 1 >>> make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 >>> make: *** [all] Error 2 >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> https://public.kitware.com/mailman/listinfo/rtk-users >>> >> > From lomahu at gmail.com Tue Jun 25 18:55:27 2019 From: lomahu at gmail.com (Howard) Date: Tue, 25 Jun 2019 18:55:27 -0400 Subject: [Rtk-users] RTK compilation Message-ID: Hi, I followed the instructions on the RTK wiki page to build the latest RTK. With upgrading ITK to v4.13.0, during the build I encountered the following error: CMake Error at CMakeLists.txt:94 (find_package): By not providing "FindITK.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "ITK", but CMake did not find one. Could not find a package configuration file provided by "ITK" (requested version 4.12.0) with any of the following names: ITKConfig.cmake itk-config.cmake Add the installation prefix of "ITK" to CMAKE_PREFIX_PATH or set "ITK_DIR" to a directory containing one of the above files. If "ITK" provides a separate development package or SDK, be sure it has been installed. I searched online and found some people said "The file FindITK.cmake was removed in CMake 3.0.", but RTK wiki page never said anything like that. With the older version RTK, I never had this trouble building RTK. It is supposed to be very smooth process but becomes so frustrating!!!! Can anyone out there help me out? Thanks, Howard From simon.rit at creatis.insa-lyon.fr Wed Jun 26 01:24:14 2019 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 26 Jun 2019 07:24:14 +0200 Subject: [Rtk-users] RTK compilation In-Reply-To: References: Message-ID: Hi Howard, Sorry to hear you're struggling. You need to set ITK_DIR to the location of your ITK build. It may have been removed from cmake but it's provided by ITK. The simplest is to build the latest ITK 5.0.0 and to simply turn on the option Module_RTK. Simon On Wed, Jun 26, 2019 at 12:55 AM Howard wrote: > Hi, > > I followed the instructions on the RTK wiki page to build the latest > RTK. With upgrading ITK to v4.13.0, during the build I encountered the > following error: > > CMake Error at CMakeLists.txt:94 (find_package): > By not providing "FindITK.cmake" in CMAKE_MODULE_PATH this project has > asked CMake to find a package configuration file provided by "ITK", but > CMake did not find one. > > Could not find a package configuration file provided by "ITK" (requested > version 4.12.0) with any of the following names: > > ITKConfig.cmake > itk-config.cmake > > Add the installation prefix of "ITK" to CMAKE_PREFIX_PATH or set > "ITK_DIR" > to a directory containing one of the above files. If "ITK" provides a > separate development package or SDK, be sure it has been installed. > > I searched online and found some people said "The file FindITK.cmake > was removed in CMake 3.0.", but RTK wiki page never said anything like > that. > > With the older version RTK, I never had this trouble building RTK. It > is supposed to be very smooth process but becomes so frustrating!!!! > Can anyone out there help me out? > > Thanks, > Howard > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > https://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lomahu at gmail.com Wed Jun 26 14:26:52 2019 From: lomahu at gmail.com (Howard) Date: Wed, 26 Jun 2019 14:26:52 -0400 Subject: [Rtk-users] RTK compilation In-Reply-To: References: Message-ID: Hi Simon, Following your suggestion to build ITK5.0.0 with the option Module_RTK turned on, I finally succeeded in running the first reconstruction example. The problem from ThreeDCircularProjectionGeometry GeometryType I posted yesterday was also fixed with the new ITK5.0.0 build. For your reference, while building ITK 5.0.0, I still could not turn on ITK_USE_FFTWD and ITK_USE_FFTWF. Not sure this would affect the RTK application, though. Howard On Wed, Jun 26, 2019 at 1:23 AM Simon Rit wrote: > Hi Howard, > Sorry to hear you're struggling. You need to set ITK_DIR to the location > of your ITK build. It may have been removed from cmake but it's provided by > ITK. > The simplest is to build the latest ITK 5.0.0 and to simply turn on the > option Module_RTK. > Simon > > On Wed, Jun 26, 2019 at 12:55 AM Howard wrote: > >> Hi, >> >> I followed the instructions on the RTK wiki page to build the latest >> RTK. With upgrading ITK to v4.13.0, during the build I encountered the >> following error: >> >> CMake Error at CMakeLists.txt:94 (find_package): >> By not providing "FindITK.cmake" in CMAKE_MODULE_PATH this project has >> asked CMake to find a package configuration file provided by "ITK", but >> CMake did not find one. >> >> Could not find a package configuration file provided by "ITK" >> (requested >> version 4.12.0) with any of the following names: >> >> ITKConfig.cmake >> itk-config.cmake >> >> Add the installation prefix of "ITK" to CMAKE_PREFIX_PATH or set >> "ITK_DIR" >> to a directory containing one of the above files. If "ITK" provides a >> separate development package or SDK, be sure it has been installed. >> >> I searched online and found some people said "The file FindITK.cmake >> was removed in CMake 3.0.", but RTK wiki page never said anything like >> that. >> >> With the older version RTK, I never had this trouble building RTK. It >> is supposed to be very smooth process but becomes so frustrating!!!! >> Can anyone out there help me out? >> >> Thanks, >> Howard >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> https://public.kitware.com/mailman/listinfo/rtk-users >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jun 26 18:31:17 2019 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 27 Jun 2019 00:31:17 +0200 Subject: [Rtk-users] RTK compilation In-Reply-To: References: Message-ID: Hi, Great, thanks for the feedback. The FFTW stuff is probably a question for the ITK forum but you can probably get around by using a pre-compiled version of FFTW (I presume you're on windows). It's not mandatory for RTK but improves the speed of filtering on the CPU. Simon On Wed, Jun 26, 2019 at 8:27 PM Howard wrote: > Hi Simon, > > Following your suggestion to build ITK5.0.0 with the option Module_RTK > turned on, I finally succeeded in running the first reconstruction example. > The problem from ThreeDCircularProjectionGeometry GeometryType I posted > yesterday was also fixed with the new ITK5.0.0 build. > > For your reference, while building ITK 5.0.0, I still could not turn on ITK_USE_FFTWD > and ITK_USE_FFTWF. Not sure this would affect the RTK application, though. > > Howard > > On Wed, Jun 26, 2019 at 1:23 AM Simon Rit > wrote: > >> Hi Howard, >> Sorry to hear you're struggling. You need to set ITK_DIR to the location >> of your ITK build. It may have been removed from cmake but it's provided by >> ITK. >> The simplest is to build the latest ITK 5.0.0 and to simply turn on the >> option Module_RTK. >> Simon >> >> On Wed, Jun 26, 2019 at 12:55 AM Howard wrote: >> >>> Hi, >>> >>> I followed the instructions on the RTK wiki page to build the latest >>> RTK. With upgrading ITK to v4.13.0, during the build I encountered the >>> following error: >>> >>> CMake Error at CMakeLists.txt:94 (find_package): >>> By not providing "FindITK.cmake" in CMAKE_MODULE_PATH this project has >>> asked CMake to find a package configuration file provided by "ITK", >>> but >>> CMake did not find one. >>> >>> Could not find a package configuration file provided by "ITK" >>> (requested >>> version 4.12.0) with any of the following names: >>> >>> ITKConfig.cmake >>> itk-config.cmake >>> >>> Add the installation prefix of "ITK" to CMAKE_PREFIX_PATH or set >>> "ITK_DIR" >>> to a directory containing one of the above files. If "ITK" provides a >>> separate development package or SDK, be sure it has been installed. >>> >>> I searched online and found some people said "The file FindITK.cmake >>> was removed in CMake 3.0.", but RTK wiki page never said anything like >>> that. >>> >>> With the older version RTK, I never had this trouble building RTK. It >>> is supposed to be very smooth process but becomes so frustrating!!!! >>> Can anyone out there help me out? >>> >>> Thanks, >>> Howard >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> https://public.kitware.com/mailman/listinfo/rtk-users >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.a.gh72 at gmail.com Sun Jun 30 08:05:45 2019 From: e.a.gh72 at gmail.com (Ali ghorbanian) Date: Sun, 30 Jun 2019 16:35:45 +0430 Subject: [Rtk-users] Use RTK library for fan beam CT Message-ID: Hi, How to use RTK library for fan beam CT (cone beam x-ray with curve shape detector)? As figure : [image: image.png] Best regards -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 56586 bytes Desc: not available URL: