Hi Robert,
> /usr/bin/ld: /dls_sw/apps/itk/itk-master-static/lib/libitkgdcmjpeg8-4.10.a(jerror.c.o): relocation R_X86_64_32S against `.text' can not be used when making a shared object; recompile with -fPIC
This means that "-fPIC" should be added to the CMAKE_CXX_FLAGS for ITK.
HTH,
Matt
On Wed, Mar 23, 2016 at 11:58 AM, <Robert.Atwood at diamond.ac.uk> wrote:
> Hi, Dženan, and List :
>
>
>
> Thanks for the tips, but, building the executable by pointing to the
> itk-build folder for linking is exactly what I did not want to do. I want
> the compiled instances of the specific templated objects to be put into a
> stand-alone library that could then be linked , in an environment where the
> ITK build directory may not be available, and within a project that’s not
> using cmake (yet? J ) just for a small single-data-type-specific filter
> chain that would be a bit nontrivial to just re-implement myself!
>
>
>
> I had some success with the following, for the example ITKFilterLib:
>
>
>
> Using the itk-master-git-static as built before, (BUILD_SHARED_LIBS OFF)
>
>
>
>
>
> In CMakeLists.txt for the project, add SHARED keyword to the library
> defninition:
>
>
>
> 15 ADD_LIBRARY(Example_ITKFilterLib SHARED ITKFilterLib.cxx )
>
> Then use cmake + make to build the libExample_ITKFilterLib.so library.
>
>
>
>
>
> Then I can invoke g++ as follows
>
>
>
>
>
>
>
> build]$ g++ ../ITKFilterLib/ITKFilterLibTest.cxx -o testcomp -L . -l
> Example_ITKFilterLib -I ../ITKFilterLib/
>
>
>
> Even if the itk-master-static is not available in that environment, this
> succeeds, and I believe this is what I want. I don’t want to have a
> statically linked final executable, but rather a .so library.
>
>
>
>
>
> However …
>
>
>
> I encountered another hitch trying to apply this to my actual project. If
> there were any FileWriter and FileReader present in the library, it would
> not build, complaining about position-dependent symbols in several IO
> libraries , most of which I was not actually wanting to use at all. This
> happened at the step of trying to build the .so library using the makefile
> created by cmake:
>
>
>
> /usr/bin/ld:
> /dls_sw/apps/itk/itk-master-static/lib/libitkgdcmjpeg8-4.10.a(jerror.c.o):
> relocation R_X86_64_32S against `.text' can not be used when making a shared
> object; recompile with -fPIC
>
> /dls_sw/apps/itk/itk-master-static/lib/libitkgdcmjpeg8-4.10.a: could not
> read symbols: Bad value
>
>
>
>
>
> Removing any reference to FileReader and FileWriter gets rid of this
> problem.
>
>
>
> Thanks!
>
>
>
>
>
> As a further note:
>
>
>
> There are also some directions in the comments of the ITKFilterLib example
> that did not turn out to be necessary in my project. I did not have to
> create global objects for poitners or image containiers outside the scope of
> the class and still did not have to #include itkImage.h in the main program.
> I placed the typedef’s inside the class and the instantiations of the smart
> poitners in the class constructor. I don’t see that this extra complication
> in the example is necessary unless it is platform dependent?
>
>
>
> ITKFilterLib.cxx from ItkApps example:
>
>
>
>
>
> 23 #include "ITKFilterLib.h"
>
> 24
>
> 25 // Nasty local globals inside .cxx file to hide itk from the real world.
>
> 26 // Can't put this variable in the class definition otherwise we'd have
> to
>
> 27 // include itkImage.h in every program using this class.
>
> 28 // The typedef h_itkFilterLibeDataType is in itkFilterLib.h to hide
>
> 29 // templates
>
> 30 typedef itk::Image<g_ItkFilterLibDataType,3> g_ImageType;
>
> 31 g_ImageType::Pointer g_InputImage;
>
> 32 g_ImageType::Pointer g_OutputImage;
>
>
>
> I did not find this to be necessary in my project.
>
>
>
>
>
> 33
>
> 34
>
> 35 //
>
> 36 //
>
> 37 // The first filter in the .lib
>
> 38 //
>
> 39 //
>
> 40
>
> 41 /** The next lines are used to include the definition of the filter
>
> 42 * we want to install in the .lib, define a typedef for it, and create
>
> 43 * a "smart" pointer to hold it.
>
> 44 * CHANGE HERE: The filter to be instantiated.
>
> 45 **/
>
> 46 #include "itkCurvatureAnisotropicDiffusionImageFilter.h"
>
> 47 typedef itk::CurvatureAnisotropicDiffusionImageFilter<g_ImageType,
>
> 48 g_ImageType> g_AnisoFilterType;
>
> 49 g_AnisoFilterType::Pointer g_anisoFilter;
>
> 50
>
>
>
> I also did not find it to be necessary to have this sort of typedef and
> instantiation of the object at global scope in my project.
>
>
>
>
>
>
>
>
>
>
>
>
>
> From: Dženan Zukić [mailto:dzenanz at gmail.com]
> Sent: 23 March 2016 14:39
> To: Atwood, Robert (DLSLtd,RAL,SCI)
> Cc: Insight-users
> Subject: Re: [ITK-users] stand-alone lib -- ITKApps/ITKFilterLib
>
>
>
> Hi Robert,
>
>
>
> BUILD_SHARED_LIBS OFF is the crucial setting. You can keep the rest of
> options on defaults.
>
>
>
> Your CMake code looks OK. You should execute the following from your folder:
>
> cmake .
>
> make
>
>
>
> During CMake step you should configure options (point to the itk-build
> folder which was configured with BUILD_SHARED_LIBS OFF). Afterwards, do not
> invoke g++ directly - invoke make, which supplies correct include
> directories and link libraries so you don't run into a thousand errors.
>
>
>
> Regards,
>
> Dženan
>
>
>
> On Tue, Mar 22, 2016 at 6:25 AM, <Robert.Atwood at diamond.ac.uk> wrote:
>
> Hi,
> Thanks, Dženan, for the hint. But, does anyone have specific information on
> exactly which options to set in each of: the ITK cmake options; and the
> project cmake options, or the plain g++ for building an external program to
> link to the library, for this to work ? There appear to be a few that might
> be related to this. Because, so far, simply changing the build options of
> the ITK installation didn’t work. See below for even more details .
>
> Thanks
>
> Robert
>
>
>
>
>
>
>
> Options selected in the project:
>
> ITK_DIR
> /dls_sw/apps/itk/itk-master-static/lib/cmake/ITK-4.10
>
>
>
>
>
>
>
> In the ITK with installation to itk-master-static:
>
> I have tried some combinations of these options but, you know, it takes a
> while to rebuild ITK even though the computer is pretty good.
>
>
>
> BUILD_POSITION_DEPENDENT_CODE OFF (I don’t think this should be ON
> because that really wouldn’t work? )
>
> BUILD_SHARED_LIBS OFF (or ON)
>
> CMAKE_CXX_FLAGS -fPIC (or default)
>
> CMAKE_EXE_LINKER_FLAGS -fPIC (or default)
>
> CMAKE_STATIC_LINKER_FLAGS (should this be set too? )
>
>
>
>
>
>
>
> The CMakeLists in the project file – only small modification from the
> original to ‘BUILD_OUTSIDE_INSIGHT_APPICATIONS’. The project builds using
> the Cmake makefile, producing the library and the executable
>
> But trying to build either the ‘main’ procedure provided with linking to
> that library, or even simplifying the ‘main’ to do virtually nothing except
> instantiate the object, results in 1000 error messages of ‘undefined
> symbols’
>
>
>
> 1 PROJECT(Example_ITKFilterLib)
>
> 2
>
> 3 #REMOVED 'IF (BUILD_OUTSIDE_INSIGHT_APPLICATIONS)'
>
> 4
>
> 5 FIND_PACKAGE(ITK)
>
> 6 IF(ITK_FOUND)
>
> 7 INCLUDE(${ITK_USE_FILE})
>
> 8 ELSE(ITK_FOUND)
>
> 9 MESSAGE(FATAL_ERROR
>
> 10 "Cannot build ITKApps without ITK. Please set ITK_DIR.")
>
> 11 ENDIF(ITK_FOUND)
>
> 12
>
> 13 #REMOVED 'ENDIF(BUILD_OUTSIDE_INSIGHT_APPLICATIONS)'
>
> 14
>
> 15 ADD_LIBRARY(Example_ITKFilterLib ITKFilterLib.cxx )
>
> 16 INSTALL_TARGETS(/lib Example_ITKFilterLib)
>
> 17 TARGET_LINK_LIBRARIES(Example_ITKFilterLib ${ITK_LIBRARIES})
>
> 18
>
> 19 ADD_EXECUTABLE(Example_ITKFilterLibTest ITKFilterLibTest.cxx )
>
> 20 INSTALL_TARGETS(/bin Example_ITKFilterLibTest)
>
> 21 TARGET_LINK_LIBRARIES(Example_ITKFilterLibTest Example_ITKFilterLib)
>
>
>
>
>
> build]$ ls -l
>
> total 2508
>
> -rw-rw-r-- 1 kny48981 kny48981 14393 Mar 22 10:02 CMakeCache.txt
>
> drwxrwxr-x 6 kny48981 kny48981 4096 Mar 22 10:05 CMakeFiles
>
> -rwxrwxr-x 1 kny48981 kny48981 1417263 Mar 22 10:05 Example_ITKFilterLibTest
>
> drwxrwxr-x 2 kny48981 kny48981 4096 Mar 22 10:02 ITKIOFactoryRegistration
>
> -rw-rw-r-- 1 kny48981 kny48981 7933 Mar 22 10:02 Makefile
>
> -rw-rw-r-- 1 kny48981 kny48981 1092874 Mar 22 10:05
> libExample_ITKFilterLib.a
>
>
>
>
>
>
>
> build]$ g++ -o testcomp ../ITKFilterLib/ITKFilterLibTest.cxx -I
> ../ITKFilterLib -L . -l Example_ITKFilterLib >& out &
>
>
>
> … generates 1100 messages …
>
>
>
>
>
> 1 ./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
> `itk::MemoryAllocationError::MemoryAllocationError(std::basic_string<char,
> std::char_traits<char>, std::allocat
>
> 2
> ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x39):
> undefined reference to `itk::ExceptionObject:
>
> …
>
> 1106
> ITKFilterLib.cxx:(.text._ZNK3itk12NeighborhoodIPfLj3ENS_21NeighborhoodAllocatorIS1_EEE9PrintSelfERSoNS_6IndentE[itk::Neighborhood<float*,
> 3u, itk::NeighborhoodAllocato
>
> 1107 collect2: ld returned 1 exit status
>
>
>
>
>
> Minimal example main:
>
>
>
> 1 #include "ITKFilterLib.h"
>
> 2 int main(int, char **) {
>
> 3 int inputDimSize[3];
>
> 4 float inputOrigin[3];
>
> 5 float inputSpacing[3];
>
> 6 inputDimSize[0] = 5;
>
> 7 inputDimSize[1] = 5;
>
> 8 inputDimSize[2] = 5;
>
> 9 inputOrigin[0] = 0;
>
> 10 inputOrigin[1] = 0;
>
> 11 inputOrigin[2] = 0;
>
> 12 inputSpacing[0] = 1;
>
> 13 inputSpacing[1] = 1;
>
> 14 inputSpacing[2] = 1;
>
> 15
>
> 16 itkFilterLib filter(inputDimSize, inputOrigin, inputSpacing);
>
> 17 return (true);
>
> 18 }
>
>
>
> g++ -o testmin minimal_example.cxx -I ../ITKFilterLib -L . -l
> Example_ITKFilterLib >& out
>
>
>
>
>
> Same output AFAICT:
>
>
>
>
>
> 1 ./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
> `itk::MemoryAllocationError::MemoryAllocationError(std::basic_string<char,
> std::char_traits<char>, std::alloca
>
> 2
> ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x39):
> undefined reference to `itk::ExceptionObject:
>
> ….
>
>
>
> From: Dženan Zukić [mailto:dzenanz at gmail.com]
> Sent: 21 March 2016 20:21
> To: Atwood, Robert (DLSLtd,RAL,SCI)
> Cc: Insight-users
> Subject: Re: [ITK-users] stand-alone lib -- ITKApps/ITKFilterLib
>
>
>
> Hi Robert,
>
>
>
> maybe you need to link to ITK statically? To accomplish this you probably
> need to build ITK as static libraries (it is a configuration option in
> CMake).
>
>
>
> Regards,
>
> Dženan
>
>
>
> On Mon, Mar 21, 2016 at 12:50 PM, <Robert.Atwood at diamond.ac.uk> wrote:
>
> Hi,
> This example, ITKApps/ITKFilterLib, appears to be an example of what I want
> to do , bundle or encapsulate a specific ITK-based filter into a library so
> that another program may just call it without having to have the ITK source
> installation available.
> However, a basic test for me is not working.
>
> I just tried to compile the test example from command line after building
> the library with Cmake as usual. I get hundreds of 'undefined reference', as
> if I have to link with all the ITK libs anyways.
> Am I missing something?
> Thanks
>
>
>
>
> g++ -o testcomp ../ITKFilterLib/ITKFilterLibTest.cxx -I ../ITKFilterLib/ -L
> . -l Example_ITKFilterLib
>
>
> First few lines of output:
>
> ./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
> `itk::MemoryAllocationError::MemoryAllocationError(std::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&, unsigned int,
> std::basic_string<char, std::char_traits<char>, std::allocator<char> >
> const&, std::basic_string<char, std::char_traits<char>, std::allocator<char>
>> const&)':
> ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x39):
> undefined reference to
> `itk::ExceptionObject::ExceptionObject(std::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&, unsigned int,
> std::basic_string<char, std::char_traits<char>, std::allocator<char> >
> const&, std::basic_string<char, std::char_trait
> ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x44):
> undefined reference to `vtable for itk::MemoryAllocationError'
> ./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
> `itk::ProcessAborted::ProcessAborted(char const*, unsigned int)':
> ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAbortedC5EPKcj]+0x33):
> undefined reference to `itk::ExceptionObject::ExceptionObject(char const*,
> unsigned int, char const*, char const*)'
> ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAbortedC5EPKcj]+0x3e):
> undefined reference to `vtable for itk::ProcessAborted'
> ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAbortedC5EPKcj]+0x4f):
> undefined reference to `itk::ExceptionObject::SetDescription(char const*)'
> ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAbortedC5EPKcj]+0x62):
> undefined reference to `itk::ExceptionObject::~ExceptionObject()'
>
>
>
> This is on a Linux Red Hat with ITK git master today (March 21 2016)
>
> cmake --version
> cmake version 2.8.12.2
>
> /proc/version:
>
> Linux version 2.6.32-573.18.1.el6.x86_64
> (mockbuild at x86-010.build.bos.redhat.com) (gcc version 4.4.7 20120313 (Red
> Hat 4.4.7-16) (GCC) ) #1 SMP Wed Jan 6 11:20:49 EST 2016
>
>
>
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> This e-mail and any attachments may contain confidential, copyright and or
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> use, copy, retain, distribute or disclose the information in or attached to
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> Any opinions expressed within this e-mail are those of the individual and
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> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
>
>
>
>
> --
>
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
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>
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_____________________________________
Powered by www.kitware.com
Visit other Kitware open-source projects at
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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php
Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ
Follow this link to subscribe/unsubscribe:
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