[ITK-users] stand-alone lib -- ITKApps/ITKFilterLib

Tue Mar 22 06:25:33 EDT 2016

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<mailto: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<mailto: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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