The problem is even stranger than that.
In my CMakeLists.txt I am using (sort of) the 'stub + library' method
suggested by Matt McCormick. But I'm not doing exactly what he did; I try
and get all the libraries needed to link and pass them in to MEX. This
ALMOST works, but ITK_LIBRARIES doesn't list all the libraries needed,
hence I still get undefined externals -- stuff from vnl and gdcm.
Apparently there are library dependencies that are handled down in the
murk of CMake's build logic.
CMAKELISTS.TXT---
find_package(Matlab REQUIRED)
set(MEX_SOURCES nrrdLoadWithMetadata nrrdSaveWithMetadata
itkLoadWithMetadata itkSaveWithMetadata)
set(MEX_SHARED_OBJECTS "")
# get library locations for ITK libraries
set(_ITK_LIBS)
foreach(itklib ${ITK_LIBRARIES})
if(TARGET ${itklib})
get_property(itk_lib_path TARGET ${itklib} PROPERTY LOCATION)
list(APPEND _ITK_LIBS "${itk_lib_path}")
else()
list(APPEND _ITK_LIBS "${itklib}")
endif()
endforeach()
foreach(MEX_PREFIX ${MEX_SOURCES})
# stick actual code in static lib
add_library(${MEX_PREFIX} STATIC ${MEX_PREFIX}.cxx)
# link in all necessary libraries
target_link_libraries(${MEX_PREFIX} ${Teem_LIBRARIES}
${ITK_LIBRARIES}
${ZLIB_LIBRARY})
get_property(mex_lib_path TARGET ${MEX_PREFIX} PROPERTY LOCATION)
set(MEX_SRC_PATH ${CMAKE_CURRENT_SOURCE_DIR}/${MEX_PREFIX}Stub.cxx)
set(MEX_OBJECT_NAME ${MEX_PREFIX}.${MATLAB_MEX_EXT})
list(APPEND MEX_SHARED_OBJECTS ${MEX_OBJECT_NAME})
add_custom_command(OUTPUT ${MEX_PREFIX}.${MATLAB_MEX_EXT}
## HACK: The next line needs to be more general
COMMAND ${MATLAB_MEX_PATH} -cxx ${CMAKE_CXX_FLAGS_Release}
${MEX_SRC_PATH}
${mex_lib_path}
${_ITK_LIBS}
-L${Teem_LIBRARY_DIR} -lteem
${ZLIB_LIBRARY}
DEPENDS ${MEX_PREFIX} ${MEX_SRC_PATH}
IMPLICIT_DEPENDS C ${MEX_SRC_PATH}
WORKING_DIRECTORY ${${PRIMARY_PROJECT_NAME}_SOURCE_DIR}/MATLAB_SCRIPTS
COMMENT "BUILDING MEX_FILE: ${MEX_SRC_PATH}" )
endforeach()
add_custom_target(MEX_BLD ALL
DEPENDS ${MEX_SHARED_OBJECTS}
#[WORKING_DIRECTORY dir]
COMMENT "BUILDING TARGET MEX_FILE: ${MEX_SRC}"
SOURCES ${MATLAB_MEX_PATH} )
-Build
Output-
make-- Configuring done
-- Generating done
-- Build files have been written to:
/Volumes/scratch/kent/CompressedSensingDWI/build/CompressedSensingDWI-build
[ 0%] Built target CompressedSensingDWIFetchData
[ 11%] Built target itkSaveWithMetadata
[ 22%] Built target nrrdSaveWithMetadata
[ 33%] Built target nrrdLoadWithMetadata
[ 44%] Built target itkLoadWithMetadata
[ 55%] BUILDING MEX_FILE:
/Volumes/scratch/kent/CompressedSensingDWI/CompressedSensingDWI/mexFiles/it
kSaveWithMetadataStub.cxx
[ 66%] BUILDING MEX_FILE:
/Volumes/scratch/kent/CompressedSensingDWI/CompressedSensingDWI/mexFiles/nr
rdLoadWithMetadataStub.cxx
[ 77%] BUILDING MEX_FILE:
/Volumes/scratch/kent/CompressedSensingDWI/CompressedSensingDWI/mexFiles/nr
rdSaveWithMetadataStub.cxx
[ 88%] BUILDING MEX_FILE:
/Volumes/scratch/kent/CompressedSensingDWI/CompressedSensingDWI/mexFiles/it
kLoadWithMetadataStub.cxx
Undefined symbols for architecture x86_64:
"vnl_vector::set_size(unsigned int)", referenced from:
itk::Array::SetSize(unsigned int) in
libITKIOHDF5-4.5.a(itkHDF5ImageIO.cxx.o)
"vnl_vector::vnl_vector(vnl_vector const&)", referenced from:
itk::Array::Array(itk::Array const&) in
libITKIOHDF5-4.5.a(itkHDF5ImageIO.cxx.o)
"vnl_vector::vnl_vector(unsigned int)", referenced from:
itk::Array::Array(unsigned int) in
libITKIOHDF5-4.5.a(itkHDF5ImageIO.cxx.o)
"vnl_vector::~vnl_vector()", referenced from:
itk::Array::~Array() in
libITKIOHDF5-4.5.a(itkHDF5ImageIO.cxx.o)
"vnl_vector::operator=(vnl_vector const&)", referenced from:
itk::Array::operator=(itk::Array const&) in
libITKIOHDF5-4.5.a(itkHDF5ImageIO.cxx.o)
"vnl_vector::set_size(unsigned int)", referenced from:
itk::Array::SetSize(unsigned int) in
libITKIOHDF5-4.5.a(itkHDF5ImageIO.cxx.o)
"vnl_vector::vnl_vector(vnl_vector const&)", referenced
from:
itk::Array::Array(itk::Array const&) in
libITKIOHDF5-4.5.a(itkHDF5ImageIO.cxx.o)
"vnl_vector::vnl_vector(unsigned int)", referenced from:
itk::Array::Array(unsigned int) in
libITKIOHDF5-4.5.a(itkHDF5ImageIO.cxx.o)
"vnl_vector::~vnl_vector()", referenced from:
itk::Array::~Array() in
libITKIOHDF5-4.5.a(itkHDF5ImageIO.cxx.o)
"vnl_vector::operator=(vnl_vector const&)", referenced
from:
itk::Array::operator=(itk::Array const&) in
libITKIOHDF5-4.5.a(itkHDF5ImageIO.cxx.o)
"gdcm::DataElement::SetVLToUndefined()", referenced from:
gdcm::ImageHelper::SetSpacingValue(gdcm::DataSet&,
std::vector > const&) in
libitkgdcmMSFF-4.5.a(gdcmImageHelper.cxx.o)
gdcm::SetDataElementInSQAsItemNumber(gdcm::DataSet&,
gdcm::DataElement const&, gdcm::Tag const&, unsigned int) in
libitkgdcmMSFF-4.5.a(gdcmImageHelper.cxx.o)
gdcm::ImageHelper::SetDirectionCosin
