undefined symbol: PyVTKAddFile_vtkNIFTIWriter

[malaterre]

I cannot build + run vtk-dicom with the following settings:

$ export CFLAGS = -fvisibility=hidden -fvisibility-inlines-hidden
$ export CXXFLAGS = -fvisibility=hidden -fvisibility-inlines-hidden
$ cmake
$ make && make test
[...]
8/9 Test #9: TestDICOMJava ....................***Failed 1.21 sec
Ran the vtk-dicom Java test.
Exception in thread "main" java.lang.UnsatisfiedLinkError: vtk.vtkDICOMReader.VTKInit()J
at vtk.vtkDICOMReader.VTKInit(Native Method)
at vtk.vtkObject.(vtkObject.java:97)
at vtk.vtkAlgorithm.(vtkAlgorithm.java:378)
at vtk.vtkImageAlgorithm.(vtkImageAlgorithm.java:78)
at vtk.vtkImageReader2.(vtkImageReader2.java:258)
at vtk.vtkDICOMReader.(vtkDICOMReader.java:166)
at TestDICOMJava.main(TestDICOMJava.java:72)

9/9 Test #8: TestDICOMPython ..................***Failed 2.74 sec
Traceback (most recent call last):
File "/home/mathieu/debian/debian-med/trunk/packages/vtk-dicom/trunk/vtk-dicom-0.5.0/Testing/TestDICOMPython.py", line 5, in
import vtkDICOMPython
ImportError: /home/mathieu/debian/debian-med/trunk/packages/vtk-dicom/trunk/vtk-dicom-0.5.0/obj-x86_64-linux-gnu/lib/vtkDICOMPython.so: undefined symbol: PyVTKAddFile_vtkNIFTIWriter

[malaterre]

Same goes for python.

Troubles starts here:

#if defined(WIN32)
extern "C" { __declspec( dllexport ) void PyVTKAddFile_vtkDICOMParser(PyObject *, const char *); }
#else
extern "C" { void PyVTKAddFile_vtkDICOMParser(PyObject *, const char *); }
#endif

[malaterre]

I am using vtk 5.8, which may be the root of the actual issue.

[dgobbi]

I don't think these visibility issues were fixed until VTK 6.0, I'll investigate this tomorrow.

[dgobbi]

The Python visibility issues are due to vtkWrapPython.c, which didn't correctly set gcc visibility attributes until VTK 6.0. There isn't any way to fix them without upgrading VTK.

The Java visibility issues can be avoided by using java-7-openjdk, which adds visibility attributes to JNIEXPORT. There might be other ways, but at least on my Mac and Linux boxes, using java-7-openjdk was enough to fix the issue.

[dgobbi]

Closing. Visibility works with python and vtk 6, but not with earlier versions of vtk.