[Insight-users] Problems with SCIFIO

[Bradley Lowekamp]

Hello Sami,

This sounds like an installation issue.

Did you reinstall ITK w/ WrapITK after rebuilding? Are you running out of the build directory? Where is the libitkSCIFIO-4.5.so.1 file?

Brad

On Feb 14, 2014, at 4:00 AM, Sami Koho <sami.koho at gmail.com> wrote:

> Hello,
> 
> I have been having some problems with reading my image data with ITK. My images are microscope images, originally from a Leica confocal, saved as 3D tiff volumes in ImageJ. When I open such a file with ITK (version 4.5), I get a complaint about unknown tags and lose all my metadata (such as voxel size information). SImilarly. when I save a tiff file with ITK, I seem to lose all the metadata – at least ImageJ does not understand it.
> 
> I ended up installing MetaImage plugin to ImageJ, allowing me to export to mhd format, which seems to work, for reading data into my ITK application at least. I still have problems showing the results in ImageJ, as the voxel sizes go wrong on save.
> 
> Last night I compiled ITK with SCIFIO module enabled, as I thought that this would make handling microscope images a bit more easy. Everything compiled nicely, but now I get a following error:
> 
> python rescaling_test.py psf_red.tif
> Traceback (most recent call last):
>   File "rescaling_test.py", line 18, in <module>
>     image = itkio.itk_read_image(image_path)
>   File "/usr/local/lib/python2.7/dist-packages/iocbio/io/itk_io_utilites.py", line 18, in itk_read_image
>     itk_image_reader = getattr(itk.ImageFileReader, image_type).New()
>   File "/usr/local/lib/ITK-4.5/Python/itkLazy.py", line 37, in __getattribute__
>     itkBase.LoadModule(module, namespace)
>   File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 95, in LoadModule
>     LoadModule(dep, namespace)
>   File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 103, in LoadModule
>     if not swigModuleName in sys.modules: module = loader.load(swigModuleName)
>   File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 214, in load
>     return imp.load_module(name, fp, pathname, description)
>   File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 30, in <module>
>     _ITKCommonPython = swig_import_helper()
>   File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 26, in swig_import_helper
>     _mod = imp.load_module('_ITKCommonPython', fp, pathname, description)
> ImportError: libitkSCIFIO-4.5.so.1: cannot open shared object file: No such file or directory
> 
> I am using ITK on 64bit Debian Wheezy (with Python wrapping). I checked, and there is a file called  libitkSCIFIO-4.5.so.1 in /usr/local/lib. Does someone have an idea, what is going wrong here?
> 
> Best,
> 
> Sami
> 
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