[Insight-users] Problems with SCIFIO

[Bradley Lowekamp]

Hello,

What is the output of "ldd /usr/local/libitkSCIFIO-4.5.so.1"?

Do all the ITK tests pass? If you run WrapITK out of the build directory does it work?

Brad

On Feb 18, 2014, at 6:16 AM, Sami Koho <sami.koho at gmail.com> wrote:

> Hello again,
> 
> I finally had some time to dedicate to this SCIFIO problem. Just to make sure that I did not do anything stupid, I made a clean build of the whole ITK (with the new 4.5.1 version), with SCIFIO module enabled. Then I removed my old installation from /usr/local/lib - by manually deleting the .so files, the ITK4.5 directory and the cmake directory containing some ITK files - after which I installed my new build of the ITK4.5.1. I still have the same problem:
> 
> Traceback (most recent call last):
>   File "itk_image_load_test.py", line 13, in <module>
>     image = itkutils.itk_read_image(image_path, image_type='IUC2')
>   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
> 
> Yet, as I reported last time around, the libitkSCIFIO-4.5.so.1 is there in /usr/local/lib with all the other ITK shared object files. Is there something I may still be doing wrong, or is this a bug? 
> 
> I will just have to use ITK without SCIFIO for now...
> 
> Best,
> 
> Sami
> 
> 
> 
> On Fri, Feb 14, 2014 at 8:41 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> 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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