[ITK] ERROR: SCIFIOImageIO

[Hans.Koch at ptb.de]

Hi Mark, thank you as well for the‎ additional tips.
 I think the problem is caused by the wrapping to Python and the building done by python(xy). 
 When I find the cause I'll call back. 
 Best regards 
 Hans
 
 
 
 Gesendet von meinem BlackBerry 10-Smartphone.
   
 
   Von: Mark Hiner
    Gesendet: Montag, 19. Oktober 2015 20:44
    An: Matt McCormick
    Cc: Hans.Koch at ptb.de; community at itk.org
    Betreff: Re: [ITK] ERROR: SCIFIOImageIO
 
          Hi Hans & Matt,
    
    
   For reference, the SCIFIO_PATH use is documented in the source[1].
   
   
  I have no idea how the Python build lifecycle works, but given your error message I'm assuming manually setting a SCIFIO_PATH environment variable[2] to the folder containing the "scifio-itk-bridge.jar" and "bio-formats_package.jar" would fix your problem.
  
     
       When ITK is built with the SCIFIO module enabled it will automatically download these jars. If your build method failed to acquire them, the CMakeLists.txt references the appropriate URLs[3].
   
       
       Best,
   
       Mark
   
       [1] https://github.com/scifio/scifio-imageio/blob/0563ee24dcb972711bc0fc5cceb1c549825c2f3e/include/itkSCIFIOImageIO.h#L65-L68
   [2] http://stackoverflow.com/questions/5971312/how-to-set-environment-variables-in-python
   [3] https://github.com/scifio/scifio-imageio/blob/0563ee24dcb972711bc0fc5cceb1c549825c2f3e/src/CMakeLists.txt#L22-L23
   
      
     On Mon, Oct 19, 2015 at 12:28 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
   Hi Hans,
    
    Is there a "jars" directory? Does it contain "scifio-itk-bridge.jar"
    and "bioformats_package.jar".  This error indicates that this
    directory cannot be found.
    
    Thanks,
    Matt
    
             On Sun, Oct 18, 2015 at 11:06 AM,  <Hans.Koch at ptb.de> wrote:
      > Hi,
      >
      > When running some itk programs, which worked a year ago, e.g. the first few
      > lines of the itk test:  MeanImageFilter.py:
      >
      > import itk
      > dim = 2
      > IType = itk.Image[itk.F, dim]
      > imageFileName='BrainProtonDensitySliceBorder20.png'
      > reader = itk.ImageFileReader[IType].New()
      > reader.SetFileName(imageFileName)
      > reader.Update()
      >
      > I now receive the following output and error message when running it with
      > Spyder (Python 2.7) :
      >
      > Python 2.7.10 (default, May 23 2015, 09:40:32) [MSC v.1500 32 bit (Intel)]
      > on win32
      > Type "help", "copyright", "credits" or "license" for more information.
      >>>>
      >>>> runfile('C:/Users/koch05/Documents/WS_14_15/Book/py_mybook/codes/ch11/my_Filter.py',
      >>>> wdir='C:/Users/koch05/Documents/WS_14_15/Book/py_mybook/codes/ch11')
      > Traceback (most recent call last):
      >   File "<stdin>", line 1, in <module>
      >   File
      > "C:\Python27\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",
      > line 688, in runfile
      >     execfile(filename, namespace)
      >   File
      > "C:\Python27\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",
      > line 72, in execfile
      >     exec(compile(scripttext, filename, 'exec'), glob, loc)
      >   File
      > "C:/Users/koch05/Documents/WS_14_15/Book/py_mybook/codes/ch11/my_Filter.py",
      > line 30, in <module>
      >     reader.Update()
      > RuntimeError:
      > C:\u\itk-git\_b\Modules\Remote\SCIFIO\src\itkSCIFIOImageIO.cxx:274:
      > itk::ERROR: SCIFIOImageIO(103ADF70): SCIFIO_PATH is not set. This
      > environment variable must point to the directory containing the SCIFIO JAR
      > files
      >>>>
      >
      > Additional remark: in the Python27 site-package, inside the itk folder are
      > the files SCIFIO.py and SCIFIOPython.py and in the Configuration folder:
      > SCIFIOConfig.py
      >
      > How can I fix this problem? Any help is highly appreciated.
      >
      > Hans
      >
      >
      
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