[ITK] ERROR: SCIFIOImageIO

[Mark Hiner]

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
> >
> >
> > _______________________________________________
> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
> >
> _______________________________________________
> Community mailing list
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>
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