<div dir="ltr"><div><div>Hi Hans & Matt,<br><br></div>For reference, the SCIFIO_PATH use is documented in the source[1].<br><br></div>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.<br><div><br></div><div>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].<br></div><div><br></div><div>Best,<br></div><div>Mark<br></div><div><br>[1] <a href="https://github.com/scifio/scifio-imageio/blob/0563ee24dcb972711bc0fc5cceb1c549825c2f3e/include/itkSCIFIOImageIO.h#L65-L68">https://github.com/scifio/scifio-imageio/blob/0563ee24dcb972711bc0fc5cceb1c549825c2f3e/include/itkSCIFIOImageIO.h#L65-L68</a><br>[2] <a href="http://stackoverflow.com/questions/5971312/how-to-set-environment-variables-in-python">http://stackoverflow.com/questions/5971312/how-to-set-environment-variables-in-python</a><br>[3] <a href="https://github.com/scifio/scifio-imageio/blob/0563ee24dcb972711bc0fc5cceb1c549825c2f3e/src/CMakeLists.txt#L22-L23">https://github.com/scifio/scifio-imageio/blob/0563ee24dcb972711bc0fc5cceb1c549825c2f3e/src/CMakeLists.txt#L22-L23</a><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Oct 19, 2015 at 12:28 PM, Matt McCormick <span dir="ltr"><<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Hans,<br>
<br>
Is there a "jars" directory? Does it contain "scifio-itk-bridge.jar"<br>
and "bioformats_package.jar". This error indicates that this<br>
directory cannot be found.<br>
<br>
Thanks,<br>
Matt<br>
<div><div class="h5"><br>
On Sun, Oct 18, 2015 at 11:06 AM, <<a href="mailto:Hans.Koch@ptb.de">Hans.Koch@ptb.de</a>> wrote:<br>
> Hi,<br>
><br>
> When running some itk programs, which worked a year ago, e.g. the first few<br>
> lines of the itk test: MeanImageFilter.py:<br>
><br>
> import itk<br>
> dim = 2<br>
> IType = itk.Image[itk.F, dim]<br>
> imageFileName='BrainProtonDensitySliceBorder20.png'<br>
> reader = itk.ImageFileReader[IType].New()<br>
> reader.SetFileName(imageFileName)<br>
> reader.Update()<br>
><br>
> I now receive the following output and error message when running it with<br>
> Spyder (Python 2.7) :<br>
><br>
> Python 2.7.10 (default, May 23 2015, 09:40:32) [MSC v.1500 32 bit (Intel)]<br>
> on win32<br>
> Type "help", "copyright", "credits" or "license" for more information.<br>
>>>><br>
>>>> runfile('C:/Users/koch05/Documents/WS_14_15/Book/py_mybook/codes/ch11/my_Filter.py',<br>
>>>> wdir='C:/Users/koch05/Documents/WS_14_15/Book/py_mybook/codes/ch11')<br>
> Traceback (most recent call last):<br>
> File "<stdin>", line 1, in <module><br>
> File<br>
> "C:\Python27\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",<br>
> line 688, in runfile<br>
> execfile(filename, namespace)<br>
> File<br>
> "C:\Python27\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",<br>
> line 72, in execfile<br>
> exec(compile(scripttext, filename, 'exec'), glob, loc)<br>
> File<br>
> "C:/Users/koch05/Documents/WS_14_15/Book/py_mybook/codes/ch11/my_Filter.py",<br>
> line 30, in <module><br>
> reader.Update()<br>
> RuntimeError:<br>
> C:\u\itk-git\_b\Modules\Remote\SCIFIO\src\itkSCIFIOImageIO.cxx:274:<br>
> itk::ERROR: SCIFIOImageIO(103ADF70): SCIFIO_PATH is not set. This<br>
> environment variable must point to the directory containing the SCIFIO JAR<br>
> files<br>
>>>><br>
><br>
> Additional remark: in the Python27 site-package, inside the itk folder are<br>
> the files SCIFIO.py and SCIFIOPython.py and in the Configuration folder:<br>
> SCIFIOConfig.py<br>
><br>
> How can I fix this problem? Any help is highly appreciated.<br>
><br>
> Hans<br>
><br>
><br>
</div></div>> _______________________________________________<br>
> Community mailing list<br>
> <a href="mailto:Community@itk.org">Community@itk.org</a><br>
> <a href="http://public.kitware.com/mailman/listinfo/community" rel="noreferrer" target="_blank">http://public.kitware.com/mailman/listinfo/community</a><br>
><br>
_______________________________________________<br>
Community mailing list<br>
<a href="mailto:Community@itk.org">Community@itk.org</a><br>
<a href="http://public.kitware.com/mailman/listinfo/community" rel="noreferrer" target="_blank">http://public.kitware.com/mailman/listinfo/community</a><br>
</blockquote></div><br></div>