[ITK] SCIFIO throws exception

[Michael Meuli]

Hi Matt,

If JAVA_HOME is unset:

Problem encoutered while reading image file : single-channel.ome.tif

itk::ExceptionObject (0x81520e0)
Location: "unknown"
File: /home/michael/Colocalization/ITK-4.5.1-build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
Line: 180
Description: itk::ERROR: SCIFIOImageIO(0x8150fb0): SCIFIOImageIO
exited abnormally. Exception in thread "main"
java.lang.IllegalStateException: ImageReader.getSeries: Current file
should not be null; call setId(String) first
at loci.formats.FormatTools.assertId(FormatTools.java:724)
at loci.formats.ImageReader.getReader(ImageReader.java:200)
at loci.formats.ImageReader.getSeries(ImageReader.java:441)
at loci.formats.ReaderWrapper.getSeries(ReaderWrapper.java:343)
at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:116)
at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:108)
at loci.scifio.itk.SCIFIOITKBridge.waitForInput(SCIFIOITKBridge.java:83)
at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:161)
at loci.scifio.itk.SCIFIOITKBridge.main(SCIFIOITKBridge.java:693)

Thanks,
Michael

On 8 April 2014 20:19, Matt McCormick <matt.mccormick at kitware.com> wrote:
> Hi Michael,
>
> If JAVA_HOME is unset?
>
> Thanks,
> Matt
>
> On Tue, Apr 8, 2014 at 1:57 PM, Michael Meuli <michael.meuli at gmail.com> wrote:
>> Hi Matt,
>>
>> Thanks a lot.
>> I set JAVA_HOME to
>> "/home/michael/Colocalization/ITK-4.5.1-build/lib/jre/bin" and still
>> get the same error.
>>
>> Thanks again,
>> Michael
>>
>>
>>
>>
>> On 7 April 2014 22:10, Matt McCormick <matt.mccormick at kitware.com> wrote:
>>> Hi Michael,
>>>
>>> Does it work with the JRE distributed with the module?  I do not think
>>> Java 8 has been tested yet.
>>>
>>> Thanks,
>>> Matt
>>>
>>> On Mon, Apr 7, 2014 at 3:34 PM, Michael Meuli <michael.meuli at gmail.com> wrote:
>>>> Hi,
>>>>
>>>> I'm trying to read the test image "single-channel.ome.tif" from
>>>> http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/data.html
>>>> JAVA_HOME is set to "/usr/lib/jvm/java-8-oracle/jre/bin/java"
>>>> Running "SCIFIOTestDriver itkSCIFIOImageIOTest" gives me a very similar error.
>>>> I'm running Ubuntu 13.10 32bit with ITK-4.5.1
>>>>
>>>> Below is the text of the error message:
>>>>
>>>> Problem encoutered while reading image file :
>>>> /home/michael/Colocalization/Data/single-channel.ome.tif
>>>>
>>>> itk::ExceptionObject (0x8e283f0)
>>>> Location: "unknown"
>>>> File: /home/michael/Colocalization/ITK-4.5.1-build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
>>>> Line: 408
>>>> Description: itk::ERROR: SCIFIOImageIO(0x8e27000): SCIFIOImageIO:
>>>> ITKReadImageInformation error:
>>>> Not a directory
>>>>
>>>>
>>>> Many thanks
>>>> Michael
>>>>
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