[ITK] SCIFIO throws exception

[Michael Meuli]

Hi Matt,

I'm sorry for my presumably stupid questions.
I guess I just have to install the appropriate plug-in, as my format
is not listed here:
https://github.com/scifio/scifio
(Didn't figure out yet how but I guess I eventually will)

Best regards and thanks again,
Michael

On 9 April 2014 22:14, Michael Meuli <michael.meuli at gmail.com> wrote:
> 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
>>>>>
>>>>> _______________________________________________
>>>>> Community mailing list
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>>>>>