[ITK] Fwd: SCIFIO throws exception

[Mark Hiner]

Hi Michael,


I guess I just have to install the appropriate plug-in, as my format
> is not listed here:
> https://github.com/scifio/scifio
>

I just wanted to let you know that the SCIFIOImageIO always checks formats
using Bio-Formats. So there are no extra plugins you need to install; you
were using it correctly (assuming your Java version is compatible).

Anyway, this looks like there could be legitimate bugs coming from Java
land. I filed an issue
<https://github.com/scifio/scifio-imageio/issues/14>for it, although I
haven't been able to reproduce it yet as I am having a
completely different issue regarding pixel types right now.

Once I can better reproduce/resolve these issues I'll let you know.

Thanks,
Mark



On Thu, Apr 10, 2014 at 2:42 AM, Michael Meuli <michael.meuli at gmail.com>wrote:

> 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
> >>>>> Community at itk.org
> >>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/community
> >>>>>
>
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