[ITK] SCIFIO throws exception

Thu Apr 10 13:43:07 EDT 2014

Hi Michael,

 I just updated<https://github.com/scifio/scifio-itk-bridge/commit/8ffccf457e0f41245167402d318d7e0c57eb127f>the
Java-side handling of null readers/ids. I couldn't reproduce your
exact
issue, but it did look like there was the potential for an unintended state
that would cause the null id error you said.

 Could you clear your /build directory and rebuild? (this will trigger a
download of the latest Java code) Then try again with the unset JAVA_HOME.

/home/michael/Colocalization/ITK-4.5.1-build/lib/jre/bin
>

As a side note, I believe you need to set JAVA_HOME to the base of your
java directory (e.g. just
"/home/michael/Colocalization/ITK-4.5.1-build/lib/jre"). At least on OSX
10.8.5, if I set include the /bin sub-directory, it doesn't actually
discover Java (slightly counter-intuitive if you're used to adding stuff to
your PATH). So you could try again with the distributed JRE as well.

 For what it's worth, I am able to read/write the single-channel.ome.tif
dataset with the itkSCIFIOImageIOTest utility, on OSX with java 1.6.0_45.

Let us know how it goes!

Thanks,
Mark

On Thu, Apr 10, 2014 at 11:48 AM, Mark Hiner <hinerm at gmail.com> wrote:

> 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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