[ITK] SCIFIO throws exception
Michael Meuli
michael.meuli at gmail.com
Fri Apr 11 01:20:44 EDT 2014
Hi Mark
I've rebuilt and get the same error when trying to read the
single-channel.ome.tif dataset with my little program which is the
same whether JAVA_HOME is unset or set to e.g.
"/home/michael/Colocalization/ITK-4.5.1-build/lib/jre":
Problem encoutered while reading image file : single-channel.ome.tif
itk::ExceptionObject (0x8c280e0)
Location: "unknown"
File: /home/michael/Colocalization/ITK-4.5.1-build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
Line: 180
Description: itk::ERROR: SCIFIOImageIO(0x8c26fb0): 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)
Trying to read/write the single-channel.ome.tif dataset with the
itkSCIFIOImageIOTest utility I get the following error:
reader->GetUseStreaming(): 1
done checking streaming usage
ITK test driver caught an ITK exception:
itk::ExceptionObject (0x9faaf70)
Location: "unknown"
File: /home/michael/Colocalization/ITK-4.5.1-build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
Line: 780
Description: itk::ERROR: SCIFIOImageIO(0x9fa1ef8): Unknown pixel type: 0
Trying to read/write a .jpg file to a .tif file with the
itkSCIFIOImageIOTest utility I don't really get an error but a black
picture:
reader->GetUseStreaming(): 1
done checking streaming usage
Notes:
Could I set some parameter using the itkSCIFIOImageIOTest utility?
Where would I find some information about this?
When I try to explicit instantiate an IO class like e.g.:
ImageIOType::Pointer scifioIO = ImageIOType::New();
writer->SetImageIO( scifioIO );
I get the following compile time error:
'SCIFIOImageIO' in namespace 'itk' does not name a type
typedef itk::SCIFIOImageIO ImageIOType
Will this be different in ITK 4.6.0? (as I can see it there in Doxygen
but not in ITK 4.5.1)
Thanks a lot
Michael
On 10 April 2014 19:43, Mark Hiner <hinerm at gmail.com> wrote:
> Hi Michael,
>
> I just updated 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 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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