[ITK] SCIFIO throws exception
Mark Hiner
hinerm at gmail.com
Fri Apr 11 08:30:10 EDT 2014
Hi Michael,
This is actually potentially some good news.
Description: itk::ERROR: SCIFIOImageIO(0x9fa1ef8): Unknown pixel type: 0
>
This was the bug I found
yesterday<http://review.source.kitware.com/#/c/15092/>.
It is fixed on the latest master.
Could I set some parameter using the itkSCIFIOImageIOTest utility?
> Where would I find some information about this?
>
Run itkSCIFIOImageIOTest with no params and it will print out all the
possible options. You might want to try -w to get it to use the Bio-Formats
writers for conversion. You also will want to set the # dimensions, pixel
type, etc.. to match your dataset I believe, which could be why it failed
on your .jpg.
When I try to explicit instantiate an IO class like e.g.:
> ImageIOType::Pointer scifioIO = ImageIOType::New();
> writer->SetImageIO( scifioIO );
>
You might want to take a look at the itkSCIFIOImageIOTest
source<https://github.com/scifio/scifio-imageio/blob/master/test/itkSCIFIOImageIOTest.cxx#L45>.
It sounds like you're trying to do the same thing, right?
I've rebuilt and get the same error when trying to read the
> single-channel.ome.tif dataset with my little program which
>
OK! Back to the original problem. So I apologize, but I misunderstood your
question.. I didn't realize this was coming up in a program you wrote (I
thought it was in the itkSCIFIOImageIOTest). So can you share the code from
your program that uses the SCIFIOImageIO? It looks like, however it's being
used, the Java-side Bio-Formats reader isn't being initialized properly.
This should be easy to fix, I just need to be able to reproduce the issue,
to see if it's a bug in your code, or either the C++ or Java portions of
the SCIFIOImageIO.
Thanks!
Mark
On Fri, Apr 11, 2014 at 12:20 AM, Michael Meuli <michael.meuli at gmail.com>wrote:
> 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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