Re: making JPEG-XR work with CZIs

[ctrueden]

Hi Roman,

> Is there a reason JPEG-XR is not yet supported by the ZeissCZIReader

Sorry, I do not know.

This question would be better posed to the Bio-Formats developers; see:

http://www.openmicroscopy.org/site/community
http://www.openmicroscopy.org/site/community/mailing-lists
http://www.openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
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On Mon, Feb 29, 2016 at 9:45 AM, Grothausmann, Roman Dr. <
[hidden email]> wrote:

> Dear mailing list members,
>
>
> Curtis pointed out in this post
>
> https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;33157c9b.1409
>
> that there is an ongoing effort to support JPEG-XR.
> Investigating the parent tags this contribution should already be in
> bftools (and fiji). However, when I try to open a CZI-file with such
> content I still get:
>
> Checking file format [Zeiss CZI]
> Initializing reader
> ZeissCZIReader initializing test.czi
> Exception in thread "main" loci.formats.UnsupportedCompressionException:
> JPEG-XR not yet supported
>
> So I had a look at
>
>
> https://github.com/openmicroscopy/bioformats/blob/master/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L2948
>
> where an UnsupportedCompressionException is still issued.
>
> Is there a reason JPEG-XR is not yet supported by the ZeissCZIReader or
> was it merely forgotten after JPEG-XR got merged into bioformats?
>
>
> I gave it a quick try to replace the UnsupportedCompressionException with:
>
>
> https://github.com/romangrothausmann/bioformats/commit/625ab357a2d20dbd81c00dd2c151d00910921096
>
> but I can't get
>
> import ome.jxr.*;
>
> to work with ant and I'm lost in finding the right build.xml to extend the
> classpath for ZeissCZIReader.java.
>
>
> Running javac by hand and using ant just to pack the *.class I get
> bfconvert to get this far:
>
> Checking file format [Zeiss CZI]
> Initializing reader
> ZeissCZIReader initializing test.czi
> Exception in thread "main" loci.formats.UnsupportedCompressionException:
> ome.jxr.JXRException: Wrong file format version. Found: 82
>         at loci.formats.in
> .ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2954)
>         at loci.formats.in
> .ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2921)
>         at loci.formats.in
> .ZeissCZIReader.initFile(ZeissCZIReader.java:567)
>         at loci.formats.FormatReader.setId(FormatReader.java:1433)
>         at loci.formats.ImageReader.setId(ImageReader.java:835)
>         at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
>         at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1034)
>         at loci.formats.tools.ImageInfo.main(ImageInfo.java:1123)
> Caused by: ome.jxr.JXRException: Wrong file format version. Found: 82
>         at
> ome.jxr.parser.FileParser.checkFileStructureVersion(FileParser.java:107)
>         at ome.jxr.parser.FileParser.parse(FileParser.java:79)
>         at ome.jxr.parser.Parser.parse(Parser.java:62)
>         at ome.jxr.JXRReader.<init>(JXRReader.java:65)
>         at loci.formats.in
> .ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2950)
>         ... 7 more
>
>
> Any help or hints how to use bfconvert to process CZIs with JPEG-XR are
> very appreciated.
>
> Roman
>
>
> --
> Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
>
> Institut für Funktionelle und Angewandte Anatomie, OE 4120
> Medizinische Hochschule Hannover
> Carl-Neuberg-Str. 1
> D-30625 Hannover
>
> Tel. [phone]
>

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