[ome-users] making JPEG-XR work with CZIs

[Grothausmann, Roman Dr.]

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 wasit 
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. +49 511 532-2900