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Bug 284 - Deltavision import failure
Deltavision import failure
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P2 major
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2011-02-09 22:22 CST by Colin
Modified: 2011-02-16 16:37 CST
1 user (show)

See Also:
Description Colin 2011-02-09 22:22:32 CST 
IJ 1.44o

I have a series of large (4GB) .dv TIFF files. The first time I open one of these images, it imports fine. After that it give the following exception:

java.lang.IllegalArgumentException: ZCT size vs image count mismatch (sizeZ=9, sizeC=1, sizeT=217, total=2047)
	at loci.formats.FormatTools.getZCTCoords(FormatTools.java:395)
	at loci.formats.FormatTools.getZCTCoords(FormatTools.java:340)
	at loci.formats.FormatReader.getZCTCoords(FormatReader.java:928)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:162)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:96)
	at loci.formats.in.DeltavisionReader.initPixels(DeltavisionReader.java:328)
	at loci.formats.in.DeltavisionReader.initFile(DeltavisionReader.java:204)
	at loci.formats.FormatReader.setId(FormatReader.java:1058)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:475)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
	at loci.plugins.in.Importer.showDialogs(Importer.java:125)
	at loci.plugins.in.Importer.run(Importer.java:77)
	at loci.plugins.LociImporter.run(LociImporter.java:77)
	at ij.IJ.runUserPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:154)
	at ij.IJ.runPlugIn(IJ.java:143)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:343)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:52)
	at ij.IJ.runUserPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:154)
	at ij.IJ.runPlugIn(IJ.java:143)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:412)
	at ij.io.Opener.openImage(Opener.java:289)
	at ij.io.Opener.openImage(Opener.java:308)
	at ij.io.Opener.open(Opener.java:142)
	at ij.io.Opener.openAndAddToRecent(Opener.java:228)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:182)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:158)
	at java.lang.Thread.run(Thread.java:680)

Other .dv TIFF files open fine.
Comment 1 Curtis Rueden 2011-02-11 19:21:08 CST 
Thanks for the bug report. Please note that the plugin which handles reading Deltavision files is the Bio-Formats Importer (even if you choose File > Open).

So first of all, have you tried the latest Bio-Formats trunk build? You can choose Plugins > LOCI > Update LOCI Plugins from the menu and select "Trunk build" to upgrade (restart Fiji afterward). Verify that it's the new version using Help > About Plugins > LOCI Plugins and checking that the build date is very recent (probably that day). Then retry opening your Deltavision file.

If you still have problems, you can upload a sample dataset (4GB is large I know, but we have space) to our SFTP server; just let me know and I'll email the connection details to you.
Comment 2 Melissa Linkert 2011-02-15 21:20:51 CST 
This problem should be fixed in the very latest trunk build of Bio-Formats and commit f98a4493771996795a97f28ce67d64a79e7eb23e on the 4_2 branch of bio-formats.git.

Note that the file in question has been truncated - the final 123 images are missing.  In their place you should see completely black images.
Comment 3 Colin 2011-02-16 16:37:02 CST 
Wonderful! Works great. I aborted the experiment before the scheduled time, which must have caused the error. Thanks for adding in the flexibility!