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Task #7869 (closed)

Opened 12 years ago

Closed 12 years ago

Bug: cannot import OME-TIFF that has adjusted dimensions

Reported by:	mlinkert	Owned by:	mlinkert
Priority:	major	Milestone:	OMERO-4.4
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:	Heinrich.Grabmayr@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	0.0d
Sprint:	2012-02-14 (8)

Description

This ImageJ macro shows the problem:

run("Bio-Formats Importer", "open=/home/melissa/test_images_good/ome-tiff/multi-channel-z-series.ome.tif autoscale color_mode=Default specify_range view=Hyperstack stack_order=XYCZT c_begin=1 c_end=3 c_step=1 z_begin=1 z_end=1 z_step=1");
run("Bio-Formats Exporter", "save=/home/melissa/all-channels.ome.tiff compression=Uncompressed");
close();
run("Bio-Formats Importer", "open=/home/melissa/all-channels.ome.tiff autoscale color_mode=Default specify_range view=Hyperstack stack_order=XYCZT c_begin=1 c_end=1 c_step=1");
run("Bio-Formats Exporter", "save=/home/melissa/single-channel.ome.tiff compression=Uncompressed");
close();
run("Bio-Formats Importer", "open=/home/melissa/single-channel.ome.tiff autoscale color_mode=Default specify_range view=Hyperstack stack_order=XYCZT");

The resulting exception is:

java.lang.IllegalArgumentException: Invalid C index: -1/1
	at loci.formats.FormatTools.getIndex(FormatTools.java:312)
	at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:525)
	at loci.formats.FormatReader.setId(FormatReader.java:1087)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:480)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:139)
	at loci.plugins.in.Importer.run(Importer.java:77)
	at loci.plugins.LociImporter.run(LociImporter.java:79)
	at ij.IJ.runUserPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:154)
	at ij.Executer.runCommand(Executer.java:150)
	at ij.Executer.run(Executer.java:78)
	at java.lang.Thread.run(Thread.java:662)

References

Change History (2)

comment:1 Changed 12 years ago by mlinkert

Sprint set to 2012-02-14 (8)

comment:2 Changed 12 years ago by mlinkert

Remaining Time set to 0
Resolution set to fixed
Status changed from new to closed

Should be sorted with this commit on my sprint8-bug-fixes branch:
https://github.com/melissalinkert/bioformats/commit/3542354dc8ee3bf6df4686d16817bc38cce03813

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