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