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Task #12268 (closed)

Opened 5 years ago

Closed 5 years ago

Bug: bfconvert fails to save z sections other than zero

Reported by:	rleigh	Owned by:	mlinkert
Priority:	minor	Milestone:	5.1.0
Component:	Bio-Formats	Version:	5.0.1
Keywords:	n.a.	Cc:	Sabine.Fischer@…, l.maier@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description

bfconvert -z 6 ~/code/bioformats-examples/cpp/glview/vessels.ome.tiff test.ome.tiff
/home/rleigh/code/bioformats-examples/cpp/glview/vessels.ome.tiff
OMETiffReader initializing /home/rleigh/code/bioformats-examples/cpp/glview/vessels.ome.tiff
Reading IFDs
Populating metadata
[OME-TIFF] -> test.ome.tiff [OME-TIFF]
Exception in thread "main" loci.formats.FormatException: Plane index:12 must be < 2
        at loci.formats.FormatWriter.checkParams(FormatWriter.java:325)
        at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:170)
        at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:197)
        at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:183)
        at loci.formats.FormatWriter.saveBytes(FormatWriter.java:126)
        at loci.formats.ImageWriter.saveBytes(ImageWriter.java:201)
        at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:547)
        at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:483)
        at loci.formats.tools.ImageConverter.main(ImageConverter.java:677)

The same applies to any section number other than zero. This is a 2C 144Z image, but appears to fail with any image with z>0. Tested with C=1, and still the same. Looks like the saved image isn't using indexes based from zero but might be using unconverted indexes from the source image?

References

Change History (2)

comment:1 Changed 5 years ago by rleigh

Cc l.maier@… added

comment:2 Changed 5 years ago by mlinkert

Milestone changed from Unscheduled to 5.1.0
Resolution set to fixed
Status changed from new to closed

PR open: https://github.com/openmicroscopy/bioformats/pull/1555

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