Task #12268 (closed)
Opened 10 years ago
Closed 9 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?
Change History (2)
comment:1 Changed 10 years ago by rleigh
- Cc l.maier@… added
comment:2 Changed 9 years ago by mlinkert
- Milestone changed from Unscheduled to 5.1.0
- Resolution set to fixed
- Status changed from new to closed
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PR open: https://github.com/openmicroscopy/bioformats/pull/1555