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Task #12926 (closed)

Opened 9 years ago

Closed 9 years ago

Last modified 9 years ago

BUG: Converting of liff to ome.tiff

Reported by:	pwalczysko	Owned by:	mlinkert
Priority:	major	Milestone:	5.1.3
Component:	Bio-Formats	Version:	5.1.2
Keywords:	n.a.	Cc:	ux@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	0.0d
Sprint:	n.a.

Description

During 5.1.1 release detected by Mark, tesing https://trello.com/c/Vmp0twk8/14-cl-tools

"
I had a go at converting Beta Catenin.lif to an ome.tiff file but got,

[Leica Image File Format] -> /tmp/foo.ome.tiff [OME-TIFF]
Switching to BigTIFF (by file size)
    Series 0: converted 1/1 planes (100%)
Exception in thread "main" loci.formats.FormatException: Plane index:1 must be < 1
    at loci.formats.FormatWriter.checkParams(FormatWriter.java:357)
    at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:211)
    at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:196)
    at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:181)
    at loci.formats.FormatWriter.saveBytes(FormatWriter.java:124)
    at loci.formats.ImageWriter.saveBytes(ImageWriter.java:199)
    at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:609)
    at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:541)
    at loci.formats.tools.ImageConverter.main(ImageConve

References

Change History (2)

comment:1 Changed 9 years ago by mlinkert

Resolution set to fixed
Status changed from new to closed

Fixed with: https://github.com/openmicroscopy/bioformats/pull/1839

This was serious enough that it probably should have blocked 5.1.1 - for things like this in the future, please do raise sooner rather than later.

comment:2 Changed 9 years ago by Melissa Linkert <melissa@…>

Remaining Time set to 0

(In [37b57c264ba83fbbef327f86bc6e825be4a40da2/bioformats.git] on branch develop) bfconvert: fix plane indexes for multi-series exports

Fixes #12926. This prevents the plane index from being too large for
series beyond the first.

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