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Task #12848 (closed)

Opened 9 years ago

Closed 9 years ago

Last modified 9 years ago

Bug: VSI multi-channel fluorescent images fail

Reported by:	omero-qa	Owned by:	mlinkert
Priority:	major	Milestone:	5.1.2
Component:	Bio-Formats	Version:	5.1.0
Keywords:	CellSensReader	Cc:	olivier.burri@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	0.0d
Sprint:	n.a.

Description

See https://www.openmicroscopy.org/qa2/qa2/qa/feedback/11039/ and https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=7501&start=20#p15678.

CellSensReader? fails on multi-channel fluorescent data with

sbesson@necromancer ~ $ ./bftools5.1.0/showinf Image_01.vsi 
Checking file format [CellSens VSI]
Initializing reader
CellSensReader initializing Image_01.vsi
Exception in thread "main" java.lang.IllegalArgumentException: Invalid C index: 1/1
	at loci.formats.FormatTools.getIndex(FormatTools.java:410)
	at loci.formats.FormatTools.getIndex(FormatTools.java:337)
	at loci.formats.FormatReader.getIndex(FormatReader.java:1083)
	at loci.formats.in.CellSensReader.initFile(CellSensReader.java:805)
	at loci.formats.FormatReader.setId(FormatReader.java:1395)
	at loci.formats.ImageReader.setId(ImageReader.java:835)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:988)
	at loci.formats.tools.ImageInfo.main(ImageInfo.java:1070)

References

Change History (4)

comment:1 Changed 9 years ago by sbesson

Component changed from from QA to Bio-Formats
Keywords CellSensReader added
Milestone changed from Unscheduled to 5.1.2
Priority changed from minor to major

comment:2 Changed 9 years ago by mlinkert

Resolution set to fixed
Status changed from new to closed

Fixed with: https://github.com/openmicroscopy/bioformats/pull/1797

comment:3 Changed 9 years ago by Melissa Linkert <melissa@…>

Remaining Time set to 0

(In [b2c472359c0e840bcc2154d951a0b34f0f532774/bioformats.git] on branch develop) CellSens?: fix SizeC for datasets with multiple pyramids

Fixes #12848.

comment:4 Changed 9 years ago by Melissa Linkert <melissa@…>

(In [2bdc569ba5c88a5d3973d32d8113c48c9daf8075/bioformats.git] on branch develop) CellSens?: calculate dimension order for each pyramid

Fixes #12848.

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