Context Navigation

Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #10515 (closed)

Opened 6 years ago

Closed 6 years ago

Bug: LSM file with ROI fails to convert

Reported by:	rleigh	Owned by:	rleigh
Priority:	minor	Milestone:	Unscheduled
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description

/ome/data_repo/from_skyking/zeiss-lsm/roger/villipatch.lsm

% ./tools/bfconvert ~/images/rleigh/zeiss-lsm/confocal.mdb/villipatch.lsm ./test.ome.tiff
/Users/rleigh/images/rleigh/zeiss-lsm/confocal.mdb/villipatch.lsm
ZeissLSMReader initializing /Users/rleigh/images/rleigh/zeiss-lsm/confocal.mdb/villipatch.lsm
Reading LSM metadata for series #0
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 1, Size: 0
	at java.util.ArrayList.RangeCheck(ArrayList.java:547)
	at java.util.ArrayList.get(ArrayList.java:322)
	at ome.xml.model.OME.getROI(OME.java:671)
	at loci.formats.ome.OMEXMLMetadataImpl.setLabelText(OMEXMLMetadataImpl.java:8844)
	at loci.formats.meta.FilterMetadata.setLabelText(FilterMetadata.java:1431)
	at loci.formats.in.ZeissLSMReader.parseOverlays(ZeissLSMReader.java:1511)
	at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:915)
	at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:540)
	at loci.formats.FormatReader.setId(FormatReader.java:1333)
	at loci.formats.ImageReader.setId(ImageReader.java:757)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:337)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:667)

References

Change History (2)

comment:1 Changed 6 years ago by rleigh

Fixed with

https://github.com/openmicroscopy/bioformats/pull/460
https://github.com/openmicroscopy/bioformats/pull/461

comment:2 Changed 6 years ago by rleigh

Resolution set to fixed
Status changed from new to closed

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

Download in other formats: