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Task #10507 (closed)

Opened 11 years ago

Closed 11 years ago

Bug: ND2 reader StringIndexOutOfBoundsException

Reported by:	omero-qa	Owned by:	mlinkert
Priority:	minor	Milestone:	OMERO-4.4.7
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:	wjbian@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	Bugs Fixing

Description

http://qa.openmicroscopy.org.uk/qa/feedback/4958/

File /ome/apache_repo/4958/556_t2.nd2 (could this be added to from_skyking?)

 CLASSPATH=artifacts/loci_tools.jar LOCI_DEVEL=1 ./tools/showinf -nopix /ome/apache_repo/4958/556_t2.nd2
Checking file format [Nikon ND2]
Initializing reader
Searching for blocks
Parsing block 'ND2 FILE SIG' 0%
Parsing block 'ImageMetadat' 0%
Parsing block 'ImageCalibra' 0%
Parsing block 'ImageMetadat' 0%
Parsing block 'ImageCalibra' 0%
Parsing block 'ImageMetadat' 0%
Parsing block 'ImageAttribu' 0%
Parsing block 'ImageDataSeq' 0%
Parsing block 'ImageDataSeq' 14%
Parsing block 'ImageDataSeq' 28%
Parsing block 'ImageDataSeq' 42%
Parsing block 'ImageDataSeq' 57%
Parsing block 'ImageDataSeq' 71%
Parsing block 'ImageDataSeq' 85%
Parsing block 'ImageMetadat' 99%
Parsing block 'ImageEventsL' 99%
Parsing block 'ImageTextInf' 99%
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -409
	at java.lang.String.substring(String.java:1937)
	at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:493)
	at loci.formats.FormatReader.setId(FormatReader.java:1183)
	at loci.formats.DelegateReader.setId(DelegateReader.java:259)
	at loci.formats.ImageReader.setId(ImageReader.java:727)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:988)
	at loci.formats.tools.ImageInfo.main(ImageInfo.java:1031)

References

Change History (2)

comment:1 Changed 11 years ago by rleigh

Component changed from from QA to Bio-Formats
Owner changed from mlinkert-x to mlinkert

comment:2 Changed 11 years ago by mlinkert

Milestone changed from Unscheduled to OMERO-4.5
Resolution set to fixed
Sprint set to Bugs Fixing
Status changed from new to closed

Fixed with: https://github.com/openmicroscopy/bioformats/pull/408

Files added to the repository.

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