Context Navigation

← Previous Ticket
Next Ticket →

Warning: Can't synchronize with repository "(default)" (/home/git/ome.git does not appear to be a Git repository.). Look in the Trac log for more information.

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 #6926 (closed)

Opened 13 years ago

Closed 13 years ago

Last modified 13 years ago

BUG:Zeiss lsm file

Reported by:	omero-qa	Owned by:	mlinkert
Priority:	minor	Milestone:	Unscheduled
Component:	from QA	Version:	n.a.
Keywords:	n.a.	Cc:	CJW@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	0.0d
Sprint:	n.a.

Description

http://qa.openmicroscopy.org.uk/qa/feedback/4009/

Comment: Importing a Zeiss lsm file. Taken with multi-time, many other images just the same are imported fine. ImageJ using the bio-formats plugin shows the same error. ImageJ File->Open can open the file, Zeiss Axiovision can open the file, and our lsm reader written in IDL can also open the file.

Thanks
Chris

java.lang.IllegalArgumentException
	at java.nio.Buffer.position(Buffer.java:218)
	at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:513)
	at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:304)
	at loci.common.RandomAccessInputStream.readInt(RandomAccessInputStream.java:336)
	at loci.formats.in.ZeissLSMReader.readEntry(ZeissLSMReader.java:1967)
	at loci.formats.in.ZeissLSMReader.access$100(ZeissLSMReader.java:69)
	at loci.formats.in.ZeissLSMReader$SubBlock.read(ZeissLSMReader.java:2087)
	at loci.formats.in.ZeissLSMReader$SubBlock.<init>(ZeissLSMReader.java:2051)
	at loci.formats.in.ZeissLSMReader$Timer.<init>(ZeissLSMReader.java:2301)
	at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:1107)
	at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:514)
	at loci.formats.FormatReader.setId(FormatReader.java:1072)
	at loci.formats.ImageReader.setId(ImageReader.java:672)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:312)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:488)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6373)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1226)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

References

Change History (4)

comment:1 Changed 13 years ago by Melissa Linkert <melissa@…>

Remaining Time set to 0
Resolution set to fixed
Status changed from new to closed

(In [fcc0ccced4820b17fc36ada23dcdfc0238d6764e/bioformats.git]) Stop reading metadata once we reach the end of the file.

Closes #6926.

comment:2 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [fcc0ccced4820b17fc36ada23dcdfc0238d6764e/bioformats.git]) Stop reading metadata once we reach the end of the file.

Closes #6926.

comment:3 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [5a33bda6473f81a850a9efe1d49455ef93abbb5e/bioformats.git]) Stop reading metadata once we reach the end of the file.

Closes #6926.
(cherry picked from commit fcc0ccced4820b17fc36ada23dcdfc0238d6764e)

comment:4 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [5a33bda6473f81a850a9efe1d49455ef93abbb5e/bioformats.git]) Stop reading metadata once we reach the end of the file.

Closes #6926.
(cherry picked from commit fcc0ccced4820b17fc36ada23dcdfc0238d6764e)

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

Download in other formats: