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Task #6929 (closed)

Opened 13 years ago

Closed 12 years ago

Reduce memory required to open .nd2 tiles

Reported by:	omero-qa	Owned by:	mlinkert
Priority:	minor	Milestone:	OMERO-4.4.4
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:	Judy.Callaghan@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description

http://qa.openmicroscopy.org.uk/qa/feedback/3994/

Comment: this file opened OK in FIJI
regards
Judy

java.lang.OutOfMemoryError: Java heap space
	at loci.formats.codec.ByteVector.toByteArray(ByteVector.java:90)
	at loci.formats.codec.ZlibCodec.decompress(ZlibCodec.java:77)
	at loci.formats.in.NativeND2Reader.openBytes(NativeND2Reader.java:221)
	at loci.formats.DelegateReader.openBytes(DelegateReader.java:184)
	at loci.formats.ImageReader.openBytes(ImageReader.java:396)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:183)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:209)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
	at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
	at ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:871)
	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:796)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:573)
	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(Unknown Source)

References

Change History (3)

comment:1 Changed 13 years ago by jmoore

Component changed from from QA to Bio-Formats

comment:2 Changed 12 years ago by mlinkert

Milestone changed from Unscheduled to OMERO-4.4.1

comment:3 Changed 12 years ago by mlinkert

Resolution set to fixed
Status changed from new to closed

This commit: https://github.com/melissalinkert/bioformats/commit/42ea8831ff8149149ef8ae948682bcc8fb5fefe6

substantially reduces the amount of memory needed to read .nd2 files.

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