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Task #5251 (closed)

Opened 13 years ago

Closed 13 years ago

Last modified 13 years ago

RFE: Phase_1-File Formats -1 : speed up NikonReader

Reported by:	jamoore	Owned by:	mlinkert
Priority:	minor	Milestone:	OMERO-Beta4.3
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	0.0d
Sprint:	2011-06-02 (13)

Description

I don't know if it's possible but the scanning of a nikon directory is quite slow. See stack trace below.

References

Referenced by:
← User Story (#5371): File Formats Phase I BUGS

Change History (4)

comment:1 Changed 13 years ago by jmoore

"Thread-56" prio=6 tid=104320000 nid=0x121fb2000 runnable [121fb0000]
   java.lang.Thread.State: RUNNABLE
	at loci.formats.codec.HuffmanCodec$Decoder.createDecoder(HuffmanCodec.java:138)
	at loci.formats.codec.HuffmanCodec$Decoder.createDecoder(HuffmanCodec.java:152)
	at loci.formats.codec.HuffmanCodec$Decoder.createDecoder(HuffmanCodec.java:138)
	at loci.formats.codec.HuffmanCodec$Decoder.createDecoder(HuffmanCodec.java:153)
	at loci.formats.codec.HuffmanCodec$Decoder.createDecoder(HuffmanCodec.java:138)
	at loci.formats.codec.HuffmanCodec$Decoder.createDecoder(HuffmanCodec.java:152)
	at loci.formats.codec.HuffmanCodec$Decoder.<init>(HuffmanCodec.java:133)
	at loci.formats.codec.HuffmanCodec.getSample(HuffmanCodec.java:111)
	at loci.formats.codec.NikonCodec.decompress(NikonCodec.java:207)
	at loci.formats.codec.BaseCodec.decompress(BaseCodec.java:170)
	at loci.formats.in.NikonReader.openBytes(NikonReader.java:189)
	at loci.formats.FormatReader.openBytes(FormatReader.java:739)
	at loci.formats.ImageReader.openBytes(ImageReader.java:380)
	at loci.formats.ChannelFiller.getLookupTableComponentCount(ChannelFiller.java:267)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:250)
	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.ImportCandidates.singleFile(ImportCandidates.java:406)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:574)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:367)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:364)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:335)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:367)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:228)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6201)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1165)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:84)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:55)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:105)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

comment:2 Changed 13 years ago by mlinkert

Remaining Time set to 0.5
Sprint set to 2011-06-02 (13)

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

Remaining Time changed from 0.5 to 0
Resolution set to fixed
Status changed from new to closed

(In [ac515babe464fdef447b226185a95e40af4606ec/bioformats.git]) Cache Decoder objects when possible.

This substantially speeds up Nikon NEF decompression, as we are not
creating a new Decoder for each pixel. Closes #5251.

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

(In [ac515babe464fdef447b226185a95e40af4606ec/bioformats.git]) Cache Decoder objects when possible.

This substantially speeds up Nikon NEF decompression, as we are not
creating a new Decoder for each pixel. Closes #5251.

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