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Task #9596 (closed)

Opened 12 years ago

Closed 12 years ago

Bug: Hamamatsu VMS import fails with OOM error

Reported by: bpindelski Owned by: mlinkert
Priority: critical Milestone: OMERO-4.4.7
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: mlinkert
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2013-05-07 (8)

Description (last modified by bpindelski)

Insight build: OMERO.insight-4.4.1-486-b319a8c-ice33-b3078-mac

OS: OS X 10.6.8, Windows

java.lang.OutOfMemoryError: Java heap space
	at java.awt.image.DataBufferByte.<init>(DataBufferByte.java:59)
	at java.awt.image.ComponentSampleModel.createDataBuffer(ComponentSampleModel.java:397)
	at java.awt.image.Raster.createWritableRaster(Raster.java:938)
	at javax.imageio.ImageTypeSpecifier.createBufferedImage(ImageTypeSpecifier.java:1056)
	at javax.imageio.ImageReader.getDestination(ImageReader.java:2879)
	at com.sun.imageio.plugins.jpeg.JPEGImageReader.readInternal(JPEGImageReader.java:980)
	at com.sun.imageio.plugins.jpeg.JPEGImageReader.read(JPEGImageReader.java:948)
	at javax.imageio.ImageIO.read(ImageIO.java:1422)
	at javax.imageio.ImageIO.read(ImageIO.java:1326)
	at loci.formats.in.ImageIOReader.initFile(ImageIOReader.java:118)
	at loci.formats.FormatReader.setId(FormatReader.java:1178)
	at loci.formats.DelegateReader.setId(DelegateReader.java:259)
	at loci.formats.in.JPEGReader.setId(JPEGReader.java:85)
	at loci.formats.ImageReader.setId(ImageReader.java:727)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:595)
	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:364)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:335)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:368)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6404)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1270)
	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.OMEROGateway.getImportCandidates(OMEROGateway.java:6408)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1270)
	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$1.doCall(ImagesImporter.java:110)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.OutOfMemoryError: Java heap space
	at java.awt.image.DataBufferByte.<init>(DataBufferByte.java:59)
	at java.awt.image.ComponentSampleModel.createDataBuffer(ComponentSampleModel.java:397)
	at java.awt.image.Raster.createWritableRaster(Raster.java:938)
	at javax.imageio.ImageTypeSpecifier.createBufferedImage(ImageTypeSpecifier.java:1056)
	at javax.imageio.ImageReader.getDestination(ImageReader.java:2879)
	at com.sun.imageio.plugins.jpeg.JPEGImageReader.readInternal(JPEGImageReader.java:980)
	at com.sun.imageio.plugins.jpeg.JPEGImageReader.read(JPEGImageReader.java:948)
	at javax.imageio.ImageIO.read(ImageIO.java:1422)
	at javax.imageio.ImageIO.read(ImageIO.java:1326)
	at loci.formats.in.ImageIOReader.initFile(ImageIOReader.java:118)
	at loci.formats.FormatReader.setId(FormatReader.java:1178)
	at loci.formats.DelegateReader.setId(DelegateReader.java:259)
	at loci.formats.in.JPEGReader.setId(JPEGReader.java:85)
	at loci.formats.ImageReader.setId(ImageReader.java:727)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:595)
	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:364)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:335)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:368)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6404)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1270)
	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)

Change History (13)

comment:1 Changed 12 years ago by bpindelski

  • Description modified (diff)

comment:2 Changed 12 years ago by bpindelski

After increasing the heap memory to 2 GB (-Xmx2048), the image fails with the error "Image Not Valid". insight.log follows

2012-09-12 13:19:35,444 INFO  [       ome.formats.importer.ImportConfig] ( Thread-17) OMERO Version: 4.4.1-486-b319a8c-ice33-b3078
2012-09-12 13:19:35,445 INFO  [       ome.formats.importer.ImportConfig] ( Thread-17) Bioformats version: 4.4-DEV revision: 6733597 date: 12 September 2012
2012-09-12 13:19:35,458 INFO  [   ome.formats.importer.ImportCandidates] ( Thread-17) Depth: 4 Metadata Level: MINIMUM
2012-09-12 13:19:35,475 INFO  [              loci.formats.FormatHandler] ( Thread-17) Populating metadata
2012-09-12 13:19:35,517 INFO  [              loci.formats.FormatHandler] ( Thread-17) Populating metadata
2012-09-12 13:19:35,521 INFO  [              loci.formats.FormatHandler] ( Thread-17) Populating metadata
2012-09-12 13:20:15,591 INFO  [   ome.formats.importer.ImportCandidates] ( Thread-17) 35 file(s) parsed into 0 group(s) with 23 call(s) to setId in 40072ms. (40132ms total) [4 unknowns]

comment:3 Changed 12 years ago by jburel

  • Cc mlinkert-x added

comment:4 Changed 12 years ago by mlinkert

  • Component changed from Insight to Bio-Formats
  • Milestone changed from OMERO-4.4.4 to OMERO-4.5
  • Owner changed from jburel to mlinkert-x
  • Sprint 2012-09-25 (5) deleted

That's a known problem, and is not going to be anywhere close to fixed for 4.4.4.

This is closely related to #5092, and basically comes down to the fact that we have no way of retrieving tiles from JPEG images (like we can for nearly every other format).

comment:5 Changed 12 years ago by mlinkert

  • Sprint set to 2012-10-23 (1)

comment:6 Changed 12 years ago by jburel

  • Sprint changed from 2012-10-23 (1) to 2012-11-20 (2)

Moved from sprint 2012-10-23 (1)

comment:7 Changed 12 years ago by jburel

  • Sprint changed from 2012-11-20 (2) to 2012-12-18 (3)

Moved from sprint 2012-11-20 (2)

comment:8 Changed 12 years ago by jburel

  • Sprint changed from 2012-12-18 (3) to 2013-01-15 (4)

Moved from sprint 2012-12-18 (3)

comment:9 Changed 12 years ago by jburel

  • Sprint changed from 2013-01-15 (4) to 2013-02-12 (5)

Moved from sprint 2013-01-15 (4)

comment:10 Changed 12 years ago by jburel

  • Sprint changed from 2013-02-12 (5) to 2013-03-12 (6))

Moved from sprint 2013-02-12 (5)

comment:11 Changed 12 years ago by jburel

  • Sprint changed from 2013-03-12 (6)) to 2013-04-09 (7))

Moved from sprint 2013-03-12 (6))

comment:12 Changed 12 years ago by jburel

  • Sprint changed from 2013-04-09 (7)) to 2013-05-07 (8)

Moved from sprint 2013-04-09 (7))

comment:13 Changed 12 years ago by mlinkert

  • Resolution set to fixed
  • Status changed from new to closed

Should be fixed with ​https://github.com/openmicroscopy/bioformats/pull/159

Not expected to work on dev_4_4; PR 159 will not be backported.

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