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Task #9101 (closed)

Opened 12 years ago

Closed 12 years ago

Last modified 12 years ago

Bug: Import failed (imacom/ss1.fff)

Reported by: bpindelski Owned by: mlinkert
Priority: major Milestone: OMERO-4.4
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: bpindelski, saloynton, mlinkert
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2012-06-19 (17)

Description (last modified by bpindelski)

Import failed on Windows with Imacom image (ss1.fff)

java.io.IOException: The parameter is incorrect
	at sun.nio.ch.FileDispatcherImpl.read0(Native Method)
	at sun.nio.ch.FileDispatcherImpl.read(Unknown Source)
	at sun.nio.ch.IOUtil.readIntoNativeBuffer(Unknown Source)
	at sun.nio.ch.IOUtil.read(Unknown Source)
	at sun.nio.ch.FileChannelImpl.read(Unknown Source)
	at loci.common.NIOFileHandle.read(NIOFileHandle.java:229)
	at loci.common.NIOFileHandle.read(NIOFileHandle.java:221)
	at loci.common.NIOFileHandle.read(NIOFileHandle.java:211)
	at loci.common.NIOFileHandle.readFully(NIOFileHandle.java:303)
	at loci.common.RandomAccessInputStream.readFully(RandomAccessInputStream.java:433)
	at loci.formats.tiff.TiffParser.getIFDValue(TiffParser.java:453)
	at loci.formats.tiff.TiffParser.fillInIFD(TiffParser.java:428)
	at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:408)
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:505)
	at loci.formats.FormatReader.setId(FormatReader.java:1092)
	at loci.formats.ImageReader.setId(ImageReader.java:682)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:492)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:250)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:492)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:261)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:492)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:310)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:486)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6253)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1247)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:86)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:55)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:113)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Unknown Source)

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6301)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1247)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:86)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:55)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:113)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: The parameter is incorrect
	at sun.nio.ch.FileDispatcherImpl.read0(Native Method)
	at sun.nio.ch.FileDispatcherImpl.read(Unknown Source)
	at sun.nio.ch.IOUtil.readIntoNativeBuffer(Unknown Source)
	at sun.nio.ch.IOUtil.read(Unknown Source)
	at sun.nio.ch.FileChannelImpl.read(Unknown Source)
	at loci.common.NIOFileHandle.read(NIOFileHandle.java:229)
	at loci.common.NIOFileHandle.read(NIOFileHandle.java:221)
	at loci.common.NIOFileHandle.read(NIOFileHandle.java:211)
	at loci.common.NIOFileHandle.readFully(NIOFileHandle.java:303)
	at loci.common.RandomAccessInputStream.readFully(RandomAccessInputStream.java:433)
	at loci.formats.tiff.TiffParser.getIFDValue(TiffParser.java:453)
	at loci.formats.tiff.TiffParser.fillInIFD(TiffParser.java:428)
	at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:408)
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:505)
	at loci.formats.FormatReader.setId(FormatReader.java:1092)
	at loci.formats.ImageReader.setId(ImageReader.java:682)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:492)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:250)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:492)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:261)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:492)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:310)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:486)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6253)
	... 11 more

Attachments (2)

omero log​ (62.2 KB) - added by saloynton 12 years ago.
Screen shot 2012-06-12 at 17.36.10.png​ (59.8 KB) - added by saloynton 12 years ago.

Download all attachments as: .zip

Change History (9)

comment:1 Changed 12 years ago by mlinkert

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

imacom/ss1.fff imports for me, using OMERO.insight-4.3.3-2956-876edcf-ice33-b79 (on Linux) with 512 MB allocated to Insight.

comment:2 Changed 12 years ago by bpindelski

  • Description modified (diff)
  • Resolution worksforme deleted
  • Status changed from closed to reopened

Imports ok on OS X, but fails on Windows.

comment:3 Changed 12 years ago by mlinkert

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

Fixed with: ​https://github.com/melissalinkert/bioformats/commit/ec76136356c44109cf10a0d5add26118718cb2de

comment:4 Changed 12 years ago by saloynton

I have retested FEI tiff and czi successfully, I have tried to import improvision tiff and Tagged Image File Format but I have had the following error in the omero.log file. I have also attached a screenshot as no information is shown in the importer window.

Changed 12 years ago by saloynton

Changed 12 years ago by saloynton

comment:5 Changed 12 years ago by saloynton

  • Cc saloynton jburel added
  • Resolution fixed deleted
  • Status changed from closed to reopened

comment:6 Changed 12 years ago by saloynton

  • Cc mlinkert-x added; jburel removed
  • Resolution set to fixed
  • Status changed from reopened to closed

comment:7 Changed 12 years ago by saloynton

I have closed this ticket and opened ticket #9166 to document the separate issue of not knowing if the import has completed.

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