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Task #12602 (closed)

Opened 10 years ago

Closed 9 years ago

Last modified 9 years ago

Bug: ICSWriter can't handle large >2gb images

Reported by: rleigh Owned by: mlinkert
Priority: minor Milestone: 5.1.1
Component: Bio-Formats Version: 5.0.5
Keywords: ICSWriter our-fault Cc: charles@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: n.a.

Description

Testing with a 5.9GB test image (2048x2048x1500 8bit)

Looking at the failure point, it looks like the hard limit might be even lower at ~2GB (exception at ~488/1500 planes):

ImageJ 1.49b; Java 1.7.0_65 [64-bit]; Linux 3.13.0-37-generic; 6433MB of 8000MB (80%)
 
java.lang.IllegalArgumentException: Negative position
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:676)
	at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:131)
	at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:116)
	at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:551)
	at loci.common.NIOFileHandle.seek(NIOFileHandle.java:273)
	at loci.common.RandomAccessOutputStream.seek(RandomAccessOutputStream.java:83)
	at loci.formats.out.ICSWriter.saveBytes(ICSWriter.java:139)
	at loci.formats.FormatWriter.saveBytes(FormatWriter.java:126)
	at loci.plugins.out.Exporter.run(Exporter.java:629)
	at loci.plugins.LociExporter.run(LociExporter.java:77)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)
	at ij.IJ.runUserPlugIn(IJ.java:203)
	at ij.IJ.runPlugIn(IJ.java:165)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:745)

Change History (5)

comment:2 Changed 10 years ago by rleigh

  • Component changed from General to Bio-Formats
  • Owner set to mlinkert

comment:3 Changed 9 years ago by mlinkert

  • Milestone changed from Unscheduled to 5.1.1

Moving to 5.1.1 for triage.

comment:4 Changed 9 years ago by mlinkert

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

Fixed with ​https://github.com/openmicroscopy/bioformats/pull/1738

comment:5 Changed 9 years ago by Melissa Linkert <melissa@…>

  • Remaining Time set to 0

(In [b12da62709ba4b301322e8c91091377a065474f0/bioformats.git] on branch develop) ICS writer: fix saving of > 2GB of pixel data

Fixes #12602.

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