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Task #12941 (closed)

Opened 9 years ago

Closed 9 years ago

Bug: ImageJ "Open files individually" and "Group files..."

Reported by: mlinkert Owned by: mlinkert
Priority: major Milestone: B-F-5.1.5
Component: Bio-Formats Version: 5.1.2
Keywords: imagej, external, our-fault Cc: jsoriano@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

See ​http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-June/005451.html.

Opening one of the attached files in ImageJ using both the "Open files individually" and "Group files with similar names" options results in this exception:

java.lang.IndexOutOfBoundsException: Index: 2, Size: 2
	at java.util.ArrayList.RangeCheck(ArrayList.java:547)
	at java.util.ArrayList.get(ArrayList.java:322)
	at ome.xml.model.OME.getImage(OME.java:647)
	at ome.xml.meta.OMEXMLMetadataImpl.getImageName(OMEXMLMetadataImpl.java:2232)
	at loci.plugins.in.ImportProcess.computeSeriesLabels(ImportProcess.java:718)
	at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:536)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:148)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:195)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.Executer.runCommand(Executer.java:128)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)

I would assume this is due to each file having multiple series, but am not certain.

Change History (3)

comment:1 Changed 9 years ago by jamoore

  • Milestone changed from 5.1.4 to B-F-5.1.4

Splitting 5.1.4 due to milestone decoupling

comment:2 Changed 9 years ago by sbesson

  • Milestone changed from B-F-5.1.4 to BF-5.1.5

comment:3 Changed 9 years ago by mlinkert

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

Fixed by ​https://github.com/openmicroscopy/bioformats/pull/1967

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