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Task #8013 (closed)

Opened 12 years ago

Closed 12 years ago

Bug: Single-channel CellWorX datasets fail

Reported by: omero-qa Owned by: mlinkert
Priority: minor Milestone: OMERO-4.4
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: john.lim@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2012-03-13 (10)

Description

​http://qa.openmicroscopy.org.uk/qa/feedback/4207/

Comment: Unable to import image file

java.io.FileNotFoundException: Z:\IMU\John\96w plate- Empty\NSC_A01_s1.TIF (The system cannot find the file specified)
	at java.io.RandomAccessFile.open(Native Method)
	at java.io.RandomAccessFile.<init>(Unknown Source)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:105)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:116)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:125)
	at loci.common.Location.getHandle(Location.java:284)
	at loci.common.Location.getHandle(Location.java:255)
	at loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.java:80)
	at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:367)
	at loci.formats.FormatReader.setId(FormatReader.java:1072)
	at loci.formats.in.CellWorxReader.getReader(CellWorxReader.java:592)
	at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:331)
	at loci.formats.FormatReader.setId(FormatReader.java:1072)
	at loci.formats.ImageReader.setId(ImageReader.java:677)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
	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.ImportLibrary.open(ImportLibrary.java:310)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:486)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6402)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1228)
	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$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Unknown Source)

See QA #4208 for the corresponding .htd file.

Change History (4)

comment:1 Changed 12 years ago by mlinkert

  • Component changed from from QA to Bio-Formats
  • Milestone changed from Unscheduled to OMERO-Beta4.4
  • Remaining Time set to 0.01
  • Sprint set to 2012-02-14 (8)
  • Status changed from new to accepted

​https://github.com/melissalinkert/bioformats/commit/269b8463a6ca23931464d3e35b62d7a90631ebdc

comment:2 Changed 12 years ago by jburel

  • Sprint changed from 2012-02-14 (8) to 2012-02-28 (9)

Moved from sprint 2012-02-14 (8)

comment:3 Changed 12 years ago by jburel

  • Sprint changed from 2012-02-28 (9) to 2012-03-13 (10)

Moved from sprint 2012-02-28 (9)

comment:4 Changed 12 years ago by mlinkert

  • Remaining Time changed from 0.01 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed
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