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Task #11951 (closed)

Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

Bug: BinaryOnly import fails

Reported by: jamoore Owned by: mlinkert
Priority: critical Milestone: 5.0.2
Component: Bio-Formats Version: 5.0.0-rc1
Keywords: n.a. Cc: pwalczysko, ajpatterson, rleigh, cxallan, bramalingam
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: n.a.

Description

Importing https://github.com/openmicroscopy/bioformats/blob/develop/components/specification/samples/2013-06/set-1-meta-companion/18x24y5z1t1c8b-text-companion.ome fails with:

2014-01-29 17:20:17,109 287        [      main] ERROR     ome.formats.importer.cli.ErrorHandler  - FILE_EXCEPTION: /opt/ome2/components/bioformats/components/specification/samples/2013-06/set-1-meta-companion/18x24y5z1t1c8b-text-companion.ome
loci.formats.FormatException: Pixel data not found
	at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:241)
	at loci.formats.FormatReader.setId(FormatReader.java:1360)
	at loci.formats.ImageReader.setId(ImageReader.java:781)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at loci.formats.Memoizer.setId(Memoizer.java:471)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:595)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:99)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:548)

This is currently being investigated as a way to "export" an entire plate. In general, we will need to make sure that our own sample files are all importable. This could happen along with the /ome/data_repo cleanup that should be happening in February.

Change History (4)

comment:1 Changed 10 years ago by jamoore

  • Cc bramalingam added

There's some question of whether the plate.ome.xml file could exist (validly) without all the IFD blocks.

comment:2 Changed 10 years ago by mlinkert

  • Milestone changed from 5.0.1 to 5.0.2

Pushing to 5.0.2 until we can get proper test cases in place. See https://trello.com/c/RTlxoIdn/22-plate-binary-only-samples

comment:3 Changed 10 years ago by mlinkert

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

comment:4 Changed 10 years ago by Melissa Linkert <melissa@…>

  • Remaining Time set to 0

(In [5e6eecfd0970b64eb9f831bf7d88814ad1292454/bioformats.git] on branch develop) Add initial support for reading BinaryOnly? OME-TIFF datasets

This adjusts the type detection slightly so that .companion.ome files
are detected as OME-TIFF, not OME-XML (as this makes finding and reading
the corresponding OME-TIFF files much easier). Selecting either a
BinaryOnly? OME-TIFF file or the corresponding companion OME-XML file
should result in the entire dataset being read.

Fixes #11951.

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