Task #11951 (closed)
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
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.
There's some question of whether the plate.ome.xml file could exist (validly) without all the IFD blocks.