Task #12144 (closed)
Bug : newer .lif files fail to initialize
| Reported by: | bramalingam | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | major | Milestone: | 5.0.6 |
| Component: | Bio-Formats | Version: | 5.0.0 |
| Keywords: | n.a. | Cc: | r.a.hoebe@…, e.mackay@…, astout@…, mendelsm@…, rebecca.richardson@… |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | n.a. |
Description (last modified by mlinkert)
Location.mapFile: embedded-stream.raw -> null
FILE_EXCEPTION: /ome/data_repo/from_Biozentrum_Basel/Charles/SP5/01-31hpi-Experiment.lif
loci.formats.FormatException: Invalid Memory Block: found magic bytes 0, expected 112
at loci.formats.in.LIFReader.initFile(LIFReader.java:416)
at loci.formats.FormatReader.setId(FormatReader.java:1319)
at loci.formats.ImageReader.setId(ImageReader.java:757)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:573)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:573)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:573)
at loci.formats.Memoizer.setId(Memoizer.java:471)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:573)
at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:595)
at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:367)
at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:335)
at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:368)
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
SCANNING: Depth:0 Num: 2 Tot: 2 File: asel/Charles/SP5
2 file(s) parsed into 0 group(s) with 1 call(s) to setId in 68ms. (77ms total) [0 unknowns]
Change History (14)
comment:1 Changed 10 years ago by mlinkert
- Component changed from General to Bio-Formats
- Priority changed from minor to major
- Summary changed from Bug : bug in Bio-Formats with LIF file to Bug : newer .lif files fail to initialize
comment:2 Changed 10 years ago by mlinkert
- Description modified (diff)
comment:3 Changed 10 years ago by mlinkert
- Milestone changed from Unscheduled to 5.1.0-m1
comment:4 Changed 10 years ago by mlinkert
- Milestone changed from 5.1.0-m1 to 5.0.4
comment:5 Changed 10 years ago by mlinkert
comment:6 Changed 10 years ago by mlinkert
- Cc r.a.hoebe@… added
comment:8 Changed 10 years ago by mlinkert
comment:9 Changed 10 years ago by crueden-x
See also http://fiji.sc/bugzilla/show_bug.cgi?id=911, which includes a small (~2.6MB) sample dataset attachment.
comment:10 Changed 10 years ago by crueden-x
- Cc astout@… added
comment:11 Changed 10 years ago by mlinkert
- Cc mendelsm@… added
comment:12 Changed 10 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
Fixed with: https://github.com/openmicroscopy/bioformats/pull/1382
New builds containing this fix are not yet available.
comment:13 Changed 10 years ago by mtbcarroll
- Cc rebecca.richardson@… added
comment:14 Changed 10 years ago by Melissa Linkert <melissa@…>
- Remaining Time set to 0
(In [d2bd3e20e05a1c37a84c524da4075aabf6c1141f/bioformats.git] on branch develop) Leica LIF: fix support for new files with 0 padding
Fixes #12144
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You may also have a look at Agilo extensions to the ticket.
See also datasets in leica-lif/fabrice/new/ and leica-lif/ron/. As far as I can tell, the last block has a 0 identifier, and is then padded with 0s (though it could also be that the length for the last "real" block needs adjusting).