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Task #12938 (new)

Opened 9 years ago

Last modified 8 years ago

Text image file support

Reported by:	omero-qa	Owned by:
Priority:	minor	Milestone:	Unscheduled
Component:	Bio-Formats	Version:	5.1.2
Keywords:	new-format, external	Cc:	pognonec@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description

https://www.openmicroscopy.org/qa2/qa2/qa/feedback/11126/

Comment: This is a .txt image file, that can be open succesfuly in ImageJ through File/Import/Text? Image. OMERO nimporter does not recognize it though (Unknown format). Is there a way to load that type of images onto OMERO nevetheless?
Thanks!
Philippe

loci.formats.UnknownFormatException: Unknown file format: /home/philippe/Desktop/PHA aplani_ SID4Bio 20130727-071005.935.txt
	at loci.formats.ImageReader.getReader(ImageReader.java:190)
	at loci.formats.ImageReader.setId(ImageReader.java:832)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.Memoizer.setId(Memoizer.java:614)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:570)
	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 org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6849)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1035)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:79)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:55)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:104)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:745)

References

Change History (3)

comment:1 Changed 9 years ago by jburel

Card added to trello board
Ticket to link all the pieces together

comment:2 Changed 9 years ago by jburel

see also https://www.openmicroscopy.org/qa2/qa/feedback/11132/

comment:3 Changed 8 years ago by mlinkert

Component changed from from QA to Bio-Formats
Keywords new-format external added
Owner mlinkert deleted

Not sure there is anything we can do with QA 11132 - those don't look like images. The QA 11126 file should be easy to parse - the only difficult part is figuring out how to do type detection, since there is no unique extension or header. Note that we do have a TextReader? already, but it reads a different format of text pixels (see data_repo/curated/text).

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