Task #12938 (new)
Opened 9 years ago
Last modified 8 years ago
Text image file support
Reported by: | omero-qa | Owned by: | |
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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)
Change History (3)
comment:1 Changed 9 years ago by jburel
comment:2 Changed 9 years ago by jburel
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).
Card added to trello board
Ticket to link all the pieces together