BUG:Dicom Positive integer

[omero-qa]

​https://www.openmicroscopy.org/qa2/qa2/qa/feedback/9283/

Comment: Problem when importing DICOM sample image from Osirix

java.lang.IllegalArgumentException: 0 must not be null and positive.
	at ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:56)
	at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:275)
	at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:236)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:138)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:101)
	at loci.formats.in.DicomReader.initFile(DicomReader.java:706)
	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 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:6384)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1199)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:701)

[jburel]

File already submitted. Roger could you have a look at it? If you can hand is better of course.

[rleigh]

No longer reproducible on either current dev_5_0 or develop. Tested with current Insight for both branches, and both import and view without problems. Tested with showinf on dev_5_0 and with the tagged 5.0.[012] releases and no problems found using the sample IM-0001-0001.dcm.

Note that in the original QA upload, there was a version discrepancy betweeen client (5.0.0) and server (5.0.1). I would suggest to odebeir that it would be worth checking the current server version and ensuring that the client version matches since I can't reproduce the original problem.

I'm closing the ticket, but if after checking the client version you still have this problem, please do let me know with some more details about how you triggered the problem.

Regards,
Roger

[khgillen]

I have example Dicom which crashes with this exception in 5.0.4 release OMERO. (It uploaded fine in an older version of OMERO, I don't remember which version)

This was just raised on the ome-users list, ​http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-September/004782.html, so I'm re-opening.

[mlinkert]

Corresponding QA is 9553. This is likely a bit different from the original problem reported in this ticket due to the slight difference in stack trace. rleigh, feel free to re-assign if you don't have the time to work on this.

[mlinkert]

I still can't reproduce with either QA fileset, using 5.0.4 and current develop. We don't have confirmation of which version produced a stack trace with QA 9553, and there has been no follow-up to confirm whether upgrading to 5.0.4 solved the problem.

Kenny, are you still seeing this with your files? If so, would you be willing to discuss briefly, so that we can at least figure out how to reproduce the problem?

[khgillen]

@mlinkert, yes, I am still seeing this with 5.1 and 5.0.5.

FWIW it's imported in the past (on an analysis OMERO instance, in Sep 2013 - not sure what our version was at that time).

More than happy to discuss / assist in testing.

Best,

Kenny

[mlinkert]

PR opened: ​https://github.com/openmicroscopy/bioformats/pull/1424

[Melissa Linkert <melissa@…>]

(In [6ef4691dd7264276ef44437d892f357d57569d81/bioformats.git] on branch develop) DICOM: fix dimension population for multi-series filesets

Fixes #12369