Task #12484 (closed)
Opened 10 years ago
Closed 10 years ago
BUG: ome-tiff reader throwing exception
Reported by: | bramalingam | Owned by: | mlinkert |
---|---|---|---|
Priority: | minor | Milestone: | 5.1.0-m3 |
Component: | Bio-Formats | Version: | 5.0.2 |
Keywords: | n.a. | Cc: | |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
Import within OMERO : QA9412
The file seems to be a file set, and only one file has been submitted.
But omero importer gives a null pointer exception, discussed with Roger and he suggested that it should still give the same error as ImageJ, where we see the error : Unmatched UUID
exception.
java.lang.NullPointerException at loci.formats.in.OMETiffReader.close(OMETiffReader.java:339) at loci.formats.ImageReader.close(ImageReader.java:536) at loci.formats.ReaderWrapper.close(ReaderWrapper.java:339) at loci.formats.ReaderWrapper.close(ReaderWrapper.java:339) at loci.formats.ChannelSeparator.close(ChannelSeparator.java:241) at loci.formats.ReaderWrapper.close(ReaderWrapper.java:339) at loci.formats.Memoizer.close(Memoizer.java:492) at loci.formats.MinMaxCalculator.close(MinMaxCalculator.java:277) at ome.formats.importer.OMEROWrapper.close(OMEROWrapper.java:269) at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:440) at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:596) 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:6706) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1140) 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:695) at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:667) at ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:556) at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:464) at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:596) 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:6706) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1140) 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:695) Caused by: java.lang.NullPointerException at loci.formats.in.OMETiffReader.close(OMETiffReader.java:339) at loci.formats.ImageReader.close(ImageReader.java:536) at loci.formats.ReaderWrapper.close(ReaderWrapper.java:339) at loci.formats.ReaderWrapper.close(ReaderWrapper.java:339) at loci.formats.ChannelSeparator.close(ChannelSeparator.java:241) at loci.formats.ReaderWrapper.close(ReaderWrapper.java:339) at loci.formats.Memoizer.close(Memoizer.java:492) at loci.formats.MinMaxCalculator.close(MinMaxCalculator.java:277) at ome.formats.importer.OMEROWrapper.close(OMEROWrapper.java:269) at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:440) ... 16 more
Import within ImageJ
loci.formats.FormatException: Unmatched UUID: urn:uuid:28c3ca1b-b7e5-428e-ae81-3e84aa56f043 at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:540) at loci.formats.FormatReader.setId(FormatReader.java:1317) at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494) at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144) at loci.plugins.in.Importer.showDialogs(Importer.java:141) at loci.plugins.in.Importer.run(Importer.java:79) at loci.plugins.LociImporter.run(LociImporter.java:81) at ij.IJ.runUserPlugIn(IJ.java:201) at ij.IJ.runPlugIn(IJ.java:165) at ij.Executer.runCommand(Executer.java:131) at ij.Executer.run(Executer.java:64) at java.lang.Thread.run(Thread.java:695)
Change History (2)
comment:1 Changed 10 years ago by mlinkert
- Milestone changed from Unscheduled to 5.0.4
comment:2 Changed 10 years ago by mlinkert
- Resolution set to worksforme
- Status changed from new to closed
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I cannot reproduce either error using QA 9412 and current develop. Feel free to re-open if you find that this is still reproducible.