Task #12864 (closed)
Bug: LeicaSCNReader IndexOutOfBoundsException
| Reported by: | omero-qa | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | minor | Milestone: | OMERO-5.1.4 |
| Component: | from QA | Version: | 5.1.1 |
| Keywords: | n.a. | Cc: | pognonec@… |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | n.a. |
Description
https://www.openmicroscopy.org/qa2/qa/feedback/11049/
Comment: This file is from a Leica virtual slide scanner. Strangely, it is the only one from 14 scans from the same batch to be rejected by Omero.
java.lang.IndexOutOfBoundsException: Index: 3, Size: 3 at java.util.ArrayList.rangeCheck(ArrayList.java:653) at java.util.ArrayList.get(ArrayList.java:429) at loci.formats.in.LeicaSCNReader.initStandardMetadata(LeicaSCNReader.java:322) at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:95) at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:542) at loci.formats.FormatReader.setId(FormatReader.java:1395) at loci.formats.ImageReader.setId(ImageReader.java:835) 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:1174) 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 (4)
comment:1 Changed 9 years ago by mlinkert
- Milestone changed from Unscheduled to 5.1.4
comment:2 Changed 9 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
comment:3 Changed 9 years ago by Melissa Linkert <melissa@…>
- Remaining Time set to 0
(In [dcad0e408a8ffff2999e721e905a64dfd7f06c7b/bioformats.git] on branch develop) Leica SCN: do not report more resolutions than there are IFDs
Fixes #12864.
comment:4 Changed 9 years ago by jamoore
- Milestone changed from 5.1.4 to OMERO-5.1.4
Splitting 5.1.4 due to milestone decoupling
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PR open: https://github.com/openmicroscopy/bioformats/pull/1948