Task #12741 (closed)
Opened 9 years ago
Closed 9 years ago
BUG:LIFReader, IllegalArgumentException
Reported by: | omero-qa | Owned by: | jburel |
---|---|---|---|
Priority: | minor | Milestone: | 5.1.1 |
Component: | Bio-Formats | Version: | 5.0.8 |
Keywords: | n.a. | Cc: | holger.vogel@…, mlinkert |
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/10480/
java.lang.IllegalArgumentException: 0 must not be null and positive. at ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:48) at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:271) at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:234) at loci.formats.MetadataTools.populatePixels(MetadataTools.java:134) at loci.formats.in.LIFReader.initMetadata(LIFReader.java:566) at loci.formats.in.LIFReader.initFile(LIFReader.java:459) 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: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:6738) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1186) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:80) 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) at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:668) 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:6738) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1186) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:80) 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) Caused by: java.lang.IllegalArgumentException: 0 must not be null and positive. at ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:48) at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:271) at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:234) at loci.formats.MetadataTools.populatePixels(MetadataTools.java:134) at loci.formats.in.LIFReader.initMetadata(LIFReader.java:566) at loci.formats.in.LIFReader.initFile(LIFReader.java:459) 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) ... 16 more
Change History (8)
comment:1 Changed 9 years ago by mlinkert
- Component changed from from QA to Bio-Formats
- Milestone changed from Unscheduled to 5.1.1
- Owner changed from mlinkert-x to mlinkert
comment:2 Changed 9 years ago by jburel
comment:3 Changed 9 years ago by mlinkert
Does LAS AF Lite (the free viewer from Leica) also show sizeX == 0 for those 6 images? If so, it's probably fine to ignore them and keep the remaining 3; otherwise, the sizeX setting will need to be fixed.
comment:4 Changed 9 years ago by jburel
I have not tried it yet.
comment:5 Changed 9 years ago by jburel
- Owner changed from mlinkert to jburel
comment:6 Changed 9 years ago by jburel
- Cc mlinkert added
comment:7 Changed 9 years ago by jburel
6 out of the 9 are listed under LAS AF lite as ClimateDataGraph(Value, t) Value being 22, 72 etc
comment:8 Changed 9 years ago by jburel
- Resolution set to fixed
- Status changed from new to closed
The file is composed of 9 images. 6 of them have a sizeX = 0 leading to the error
The other sizes (y,c,z,t) are > 0.
Do we exclude those images in that case?