Task #9600 (closed)
Opened 12 years ago
Closed 12 years ago
Bug: Some Ultraview datasets do not open
Reported by: | omero-qa | Owned by: | mlinkert |
---|---|---|---|
Priority: | blocker | Milestone: | OMERO-4.4.4 |
Component: | Bio-Formats | Version: | n.a. |
Keywords: | n.a. | Cc: | helio.roque@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | 2012-09-25 (5) |
Description
The source of the problem seems to be having some pixels files that contain a single Z section mixed with some pixels files that contain all of the Z sections for a particular timepoint. See the file listing in the QA comment.
http://qa.openmicroscopy.org.uk/qa/feedback/4625/
Comment: Even choosing the htm file the dataset still fails.
java.lang.ArrayIndexOutOfBoundsException: 6698 at loci.formats.in.PerkinElmerReader.initFile(PerkinElmerReader.java:385) at loci.formats.FormatReader.setId(FormatReader.java:1105) at loci.formats.ImageReader.setId(ImageReader.java:695) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505) at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505) at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:310) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:486) at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6335) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1248) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110) at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) at java.lang.Thread.run(Thread.java:680)
Change History (3)
comment:1 Changed 12 years ago by mlinkert
- Component changed from from QA to Bio-Formats
- Milestone changed from Unscheduled to OMERO-4.4.4
- Priority changed from minor to major
- Sprint set to 2012-09-25 (5)
comment:2 Changed 12 years ago by jmoore
- Priority changed from major to blocker
comment:3 Changed 12 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
Elevating to blocker if it's to be included in 4.4.4