Task #10234 (closed)
Bug: truncated .fits files cannot be imported
Reported by: | omero-qa | Owned by: | mlinkert |
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Priority: | minor | Milestone: | OMERO-4.4.7 |
Component: | Bio-Formats | Version: | n.a. |
Keywords: | n.a. | Cc: | jacques.pecreaux@… |
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/4825/
Comment: Importing a fits file created on an andor iXon+ with software iXon (now named solis). This file contain an inherent bug: the fits file is announced to be of its maximum size (about 4096) but is in fact shorter since acquisition was interupted. It seems to fool the importer since it do import a large number of plane before crashing
java.lang.IllegalArgumentException at java.nio.Buffer.position(Buffer.java:218) at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:535) at loci.common.NIOFileHandle.seek(NIOFileHandle.java:254) at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:140) at loci.formats.in.FitsReader.openBytes(FitsReader.java:87) at loci.formats.ImageReader.openBytes(ImageReader.java:414) at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:226) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:317) at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:273) at ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:876) at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:801) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:577) at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6443) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1250) 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:662)
See also QA 4827.
Change History (3)
comment:1 Changed 11 years ago by mlinkert
- Owner changed from mlinkert-x to mlinkert
comment:2 Changed 11 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
comment:3 Changed 11 years ago by jmoore
- Component changed from from QA to Bio-Formats
- Milestone changed from Unscheduled to OMERO-4.5
Fixed with https://github.com/openmicroscopy/bioformats/pull/408