search

ome / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
378 stars 242 forks source link

Imaris: null PixelType exception #3653

Open dgault opened 3 years ago

dgault commented 3 years ago

Issue was raised by QA-29769 and a sample file was provided which reproduces the issue with Bio-Formats 6.6.0

The stack trace for the exception is:

loci.formats.FormatException: Unknown pixel type: null
    at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:315)
    at loci.formats.FormatReader.setId(FormatReader.java:1392)
    at loci.formats.ImageReader.setId(ImageReader.java:849)
    at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at loci.formats.Memoizer.setId(Memoizer.java:662)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
    at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
    at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)
    at ome.formats.importer.ImportCandidates.(ImportCandidates.java:222)
    at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174)
    at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5965)
    at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1113)
    at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:103)
    at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:49)
    at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:127)
    at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
    at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
    at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
    at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
    at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
    at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
    at java.lang.Thread.run(Thread.java:748)
sbesson commented 3 years ago

Unsure whether this could help this problem here but https://github.com/ome/bioformats/pull/2928 originally included an extra feature to related to the pixel type detection logic in the Imaris HDF reader (see https://github.com/ome/bioformats/pull/2928/commits/00de4a997115084294de5a4bdc9befdf776653ba).

If the change was sufficient to address issue, it might be possible to reintroduce it for a minor release. The blocker back then was the addition of a new method to the NetCDFService interface is a breaking change. Since then, the minimal Java version was increased to 8+ and we should be able to make use of the default methods introduced in Java 8.