[ome-devel] Importing .dm4 files

[Andrii Iudin]

Dear OMERO Developers,

As we are developing the EMPIAR (Electron Microscopy Pilot Image 
Archive) and would like to use OMERO to visualize data, we would like to 
ask if you could, please, check some of the files that are stored in 
EMPIAR for issues when doing an import using 
OMERO.insight-5.1.4-ice35-b55-mac_Java6.
For .mrcs, dat (Spider) and .img files we have submitted a ticket
http://qa.openmicroscopy.org.uk/qa/feedback/16850/

However, one of the cases cannot be submitted due to the limitation of 2 
GB for the upload. Please could you check the following file (size 8.66 GB):
BGal_000438_frames.dm4
which can be downloaded on the page 
http://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10013/ in "sample" directory?

It produces the "File Not Valid" error

loci.formats.FormatException: Unsupported byte depth: 472
     at loci.formats.FormatTools.pixelTypeFromBytes(FormatTools.java:883)
     at loci.formats.in.GatanReader.initFile(GatanReader.java:216)
     at loci.formats.FormatReader.setId(FormatReader.java:1426)
     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:650)
     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:6871)
     at 
org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1033)
     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:695)

     at 
org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:673)
     at 
ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:530)
     at 
ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:465)
     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:6871)
     at 
org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1033)
     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:695)
Caused by: loci.formats.FormatException: Unsupported byte depth: 472
     at loci.formats.FormatTools.pixelTypeFromBytes(FormatTools.java:883)
     at loci.formats.in.GatanReader.initFile(GatanReader.java:216)
     at loci.formats.FormatReader.setId(FormatReader.java:1426)
     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:650)
     at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
     at 
ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
     ... 16 more


Please note that other .dm4 files can be imported fine. For example, on 
page
http://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10013/

in folder 2dxtal_B for file JapanB0021.dm4 import works.

Thank you and best regards,
Andrii