[ome-devel] Importing .dm4 files

Andrii Iudin andrii at ebi.ac.uk
Wed Oct 14 15:17:12 BST 2015 

Dear Balaji,

What got me confused was that IMOD was able to open the file even 
without .hed present. But since the import works fine when there is 
.hed, then it is okay.

Best regards,
Andrii

On 14/10/2015 15:05, Balaji Ramalingam (Staff) wrote:
> Hi,
>
> That makes complete sense.
> The .hed file is the header file, and it needs to be in the same folder as
> the .img file.
>
> Best,
> Balaji
>
> __________________
> Mr Balaji Ramalingam
> Software Developer
>
> OME Team
> College of Life Sciences
> University of Dundee
>
>
>
>
>
>
> On 13/10/2015 17:19, "Andrii Iudin" <andrii at ebi.ac.uk> wrote:
>
>> Dear Balaji,
>>
>> Thank you for the prompt response and confirming the issues.
>> Sorry, the problem with .img (Imagic) file was that when we tried to
>> import it, we got the "Unknown format" error. However, it imported fine
>> when a corresponding .hed file was placed in the same directory.
>>
>> Best regards,
>> Andrii
>>
>>
>> On 13/10/2015 17:00, Balaji Ramalingam (Staff) wrote:
>>> Hi,
>>>
>>> Thank you for submitting your files to our QA system.
>>> We were able to reproduce the issues on both the cases.
>>>
>>> We have created tickets for the same,
>>> https://trac.openmicroscopy.org/ome/ticket/13057 (Reg: dm4 files)
>>> https://trac.openmicroscopy.org/ome/ticket/13058 (Reg: mrcs files)
>>> https://trac.openmicroscopy.org/ome/ticket/13059 (Reg: Spider files)
>>> and you have been added to the cc list. You will be notified when there
>>> is
>>> a status change on these tickets.
>>>
>>> On a related note,
>>> In the list of files submitted under :
>>> http://qa.openmicroscopy.org.uk/qa/feedback/16850/
>>>
>>> We could identify the .mrcs format
>>> (http://www.ccp4.ac.uk/html/maplib.html#description) and .dat files
>>> (Spider).
>>> Could you please give us a bit of information on the role of the .img
>>> file?
>>> This would help us troubleshoot the issue in better detail.
>>>
>>> Thank you,
>>>
>>> Best,
>>> Balaji
>>>
>>>
>>>
>>> __________________
>>> Mr Balaji Ramalingam
>>> Software Developer
>>>
>>> OME Team
>>> College of Life Sciences
>>> University of Dundee
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 12/10/2015 17:06, "Andrii Iudin" <andrii at ebi.ac.uk> wrote:
>>>
>>>> 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:4
>>>> 14
>>>> )
>>>>       at
>>>>
>>>> ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:5
>>>> 70
>>>> )
>>>>       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(OMER
>>>> OG
>>>> ateway.java:6871)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(Omer
>>>> oI
>>>> mageServiceImpl.java:1033)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile
>>>> (I
>>>> magesImporter.java:79)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000
>>>> (I
>>>> magesImporter.java:55)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(I
>>>> ma
>>>> gesImporter.java:104)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java
>>>> :1
>>>> 44)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(Composi
>>>> te
>>>> Task.java:226)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(Compo
>>>> si
>>>> teBatchCall.java:126)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand
>>>> .j
>>>> ava:165)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.
>>>> ja
>>>> va:276)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(As
>>>> yn
>>>> cProcessor.java:91)
>>>>       at java.lang.Thread.run(Thread.java:695)
>>>>
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.j
>>>> av
>>>> a:673)
>>>>       at
>>>>
>>>> ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:5
>>>> 30
>>>> )
>>>>       at
>>>>
>>>> ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:4
>>>> 65
>>>> )
>>>>       at
>>>>
>>>> ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:5
>>>> 70
>>>> )
>>>>       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(OMER
>>>> OG
>>>> ateway.java:6871)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(Omer
>>>> oI
>>>> mageServiceImpl.java:1033)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile
>>>> (I
>>>> magesImporter.java:79)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000
>>>> (I
>>>> magesImporter.java:55)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(I
>>>> ma
>>>> gesImporter.java:104)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java
>>>> :1
>>>> 44)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(Composi
>>>> te
>>>> Task.java:226)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(Compo
>>>> si
>>>> teBatchCall.java:126)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand
>>>> .j
>>>> ava:165)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.
>>>> ja
>>>> va:276)
>>>>       at
>>>>
>>>> org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(As
>>>> yn
>>>> cProcessor.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:4
>>>> 14
>>>> )
>>>>       ... 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
>>>> _______________________________________________
>>>> ome-devel mailing list
>>>> ome-devel at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
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>
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