[ome-devel] Importing .dm4 files

Balaji Ramalingam (Staff) b.ramalingam at dundee.ac.uk
Wed Oct 14 15:05:04 BST 2015 

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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