Omero and amira files

[robert.stanislawiak]

hello, i can`t upload amira .hx files to the system - it says "not amira file". Can I know somehow attach .hx files to recently uploaded amira .am files to achieve somekind 3D visualization ?

loci.formats.FormatException: Syntax Error:0:0: Doesn't seem to be an Amira file
at loci.formats.tools.AmiraParameters.syntaxError(AmiraParameters.java:160)
at loci.formats.tools.AmiraParameters.readFile(AmiraParameters.java:112)
at loci.formats.tools.AmiraParameters.<init>(AmiraParameters.java:82)
at loci.formats.in.AmiraReader.initFile(AmiraReader.java:123)
at loci.formats.FormatReader.setId(FormatReader.java:1244)
at loci.formats.ImageReader.setId(ImageReader.java:727)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:323)
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:499)
at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6369)
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1347)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Unknown Source)

at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6423)
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1347)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Unknown Source)
Caused by: loci.formats.FormatException: Syntax Error:0:0: Doesn't seem to be an Amira file
at loci.formats.tools.AmiraParameters.syntaxError(AmiraParameters.java:160)
at loci.formats.tools.AmiraParameters.readFile(AmiraParameters.java:112)
at loci.formats.tools.AmiraParameters.<init>(AmiraParameters.java:82)
at loci.formats.in.AmiraReader.initFile(AmiraReader.java:123)
at loci.formats.FormatReader.setId(FormatReader.java:1244)
at loci.formats.ImageReader.setId(ImageReader.java:727)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:323)
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:499)
at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6369)
... 11 more

Regards
Robert Stanislawiak

[rleigh]

Dear Robert,

If the uploader doesn't recognise the specific file format (its list isn't comprehensive), you can always put it into a .zip file and upload the zip. This is also the easiest way to upload multiple files.


Regards,
Roger

[rleigh]

Dear Robert,

Sorry, my previous reply was due to misreading your problem.

If the import process isn't recognising your file as being valid, it's possible that it's a variant of the Amira format which we haven't seen before and don't yet support. If you could possibly upload a zipfile containing an example file (plus any companion files which accompany it) using https://www.openmicroscopy.org/qa2/qa/upload/ we can take a look in more detail at where the problem lies, and if the Amira reader doesn't support this file type yet, we can investigate adding support for it.


Many thanks,
Roger Leigh