[ome-users] LSM import failed.

Thu Nov 25 12:13:46 GMT 2010

Hi Melissa,

Here are the MDB/LDB files and the first LSM:
http://cmpdartsvr1.cmp.uea.ac.uk/downloads/data/Tubulin_101108.mdb/

Here is the exact original folder contents:

All_tub_40_25min_01__Sum0.lsm
All_tub_40_25min_01__Sum.lsm
All_tub_40_25min_02__Sum.lsm
All_tub_40_25min_03__Sum0.lsm
All_tub_40_25min_03__Sum1.lsmAll_tub_40_25min_03__Sum.lsm
All_tub_40_25min_07__Sum0.lsm
All_tub_40_25min_07__Sum1.lsm
All_tub_40_25min_07__Sum2.lsm
All_tub_40_25min_07__Sum3.lsm
All_tub_40_25min_07__Sum4.lsm
All_tub_40_25min_07__Sum5.lsm
All_tub_40_25min_07__Sum.lsm
All_tub_40_25min_15__Sum.lsm
kimkong_z15.lsm
MT_z05_thurs.lsm
Tubulin_101108.ldb
Tubulin_101108.mdb

Total is about 20GB so not easy to make them all available to you... Though you might not need everything anyways... Full error log from OMERO.importer attached.
I've attached the DEBUG and  OUTPUT logs from OMERO.importer... See the previous emails for the ERROR prompt and the JavaIO error generated.

I also tried loading one of the LSM files (first one) from that folder, with FIJI with the trunk of bioformats and get the same error.. Full stack trace from FIJI found below:

java.io.EOFException: Attempting to read beyond end of file.
 at loci.common.NIOFileHandle.readByte(NIOFileHandle.java:219)
 at loci.common.RandomAccessInputStream.readByte(RandomAccessInputStream.java:286)
 at loci.common.RandomAccessInputStream.read(RandomAccessInputStream.java:403)
 at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:351)
 at loci.formats.FormatReader.setId(FormatReader.java:1067)
 at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:328)
 at loci.formats.FormatReader.setId(FormatReader.java:1067)
 at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:432)
 at loci.plugins.in.ImportProcess.execute(ImportProcess.java:136)
 at loci.plugins.in.Importer.showDialogs(Importer.java:125)
 at loci.plugins.in.Importer.run(Importer.java:77)
 at loci.plugins.LociImporter.run(LociImporter.java:77)
 at ij.IJ.runUserPlugIn(IJ.java:193)
 at ij.IJ.runPlugIn(IJ.java:154)
 at ij.Executer.runCommand(Executer.java:147)
 at ij.Executer.run(Executer.java:78)
 at java.lang.Thread.run(Thread.java:619)
Caused by: java.nio.BufferUnderflowException
 at java.nio.Buffer.nextGetIndex(Buffer.java:474)
 at java.nio.HeapByteBuffer.get(HeapByteBuffer.java:117)
 at loci.common.NIOFileHandle.readByte(NIOFileHandle.java:217)
 ... 16 more

Let me know if you need anything else,
And thanks for your time/help!!

Jerome.

> Date: Wed, 24 Nov 2010 11:52:18 -0600
> From: melissa at glencoesoftware.com
> To: jeromeavondo at msn.com
> CC: j.burel at dundee.ac.uk; ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] LSM import failed.
> 
> Hi Jerome,
> 
> > That file is from a user's directory that contains more then one LSM in it (raw data and projections) and an .mdb file...
> > If I add all the LSM files and ignore the .mdb file to the import queue in OMERO.importer, and try an import that is when it fails.
> 
> That's certainly something we can fix, but we'll need to see the .mdb file in
> order to do so. Could you please send the corresponding .mdb file and perhaps
> the full text of the error message? If you need somewhere to upload it, just
> let me know and I can send you our SFTP server information off-list.
> 
> > So, OMERO.importer is still reading the mdb file even if I don't select it for import. Would it not be better to read the mdb file only if selected? If I don't select something for import I would excpect that to be the outcome.... But again there might be good reasons for you to do what you do... :)
> 
> The .mdb file is always included if it references one of the selected LSM files.
> It should not be included if you only select LSM files that are not referenced
> by the .mdb file.
> 
> Regards,
> -Melissa
> 
> On Tue, Nov 23, 2010 at 02:49:58PM +0000, Jerome Avondo wrote:
> > 
> > Hi Jmarie,
> > 
> > Right I have understood what is going on...
> > 
> > That file is from a user's directory that contains more then one LSM in it (raw data and projections) and an .mdb file...
> > If I add all the LSM files and ignore the .mdb file to the import queue in OMERO.importer, and try an import that is when it fails.
> > 
> > If I move all the LSM files to a new directory, without the .mdb file, then the import succeeds....
> > 
> > So, OMERO.importer is still reading the mdb file even if I don't select it for import. Would it not be better to read the mdb file only if selected? If I don't select something for import I would excpect that to be the outcome.... But again there might be good reasons for you to do what you do... :)
> > 
> > I think the problem we have with the current approach is that users like to create their data by some imaging runs, so lots of LSMs and the mdb, then also produce projections for this data, so there are further LSMs not associated to the .mdb and all of these are stored in the same experiment folder....
> > 
> > J.
> > 
> > 
> > 
> > Date: Tue, 23 Nov 2010 13:14:39 +0000
> > From: j.burel at dundee.ac.uk
> > To: jeromeavondo at msn.com
> > CC: ome-users at lists.openmicroscopy.org.uk
> > Subject: Re: [ome-users] LSM import failed.
> > 
> > 
> > 
> > Hi Jerome 
> > 
> > If you use the released version 4.2.1, it should work. 
> > I have just imported the LSM file. 
> > 
> > http://www.openmicroscopy.org.uk/site/support/omero4/downloads 
> > 
> > 
> > Jmarie 
> > 
> > 
> > ************************************************************
> > Please consider the environment. Do you really need to print this email? 
> > 
> > 
> > 
> 
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> 

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