[ome-users] OMERO 5 Flex Import Problem
Melissa Linkert
melissa at glencoesoftware.com
Thu Nov 14 01:21:26 GMT 2013
Hi Christophe,
> I tried using the new OMER 5.0 beta to import flex files from the PerkinElmer Opera.
>
> I configure a CIA in the import.ini file and it starts to import correctly but then fails on importing the metadata.
>
> I then used Insight -> Import and selected the corresponding .mea file. Then I clicked Import.
>
> Here is an excerpt from the log file.
Thank you for the report.
Unfortunately, that piece of the log file doesn't show the import
failure. Could you please send the complete log file, either to the
list or as a Zip file to http://qa.openmicroscopy.org.uk/qa/upload/ ?
Alternately, you can try the import again and then click the button in
the error window to submit the error report directly from Insight.
Regards,
-Melissa
On Tue, Nov 12, 2013 at 05:47:58PM +0000, Christophe TREFOIS wrote:
> Dear all,
>
> I tried using the new OMER 5.0 beta to import flex files from the PerkinElmer Opera.
>
> I configure a CIA in the import.ini file and it starts to import correctly but then fails on importing the metadata.
>
> I then used Insight -> Import and selected the corresponding .mea file. Then I clicked Import.
>
> Here is an excerpt from the log file.
>
> 2013-11-12 18:15:53,280 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470
> 2013-11-12 18:15:53,280 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader map values: \\10.79.2.101\hcs\OperaArchiveCol<file:///\\10.79.2.101\hcs\OperaArchiveCol>
> 2013-11-12 18:15:53,285 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Added Flex reader server map 'CIA-1' = '\\10.79.2.101\hcs\OperaArchiveCol'.
> 2013-11-12 18:15:53,285 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) Bioformats version: 5.0.0-beta1 revision: 3a84df1 date: 19 June 2013
> 2013-11-12 18:15:53,385 DEBUG [penmicroscopy.shoola.util.NetworkChecker] ( Thread-22) Network status: true (in 99 ms.)
> 2013-11-12 18:15:54,383 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470
> 2013-11-12 18:15:54,383 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader map values: \\10.79.2.101\hcs\OperaArchiveCol<file:///\\10.79.2.101\hcs\OperaArchiveCol>
> 2013-11-12 18:15:54,386 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Added Flex reader server map 'CIA-1' = '\\10.79.2.101\hcs\OperaArchiveCol'.
> 2013-11-12 18:15:54,386 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) Bioformats version: 5.0.0-beta1 revision: 3a84df1 date: 19 June 2013
> 2013-11-12 18:16:01,674 DEBUG [ ome.scifio.io.Location] ( Thread-22) Location.mapFile: embedded-stream.raw -> null
> 2013-11-12 18:16:01,980 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470
> 2013-11-12 18:16:01,980 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader map values: \\10.79.2.101\hcs\OperaArchiveCol<file:///\\10.79.2.101\hcs\OperaArchiveCol>
> 2013-11-12 18:16:01,984 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Added Flex reader server map 'CIA-1' = '\\10.79.2.101\hcs\OperaArchiveCol'.
> 2013-11-12 18:16:01,984 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) Bioformats version: 5.0.0-beta1 revision: 3a84df1 date: 19 June 2013
> 2013-11-12 18:16:01,986 INFO [ ome.formats.importer.ImportCandidates] ( Thread-22) Depth: 4 Metadata Level: MINIMUM
> 2013-11-12 18:16:02,008 DEBUG [ ome.scifio.io.Location] ( Thread-22) Location.mapFile: embedded-stream.raw -> null
> 2013-11-12 18:16:02,182 INFO [ loci.formats.ImageReader] ( Thread-22) FlexReader initializing V:\OperaDB_Backups\2013\2013_11\OperaDB_2013_Nov\Christophe Trefois\CT 2013.11.08_Rotenone_Paraquat\Settings\Beads control\CT 20131109_BeadsControl\Meas_01\Meas_01(2013-11-09_13-13-12).mea
> 2013-11-12 18:16:02,183 INFO [ loci.formats.FormatHandler] ( Thread-22) Reading contents of .mea file
> 2013-11-12 18:16:02,183 INFO [ loci.formats.FormatHandler] ( Thread-22) Parsing XML from .mea file
> 2013-11-12 18:16:03,094 INFO [ loci.formats.FormatHandler] ( Thread-22) Looking for corresponding .res file
> 2013-11-12 18:16:03,094 INFO [ loci.formats.FormatHandler] ( Thread-22) Looking for files that are in the same dataset as V:\OperaDB_Backups\2013\2013_11\OperaDB_2013_Nov\Christophe Trefois\CT 2013.11.08_Rotenone_Paraquat\Settings\Beads control\CT 20131109_BeadsControl\Meas_01\Meas_01(2013-11-09_13-13-12).mea
> 2013-11-12 18:16:03,208 INFO [ loci.formats.FormatHandler] ( Thread-22) Grouping together files in the same dataset
> 2013-11-12 18:16:34,782 INFO [ loci.formats.FormatHandler] ( Thread-22) Parsing IFDs for well D6
> 2013-11-12 18:16:35,084 INFO [ loci.formats.FormatHandler] ( Thread-22) Parsing .flex file (well D6)
> 2013-11-12 18:16:35,086 INFO [ loci.formats.FormatHandler] ( Thread-22) Parsing XML in .flex file
> 2013-11-12 18:16:35,090 INFO [ loci.formats.FormatHandler] ( Thread-22) Populating core metadata for well row 3, column 5
> 2013-11-12 18:16:35,090 INFO [ loci.formats.FormatHandler] ( Thread-22) Populating pixel scaling factors
> 2013-11-12 18:16:35,090 WARN [ loci.formats.FormatHandler] ( Thread-22) mismatch between image count, names and factors (count=9, names=3, factors=3)
>
> Any help on this might be very helpful as I think I'm missing something here...
>
> Thank you for your help.
>
>
>
> ................................................................................
>
> Dipl.-Ing. Christophe TREFOIS
> Ing. Sys. Com. Dipl. EPF
>
> PhD Candidate
>
>
> Université du Luxembourg | University of Luxembourg
>
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>
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