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Task #11104 (closed)

Opened 11 years ago

Closed 11 years ago

Bug: instrument not properly linked during OME-TIFF import

Reported by: sbesson Owned by: jburel
Priority: major Milestone: OMERO-4.4.9
Component: Import Version: n.a.
Keywords: n.a. Cc: jamoore, mlinkert
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Generated an OME-TIFF using Matlab containing one instrument with one objective linked to the image with an ObjectiveSettings? object.

sebastien@jrs-macbookpro-25399:Desktop $ tiffcomment case1_higherSNR.ome.tiff | xmllint -format -
<?xml version="1.0" encoding="utf-8"?>
<!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://ome-xml.org/wiki/OmeTiff. -->
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2012-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:56afc563-14f9-4531-8089-e0f6f20193d2" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2012-06 http://www.openmicroscopy.org/Schemas/OME/2012-06/ome.xsd">
  <Instrument ID="Instrument:0">
    <Objective ID="Objective:0:0" LensNA="1.45"/>
  </Instrument>
  <Image ID="Image:0">
    <AcquisitionDate>2013-05-06T00:08:47</AcquisitionDate>
    <ObjectiveSettings ID="Objective:0:0"/>
  ...

Imported this OME-TIFF under howe:

hudson@howe:~/OMERO-CURRENT$ bin/omero import ~/case1_higherSNR.ome.tiff -- --debug=DEBUG
Using session 5bbc40e6-775c-4c7a-8dc4-579f114460ea (user-1@localhost:4064). Idle timeout: 10.0 min. Current group: private-1
2013-06-11 21:18:32,572 0          [      main] INFO          ome.formats.importer.ImportConfig  - OMERO Version: 4.4.8-178-195069d-ice33-b266
2013-06-11 21:18:32,578 6          [      main] INFO          ome.formats.importer.ImportConfig  - Bioformats version: 4.4.9-DEV revision: 620cfdf date: 11 June 2013
...
2013-06-11 21:18:35,862 3290       [      main] DEBUG  ormats.importer.cli.LoggingImportMonitor  - BEGIN_SAVE_TO_DB
2013-06-11 21:18:35,862 3290       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - Starting containers....
2013-06-11 21:18:35,862 3290       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Image:0 == omero.model.ImageI@4b3ec2dd,Image:0
2013-06-11 21:18:35,863 3291       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Instrument:0 == omero.model.InstrumentI@56b61c3,Instrument:0
2013-06-11 21:18:35,863 3291       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Pixels:0 == omero.model.PixelsI@4cdf4bfc,Pixels:0
2013-06-11 21:18:35,863 3291       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Channel:0:0 == omero.model.ChannelI@57f5b4d1,Channel:0:0
2013-06-11 21:18:35,863 3291       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LogicalChannel:0:0 == omero.model.LogicalChannelI@44323274,omero.model.LogicalChannel:0:0
2013-06-11 21:18:35,864 3292       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Objective:0:0 == omero.model.ObjectiveI@3b8e80a6,Objective:0:0
2013-06-11 21:18:35,864 3292       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.ObjectiveSettings:0 == omero.model.ObjectiveSettingsI@8a030d6,omero.model.ObjectiveSettings:0
2013-06-11 21:18:35,864 3292       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - Starting references....
2013-06-11 21:18:35,864 3292       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.ObjectiveSettings:0 == Objective:0:0
2013-06-11 21:18:35,864 3292       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - containerCache contains 7 entries.
2013-06-11 21:18:35,864 3292       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - referenceCache contains 1 entries.
2013-06-11 21:18:35,990 3418       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - Saved Pixels with ID: 71574
2013-06-11 21:18:35,990 3418       [      main] DEBUG  ormats.importer.cli.LoggingImportMonitor  - END_SAVE_TO_DB
2013-06-11 21:18:36,078 3506       [      main] DEBUG  ormats.importer.cli.LoggingImportMonitor  - DATASET_STORED

However when loading the image (OMERO.matlab), image.getInstrument() returns null.

Failing file is under /ome/team/sbesson/case1_higherSNR.ome.tiff

Change History (1)

comment:1 Changed 11 years ago by sbesson

  • Resolution set to invalid
  • Status changed from new to closed

As pointed out by Melissa, rewriting the OME-TIFF to set the InstrumentRef? fixed the linkage issue:

  <Instrument ID="Instrument:0">
    <Objective ID="Objective:0:0" LensNA="1.45"/>
  </Instrument>
  <Image ID="Image:0">
    <AcquisitionDate>2013-05-06T00:08:47</AcquisitionDate>
    <InstrumentRef ID="Instrument:0"/>
    <ObjectiveSettings ID="Objective:0:0"/>
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