Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #5513 (closed)

Opened 8 years ago

Closed 8 years ago

Validate OME-TIFF export after schema changes

Reported by: jamoore Owned by: jamoore
Priority: minor Milestone: OMERO-Beta4.3
Component: Export Version: n.a.
Keywords: n.a. Cc: ajpatterson, cxallan, saloynton
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2011-06-02 (13)

Description

After the recent schema changes, there may be also need to be changes made to export. A few exported files should be checked visibly to ensure they are sensible, as well as using xmllint --schema and re-importing.

Change History (2)

comment:1 Changed 8 years ago by jmoore

  • Remaining Time set to 0.25
  • Status changed from new to accepted

comment:2 Changed 8 years ago by jmoore

  • Remaining Time changed from 0.25 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed

Chris, as far as I can tell, these all look fine:

~/NoBackup/SampleImages/oif $ l
total 84752
drwxr-xr-x   10 moore  wheel       340 May 25 09:41 .
drwxr-xr-x   21 moore  moore       714 May 20 12:36 ..
-rw-r--r--    1 moore  wheel      6148 Apr 16  2009 .DS_Store
-rwxr-xr-x    1 moore  wheel     59484 Apr  6  2009 31h_pea3_fgf10_01_1.oif
drwxr-xr-x  140 moore  wheel      4760 Apr  6  2009 31h_pea3_fgf10_01_1.oif.files
-rw-r--r--    1 moore  wheel  36978335 May 24 12:09 Image15737.ome.tiff
-rw-r--r--    1 moore  wheel     11028 May 25 09:40 Image15737.ome.xml
-rw-r--r--    1 moore  wheel   6319018 May 24 12:08 Image15738.ome.tiff
-rw-r--r--    1 moore  wheel      2447 May 25 09:40 Image15738.ome.xml
-rw-r--r--    1 moore  wheel      4239 Apr 23  2009 test_setup.ini
~/NoBackup/SampleImages/oif $ xmllint --schema http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd Image15738.ome.xml 
<?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/2011-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:5fe16688-74d2-4533-bde8-57def9e8d395" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2011-06 http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd">
  <Image ID="urn:lsid:export.openmicroscopy.org:Image:2c0c47c1-112a-459b-a5d6-a08e9cef59a9_15738:127171" Name="Series 2">
    <AcquiredDate>2009-04-06T05:37:49</AcquiredDate>
    <Pixels DimensionOrder="XYZCT" ID="urn:lsid:export.openmicroscopy.org:Pixels:2c0c47c1-112a-459b-a5d6-a08e9cef59a9_15638:127215" PhysicalSizeX="0.155" PhysicalSizeY="0.155" PhysicalSizeZ="1.0" SizeC="3" SizeT="1" SizeX="1024" SizeY="1024" SizeZ="1" TimeIncrement="1.0" Type="uint16">
      <Channel Color="-16776961" ID="urn:lsid:export.openmicroscopy.org:Channel:2c0c47c1-112a-459b-a5d6-a08e9cef59a9_39563:127420" IlluminationType="Epifluorescence" SamplesPerPixel="1">
        <LightPath/>
      </Channel>
      <Channel Color="16711935" ID="urn:lsid:export.openmicroscopy.org:Channel:2c0c47c1-112a-459b-a5d6-a08e9cef59a9_39564:127420" IlluminationType="Epifluorescence" SamplesPerPixel="1">
        <LightPath/>
      </Channel>
      <Channel Color="65535" ID="urn:lsid:export.openmicroscopy.org:Channel:2c0c47c1-112a-459b-a5d6-a08e9cef59a9_39565:127420" IlluminationType="Epifluorescence" SamplesPerPixel="1">
        <LightPath/>
      </Channel>
      <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
        <UUID FileName="__omero_export__2045410992254193899.ome.tiff">urn:uuid:5fe16688-74d2-4533-bde8-57def9e8d395</UUID>
      </TiffData>
      <TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1">
        <UUID FileName="__omero_export__2045410992254193899.ome.tiff">urn:uuid:5fe16688-74d2-4533-bde8-57def9e8d395</UUID>
      </TiffData>
      <TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1">
        <UUID FileName="__omero_export__2045410992254193899.ome.tiff">urn:uuid:5fe16688-74d2-4533-bde8-57def9e8d395</UUID>
      </TiffData>
    </Pixels>
  </Image>
</OME>
Image15738.ome.xml validates
~/NoBackup/SampleImages/oif $ xmllint --schema http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd Image15737.ome.xml 
<?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/2011-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:d388a6ef-7ed3-4a92-acbd-1eed7895b528" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2011-06 http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd">
  <Image ID="urn:lsid:export.openmicroscopy.org:Image:2c0c47c1-112a-459b-a5d6-a08e9cef59a9_15737:127171" Name="Series 1">
    <AcquiredDate>2009-04-06T05:37:49</AcquiredDate>
    <Pixels DimensionOrder="XYZCT" ID="urn:lsid:export.openmicroscopy.org:Pixels:2c0c47c1-112a-459b-a5d6-a08e9cef59a9_15637:127419" PhysicalSizeX="0.155" PhysicalSizeY="0.155" PhysicalSizeZ="1.0" SizeC="3" SizeT="1" SizeX="1024" SizeY="428" SizeZ="14" TimeIncrement="1.0" Type="uint16">
      <Channel Color="65535" EmissionWavelength="461" ExcitationWavelength="405" ID="urn:lsid:export.openmicroscopy.org:Channel:2c0c47c1-112a-459b-a5d6-a08e9cef59a9_39560:127420" IlluminationType="Epifluorescence" Name="CHS1" SamplesPerPixel="1">
        <LightPath/>
      </Channel>
      <Channel Color="16711935" EmissionWavelength="520" ExcitationWavelength="488" ID="urn:lsid:export.openmicroscopy.org:Channel:2c0c47c1-112a-459b-a5d6-a08e9cef59a9_39561:127420" IlluminationType="Epifluorescence" Name="CHS2" SamplesPerPixel="1">
        <LightPath/>
      </Channel>
      <Channel Color="-16776961" EmissionWavelength="603" ExcitationWavelength="561" ID="urn:lsid:export.openmicroscopy.org:Channel:2c0c47c1-112a-459b-a5d6-a08e9cef59a9_39562:127420" IlluminationType="Epifluorescence" Name="CH3" SamplesPerPixel="1">
        <LightPath/>
      </Channel>
      <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
        <UUID FileName="__omero_export__3174325851288537932.ome.tiff">urn:uuid:d388a6ef-7ed3-4a92-acbd-1eed7895b528</UUID>
      </TiffData>
      ....
    </Pixels>
  </Image>
</OME>
Image15737.ome.xml validates
Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.81480 sec.)

© 2000-2014 University of Dundee & Open Microscopy Environment. Creative Commons Attribution 3.0 Unported License
OME source code is available under the GNU General public license or through commercial license from Glencoe Software

We're Hiring!