importing ome-tiff

[jburel]

• import ome-tiff from QA 2973. Import seems to work but after we have the following exception

  Caused by: omero.InternalException
      serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.IndexOutOfBoundsException):
                          Index: 1, Size: 1
                          	at java.util.ArrayList.RangeCheck(ArrayList.java:546)
                          	at java.util.ArrayList.get(ArrayList.java:321)
                          	at ome.logic.RenderingSettingsImpl.resetChannelBindings(RenderingSettingsImpl.java:702)
                          	at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:535)
                          	at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:454)
                          	at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:1233)
                          	at ome.services.RenderingBean$13.doWork(RenderingBean.java:1542)
  

• import Ome-tiff from QA 2965. Import ok, black images

[bwzloranger]

Updated BF to 7157 in commit r8549 (which should fix this problem)

[jburel]

commit r8549 fixes the first problem
The second one is working, needs to figure out why the channels are black. If I turned then to red and white, I can see what's there.
Closing ticket

[jburel]

re-opening. Second one (i.e. QA 2965) is importing
but the metadata are not. If I open the file I can see the following

<?xml version="1.0"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2008-02" xmlns:CA="http://www.openmicroscopy.org/Schemas/CA/2008-02" xmlns:STD="http://www.openmicroscopy.org/Schemas/STD/2008-02" xmlns:Bin="http://www.openmicroscopy.org/Schemas/BinaryFile/2008-02" xmlns:SPW="http://www.openmicroscopy.org/Schemas/SPW/2008-02" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2008-02 http://www.openmicroscopy.org/Schemas/OME/2008-02/ome.xsd" UUID="urn:uuid:583e4cdd-e828-41d1-a75e-b53caa8876ee"><Experiment ID="urn:lsid:loci.wisc.edu:Experiment:OWS348" Type="PGIDocumentation"><Description>4 Cell Embryo</Description><ExperimenterRef ID="urn:lsid:loci.wisc.edu:Experimenter:116"/></Experiment><Experimenter ID="urn:lsid:loci.wisc.edu:Experimenter:116"><FirstName>Maimoon</FirstName><LastName>Nasim</LastName><Email>mnasim@wisc.edu</Email><Institution></Institution><GroupRef ID="urn:lsid:loci.wisc.edu:Group:3"/></Experimenter><Instrument ID="urn:lsid:loci.wisc.edu:Instrument:OWS1"><Microscope Manufacturer="Nikon" Model="Eclipse TE300" SerialNumber="U629762" Type="Inverted"/><LightSource ID="urn:lsid:loci.wisc.edu:LightSource:OWS1" Manufacturer="Spectral Physics" Model="Tsunami 5W" SerialNumber="2123"><Laser Type="SolidState" LaserMedium="TiSapphire"/></LightSource><Detector ID="urn:lsid:loci.wisc.edu:Detector:OWS1" Type="PMT" Manufacturer="Hamamatzu" Model="H7422"/><Detector ID="urn:lsid:loci.wisc.edu:Detector:OWS2" Type="Photodiode" Manufacturer="Bio-Rad" Model="1024TLD"/><Objective ID="urn:lsid:loci.wisc.edu:Objective:OWS2" Manufacturer="Nikon" Model="S Fluor" SerialNumber="044989"><Correction>PlanApo</Correction><Immersion>Oil</Immersion><LensNA>1.40</LensNA><NominalMagnification>100</NominalMagnification><CalibratedMagnification>100.0</CalibratedMagnification><WorkingDistance>0.13</WorkingDistance></Objective></Instrument><Image Name="tubhiswt" ID="urn:lsid:loci.wisc.edu:Image:OWS348" DefaultPixels="urn:lsid:loci.wisc.edu:Pixels:OWS348"><CreationDate>2005-12-09T17:16:09</CreationDate><ExperimenterRef ID="urn:lsid:loci.wisc.edu:Experimenter:116"/><LogicalChannel ID="urn:lsid:loci.wisc.edu:LogicalChannel:OWS348-1"><LightSourceRef ID="urn:lsid:loci.wisc.edu:LightSource:OWS1"/><DetectorRef ID="urn:lsid:loci.wisc.edu:Detector:OWS1"/><ChannelComponent Pixels="urn:lsid:loci.wisc.edu:Pixels:OWS348" Index="1"/></LogicalChannel><LogicalChannel ID="urn:lsid:loci.wisc.edu:LogicalChannel:OWS348-2"><LightSourceRef ID="urn:lsid:loci.wisc.edu:LightSource:OWS1"/><DetectorRef ID="urn:lsid:loci.wisc.edu:Detector:OWS2"/><ChannelComponent Pixels="urn:lsid:loci.wisc.edu:Pixels:OWS348" Index="0"/></LogicalChannel><Pixels PixelType="uint8" SizeX="512" SizeY="512" SizeZ="1" DimensionOrder="XYZTC" ID="urn:lsid:loci.wisc.edu:Pixels:OWS348" BigEndian="false" SizeC="2" SizeT="1"><TiffData FirstC="0"><UUID FileName="tubhiswt_C1.ome.tif">urn:uuid:1fdb0a1a-5374-46da-bd24-d04e8cbf3175</UUID></TiffData><TiffData FirstC="1"><UUID FileName="tubhiswt_C2.ome.tif">urn:uuid:583e4cdd-e828-41d1-a75e-b53caa8876ee</UUID></TiffData></Pixels></Image></OME>

[jburel]

Sorry for the cut and paste. Just open the content of the file and you will see that the metadata are not imported