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

[jburel]

Opening the image in !ImageJ using the loci-plugin, I select metadata only, microscope etc not displayed

[jburel]

Clarification:

• metadata are read
• metadata linked to channel i.e. detector, light source are imported and correctly linked
• Objective, instrument are read and inserted in the DB but not linked to the image. i.e. image.instrument = null b/c no instrument ref. Question: should we, in that case, insert instrument, objective etc?
• Nothing in Original metadata file.

[jburel]

Why do the channels are black?
Nothing in the file indicate to set the channel to black but when the image is imported
we have in the channel table, red = green = blue = 0

[mlinkert]

Replying to jburel:

Why do the channels are black?
Nothing in the file indicate to set the channel to black but when the image is imported
we have in the channel table, red = green = blue = 0

When the OME-XML in the file goes through the 2008-09 -> 2009-09 stylesheet, a default value of "4294967295" is inserted for the values of Channel.Color. When the XML then goes through the 2010-04 -> 2010-06 stylesheet, this value is converted to "-2147483648" (0x80000000). According to the schema documentation, this should correspond to 0xffffffff.

However, in OMEROMetadataStoreClient.setChannelColor, we have:

  Channel o = getChannel(imageIndex, channelIndex);
  Color c = new Color(color);
  o.setRed(toRType(c.getRed()));
  o.setGreen(toRType(c.getGreen()));
  o.setBlue(toRType(c.getBlue()));
  o.setAlpha(toRType(c.getAlpha()));

Because 'color' is 0x80000000, c.getRed(), c.getGreen(), etc. return 0. One option would be to convert the Integer color to a java.awt.Color like this:

  int unsignedColor = color;
  if (unsignedColor < 0) {
    unsignedColor += 2147483647;
    // unsignedColor should now be '0xffffffff' (but you'll want to double-check)
  }
  Color c = new Color(unsignedColor, true);

[jburel]

Thanks for the clarification, I forgot about the XML conversion discussion.

[jburel]

Black images due to a bug in the stylesheet. Adding Andrew to the ticket

[ajpatterson]

Changed the calculation used in the transform. I thought it had to work in a different way. The up-shot of this was the direction of the negative part of the range was backwards.
​http://www.ome-xml.org/changeset/691

[ajpatterson]

• Old, the version from the 2010-04 file
• New-Fix, the version now
• Bug, the version before this fix

  R   G   B   A       Decimal-Old Hex-Old     Decimal-New-Fix Decimal-Bug
  0   0   0   0       0           00000000    0               0
  0   0   0   255     255         000000FF    255 255
  0   0   255 0       65280       0000FF00    65280           65280
  0   0   255 255     65535       0000FFFF    65535           65535
  0   255 0   0       16711680    00FF0000    16711680        16711680
  0   255 0   255     16711935    00FF00FF    16711935        16711935
  0   255 255 0       16776960    00FFFF00    16776960        16776960
  0   255 255 255     16777215    00FFFFFF    16777215        16777215
  127 255 255 254     2147483646  7FFFFFFE    2147483646      2147483646
  127 255 255 255     2147483647  7FFFFFFF    2147483647      2147483647
  128 0   0   0       2147483648  80000000    -2147483648     2147483648
  128 0   0   1       2147483649  80000001    -2147483647     -1
  128 0   0   2       2147483650  80000002    -2147483646     -2
  128 255 255 254     2164260862  80FFFFFE    -2130706434     -16777214
  128 255 255 255     2164260863  80FFFFFF    -2130706433     -16777215
  129 0   0   0       2164260864  81000000    -2130706432     -16777216
  129 0   0   1       2164260865  81000001    -2130706431     -16777217
  129 255 255 255     2181038079  81FFFFFF    -2113929217     -33554431
  255 0   0   0       4278190080  FF000000    -16777216       -2130706432
  255 0   0   255     4278190335  FF0000FF    -16776961       -2130706687
  255 0   255 0       4278255360  FF00FF00    -16711936       -2130771712
  255 0   255 255     4278255615  FF00FFFF    -16711681       -2130771967
  255 255 0   0       4294901760  FFFF0000    -65536          -2147418112
  255 255 0   255     4294902015  FFFF00FF    -65281          -2147418367
  255 255 255 0       4294967040  FFFFFF00    -256            -2147483392
  255 255 255 254     4294967294  FFFFFFFE    -2              -2147483646
  255 255 255 255     4294967295  FFFFFFFF    -1              -2147483647
  

[jburel]

latest version of B-F with new stylesheet fixes the problem of black channel.

[cxallan]

(In [8593]) Ensure that an RGBA <--> ARGB conversion happens on import and export. (See #3250)