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Task #8168 (closed)

Opened 12 years ago

Closed 12 years ago

Bug: LIF Attenuation

Reported by: wmoore Owned by: wmoore
Priority: minor Milestone: OMERO-4.4
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2012-05-08 (14)

Description

For one of the images in Martin's "sample files.lif", we have an incorrect reading of Attenuation attribute.

With BF built from sprint10-bug-fixes with sprint8-bug-fixes merged in, a diff of the output from 

$ java -Xmx512m loci.formats.tools.ImageInfo -nopix -omexml-only -no-sas -xmlspaces 4 /Users/will/Documents/biology-data/Test-Import-Images/Martin/Leica-SP5/sample\ files.lif

with components/specification/Samples/Repository/MetadataOnly/Leica_LIF/sample_files.ome.xml
gives this:

"+" is what BF build above is reading
"-" is the correct value

     <Image ID="Image:2" Name="series 02 - XYZChBF">

             <Channel Color="65535" ExcitationWavelength="405" ID="Channel:2:0" Name="" PinholeSize="106.08964270380099" SamplesPerPixel="1">
-                <LightSourceSettings Attenuation="0.69999389611182295" ID="LightSource:2:0"/>
+                <LightSourceSettings Attenuation="0.7999756" ID="LightSource:2:0"/>

In the Leica metadata UI, it's displayed as 'Power: 30%'.

Afraid I have no idea why this is the only Image in that file with an incorrect value.

The value seems to currently being read from

<LDM_Block_Sequential_Master>
   <ATLConfocalSettingDefinition>
      <AotfList>
        <Aotf AotfQualifier="20" OpenVirtual="0" IsChanged="0" CanDoPulseFreq="0" PulsFreq="0" AotfType="UV">
              <LaserLineSetting LaserLine="405" IntensityDev="20.0024415552707" IntensityLowDev="0" AOBSIntensityDev="-1" AOBSIntensityLowDev="-1" EnableDoubleMode="0" LineIndex="0" Qualifier="20" SequenceIndex="0" IsLineDeactivated="0" IsLineChecked="0" OutCheckedIntensity="0" SuppressionMode="-1" AotfType="UV" IntensityShow="20.00" />
        </Aotf>

whereas the correct value for the first channel is under

<LDM_Block_Sequential_List>
   <ATLConfocalSettingDefinition>
      <AotfList>
         <Aotf AotfQualifier="20" OpenVirtual="0" IsChanged="1" CanDoPulseFreq="0" PulsFreq="0" AotfType="UV">
            <LaserLineSetting LaserLine="405" IntensityDev="30.0006103888177" IntensityLowDev="0" AOBSIntensityDev="-1" AOBSIntensityLowDev="-1" EnableDoubleMode="0" LineIndex="0" Qualifier="20" SequenceIndex="0" IsLineDeactivated="0" IsLineChecked="0" OutCheckedIntensity="0" SuppressionMode="-1" AotfType="UV" IntensityShow="30.00" />
         </Aotf>

Change History (11)

comment:1 Changed 12 years ago by mlinkert

  • Sprint set to 2012-03-13 (10)

comment:2 Changed 12 years ago by mlinkert

  • Status changed from new to accepted

comment:3 Changed 12 years ago by jburel

  • Sprint changed from 2012-03-13 (10) to 2012-03-27 (11)

Moved from sprint 2012-03-13 (10)

comment:4 Changed 12 years ago by jburel

  • Sprint changed from 2012-03-27 (11) to 2012-04-10 (12)

Moved from sprint 2012-03-27 (11)

comment:5 Changed 12 years ago by jburel

  • Sprint changed from 2012-04-10 (12) to 2012-04-24 (13)

Moved from sprint 2012-04-10 (12)

comment:6 Changed 12 years ago by mlinkert

  • Owner changed from mlinkert-x to wmoore

Should be fixed with ​https://github.com/melissalinkert/bioformats/commit/2b41d583c2fa5dcff3777e23e85abfed0e633319 (sprint13-bug-fixes)

Note that sprint12-bug-fixes hasn't been merged yet, so when you check out sprint13-bug-fixes you'll either need to merge in sprint12-bug-fixes or look past the differences in filter linkages.

comment:7 Changed 12 years ago by wmoore

  • Owner wmoore deleted
  • Status changed from accepted to new

comment:8 Changed 12 years ago by wmoore

  • Owner set to wmoore

comment:9 Changed 12 years ago by jburel

  • Sprint changed from 2012-04-24 (13) to 2012-05-08 (14)

Moved from sprint 2012-04-24 (13)

comment:10 Changed 12 years ago by wmoore

  • Status changed from new to accepted

comment:11 Changed 12 years ago by wmoore

  • Resolution set to fixed
  • Status changed from accepted to closed

Great! When I merge sprint12 and sprint13-bug-fixes I get NO MORE LIF BUGS!

BF writes exactly the LIF that I have in omexml_repo.
Updating the precision of one Attenuation attirbute:

​https://github.com/will-moore/openmicroscopy/commit/7a0e385f2b7116254bf4af4385234e4441170186

Closing...

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