Bug: sprint10 LEI TransmittanceRange & LightPath

[wmoore]

It seems that one of the commits in sprint10-bug-fixes has lost some of the <TransmittanceRange> elements from
lei files and FilterRefs? in LightPath?.

E.g. If I checkout sprint10-bug-fixes, with graph looking like this:

* a7b5b6c (HEAD, melissa/sprint10-bug-fixes, sprint10-bug-fixes) Prevent potential AIOOB exception
* 936a5fa LEI: populate detectors after parsing is complete
* eb5be58 CZI: check for null transmittance values
* 05d4dd2 Reset the tile count if there is only one series
* 99aff0e Allow 4D data of type uint8
* ab41d1e Remove anything before whitespace in lens ID
* 0692047 Exclude files that do not exist
* 95ed6d5 Increase block size for checking file type
* e74ec6c Adjust the Y coordinate before flipping the plane
* c0804c4 Interpret Leica LIF timestamps as being GMT
* a054802 Output valid MetadataOnly OME-XML
* cb76792 Avoid StringIndexOutOfBounds if units are missing
* 499562e Do not populate ExposureTime for LSM files
* 3df1ab5 Commented out Dichroic -> LightPath and Binning
* 2637b94 Correct for the stage having moved backwards
*   0099bd2 (origin/develop, origin/HEAD, develop) Merge pull request #32 from melissalinkert/sprint9-bug-fixes

I get this:

$ java -Xmx512m loci.formats.tools.ImageInfo -nopix -omexml-only -no-sas -xmlspaces 4 /Users/will/Documents/biology-data/Test-Import-Images/Martin/Leica-SP2/samples-SP2/samples-SP2.lei | grep TransmittanceRange
            <TransmittanceRange CutIn="578" CutOut="629"/>
            <TransmittanceRange CutIn="650" CutOut="700"/>
            <TransmittanceRange CutIn="575" CutOut="693"/>
            <TransmittanceRange CutIn="790" CutOut="800"/>

This is missing some TR element. I checkout develop, build and get this:

$ java -Xmx512m loci.formats.tools.ImageInfo -nopix -omexml-only -no-sas -xmlspaces 4 /Users/will/Documents/biology-data/Test-Import-Images/Martin/Leica-SP2/samples-SP2/samples-SP2.lei | grep TransmittanceRange
            <TransmittanceRange CutIn="578" CutOut="629"/>
            <TransmittanceRange CutIn="500" CutOut="540"/>
            <TransmittanceRange CutIn="650" CutOut="700"/>
            <TransmittanceRange CutIn="500" CutOut="560"/>
            <TransmittanceRange CutIn="575" CutOut="693"/>
            <TransmittanceRange CutIn="790" CutOut="800"/>

The diff looks like this: where

• - is the correct output
• + is what we're getting with sprint10-bug-fixes.

  -        <Filter ID="Filter:1:0" Model="SP Mirror 1">
  -            <TransmittanceRange CutIn="500" CutOut="540"/>
  -        </Filter>
  +        <Filter ID="Filter:1:0" Model="SP Mirror 1"/>
  ...
  -        <Filter ID="Filter:2:0" Model="SP Mirror 1">
  -            <TransmittanceRange CutIn="500" CutOut="560"/>
  -        </Filter>
  +        <Filter ID="Filter:2:0" Model="SP Mirror 1"/>
  

and

@@ -173,26 +169,24 @@
             <Channel Color="16711935" ID="Channel:1:0" PinholeSize="20.420594633792604" SamplesPerPixel="1">
                 <DetectorSettings ID="Detector:1:0"/>
                 <LightPath>
-                    <EmissionFilterRef ID="Filter:1:0"/>
+                    <EmissionFilterRef ID="Filter:1:1"/>
                 </LightPath>
             </Channel>
             <Channel Color="-16776961" ID="Channel:1:1" PinholeSize="20.420594633792604" SamplesPerPixel="1">
                 <DetectorSettings ID="Detector:1:1"/>
-                <LightPath>
-                    <EmissionFilterRef ID="Filter:1:1"/>
-                </LightPath>
+                <LightPath/>
             </Channel>

...

                 <DetectorSettings ID="Detector:2:1"/>
-                <LightPath>
-                    <EmissionFilterRef ID="Filter:2:0"/>
-                </LightPath>
+                <LightPath/>

So it seems the bug is in the list of commits above.

[mlinkert]

Same basic bug as #8213; should be fixed with ​https://github.com/melissalinkert/bioformats/commit/ed5092ac77b80aa8c8dd66921031a2ab1282f22d.

[wmoore]

All looking good now. Closing...