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Task #8213 (closed)

Opened 12 years ago

Closed 12 years ago

Bug: sprint10 LEI Channel Names

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:	n.a.

Description

On spint10-bug-fixes, we're missing a Channel Name from Martin's sample-files.lei (2nd Channel of Image:2):

With sprint10-bug-fixes I get:

$ 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 "Name="
    <Image ID="Image:0" Name="XYZ-Ch">
            <Channel Color="-16776961" ID="Channel:0:0" Name="TRITC" PinholeSize="81.40681653372008" SamplesPerPixel="1">
    <Image ID="Image:1" Name="XY-Ch-trans">
    <Image ID="Image:2" Name="XZY-Ch-trans_y000">
            <Channel Color="-16776961" ID="Channel:2:0" Name="TEXAS RED" PinholeSize="243.3357505438723" SamplesPerPixel="1">
    <Image ID="Image:3" Name="XY-lambda_la000">

On develop I get:

$ 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 "Name="
    <Image ID="Image:0" Name="XYZ-Ch">
            <Channel Color="-16776961" ID="Channel:0:0" Name="TRITC" PinholeSize="81.40681653372008" SamplesPerPixel="1">
    <Image ID="Image:1" Name="XY-Ch-trans">
    <Image ID="Image:2" Name="XZY-Ch-trans_y000">
            <Channel Color="-16776961" ID="Channel:2:0" Name="TEXAS RED" PinholeSize="243.3357505438723" SamplesPerPixel="1">
            <Channel Color="16711935" ID="Channel:2:1" Name="FITC" PinholeSize="243.3357505438723" SamplesPerPixel="1">
    <Image ID="Image:3" Name="XY-lambda_la000">

This is what my sprint10-bug-fixes branch looks like now: One of these commits has the bug:

* 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

References

Change History (2)

comment:1 Changed 12 years ago by mlinkert

Owner changed from mlinkert-x to wmoore

Same basic bug as #8211; should be fixed with https://github.com/melissalinkert/bioformats/commit/ed5092ac77b80aa8c8dd66921031a2ab1282f22d.

comment:2 Changed 12 years ago by wmoore

Resolution set to fixed
Status changed from new to closed

Bug fixed! Closing...

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