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Published 20 hours ago • verified publisher icon ome

CZI: Parse TimeSpan Default Units

Open dgault opened this issue 4 years ago • 2 comments

Fixes https://github.com/ome/bioformats/issues/3560

This issue was raised in https://forum.image.sc/t/czi-reader-illuminationtype-mapping-and-exposuretime-units/37557/4 and a sample file showing the issue is available in QA-29273

This now parses the metadata value Experiment|AcquisitionBlock|TimeSeriesSetup|Interval|TimeSpan|DefaultUnitFormat and makes use of the units which had previously been hardcoded to seconds (note, seconds remains the default if the tag is not available).

This may have a knock on effect on sample files in the data repo, in which they will need to be reviewed to ensure the new values are correct.

To test:

  • Ensure builds and tests remain green
  • Using the file QA-29273, without the PR the exposure time will be in seconds
  • With this PR included the exposure time should correctly be ms

dgault avatar May 15 '20 12:05 dgault

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/czi-reader-illuminationtype-mapping-and-exposuretime-units/37557/6

imagesc-bot avatar May 15 '20 12:05 imagesc-bot

This has caused changes to many existing files (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-test-folder/62854/consoleFull), many of those using ms are likely to be correct and worth updating. Some have updated to min which needs further investigation as this looks to be incorrect.

dgault avatar May 18 '20 16:05 dgault

@melissalinkert, as discussed, I am unable to verify the ground truth for this change. There are a significant number of failures, the ones that I would be most concerned about are the ones which have updated the units to mins which looks incorrect: https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-test-folder/62854/consoleFull

Below are a sample of some of the failures with min as units and may be worth verifying first:

/data/public/idr0011/Plate1-Blue-A_TS-Stinger/Plate1-Blue-A-26-Scene-2-P1-E5-02.czi
/data/public/idr0011/Plate1-Blue-A_TS-Stinger/Plate1-Blue-A-40-Scene-2-P2-D8-02.czi
/data/public/idr0011/Plate1-Blue-A_TS-Stinger/Plate1-Blue-A-24-Scene-1-P1-F4-01.czi

dgault avatar Nov 28 '22 15:11 dgault

@dgault: screenshots for several of the failing files are now in https://github.com/openmicroscopy/data_repo_config/issues/552 (can add to that if needed).

melissalinkert avatar Nov 28 '22 16:11 melissalinkert

Thanks Melissa, closing this PR as it is resulting in a large number of values which do not match the values in Zen.

dgault avatar Nov 29 '22 11:11 dgault