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OIR: parse time step from TIMELAPSE axis when possible #4259

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See https://forum.image.sc/t/bio-formats-reads-wrong-time-interval-from-oir-time-lapse-images/105684/

Without this change, showinf -nopix -omexml on the provided file (in curated/olympus-oir/imagesc-105684/) should show Plane.DeltaT values spaced ~2.17 seconds apart. With this change, Plane.DeltaT values should be spaced 30 seconds apart.

The time step is now being parsed the same way that the Z step is parsed, so I think this makes sense. I would expect some test failures overnight in the DeltaT test for existing .oir data; I can update configs as needed later in the week, or we can exclude temporarily.

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

https://forum.image.sc/t/bio-formats-reads-wrong-time-interval-from-oir-time-lapse-images/105684/4

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sbesson commented Dec 11, 2024

A few OIR samples failed the tests for the plane timestamp values and will need to be reconfigured accordingly - see https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-test-folder/45268/console

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As noted above, this change does modify the timestamps for a few existing files, including https://downloads.openmicroscopy.org/images/Olympus-OIR/gh-4205/zenodo-12773657/DAPI_mCherry_4T_5Lambda-420-630-w10nm-s50nm.oir.

@NicoKiaru, since that file was submitted by you, any thoughts on this change or the expected plane timestamps for the file would be welcome.

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I confirmed that there was an issue in the timestamps which is fixed by these commits, thanks @melissalinkert !

I checked on the Fluoview software, and the delay between frames is of 20 seconds, and thanks to this PR the frame interval is now detected to be of 20 secs with the file you linked.

@melissalinkert melissalinkert added this to the 8.1.0 milestone Dec 13, 2024
@sbesson sbesson self-requested a review December 19, 2024 21:25
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4 participants