Develop a script to "slice" videos to "match" DICOM series timing

[yarikoptic]

• [ ] initial script: can assume that all clocks (of reproiner and in DICOMs) are perfectly synchronized
  • I think the script should have an option to allow for a "buffer" time at the beginning/end and record that in some sidecar json file, on how many s.econds of buffer were added. This would allow later to adjust those numbers to account for in the anslysis of the video without changing/reslicing video itself
• [ ] exact alignment would dependent on the outcome of findings in #13 on either we could establish exact account of the DICOMs clock drift/offset or should resort to additional workarounds

[yarikoptic]

Might be worth aiming right away for BIDS datasets - information from _scans.tsv an possibly side car .json files (on duration).

[yarikoptic]

Script (ideally in python) should take

• location of not sliced videos
• beginning absolute time parameter
• end time or duration parameter
• optional "parameters" of how much of "buffer" to take before/after video begins/ends so we could account for time imprecision
  • all durations should accept either simple float for seconds (e.g. 121) , or ISO 8601 duration (P2M1S. note: isodurations does not take this value - wants a date! odd)
  • precision of ms is enough
  • if buffers go outside of the video times -- trim to video (so to 0 on the left, and total length on the right) and store (see below) actual values in the .json
  • if video itself doesn't overlap fully with desired time/duration -- for now just error
  • specific case: it was multiple (more than 1 video) videos captured for the single desired time duration -- we do not bother ATM to somehow join them.
• output .mkv filename.
  • in addition to .mkv generate or update (if exists) side car .json file with annotation of the parameters etc provided into "reprostim-videocapture" field. Should contain "onset" (ISO 8601 time, no date), "duration", "buffer-before", "buffer-after" in seconds (up to .ms), all reprostim-videocapture metadata from the log (https://github.com/ReproNim/reprostim/issues/83) .
  • Do not store absolute dates anywhere. Times are ok, not dates

example:

reprostim-slice --buffer-before 10 --buffer-after 10 --start 2024-02-02T17:30:00 --duration P3M  --input $VIDEOS/2024.02.02.17.20.38.680_2024.02.02.17.20.44.774.mkv --output $BIDS/sub-01/func/sub-01_task-rest_bold.mkv 

in case of input filename not satisfying the pattern to have starting time -- error

@jwodder -- please provide guidance on the python project template to start with, or tools to use. I would expect you to provide review of this work in the future.

[jwodder]

@yarikoptic

please provide guidance on the python project template to start with, or tools to use

What kind of guidance? Most decisions about Python project tooling are ultimately opinion-based, as there is no One True Packaging Tool.