Safety checks

python -m stride.stages.safety_checks is a separate command that tests a finished table or folder and returns an exit code, so a shell script can stop on it. The pipelines do not run it by themselves: stride tmaze and stride gait print warnings and never change a value (Logs, warnings and exit codes).

The checks

check	what it tests	FAIL when
--roi-coverage DIR	every video under DIR has an ROI file, next to it or in --yml-dir	no video is found, any video lacks an ROI file, or the number of videos differs from --expect-count
--gait CSV: calibration	the px_per_cm column of a gait table, read as px/cm	the file is empty or has no usable px_per_cm column; any stride, or the median, is outside 5 to 40 px/cm (this catches the 1.0 sentinel); the 98th and 2nd percentile differ by more than a factor 1.4; more than 2 % of the strides sit near twice or half the median; or, with --expect-pxcm, the median differs from the expected value by more than 5 %
--gait CSV: body length	body_length_cm	the column is missing or empty; the median is outside 4 to 11 cm; or the table has a camera or pose_model column with more than one value
--gait CSV: fps	the fps column	more than one frame rate (rounded to 0.1) in the table; a missing column is a WARN

A scale that is the same for every stride, checked without --expect-pxcm, is reported as a WARN: a uniform but wrong value cannot be caught without the expected value.

python -m stride.stages.safety_checks --roi-coverage /data/videos --yml-dir /data/stride_out/roi
python -m stride.stages.safety_checks --gait /data/stride_out/gait/gait_per_stride_filtered.csv --expect-pxcm 26.1 --strict

Exit code 2 on any FAIL, 1 on a WARN when --strict is given, 0 otherwise.

Gate ledger

Each passing step can stamp .stride_gates.json in a video folder, and a later step can require earlier stamps:

python -m stride.stages.safety_checks --stamp roi --vid /data/videos
python -m stride.stages.safety_checks --require rename,roi --vid /data/videos   # FAIL if either is missing

The gate names are free text. The authors' own intake workflow runs the gait calibration check after its gait stage (Authors' lab workflow).