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KumarLabJax / JABS-behavior-classifier

Behavior Classifier Component from the Jax Animal Behavior System
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Tc 245 #12

Closed SkepticRaven closed 1 year ago

SkepticRaven commented 1 year ago

Pull for integrating all the segmentation features and logging challenges related to it.

SkepticRaven commented 1 year ago

Known issues at this timepoint

  1. Poses are not currently matching segmentation. seg-mismatch

  2. Multiple contours per mouse are flattened to 1 contour per mouse (instead of a list of contours). multi-contour-issue Expectation (orange was the list of contours mis-drawn): rendered-all-masks

  3. Pixels to cm conversion isn't being applied to moments correctly (m00 is area, and needs to be multiplied by conversion^2) contour_moments = [[cv2.moments(trim_seg(np.reshape(seg_data[0,x,y], [-1,2])))['m00']*(cm_per_px**2)*[-1,1][seg_external_flag[0,x,y].astype(int)] for y in np.arange(np.shape(seg_data)[2])] for x in np.arange(np.shape(seg_data)[1])] Instead of figuring out how to merge the moments, it may also be simpler to render the frame and just pass that to cv2.moments

  4. My first edit for enabling the features to get passed in causes issues with other pose formats -- AttributeError: 'PoseEstimationV5' object has no attribute 'get_seg_id' is thrown when I have a project with only pose_v5 files.

SkepticRaven commented 1 year ago

This pull is being closed in favor of https://github.com/KumarLabJax/JABS-behavior-classifier/pull/16