Keypoint-moseq

Latest version: v0.4.7

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0.4.7

Pin etils and scipy versions

0.4.6

What's Changed
* fix: fixing running kruskal wallis and plotting sig syllables by versey-sherry in https://github.com/dattalab/keypoint-moseq/pull/137
* Analysis fix by versey-sherry in https://github.com/dattalab/keypoint-moseq/pull/144
* merge dev into main by versey-sherry in https://github.com/dattalab/keypoint-moseq/pull/145
* Better error catching + change default iters for apply_model by calebweinreb in https://github.com/dattalab/keypoint-moseq/pull/146


**Full Changelog**: https://github.com/dattalab/keypoint-moseq/compare/0.4.5...0.4.6

0.4.5

Added FreiPose loader and function for saving keypoints.

Loading keypoints from FreiPose

To load keypoints output by FreiPose, use:

coordinates, confidences, bodyparts = kpms.load_keypoints(filepath_pattern, "freipose")

Note that `confidences` is set uniformly to 1, since the FreiPose scores range from <0 to >1 and therefore can't be used for modeling. Also `bodyparts` is None because these are not stored in the FreiPose output.

Initializing a config from FreiPose

Its also possible to setup a kpms config using a FreiPose config:

kpms.setup_project('test', freipose_config="path/to/skeleton_config.cfg.json")

The FreiPose config will be used to populate "bodyparts", "use_bodyparts" and "skeleton" in the kpms config. In some cases, the FreiPose skeleton may use a pair of keypoints to define one end of a limb. In FreiPose, this is used to indicate a limb midpoint. Since the same option is not available in kpms, the first bodypart in the pair is selected as the end of the limb.

Export keypoints

A new convenience function has been added for exporting keypoints:

kpms.save_keypoints(save_dir, coordinates, confidences=confidences, bodyparts=bodyparts)


One csv file is saved for each recording in `coordinates`. Each row in the csv corresponds to one frame and the columns are named

"BODYPART1_x", "BODYPART1_y", "BODYPART1_conf", "BODYPART2_x", ...

Columns with confidence scores are ommitted if `confidences` is not provided. Besides confidences, there can be 2 or 3 columns for each bodypart, depending on whether the keypoints are 2D or 3D.

0.4.4

Added support for loading DLC files with unique bodyparts

0.4.3

Fixed bug in calibration widget

0.4.2

Bugfixes
- Remove "linestyle" keyword from analysis code
- Pad states before unbatch rather than after - prevents error for sequences with length < nlags

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