Keypoint MoSeq 0.5.0

• Refactored installation to work with CUDA12 and any jax version. Installation pathways for different setups are described here https://github.com/dattalab/keypoint-moseq/blob/main/docs/source/install.rst
• Bug fix related to video extensions
• Other small tweaks to docs

What's Changed

• pass video_extension in calibration by @calebweinreb in #175

Full Changelog: 0.4.10...0.5.0

Keypoint MoSeq 0.4.10

What's Changed

• refactored downsampling and added trimming options by @calebweinreb in #172

New downsampling/trimming API documented here: https://keypoint-moseq.readthedocs.io/en/latest/advanced.html#temporal-downsampling

Full Changelog: 0.4.9...0.4.10

Keypoint MoSeq 0.4.9

What's Changed

• try except in keypoint loader reraises exception by @calebweinreb in #162
• correct processing of axis order from sleap_io.Labels.numpy() by @calebweinreb in #163

Full Changelog: 0.4.8...0.4.9

Keypoint MoSeq 0.4.8

• Added support for DANNCE
• Updated link to keypoint moseq paper

Full Changelog: 0.4.7...0.4.8

Keypoint MoSeq 0.4.7

Pin etils and scipy versions

Keypoint MoSeq 0.4.6

What's Changed

• fix: fixing running kruskal wallis and plotting sig syllables by @versey-sherry in #137
• Analysis fix by @versey-sherry in #144
• merge dev into main by @versey-sherry in #145
• Better error catching + change default iters for apply_model by @calebweinreb in #146

Full Changelog: 0.4.5...0.4.6

Keypoint MoSeq 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.

Keypoint MoSeq 0.4.4

Added support for loading DLC files with unique bodyparts

Keypoint MoSeq 0.4.3

Fixed bug in calibration widget

Keypoint MoSeq 0.4.2

Bugfixes

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