Keypoint MoSeq 0.5.2

• Same as 0.5.1, but with a few errors corrected.

Keypoint MoSeq 0.5.1

• Refactored installation to remove backwards compatibility with CUDA11 - CUDA12 is now the only option.
• Removed conda environment yaml files - installation should now happen only with pip. Installation instructions here: https://github.com/dattalab/keypoint-moseq/blob/main/docs/source/install.rst
• Keypoint-moseq now requires python 3.10 or greater instead of python 3.9 or greater.

What's Changed

• setup.cfg updated to match jax-moseq's refactored installation by @JRJacoby in #200
• Installation documentation was updated to match the new setup.cfg by @JRJacoby in #200

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