movement - v0.9.0

What's Changed

New feature: compute kinetic energy

feat: computekineticenergy for per-individual KE decomposition (#228) by @vtushar06 in https://github.com/neuroinformatics-unit/movement/pull/623

The compute_kinetic_energy function is the newest addition to the movement.kinematics module. It can be used to derive the total kinetic energy per individual, or decompose it into "translational" (centre-of-mass motion) and "internal" components (motion of keypoints relative to individual's centre-of-mass). Thanks to @vtushar06 for driving this forward.

Improvements to documentation

Spearheaded by @lochhh.

Replace external links to movement docs with explicit targets by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/642
Aggregate API docs for flat modules by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/648
Add gallery of examples in API documentation by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/644

Housekeeping

Contributors-Readme-Action: Update contributors list by @github-actions[bot] in https://github.com/neuroinformatics-unit/movement/pull/650
Bump akhilmhdh/contributors-readme-action from 2.3.10 to 2.3.11 by @dependabot[bot] in https://github.com/neuroinformatics-unit/movement/pull/651
Add downloads badge by @adamltyson in https://github.com/neuroinformatics-unit/movement/pull/652
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/neuroinformatics-unit/movement/pull/653

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.8.2...v0.9.0

- Python
Published by niksirbi 10 months ago

movement - v0.8.2

A hotfix to redeploy the website

Hotfix: disable artifact.ci by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/640
Hotfix: temporarily disable linkcheck by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/641

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.8.1...v0.8.2

- Python
Published by niksirbi 10 months ago

movement - v0.8.1

What's Changed

Fix broken Aeon habitat URL and update terminology from "arena" to "habitat" by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/637
Preview docs built in CI from the browser by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/631
Upper pin numpy to 2.3 by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/638

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.8.0...v0.8.1

- Python
Published by niksirbi 10 months ago

movement - v0.8.0

✨ Highlight ✨ visualise bounding boxes

Thanks to the persistent efforts of @DPWebster, bounding boxes can now be displayed in our GUI as a napari Shapes layer 🎉 (for now this only apples to bounding boxes datasets). See the updated user guide for more info. * Visualize bounding boxes as Napari shapes layer by @DPWebster in https://github.com/neuroinformatics-unit/movement/pull/590

napari_bboxes_layer

`movement` now has a logo

movement_logo_transparent

Add movement logo and favicon to the website by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/614
Update logo, favicon, and overview images by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/632

Miscellaneous

fix: update default individual name from 'individual0' to 'id0' acr… by @vtushar06 in https://github.com/neuroinformatics-unit/movement/pull/618
Accommodate sample datasets that are ZIP archives by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/619

Housekeeping

Fetch full commit history in build-sphinx-docs by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/621
Restrict deploysphinxdocs to main branch on manual workflow dispatch by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/624
Contributors-Readme-Action: Update contributors list by @github-actions in https://github.com/neuroinformatics-unit/movement/pull/627
Apply monospace formatting for movement in CONTRIBUTING.md by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/626
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/629

New Contributors

@vtushar06 made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/618
@DPWebster made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/590

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.7.1...v0.8.0

- Python
Published by niksirbi 11 months ago

movement - v0.7.1

✨ Highlight ✨ netCDF is the file format 🗃️ of choice for saving `movement` datasets 💾

Test and document saving movement datasets to netCDF by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/606

Saving to netCDF is the recommended way to preserve the complete state of your analysis, including all variables, coordinates, and attributes. Below is an example of how you may integrate netCDF into you movement-powered workflows:

```python from movement.io import loadposes from movement.filtering import rollingfilter from movement.kinematics import compute_speed

ds = loadposes.fromfile( "path/to/mydata.h5", sourcesoftware="DeepLabCut", fps=30 )

Apply a rolling median filter to smooth the position data

ds["positionsmooth"] = rollingfilter( ds["position"], window=5, statistic="median" )

Compute speed based on the smoothed position data

ds["speed"] = computespeed(ds["positionsmooth"])

Save the dataset to a netCDF file

This includes the original position and confidence data,

the smoothed position, and the computed speed

ds.tonetcdf("mydata_processed.nc") ```

To later load the dataset back from disk:

```python import xarray as xr

ds = xr.opendataset("mydata_processed.nc") ```

Miscellaneous

Completely remove deprecated median_filter function by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/611
Add logtoattrs decorator to scale function by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/604

[!warning] The deprecated movement.filtering.median_filter() function has been completely removed. Use movement.filtering.median_filter() instead, with statistic="median".

Housekeeping

Change path to match GIN repo current status by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/603
Add note for Apple silicon users with macOS <=13 by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/605
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/607
chore: run codespell throughout fixing a typo by @yarikoptic in https://github.com/neuroinformatics-unit/movement/pull/608
Remove announcement banner for Open Software Week by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/610
Remove "easily" from some longer examples by @adamltyson in https://github.com/neuroinformatics-unit/movement/pull/612

New Contributors

@yarikoptic made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/608

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.7.0...v0.7.1

- Python
Published by niksirbi 12 months ago

movement - v0.7.0

🎉 Highlight: support for the NWB file format 🧠

movement poses datasets can now be loaded from and saved to NeuroData Without Borders (NWB) files. The pose tracks are formatted according to the ndx-pose extension.

This was a global team effort started long ago by @edeno, continued by me, and finally wrapped up by @lochhh. Many thanks go to @luiztauffer for providing advice and crash-testing.

Example usage:

```python import pynwb import xarray as xr from movement.io import loadposes, saveposes

Load pose tracks from open NWBFile objects:

with pynwb.NWBHDF5IO("path/to/file.nwb", mode="r") as io: nwbfile = io.read() ds = loadposes.fromnwbfile(nwb_file)

Or, directly load pose tracks from NWB files on disk.

Here merge data from 2 files into a multi-individual dataset:

dssingles = [loadposes.fromnwbfile(f) for f in ["id1.nwb", "id2.nwb"]] dsmulti = xr.merge(dssingles)

Create NWBFile objects for each individual and save them to disk

nwbfiles = saveposes.tonwbfile(ds) for file in nwb_files: with NWBHDF5IO(f"{file.identifier}.nwb", "w") as io: io.write(file) ```

As always, let us know if you encounter any hurdles with this.

What's Changed

Fix remaining napari future warning by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/594
Temporarily suppress napari warnings by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/592
Replace numpy legacy random generation by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/597
Update the contributing guide by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/598
Refactor reports.py by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/557
Ignore SWC URL in linkcheck by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/601
Add I/O support for the ndx-pose NWB extension: take 2 by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/360

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.6.1...v0.7.0

- Python
Published by niksirbi about 1 year ago

movement - v0.6.1

What's Changed

Small updates to documentation

Add Mahi7828 as contributor and change str to locate section by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/576
Clarify x,y data in VIA-tracks by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/577
Add announcement banner for open software week by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/578
Added a sub-gallery for "Advanced" examples by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/582
Add ShigrafS to github contributors by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/587
Contributors-Readme-Action: Update contributors list by @github-actions in https://github.com/neuroinformatics-unit/movement/pull/589
Update animovement website URL by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/588

Internal refactoring of the kinematics module

[!note] The interface for using all kinematics functions remains unchanged

Split kinematics.py and corresponding tests into multiple files by @ShigrafS and @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/583

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.6.0...v0.6.1

- Python
Published by niksirbi about 1 year ago

movement - v0.6.0

What's Changed

Highlight: ✨ See into the past and future ✨

@sfmig has worked hard to visualise point trajectories as "tracks" in napari. In effect, this means that in our GUI you can now display each point's past ("tail") and future ("head"). Read more about it the updated guide.

Add tracks to napari visualisation by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/476
Update GUI docs with tracks details by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/547

napari_tracks_layer_head_length

Documentation

Update upgrading instructions by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/551
Add people section and support for automatic contributors list update by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/554
Contributors-Readme-Action: Update contributors list by @github-actions in https://github.com/neuroinformatics-unit/movement/pull/559
Removed warning about package being in early development by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/560

Bug fixes

Fix _warn_about_nan_proportion bugs by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/541
Fix: frame slider to show max n of frames across all loaded files by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/503
Fix: update frame slider after deletion of layers by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/504
Ensure derived data variables have correct name by @Ishaan0132 in https://github.com/neuroinformatics-unit/movement/pull/523
Fix for bboxes dataset loading by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/561
Fix duplicate reference when closing and reopening napari widget by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/575

Housekeeping

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/545
Speed up test data caching in CI by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/566
Bump pyvista/setup-headless-display-action from 3 to 4 by @dependabot in https://github.com/neuroinformatics-unit/movement/pull/568
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/572
Restrict napari version to >=0.6.0 by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/570

New Contributors

@github-actions made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/559

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.5.1...v0.6.0

- Python
Published by niksirbi about 1 year ago

movement - v0.5.1

[!note] This release changes the way we do logging in movement, which fixes a bug (certain warnings were not showing up on the console) and impacts developers. We encourage contributors to the consult the "Logging" section of the updated contributing guide.

What's Changed

Small fixes to the ROI distances and angles example by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/521
Fix Runtime Warning raised by ROI plot test by @harsh-bhanushali-05 in https://github.com/neuroinformatics-unit/movement/pull/534
Add focus areas for 2025 to the roadmaps page by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/535
Replace logging with loguru by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/467

New Contributors

@harsh-bhanushali-05 made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/534

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.5.0...v0.5.1

- Python
Published by niksirbi about 1 year ago

movement - v0.5.0

Highlight

Our Regions of Interest (RoI) classes now have a .plot method for conveniently showing the RoI with matplotlib. @willGraham01 has showcased this and other cool RoI features—like computing distances and angles relative to RoIs—in a new comprehensive example.

What's Changed

.plot method for RoIs by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/447
Ensure dataset attributes are not set to None by @Ishaan0132 in https://github.com/neuroinformatics-unit/movement/pull/493
Example for Boundary Angle Calculations by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/440

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.4.0...v0.5.0

- Python
Published by niksirbi about 1 year ago

movement - v0.4.0

What's Changed

@sfmig has added the ability to load tracked bounding boxes in our GUI, and has also improved the GUI user experience by matching the colour of the text labels to the colour of the displayed points.

Data points text labels in napari by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/466
Extend napari plugin to bboxes' centroids by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/434

A small fix to the docs: * Correct confidencearray shape in fromnumpy example docstring by @Ishaan0132 in https://github.com/neuroinformatics-unit/movement/pull/492

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.3.0...v0.4.0

- Python
Published by niksirbi about 1 year ago

movement - v0.3.0

What's Changed

@willGraham01 and @stellaprins have summarised their work on spatial navigation features introduced during Jan-Feb 2025 in a blogpost.

Blog Post for Jan-Feb features by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/444

With the help of @angkul07 we've added a general rolling_filter function, which can be used to apply a rolling median, mean, max, or min filters. The more specific median_filter function is being deprecated and will be removed in a future release.

Added a general filter function for mean and median filter by @angkul07 in https://github.com/neuroinformatics-unit/movement/pull/455

New Contributors

@angkul07 made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/455

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.2.0...v0.3.0

- Python
Published by niksirbi about 1 year ago

movement - v0.2.0

New feature

Condition arrays: compute region occupancy by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/421 ## Bug fix
Updated GUI installation instructions by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/478

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.1.0...v0.1.1

- Python
Published by niksirbi about 1 year ago

movement - v0.1.0

The graphical user interface (GUI) is here!

This is the first release including our napari plugin, which we'll gradually develop into a fully fledged GUI for movement. We have been working on a minimal version of this plugin for a while and are happy to share it with the world with this release.

Read this guide on how to use it.

Minimal viable version of the movement plugin for napari. by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/450
Fix: remove NaN points before passing to points layer by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/465

Regions of interest and spatial navigation

This chunk of work was spearheaded by @willGraham01 and includes many goodies for analysing tracking data in relation to user-defined regions of interest. Stay tuned for more to come in the next releases.

Introduce decorator for broadcasting 1D methods by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/397
add pointisinside to BaseRegionOfInterest by @stellaprins in https://github.com/neuroinformatics-unit/movement/pull/413
Fix compute_signed_angle_2d using 2D boolean indexing by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/432
Add functionality for computing ego- and allocentric angles to RoIs by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/416
Remove toggles for signed angle computations by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/445

Quick plots

Mostly thanks to @stellaprins, movement now includes a plots submodule, currently offering two functions for quickly visualising trajectories and occupancy heatmaps.

Plotting wrappers: Head Trajectory by @stellaprins in https://github.com/neuroinformatics-unit/movement/pull/394
Plotting Wrappers: Occupancy Histogram by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/403
Use plot_trajectory in broadcasting example by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/414
Sp/417 bug fix plot trajectory by @stellaprins in https://github.com/neuroinformatics-unit/movement/pull/425
Rename plottrajectory --> plotcentroid_trajectory by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/474

New and overhauled examples

Many of our examples were updated in this release, but we'd like to draw special attention to the ones on pupil tracking and head direction. Our more advanced users may appreciate the new example on broadcasting functions along data dimensions.

Eye movement example by @stellaprins in https://github.com/neuroinformatics-unit/movement/pull/429
Reframe polar coordinates example around head direction by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/426
Introduce decorator for broadcasting 1D methods by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/397

Housekeeping

As usual, it takes lots of work to keep the lights on. We'd like to draw particular attention to two changes that may impact users: 1. We've updated the supported Python versions to 3.11 - 3.13 2. The print_report parameter now defaults to False for all functions in the movement.filtering module.

Tiny fix in docstrings for configure_logging by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/411
replace xarray median and mean with numpy by @Kasra-Shirvanian in https://github.com/neuroinformatics-unit/movement/pull/419
Clarify error raised by ValidHDF5 by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/424
Update Python versions to adhere to SPEC 0 by @adamltyson in https://github.com/neuroinformatics-unit/movement/pull/442
Remove Intel Macs from CI workflow by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/449
Add make docs note for PowerShell users by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/430
Use raw string for regex by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/452
Set print_report to False by default in filtering functions by @Ishaan0132 in https://github.com/neuroinformatics-unit/movement/pull/456
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/460
Update testanddeploy.yml to remove nodefaults conda channel by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/462

New Contributors

@Kasra-Shirvanian made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/419
@Ishaan0132 made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/456

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.23...v0.1.0

- Python
Published by niksirbi about 1 year ago

movement - v0.0.23

What's Changed

New features 🎉

Add computeforwardvector_angle function by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/376
Add transforms module with scale function by @stellaprins in https://github.com/neuroinformatics-unit/movement/pull/384
Introduce basic classes for regions of interest by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/396

Housekeeping

Pass kwargs to interpolate_over_time by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/383
Replaced NIU upload action with separate steps by @IgorTatarnikov in https://github.com/neuroinformatics-unit/movement/pull/391
bounding boxes' tracks --> bounding boxes tracks by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/392
Reorganise test fixtures by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/380
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/401
Use pypa/gh-action-pypi-publish stable release v1 by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/404

New Contributors

@IgorTatarnikov made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/391
@stellaprins made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/384

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.22...v0.0.23

- Python
Published by niksirbi over 1 year ago

movement - v0.0.22

New feature

Loading function for Anipose data by @vigji in https://github.com/neuroinformatics-unit/movement/pull/358

Bug fix

Fix dims and coords returned by compute_forward_vector by @willGraham01 in https://github.com/neuroinformatics-unit/movement/pull/382

Housekeeping

Badges by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/364
Fix mypy error in py3.12 by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/372
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/373

New Contributors

@willGraham01 made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/382

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.21...v0.0.22

Note

This is the 2nd attempt at this release, because of some issues uploading the artifacts to PyPI.

- Python
Published by niksirbi over 1 year ago

movement - v0.0.21

What's Changed

New features

Compute Forward Vector by @b-peri in https://github.com/neuroinformatics-unit/movement/pull/276
Compute pairwise distances by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/278
Implement compute_speed and compute_path_length by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/280
Add the option for multiple views loading - take2 by @vigji in https://github.com/neuroinformatics-unit/movement/pull/346

Breaking changes

Drop the .move accessor by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/322
Removed "analysis" level from namespace by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/333
Reorder dimensions by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/351

Docs/website improvements

Fix command for installation of docs dependencies in the guide. by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/323
Add example to convert file formats and changing keypoints by @Lauraschwarz in https://github.com/neuroinformatics-unit/movement/pull/304
Encourage R users to check out animovement by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/335
Update overview, mission, scope, and roadmaps by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/352
Restructure "Getting Started" page to a "User Guide" - take 2 by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/356
Bounding boxes example by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/312
Add inaugural blogpost by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/359

Housekeeping

Add bbox centroid fix by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/303
General validator function for checking dimensions and coordinates by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/294
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/318
Update integration tests by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/295
Refactor auto-generate API docs by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/331
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/338
Fix for check-manifest pre-commit hook in Python 3.12 by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/344
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/355
Fix and relax bboxes requirements by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/313

New Contributors

@Lauraschwarz made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/304
@vigji made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/346

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.20...v0.0.21

- Python
Published by niksirbi over 1 year ago

movement - v0.0.20

Highlight

New movement dataset type to store bounding boxes. Tracked bounding boxes can be loaded from files in VGG Image Annotator format or constructed from Numpy arrays. Spearheaded by @sfmig 🎉

movement_datasets

What's Changed

Support for bounding boxes

Add a ValidVIAtracksCSV class (2/4) by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/219
Small edits to ValidBboxesDataset (1/4) by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/230
Getting started docs update for bboxes by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/245
Load bboxes dataset from VIA tracks file (3/4) by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/229
Adapt move accessor to bboxes datasets by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/255
Simplify and expand filtering tests for bboxes by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/267
Extend tests for bboxes datasets by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/246
added new movement datasets figure, with caption by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/286
Small refactor to filtering tests by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/287
Simplify and expand kinematic tests for bboxes by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/265

New vector utilities

Add utilities for vector magnitude and normalisation by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/243

Housekeeping and docs improvements

Add citation information by @adamltyson in https://github.com/neuroinformatics-unit/movement/pull/240
Refactor names and fix docs formatting in validators by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/251
Pin pandas version for Py3.12 tests by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/259
Fix tox requires section by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/261
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/258
Update setup docs by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/264
Revert "Pin pandas version for Py3.12 tests" by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/272
Configure intersphinx by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/269
Suggestion to treat warnings as errors in sphinx-build by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/256
Refactor derivative by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/270
Remove defaults from testanddeploy.yml by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/275
Updated movement overview figure by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/288
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/296
Fix xarray FutureWarning about dims vs sizes by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/297

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.19...v0.0.20

- Python
Published by niksirbi over 1 year ago

movement - v0.0.19

What's Changed

For users

Changes in user-facing interface: * Refactor filtering module to take DataArrays as input by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/209

Bugfix: * Accessor compute_ to only validate required position data variable by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/206

For developers

Changes in code architecture, aiming at improving ease of contribution and maintainability.

Refactor validators by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/204
Move logging.py inside utils by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/216
Refactor validators tests by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/207
Make video download optional for sample datasets by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/224
Re-organise API reference by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/213

Paving the way for upcoming features: * Add a ValidBboxesDataset class by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/201 * Add bboxes sample data by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/231

Housekeeping: * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/202 * Update supported Python versions by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/208 * Use raw string for ASCII art in CLI entrypoint by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/212 * Add missing init.py files by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/215 * Update python version in README.md by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/221 * Added ruff rule to check for numpy2.0 compatibility by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/227 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/233

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.18...v0.0.19

- Python
Published by niksirbi almost 2 years ago

movement - v0.0.18

What's Changed

Tutorial polar coordinates by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/180
Suggestion to rename ValidPosesCSV to ValidDeepLabCutCSV by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/195
Added example using median_filter() and savgol_filter() by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/193
Refactored modules related to input-output by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/194

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.17...v0.018

- Python
Published by niksirbi almost 2 years ago

movement - v0.0.17

What's Changed

Unpin sphinx version in docs requirements by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/183
Fix installation link and add quick install by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/185
Suggestion to rename private loader by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/187
Rename roadmap -> roadmaps in docs by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/188
Added new smoothing functions to API index by @ivanvrlg in https://github.com/neuroinformatics-unit/movement/pull/189

New Contributors

@ivanvrlg made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/189

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.16...v0.0.17

- Python
Published by niksirbi about 2 years ago

movement - v0.0.16

What's Changed

New features

Polar kinematics by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/155
Support video and frames files associated with sample data by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/171
Add CLI entrypoint by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/176
Implement Median and Savitzky-Golay Filters by @b-peri in https://github.com/neuroinformatics-unit/movement/pull/163

Interface changes

Rename pose_tracks to position by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/149
Refactor accessor to provide methods instead of properties by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/174

Documentation

Define the "movement dataset" and reorganise the Getting Started section by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/177

Housekeeping

use Dataset.sizes instead of Dataset.dims for getting dimension sizes by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/153
add merge_group as workflow trigger by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/154
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/157
Overhaul linting and formatting by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/156
Add viz extras to xarray dependency by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/161
Enforce linting of docstrings by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/165
Remove cibuildwheel config by @adamltyson in https://github.com/neuroinformatics-unit/movement/pull/169
Changed macos runners for GitHub CI by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/170
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/173
update pypi dev status from pre-alpha to alpha by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/172

New Contributors

@adamltyson made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/169

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.15...v0.0.16

- Python
Published by niksirbi about 2 years ago

movement - v0.0.15

What's Changed

Add and configure codespell by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/143
Show short-term milestone as checklist by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/144
Kinematics tutorial by @sfmig in https://github.com/neuroinformatics-unit/movement/pull/135

New Contributors

@sfmig made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/135

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.14...v0.0.15

- Python
Published by niksirbi about 2 years ago

movement - v0.0.14

What's Changed

Add binder configuration and dependencies by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/142

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.13...v0.0.14

- Python
Published by adamltyson about 2 years ago

movement - v0.0.13

What's Changed

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/99
Update datasets.py by @b-peri in https://github.com/neuroinformatics-unit/movement/pull/86
Fix unreadable unwriteable fixtures for Windows by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/103
Remove pytables as a conda dependency by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/104
Use the updated upload_pypi action by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/108
Provide a generic loadposes.fromfile() function #107 by @DhruvSkyy in https://github.com/neuroinformatics-unit/movement/pull/110
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/111
Reorganise Accessor by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/122
Compute locomotion features by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/106
Include M1 runners in CI and update install instructions accordingly by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/125
Add dependabot config by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/128
Bump actions/cache from 3 to 4 by @dependabot in https://github.com/neuroinformatics-unit/movement/pull/130
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/131
Add codecov token to testanddeploy.yml by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/129
add setup-miniconda action and conda install pytables (instead of hdf5) by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/133
Implement functions to drop and interpolate over low-confidence datapoints by @b-peri in https://github.com/neuroinformatics-unit/movement/pull/116
Add tables pip package to docs requirements by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/137

New Contributors

@b-peri made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/86
@dependabot made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/130

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.12...v0.0.13

- Python
Published by niksirbi about 2 years ago

movement - v0.0.12

What's Changed

Export SLEAP .h5 analysis files by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/88
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/94
Fix admonition rendering in README by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/95
Added function to load poses from LightningPose by @DhruvSkyy in https://github.com/neuroinformatics-unit/movement/pull/92
Updated website with images and branding by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/96

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.11...v0.0.12

- Python
Published by niksirbi over 2 years ago

movement - v0.0.11

What's Changed

Added LightningPose data to pooch dataset registry by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/87
Add support for loading "trackless" SLEAP files by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/90

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.10...v0.0.11

- Python
Published by niksirbi over 2 years ago

movement - v0.0.10

What's Changed

Docs link check by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/80
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/82
Add sample SLEAP data containing mixed (user/predicted) labels by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/85
SLEAP read user labels by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/79
Ability to save multi-animal pose tracks to single-animal files by @DhruvSkyy in https://github.com/neuroinformatics-unit/movement/pull/83

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.9...v0.0.10

- Python
Published by niksirbi over 2 years ago

movement - v0.0.9

What's Changed

Updated docs with community section by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/72
The section contains information about the project's mission, scope, and roadmap.

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.8...v0.0.9

- Python
Published by niksirbi over 2 years ago

movement - v0.0.8

What's Changed

Updated project URLs in pyproject.toml by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/64
Refactor configure_logging by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/65
Refactor tests by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/63

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.7...v0.0.8

- Python
Published by niksirbi over 2 years ago

movement - v0.0.7

What's Changed

Added calls to join zulip chat by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/61
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/neuroinformatics-unit/movement/pull/60
Changed documentation website URL by @niksirbi in https://github.com/neuroinformatics-unit/movement/pull/62

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.6...v0.0.7

- Python
Published by niksirbi over 2 years ago

movement - v0.0.6

What's Changed

Deprecate support for python 3.8 by @DhruvSkyy in https://github.com/neuroinformatics-unit/movement/pull/54
Fix indentation error in ValidPosesCSV validator by @lochhh in https://github.com/neuroinformatics-unit/movement/pull/57

New Contributors

@DhruvSkyy made their first contribution in https://github.com/neuroinformatics-unit/movement/pull/54

Full Changelog: https://github.com/neuroinformatics-unit/movement/compare/v0.0.5...v0.0.6

- Python
Published by niksirbi over 2 years ago

movement - v0.0.5

import pose tracks from DeepLabCut and SLEAP
represent pose tracks as xarray objects
export pose track in DeepLabCut format
improved data validation
sphinx documentation deployed on GitHub pages

- Python
Published by niksirbi over 2 years ago

Recent Releases of movement

movement - v0.9.0

What's Changed

New feature: compute kinetic energy

Improvements to documentation

Housekeeping

movement - v0.8.2

A hotfix to redeploy the website

movement - v0.8.1

What's Changed

movement - v0.8.0

✨ Highlight ✨ visualise bounding boxes

movement now has a logo

Miscellaneous

Housekeeping

New Contributors

movement - v0.7.1

✨ Highlight ✨ netCDF is the file format 🗃️ of choice for saving movement datasets 💾

Apply a rolling median filter to smooth the position data

Compute speed based on the smoothed position data

Save the dataset to a netCDF file

This includes the original position and confidence data,

the smoothed position, and the computed speed

Miscellaneous

Housekeeping

New Contributors

movement - v0.7.0

🎉 Highlight: support for the NWB file format 🧠

Load pose tracks from open NWBFile objects:

Or, directly load pose tracks from NWB files on disk.

Here merge data from 2 files into a multi-individual dataset:

Create NWBFile objects for each individual and save them to disk

What's Changed

movement - v0.6.1

What's Changed

Small updates to documentation

Internal refactoring of the kinematics module

movement - v0.6.0

What's Changed

Highlight: ✨ See into the past and future ✨

Documentation

Bug fixes

Housekeeping

New Contributors

movement - v0.5.1

What's Changed

New Contributors

movement - v0.5.0

Highlight

What's Changed

movement - v0.4.0

What's Changed

movement - v0.3.0

What's Changed

New Contributors

movement - v0.2.0

New feature

movement - v0.1.0

The graphical user interface (GUI) is here!

Regions of interest and spatial navigation

Quick plots

New and overhauled examples

Housekeeping

New Contributors

movement - v0.0.23

What's Changed

New features 🎉

Housekeeping

New Contributors

movement - v0.0.22

New feature

Bug fix

Housekeeping

New Contributors

Note

movement - v0.0.21

What's Changed

New features

Breaking changes

Docs/website improvements

`movement` now has a logo

✨ Highlight ✨ netCDF is the file format 🗃️ of choice for saving `movement` datasets 💾