Deeplabcut

Funding includes [ChanZuckerberg Initiative's Essential Open Source Software for Science](https://chanzuckerberg.com/eoss/). Thanks!

What's Changed
* use filter instead of for loop by maldil in https://github.com/DeepLabCut/DeepLabCut/pull/1905
* Add keypoint horizontal flip augmentation by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1805
* Add in_random_order flag to get_list_of_videos by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1911
* Unpin statsmodels by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1910
* Rename functions in "auxfun_models.py" by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1914
* Update installation.md by P-eMartin in https://github.com/DeepLabCut/DeepLabCut/pull/1918

Bugfixes and minor editing:
* Fix empty pose plot from Analyze videos GUI tab by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1892
* Fix GUI sizing: 'float' object cannot be interpreted as an integer by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1893
* Fix TypeError for create_training_dataset when training videos are named by number by hongh-zhang in https://github.com/DeepLabCut/DeepLabCut/pull/1880
* Update pose_cfg.yaml template by sfmig in https://github.com/DeepLabCut/DeepLabCut/pull/1907
* Fix 'allow_growth' by neslihanedes in https://github.com/DeepLabCut/DeepLabCut/pull/1917
* Add copy_videos argument to extract_outlier_frames by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1924
* Fix python 'testing for equality/inequality' issue by luzpaz in https://github.com/DeepLabCut/DeepLabCut/pull/1928
* Rename functions in `auxiliaryfunctions.py` from CamelCase to underscores by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1913
* Update outdated Colab notebook cells by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1933
* Fix various typos by luzpaz in https://github.com/DeepLabCut/DeepLabCut/pull/1927
* Fix topktoretain when there are unique body parts by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1938
* Remove two dead ends from triangulate() by stes in https://github.com/DeepLabCut/DeepLabCut/pull/1944
* Handle argument errors in undistort_points() by stes in https://github.com/DeepLabCut/DeepLabCut/pull/1943
* add validation for fps when fps*1000 overflow 65535(max of 16bit) by yueoka in https://github.com/DeepLabCut/DeepLabCut/pull/1952
* Fix scorer_3d in triangulate() by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1954

New Contributors
* maldil made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1905
* hongh-zhang made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1880
* sfmig made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1907
* P-eMartin made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1918
* yueoka made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1952

Thank you!

**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.2.1.1...v2.2.2

What's Changed
* Fixes add_new_videos not using correct argument for extract_frames by louisadamian in https://github.com/DeepLabCut/DeepLabCut/pull/1780
* Add destfolder to most transreID funcs by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1779
* ffmpeg typo by mchaker in https://github.com/DeepLabCut/DeepLabCut/pull/1782
* More visible DLC version by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1786
* Update installation.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1787
* Avoid ValueError when searching for outliers in raw data by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1788
* Move ipython dependency to conda environments by hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/1794
* Update repo org name in code and docs from "AlexEMG" to "DeepLabCut" by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1781
* Experiment : API documentation in Jupyter Book docs by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1795
* Ignore "_build" directory by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1799
* Loosen pin on scikit-image by hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/1800
* Fix create dataset model comparison crashing from GUI by louisadamian in https://github.com/DeepLabCut/DeepLabCut/pull/1803
* Its "add_new_videos", not "add_new_video" by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1802
* Remove unused imports from modules by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1801
* Add more API docs in Jupyter Book by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1798
* Fix a spelling mistake in the docker doc by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1812
* Fix colorbar tick placement and color normalization by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1813
* Use cv2 named constants instead of opaque numbers to get properties by hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/1811
* Add more API documentation in user guide by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1814
* Update publish-book.yml by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1816
* Fix ZeroDivisionError during calibration by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1819
* Fix ValueError with reID when no keypoints are detected by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1822
* Ignore failing "wx" imports when building api docs by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1823
* Avoid KeyError during feature loading by yeshaokai in https://github.com/DeepLabCut/DeepLabCut/pull/1830
* Remove "_filtered" suffix from file stem by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1835
* Bugfix for 1836: Catch subprocess error on symlink failure by nickdelgrosso in https://github.com/DeepLabCut/DeepLabCut/pull/1837
* Fix IndexError in save_coords by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1841
* Fix DataFrames concatenation when refining outliers by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1845
* Handle tuple indices in SkeletonBuilder by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1851
* Cleanup internal links in documentation by rahulporuri in https://github.com/DeepLabCut/DeepLabCut/pull/1824
* doc clean up by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1861
* Update python-package.yml by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1860
* Add option to save tracks as csv by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1859
* Update post.md by diegosancarmen in https://github.com/DeepLabCut/DeepLabCut/pull/1853
* Fix direct link to conda.yaml file by neslihanedes in https://github.com/DeepLabCut/DeepLabCut/pull/1869
* Ensure data is loaded upon each function evaluation by hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/1867
* Avoid asserting specific values for tracker ids by hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/1868
* demo notebook for labeling w/napari by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1866
* Fix broken link in Demo_3D_DeepLabCut.ipynb by zhoutianxun in https://github.com/DeepLabCut/DeepLabCut/pull/1879
* Bug fix for adding videos on windows by tomsains in https://github.com/DeepLabCut/DeepLabCut/pull/1873
* fix dockerfiles by reuterk in https://github.com/DeepLabCut/DeepLabCut/pull/1871
* Rahulporuri dev/1843 network loc by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/1886

New Contributors
* mchaker made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1782
* rahulporuri made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1781
* nickdelgrosso made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1837
* diegosancarmen made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1853
* zhoutianxun made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1879
* tomsains made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1873
* reuterk made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1871

**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.2.1...v2.2.1.1

Alongside our latest paper documenting new identity tracking, multi-animal pose and tracking in Nature Methods: https://www.nature.com/articles/s41592-022-01443-0 we release 2.2.1.

`pip install 'deeplabcut[gui]'==2.2.1`

Major new feature: transformer-based unsupervised identity tracking, check out the docs! https://deeplabcut.github.io/DeepLabCut/docs/maDLC_UserGuide.html#using-unsupervised-identity-tracking

What's Changed
* Fix for restarted training not following the lr schedule by LucZot in https://github.com/DeepLabCut/DeepLabCut/pull/1653
* Introduce DLC <-> NWB data conversion by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1657
* Set confidence to 0 when instantiating Assembly by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1652
* Fix IndexError when refining tracklets by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1662
* Fix matplotlib's AttributeError by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1680
* Docs: Add recipes for varying number of animals & Using labels from other software by intergalactic-mammoth in https://github.com/DeepLabCut/DeepLabCut/pull/1675
* Revert "Docs: Add recipes for varying number of animals & Using labels from other software" by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1681
* Clean up requirements.txt by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1678
* Make the outer loop go over GT assemblies in evaluate_assembly by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1664
* Visualize edge affinity distributions by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1683
* Adding greedy oks matching as option by LucZot in https://github.com/DeepLabCut/DeepLabCut/pull/1700
* Discard empty assemblies but not those without links by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1711
* FIX: Attribute error when using skeleton tracking method by mdsmarte in https://github.com/DeepLabCut/DeepLabCut/pull/1713
* Update Overviewof3D.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1717
* Freshening up `Getlistofvideos` by sneakers-the-rat in https://github.com/DeepLabCut/DeepLabCut/pull/1704
* clarification on when to use ma=false/true 1696 by intergalactic-mammoth in https://github.com/DeepLabCut/DeepLabCut/pull/1699
* Drop smart crop aug parameters from single-animal pose_cfg by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1674
* Randomly prune large graphs by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1607
* adds frame extraction to add_new_videos by louisadamian in https://github.com/DeepLabCut/DeepLabCut/pull/1660
* edit: Enable to build skeleton from config by intergalactic-mammoth in https://github.com/DeepLabCut/DeepLabCut/pull/1719
* Fix various typos by luzpaz in https://github.com/DeepLabCut/DeepLabCut/pull/1722
* added tf-directml install tip to docs by Seyij in https://github.com/DeepLabCut/DeepLabCut/pull/1720
* Update python-package.yml -- testing 3.9 (consider dropping 3.7?), and security patch by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1729
* Minor create_labeled_video refactoring by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1731
* Added posecfg_template option to create_training_dataset by alexcwsmith in https://github.com/DeepLabCut/DeepLabCut/pull/1423
* Exit while loop prematurely if not finding valid image sizes by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1738
* Add test time image resizing by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1737
* Remove duplicate description example by vidalmaxime in https://github.com/DeepLabCut/DeepLabCut/pull/1746
* OpenVINO backend by dkurt in https://github.com/DeepLabCut/DeepLabCut/pull/1686
* WIP: Delay setting the matplotlib backend until the user asks to launch the GUI by hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/1730
* Add option to automatically jump to the next unlabeled data folder by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1733
* Add function for handling too many extracted labels by frankiechang123 in https://github.com/DeepLabCut/DeepLabCut/pull/1751
* Fix NameError: name 'config' is not defined in get_track_method by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1665
* closes 1753 by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1755
* Allow windows to resize to be smaller than the default size by hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/1613
* Address an off by one error in the TQDM progress bar in the predict steps by hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/1744
* from transID to master (1) by yeshaokai in https://github.com/DeepLabCut/DeepLabCut/pull/1764
* Fix TypeError when refining outliers by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1763
* Improved 3D data processing by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1690
* Handle MultiIndex in convertcsv2h5 by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1769
* Mwm/deployment transformer_reID by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1767
* colab for transformer reID (WIP) by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1768
* adding plotting for transformer demo by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1770
* Delay torch import by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1772
* Improved behavior of get_list_of_videos by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1773
* Stricter file search based on suffixes by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1774
* Find data transformer by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/1776

New Contributors
* LucZot made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1653
* mdsmarte made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1713
* louisadamian made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1660
* luzpaz made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1722
* Seyij made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1720
* vidalmaxime made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1746
* dkurt made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1686
* hmaarrfk made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1730
* frankiechang123 made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1751

**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.2.0.6...v2.2.1

Bugfixes (introduced in recent versions):
* Properly handle empty assemblies by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1641
* Pin pytables to fix h5 writing by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1643
* Fix merge of old and new (path agnostic) DataFrames by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1647


**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.2.0.5...v2.2.0.6

What's Changed
* Backwards compat., allowing track_method in conv2tracklets and stitching by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/1633
* Easily mine tracklets from the TrackletStitcher by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1634

**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.2.0.4...v2.2.0.5

to use:

`pip install 'deeplabcut[gui]'==2.2.0.4`

What's Changed
* updated maDLC notebook! by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1589
* clean up example directory by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1590
* colab notebook path edit, minor fix by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1591
* updated colab demo openfield by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1592
* Update examples/README.md by EitanHemed in https://github.com/DeepLabCut/DeepLabCut/pull/1598
* install update by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1594
* Refactor trackingutils.py by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1576
* Default to headless when wx backend cannot be set (Importing headless even with GUI installation) by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1597
* Minor fixes for single point tracking by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1596
* Ignore single-keypoint assemblies during mAP evaluation by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1566
* Better format for cross-platform labelling and training (storing triples) by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1584
* Optionally write data on the fly to a shelf during analyze_videos (1… by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/1603
* Betterfunctionaltests by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/1604
* black formatting by AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/1605
* Backward compatibility of training on data stored the old way by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1611
* Update installation.md by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1619
* Convert RGBA images to RGB if necessary by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1614
* Uniform analyze_videos API by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1567
* Remove hardcoded path separators by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1615
* simplified 1-click maDLC analyze video, track, create video within the GUI by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1621
--see PR notes, and new format: https://user-images.githubusercontent.com/28102185/146851326-23ecc001-a8b4-45e0-ad80-b42d591c1b61.png
* Ignore numerical DataFrame index by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1622
* Update the model zoo Colab notebook by jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/1616
* drop duplicate opencv (headless) by MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/1628
* standardized imread, and Updated demo loading and modelcomparison by AlexEMG https://github.com/DeepLabCut/DeepLabCut/pull/1632

New Contributors
* EitanHemed made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/1598

**Full Changelog**: https://github.com/DeepLabCut/DeepLabCut/compare/v2.2.0.3...v2.2.0.4