DeepLabCut Files

What's Changed

• Fix PySide6 AttributeError and uninitialized variable by @jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2622
• Niels/pcutoff arg by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2630
• Fix video overwrite by @jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2633
• Visually signal end of super animal video inference by @jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2637
• Fix GUI bugs by @jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2649
• Fix OSError: Could not find a backend to open CollectedData_Alex.csv with iomode r by @jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2650
• Fix video extension filter in filterpredictions by @jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2673
• Fix and decouple video rotation from other operations by @jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2653
• merge named snapshot evaluation into pytorch_dlc by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2657
• Handle internet connectivity issues by @jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2672
• New PyTorch DeepLabCut SuperAnimal demo notebook by @yeshaokai in https://github.com/DeepLabCut/DeepLabCut/pull/2629
• merge main to pytorch_dlc by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2677
• Update train.py: avoids error on 'unique_bodyparts' by @Zelin2001 in https://github.com/DeepLabCut/DeepLabCut/pull/2668
• Default PAF config update by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2678
• New detector options and better detector integration by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2676
• backwards compatibility by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2681
• evaluation refactor by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2679
• bug fixes for analyze_videos and unique_bodyparts by @Zelin2001 in https://github.com/DeepLabCut/DeepLabCut/pull/2685
• Fix import in deeplabcut.pose_tracking_pytorch by @jeylau in https://github.com/DeepLabCut/DeepLabCut/pull/2691
• Location Refinement for Top-Down models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2699
• Identity Predictor by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2707
• batched inference by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2708
• Bug fixes: find_closest_neighbors + ellipse tracking by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2709
• bug fix: find closest neighbors by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2717
• Minimal backward compatibility by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/2713
• Documentation Improvements - DeepLabCut PyTorch Code by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/2714
• merge main into pytorch_dlc by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2731
• Make 3D Triangulate possible with pytorch_dlc branch and MA project by @Zelin2001 in https://github.com/DeepLabCut/DeepLabCut/pull/2729
• Data compatibility - Benchmark by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2740
• Adding cropping to pose_estimation_pytorch/apis/analyze_videos.py by @YankoFelipe in https://github.com/DeepLabCut/DeepLabCut/pull/2737
• pytorch_dlc - Small updates and bug fixes by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2747
• calc_similarity_with .py ZeroDivisionError: float division by zeros via upload by @SowonKIMM in https://github.com/DeepLabCut/DeepLabCut/pull/2688
• update version by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/2748
• SuperAnimal Model Updates by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2756
• Look for uppercase video extensions when creating projects by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2763
• Fix reading gpus config by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2764
• Git ignore IDE configs by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2765
• Fix bug introduced in PR [#2764] by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2772
• Bug fix: create_video_with_all_detections fails with PAF heads by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2776
• Resume training from existing snapshots option in GUI by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2774
• Improvements to the training UX by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2775
• Fix failing DLC 3.0 tests - changes to internal implementation by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2778
• Merge changes made to main by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2779
• Fix: gui/tabs/train_network.py, AttributeError: ‘NoneType’ object has no attribute ‘lower’ by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2780
• Use architecture-specific snapshots prefixes in video adaptation by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2781
• Video Analysis with Identity - Lowering memory footprint by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2785
• Timeout retrieving latest package version from the Web by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2782
• Load scheduler state when resuming training by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2788
• DeepLabCut 3.0 - Video Analysis with use_shelve=True by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2790
• Fix: correct the early return error when save_epochs=1 and optimize the clean up way by @xiu-cs in https://github.com/DeepLabCut/DeepLabCut/pull/2793
• Fix: Video Analysis for Single Animal projects by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2798
• Model Output Visualization for PyTorch Models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2799
• Add Functions for Visualizing COCO Predictions and Ground Truth by @xiu-cs in https://github.com/DeepLabCut/DeepLabCut/pull/2792
• DLC 3.0 - Function to export PyTorch models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2800
• KeypointAwareCrop: uniform sampling when no keypoints are present by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2801
• Fix version check timeout by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2805
• Revert "Fix version check timeout" by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2807
• PyTorch model evaluation - per_keypoint_evaluation and comparisonbodyparts by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2810
• Prune PAF graphs before evaluation by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2813
• Plot detector's bboxes if Top-Down architecture by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2791
• superanimal_analyze_images: improve plotting functions by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2815
• Update superanimal_analyze_images plotting by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2817
• Set weights_only=True as a default when loading snapshot weights. by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2818
• Implement missing arguments for PyTorch models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2816
• Add missing positional arguments to SuperAnimal Colab by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2819
• New Top-Down Pose Estimation Model - RTMPose by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2795
• SuperAnimal demo colab update (for DLC3) by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2814
• Improved loading of snapshot weights withtorch.load(..., weights_only=True) by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2823
• create_labeled_video fails with single animal TensorFlow models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2826
• Merges main into pytorch_dlc by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2828
• Restore "Build skeleton" button by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2831
• Improve deeplabcut.pose_estimation_pytorch imports by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2833
• Improve train_network() docstring by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2836
• get_detector_inference_runner: resolve the device from the model config when None by @nattse in https://github.com/DeepLabCut/DeepLabCut/pull/2841
• Update docs video_inference_superanimal() by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2848
• Fix - setting cropping parameters in analyze_videos for PyTorch models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2849
• Improvements to default configs by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2860
• Dynamic update of pytorch config with dot notation by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2859
• fix broken train_network argument display_iters in the GUI by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2865
• ReID Tracking dataset creation for PyTorch models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2861
• Merges main into pytorch_dlc by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2876
• fix evaluation for ma models, following change in 'deeplabcut/core/metrics/api.py' by @Zelin2001 in https://github.com/DeepLabCut/DeepLabCut/pull/2872
• Fix check version timeout Version 2 (compatible with Windows and MacOS) by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2820
• fix entrypoint for dlc by @hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/2863
• Fix entrypoint - Requested changes by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2883
• Fix assert in compute_detection_rmse() by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2879
• Rename CLI command to dlc by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2885
• add animal_names parameter for pytorch models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2890
• Facelift for codespell config: newer codespell, annotation to PRs, codespell config centralization by @yarikoptic in https://github.com/DeepLabCut/DeepLabCut/pull/2891
• Improvements to the create project GUI by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2892
• Set pcutoff per-bodypart when evaluating PyTorch models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2889
• Fix Codespell by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2899
• Fixes failing tests by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2901
• Implement create_pretrained_project() for Pytorch engine by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2897
• Improve tracklet creation for ID-only tracking by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2903
• Error handling when extracting frames fails in the GUI by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2904
• Fixing video creation from tracks in DLC 2* by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/2910
• [WIP] DLC 3.0 - Review documentation by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2881
• DeepLabCut 3.0 - Updates to COLABs and Notebooks for the PyTorch Engine by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2868
• Option to export top-down models without detectors by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2911
• 🔥 New main backend Deep Learning Library (Engine) for DeepLabCut: PyTorch by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2613
• fix publish-book by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2912
• RC7 release from main by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/2913
• Fix testscript_superanimal_create_pretrained_project by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2915
• Fix circular import by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2917
• Add engine example to docstring in create_training_dataset() by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2921
• _create_video_from_tracks fix by @KonradDanielewski in https://github.com/DeepLabCut/DeepLabCut/pull/2908
• Save predicted poses in evaluate_multianimal_full() by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2902
• Reading apply_prob for augmentation pipeline from config by @aiyeraditya in https://github.com/DeepLabCut/DeepLabCut/pull/2843
• Tracking benchmarking - Updates by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2905
• Add a COLAB for human pose estimation using RTMPose by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2918
• NMS for DEKR models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2907
• Default net type in config set according to engine by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2924
• Add bbox_margin as a parameter to the pytorch config by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2933
• Implement snapshots_to_evaluate for PyTorch models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2936
• Fix: check assembly length before getting first element. by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2935
• Fix docstring by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2939
• Fix ModelZoo Colab by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2946
• Update DEEPLABCUT.yaml by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2948
• Dynamic cropping for top-down models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2919
• Fix missing detector in Create Training Dataset GUI with animaltokenpose and rtmpose architectures by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2938
• Correct dlc_torch README by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2941
• Update CI/CD pipeline by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2947
• Unsupervised ID tracking through the GUI - set of videos instead of list by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2956
• Update README.md by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2955
• create_training_model_comparison: check that existing_shuffles is not empty by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2957
• Addition of BUCTD Models by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2952
• Update bug_report.yml --> new assignment! by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2958
• lower default LR to 5e-4 for ResNets and CSPNeXt by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2960
• DeepLabCut: Fix pandas FutureWarning in evaluate_multianimal.py (inplace=True in .replace()) by @Denny-Hwang in https://github.com/DeepLabCut/DeepLabCut/pull/2927
• Updates to deeplabcut-docker for DeepLabCut 3.0 by @n-poulsen in https://github.com/DeepLabCut/DeepLabCut/pull/2963
• Update bug_report.yml by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2966
• Clarify the CTD evaluation conditions and fix the variable reference used for URL access by @xiu-cs in https://github.com/DeepLabCut/DeepLabCut/pull/2978
• Fix BUCTD Colab link by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2979
• Remove duplicate dlclibrary specification in the setup.py by @hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/2972
• Use R-strings in docstrings containing backslashes by @hmaarrfk in https://github.com/DeepLabCut/DeepLabCut/pull/2971
• Improve CTD preprocessors pipeline by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2984
• Update installation.md by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/2994
• [Docs] pcutoff per bodypart documentation by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2997
• Update docstring and comment by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2981
• Update test_metrics_map_computation.py by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3004
• docs updates, install and readme page by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3005
• extra ` removed by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3008
• Fix BUCTD figure in architectures docs by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/2980
• Update README.md by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3011
• Fix CTD configs and docs inconsistencies by @LucZot in https://github.com/DeepLabCut/DeepLabCut/pull/3010
• Bump torch from 2.6.0 to 2.7.1 by @dependabot in https://github.com/DeepLabCut/DeepLabCut/pull/3006
• Shaokai/faster inference by @yeshaokai in https://github.com/DeepLabCut/DeepLabCut/pull/3012
• formatting fixes by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3015
• Shaokai/rtmpose in modelzoo by @yeshaokai in https://github.com/DeepLabCut/DeepLabCut/pull/3014
• Fix deeplabcut.train_network object detector training evaluation step by @jlb112 in https://github.com/DeepLabCut/DeepLabCut/pull/3013
• Fix and Enhance Adapted Model Checkpoint Path Resolution in video_inference_superanimal(*) by @xiu-cs in https://github.com/DeepLabCut/DeepLabCut/pull/3009
• Fix reID Colab installation by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3021
• Fix Demo SuperAnimal colab by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3022
• Colab YourData SuperAnimal - add model and detector options by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3023
• Fix BUCTD Colab by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3020
• BUCTD GUI integration by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3016
• reID revert to pre-DLC3 to stay with maDLC paper by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3028
• Adding demos to Docs by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3029
• Updated to 3.0.0rc9 and remove superanimal folder by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/3025
• Fix CTDInferenceRunner by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3018
• Set matplotlib in non-interactive backend during tests by @maximpavliv in https://github.com/DeepLabCut/DeepLabCut/pull/3027
• Readme additions by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3032
• Path fix for jupyter book by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/3033
• Set default to pm 180 by @AlexEMG in https://github.com/DeepLabCut/DeepLabCut/pull/3035
• edge case fix / rc10 by @MMathisLab in https://github.com/DeepLabCut/DeepLabCut/pull/3036

New Contributors

• @Zelin2001 made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2668
• @YankoFelipe made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2737
• @SowonKIMM made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2688
• @xiu-cs made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2793
• @aiyeraditya made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2843
• @Denny-Hwang made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/2927
• @dependabot made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/3006
• @jlb112 made their first contribution in https://github.com/DeepLabCut/DeepLabCut/pull/3013

Full Changelog: https://github.com/DeepLabCut/DeepLabCut/compare/v2.3.11...v3.0.0rc10