├── .clinerules ├── .github └── workflows │ ├── publish_docs.yaml │ ├── publish_main.yaml │ └── testing.yaml ├── .gitignore ├── CHANGELOG.md ├── Dockerfile ├── Images ├── VAME_Logo-1.png ├── behavior_structure_crop.gif ├── cuttree_vis.jpg ├── vame-workflow-diagram.jpg └── workflow.png ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── README.md ├── pydoc-markdown.yml ├── requirements-docs.txt ├── vame-docs-app │ ├── .gitignore │ ├── README.md │ ├── babel.config.js │ ├── blog │ │ ├── 2021-08-26-welcome │ │ │ └── index.md │ │ └── authors.yml │ ├── docs │ │ ├── faq.mdx │ │ ├── getting_started │ │ │ ├── _category_.json │ │ │ ├── _pipeline.mdx │ │ │ ├── _step_by_step.mdx │ │ │ ├── export.mdx │ │ │ ├── installation.md │ │ │ ├── pipeline.mdx │ │ │ └── step_by_step.mdx │ │ ├── intro.md │ │ ├── project_config.mdx │ │ └── reference │ │ │ ├── __init__ │ │ │ └── __init__.md │ │ │ ├── _category_.json │ │ │ ├── analysis │ │ │ ├── __init__.md │ │ │ ├── community_analysis.md │ │ │ ├── generative_functions.md │ │ │ ├── gif_creator.md │ │ │ ├── pose_segmentation.md │ │ │ ├── tree_hierarchy.md │ │ │ ├── umap.md │ │ │ └── videowriter.md │ │ │ ├── initialize_project │ │ │ ├── __init__.md │ │ │ └── new.md │ │ │ ├── io │ │ │ ├── __init__.md │ │ │ ├── load_poses.md │ │ │ └── nwb.md │ │ │ ├── model │ │ │ ├── __init__.md │ │ │ ├── create_training.md │ │ │ ├── dataloader.md │ │ │ ├── evaluate.md │ │ │ ├── rnn_model.md │ │ │ └── rnn_vae.md │ │ │ ├── pipeline.md │ │ │ ├── preprocessing │ │ │ ├── __init__.md │ │ │ ├── align_egocentrical_legacy.md │ │ │ ├── alignment.md │ │ │ ├── cleaning.md │ │ │ ├── filter.md │ │ │ ├── inspection.md │ │ │ ├── preprocessing.md │ │ │ ├── scaling.md │ │ │ ├── to_model.md │ │ │ └── visualization.md │ │ │ ├── sidebar.json │ │ │ ├── util │ │ │ ├── __init__.md │ │ │ ├── auxiliary.md │ │ │ ├── cli.md │ │ │ ├── csv_to_npy.md │ │ │ ├── data_manipulation.md │ │ │ ├── gif_pose_helper.md │ │ │ ├── model_util.md │ │ │ ├── report.md │ │ │ └── sample_data.md │ │ │ ├── video │ │ │ ├── __init__.md │ │ │ └── video.md │ │ │ └── visualization │ │ │ ├── __init__.md │ │ │ ├── community.md │ │ │ ├── model.md │ │ │ ├── motif.md │ │ │ ├── preprocessing.md │ │ │ ├── report.md │ │ │ └── umap.md │ ├── docusaurus.config.js │ ├── package-lock.json │ ├── package.json │ ├── sidebars.js │ ├── src │ │ ├── components │ │ │ ├── HomepageFeatures │ │ │ │ ├── index.js │ │ │ │ └── styles.module.css │ │ │ └── IframeResizer │ │ │ │ └── index.js │ │ ├── css │ │ │ └── custom.css │ │ └── pages │ │ │ ├── index.js │ │ │ ├── index.module.css │ │ │ └── markdown-page.md │ ├── static │ │ ├── .nojekyll │ │ ├── img │ │ │ ├── behavior_structure_crop.gif │ │ │ ├── logo.svg │ │ │ ├── undraw_docusaurus_mountain.svg │ │ │ ├── undraw_docusaurus_react.svg │ │ │ ├── undraw_docusaurus_tree.svg │ │ │ ├── vame_social_card.jpg │ │ │ └── workflow_overview.png │ │ └── notebooks_html │ │ │ ├── pipeline.html │ │ │ └── step_by_step.html │ └── yarn.lock └── yarn.lock ├── environment-linux.yaml ├── environment-win.yaml ├── examples ├── convert_maDLC_csv_individual_csv.py ├── demo.py ├── demo_docker.py ├── pipeline.ipynb └── step_by_step.ipynb ├── memory-bank ├── activeContext.md ├── productContext.md ├── progress.md ├── projectbrief.md ├── systemPatterns.md └── techContext.md ├── pyproject.toml ├── src └── vame │ ├── __init__.py │ ├── analysis │ ├── __init__.py │ ├── community_analysis.py │ ├── generative_functions.py │ ├── gif_creator.py │ ├── pose_segmentation.py │ ├── tree_hierarchy.py │ └── videowriter.py │ ├── initialize_project │ ├── __init__.py │ └── new.py │ ├── io │ ├── __init__.py │ ├── load_poses.py │ └── nwb.py │ ├── logging │ └── logger.py │ ├── model │ ├── __init__.py │ ├── create_training.py │ ├── dataloader.py │ ├── evaluate.py │ ├── rnn_model.py │ └── rnn_vae.py │ ├── pipeline.py │ ├── preprocessing │ ├── __init__.py │ ├── align_egocentrical_legacy.py │ ├── alignment.py │ ├── cleaning.py │ ├── filter.py │ ├── inspection.py │ ├── preprocessing.py │ ├── scaling.py │ └── to_model.py │ ├── schemas │ ├── project.py │ └── states.py │ ├── util │ ├── __init__.py │ ├── auxiliary.py │ ├── cli.py │ ├── csv_to_npy.py │ ├── data_manipulation.py │ ├── gif_pose_helper.py │ ├── model_util.py │ └── sample_data.py │ ├── video │ ├── __init__.py │ └── video.py │ └── visualization │ ├── __init__.py │ ├── community.py │ ├── model.py │ ├── motif.py │ ├── preprocessing.py │ ├── report.py │ └── umap.py └── tests ├── 01_pipeline_test.py ├── 02_initialize_project_test.py ├── 03_util_test.py ├── 04_model_test.py ├── 05_analysis_test.py ├── conftest.py ├── requirements-tests.txt ├── test_project_sample_nwb └── cropped_video.nwb ├── test_traindata_aligned.py └── tests_project_sample_data ├── cropped_video.csv └── cropped_video.mp4 /.clinerules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EthoML/VAME/HEAD/.clinerules 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