├── .github └── workflows │ ├── docs.yml │ ├── lint.yml │ └── test.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── LICENSE ├── Makefile ├── README.md ├── codecov.yml ├── conda-linux-64.lock ├── conda-lock.yml ├── conda.yaml ├── docs ├── Makefile ├── api │ ├── curvature.rst │ ├── datasets.rst │ ├── dimension.rst │ ├── index.rst │ ├── topology.rst │ └── warping.rst ├── conf.py ├── index.rst ├── notebooks └── tutorials │ └── index.rst ├── method_overview.png ├── neurometry ├── __init__.py ├── datasets │ ├── __init__.py │ ├── digital_twins │ │ ├── __init__.py │ │ ├── images │ │ │ └── rotations.npy │ │ └── weights │ │ │ ├── task_driven_ensemble_model_01.pth.tar │ │ │ ├── task_driven_ensemble_model_02.pth.tar │ │ │ ├── task_driven_ensemble_model_03.pth.tar │ │ │ ├── task_driven_ensemble_model_04.pth.tar │ │ │ └── task_driven_ensemble_model_05.pth.tar │ ├── experimental │ │ ├── __init__.py │ │ ├── experimental.py │ │ └── utils.py │ ├── piRNNs │ │ ├── __init__.py │ │ ├── dual_agent │ │ │ ├── __init__.py │ │ │ ├── config.py │ │ │ ├── dual_agent_activity.py │ │ │ ├── model.py │ │ │ ├── model_dual_path_integration.py │ │ │ ├── place_cells.py │ │ │ ├── place_cells_dual_path_integration.py │ │ │ ├── single_agent_activity.py │ │ │ ├── trainer.py │ │ │ ├── trajectory_generator.py │ │ │ ├── trajectory_generator_dual_path_integration.py │ │ │ ├── utils.py │ │ │ └── visualize.py │ │ ├── load_rnn_grid_cells.py │ │ ├── saliency │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── default_config.py │ │ │ ├── eval.py │ │ │ ├── experiment.py │ │ │ ├── input_pipeline.py │ │ │ ├── main.py │ │ │ ├── model.py │ │ │ └── utils.py │ │ └── scores.py │ └── synthetic.py └── estimators │ ├── __init__.py │ ├── curvature │ ├── __init__.py │ ├── data │ │ ├── binned │ │ │ └── README.md │ │ ├── datasets_summary.csv │ │ ├── expt_to_first_second_gains.csv │ │ ├── expt_to_n_laps.csv │ │ ├── expt_to_ncells.csv │ │ ├── expt_to_ntimes_timestep100000.csv │ │ ├── expt_to_ntimes_timestep1000000.csv │ │ └── raw │ │ │ └── README.md │ ├── datasets │ │ ├── __init__.py │ │ ├── experimental.py │ │ ├── gridcells.py │ │ ├── structures.py │ │ ├── synthetic.py │ │ └── utils.py │ ├── default_config.py │ ├── evaluate.py │ ├── hyperspherical │ │ ├── __init__.py │ │ ├── distributions │ │ │ ├── __init__.py │ │ │ ├── hyperspherical_uniform.py │ │ │ └── von_mises_fisher.py │ │ └── ops │ │ │ ├── __init__.py │ │ │ └── ive.py │ ├── losses.py │ ├── main.py │ ├── models │ │ ├── __init__.py │ │ ├── klein_bottle_vae.py │ │ ├── neural_vae.py │ │ ├── regressor.py │ │ └── toroidal_vae.py │ ├── plot.html │ ├── plots.py │ ├── torus_embedding.py │ ├── train.py │ └── viz.py │ ├── dimension │ ├── __init__.py │ ├── dim_reduction.py │ └── dimension.py │ ├── geometry │ ├── __init__.py │ ├── immersion_estimator.py │ ├── metric_estimator.py │ └── models │ │ ├── __init__.py │ │ ├── hyperspherical │ │ ├── __init__.py │ │ ├── distributions │ │ │ ├── __init__.py │ │ │ ├── hyperspherical_uniform.py │ │ │ └── von_mises_fisher.py │ │ └── ops │ │ │ ├── __init__.py │ │ │ └── ive.py │ │ ├── losses.py │ │ ├── spherical_vae.py │ │ ├── toroidal_vae.py │ │ ├── train.py │ │ ├── train_config.py │ │ └── utils.py │ ├── topology │ ├── __init__.py │ ├── pd_distances.py │ ├── plotting.py │ └── topology_classifier.py │ └── warping │ ├── __init__.py │ ├── example_images │ ├── out_c2s.gif │ └── out_translation.gif │ ├── pyLDDMM │ ├── LDDMM.py │ ├── __init__.py │ ├── regularizer.py │ └── utils │ │ ├── __init__.py │ │ ├── grad.py │ │ ├── grid.py │ │ ├── sampler.py │ │ └── visualization.py │ ├── results │ └── out_c2s.gif │ └── setup.py ├── poetry.lock ├── pyproject.toml ├── tests ├── __init__.py ├── neurometry │ ├── __init__.py │ └── estimators │ │ ├── __init__.py │ │ ├── curvature │ │ ├── __init__.py │ │ └── test_curvature.py │ │ └── topology │ │ ├── __init__.py │ │ └── test_topology_classifier.py └── test_tutorials.py └── tutorials ├── 01_methods_create_synthetic_data.ipynb 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