├── .github └── workflows │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── examples ├── baselines │ ├── autolfads │ │ ├── README.md │ │ ├── config │ │ │ ├── area2_bump.yaml │ │ │ ├── area2_bump_20.yaml │ │ │ ├── dmfc_rsg.yaml │ │ │ ├── dmfc_rsg_20.yaml │ │ │ ├── mc_maze.yaml │ │ │ ├── mc_maze_20.yaml │ │ │ ├── mc_maze_large.yaml │ │ │ ├── mc_maze_large_20.yaml │ │ │ ├── mc_maze_medium.yaml │ │ │ ├── mc_maze_medium_20.yaml │ │ │ ├── mc_maze_small.yaml │ │ │ ├── mc_maze_small_20.yaml │ │ │ ├── mc_rtt.yaml │ │ │ └── mc_rtt_20.yaml │ │ ├── lfads_data_prep.py │ │ ├── post_lfads_prep.py │ │ └── run_lfads.py │ ├── gpfa │ │ ├── README.md │ │ ├── gpfa_cv_sweep.py │ │ └── run_gpfa.py │ ├── ndt │ │ └── README.md │ ├── slds │ │ ├── README.md │ │ ├── run_slds.py │ │ └── run_slds_randsearch.py │ └── smoothing │ │ ├── README.md │ │ ├── run_smoothing.py │ │ └── smoothing_cv_sweep.py └── tutorials │ ├── basic_example.ipynb │ ├── gpfa_example.ipynb │ ├── img │ ├── pipeline.png │ └── split.png │ └── slds_example.ipynb ├── nlb_tools ├── __init__.py ├── chop.py ├── evaluation.py ├── make_tensors.py └── nwb_interface.py ├── pyproject.toml ├── requirements.txt ├── setup.py └── tests ├── __init__.py ├── conftest.py ├── test_evaluate.py ├── test_make_tensors.py ├── test_nlb.py └── test_nwb_interface.py /.github/workflows/test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/.github/workflows/test.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/README.md -------------------------------------------------------------------------------- /examples/baselines/autolfads/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/README.md -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/area2_bump.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/area2_bump.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/area2_bump_20.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/area2_bump_20.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/dmfc_rsg.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/dmfc_rsg.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/dmfc_rsg_20.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/dmfc_rsg_20.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/mc_maze.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/mc_maze.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/mc_maze_20.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/mc_maze_20.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/mc_maze_large.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/mc_maze_large.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/mc_maze_large_20.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/mc_maze_large_20.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/mc_maze_medium.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/mc_maze_medium.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/mc_maze_medium_20.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/mc_maze_medium_20.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/mc_maze_small.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/mc_maze_small.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/mc_maze_small_20.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/mc_maze_small_20.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/mc_rtt.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/mc_rtt.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/config/mc_rtt_20.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/config/mc_rtt_20.yaml -------------------------------------------------------------------------------- /examples/baselines/autolfads/lfads_data_prep.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/lfads_data_prep.py -------------------------------------------------------------------------------- /examples/baselines/autolfads/post_lfads_prep.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/post_lfads_prep.py -------------------------------------------------------------------------------- /examples/baselines/autolfads/run_lfads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/autolfads/run_lfads.py -------------------------------------------------------------------------------- /examples/baselines/gpfa/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/gpfa/README.md -------------------------------------------------------------------------------- /examples/baselines/gpfa/gpfa_cv_sweep.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/gpfa/gpfa_cv_sweep.py -------------------------------------------------------------------------------- /examples/baselines/gpfa/run_gpfa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/gpfa/run_gpfa.py -------------------------------------------------------------------------------- /examples/baselines/ndt/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/ndt/README.md -------------------------------------------------------------------------------- /examples/baselines/slds/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/slds/README.md -------------------------------------------------------------------------------- /examples/baselines/slds/run_slds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/slds/run_slds.py -------------------------------------------------------------------------------- /examples/baselines/slds/run_slds_randsearch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/slds/run_slds_randsearch.py -------------------------------------------------------------------------------- /examples/baselines/smoothing/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/smoothing/README.md -------------------------------------------------------------------------------- /examples/baselines/smoothing/run_smoothing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/smoothing/run_smoothing.py -------------------------------------------------------------------------------- /examples/baselines/smoothing/smoothing_cv_sweep.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/baselines/smoothing/smoothing_cv_sweep.py -------------------------------------------------------------------------------- /examples/tutorials/basic_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/tutorials/basic_example.ipynb -------------------------------------------------------------------------------- /examples/tutorials/gpfa_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/tutorials/gpfa_example.ipynb -------------------------------------------------------------------------------- /examples/tutorials/img/pipeline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/tutorials/img/pipeline.png -------------------------------------------------------------------------------- /examples/tutorials/img/split.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/tutorials/img/split.png -------------------------------------------------------------------------------- /examples/tutorials/slds_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/examples/tutorials/slds_example.ipynb -------------------------------------------------------------------------------- /nlb_tools/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nlb_tools/chop.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/nlb_tools/chop.py -------------------------------------------------------------------------------- /nlb_tools/evaluation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/nlb_tools/evaluation.py -------------------------------------------------------------------------------- /nlb_tools/make_tensors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/nlb_tools/make_tensors.py -------------------------------------------------------------------------------- /nlb_tools/nwb_interface.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/nlb_tools/nwb_interface.py -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/pyproject.toml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/setup.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/test_evaluate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/tests/test_evaluate.py -------------------------------------------------------------------------------- /tests/test_make_tensors.py: -------------------------------------------------------------------------------- 1 | # TODO: write tests of main make_tensors functions -------------------------------------------------------------------------------- /tests/test_nlb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurallatents/nlb_tools/HEAD/tests/test_nlb.py -------------------------------------------------------------------------------- /tests/test_nwb_interface.py: -------------------------------------------------------------------------------- 1 | # TODO: write tests of main nwb_interface functions --------------------------------------------------------------------------------