├── .github └── workflows │ ├── ci.yml │ └── deploy-docs.yml ├── .gitignore ├── LICENSE ├── README.md ├── docs ├── copy_tutorials.py ├── gen_ref_pages.py ├── index.md └── stylesheets │ └── extra.css ├── mkdocs.yml ├── neuro_py ├── __init__.py ├── __init__.pyi ├── behavior │ ├── __init__.py │ ├── __init__.pyi │ ├── cheeseboard.py │ ├── circle_maze.py │ ├── get_trials.py │ ├── kinematics.py │ ├── linear_positions.py │ ├── linearization.py │ ├── linearization_pipeline.py │ ├── preprocessing.py │ └── well_traversal_classification.py ├── detectors │ ├── __init__.py │ ├── __init__.pyi │ ├── dentate_spike.py │ └── up_down_state.py ├── ensemble │ ├── __init__.py │ ├── __init__.pyi │ ├── assembly.py │ ├── assembly_reactivation.py │ ├── decoding │ │ ├── __init__.py │ │ ├── bayesian.py │ │ ├── lstm.py │ │ ├── m2mlstm.py │ │ ├── mlp.py │ │ ├── pipeline.py │ │ ├── preprocess.py │ │ └── transformer.py │ ├── dynamics.py │ ├── explained_variance.py │ ├── geometry.py │ ├── pairwise_bias_correlation.py │ ├── replay.py │ ├── similarity_index.py │ └── similaritymat.py ├── io │ ├── __init__.py │ ├── __init__.pyi │ ├── loading.py │ └── saving.py ├── lfp │ ├── CSD.py │ ├── __init__.py │ ├── __init__.pyi │ ├── preprocessing.py │ ├── spectral.py │ └── theta_cycles.py ├── plotting │ ├── __init__.py │ ├── __init__.pyi │ ├── decorators.py │ ├── events.py │ └── figure_helpers.py ├── process │ ├── __init__.py │ ├── __init__.pyi │ ├── batch_analysis.py │ ├── correlations.py │ ├── intervals.py │ ├── peri_event.py │ ├── precession_utils.py │ ├── pychronux.py │ └── utils.py ├── raw │ ├── __init__.py │ ├── __init__.pyi │ ├── preprocessing.py │ └── spike_sorting.py ├── session │ ├── __init__.py │ ├── __init__.pyi │ └── locate_epochs.py ├── spikes │ ├── __init__.py │ ├── __init__.pyi │ └── spike_tools.py ├── stats │ ├── __init__.py │ ├── __init__.pyi │ ├── circ_stats.py │ ├── regression.py │ ├── stats.py │ └── system_identifier.py ├── tuning │ ├── __init__.py │ ├── __init__.pyi │ ├── fields.py │ └── maps.py └── util │ ├── __init__.py │ ├── __init__.pyi │ ├── _dependencies.py │ └── array.py ├── pyproject.toml ├── tests ├── README.md ├── behavior │ ├── __init__.py │ ├── test_behavior_preprocessing.py │ ├── test_circle_maze.py │ ├── test_linear_positions.py │ ├── test_linearization.py │ └── test_position_estimator.py ├── detectors │ ├── __init__.py │ └── test_up_down_state.py ├── ensemble │ ├── __init__.py │ ├── decoding │ │ ├── test_bayesian_decode.py │ │ └── test_dnn_decoders.py │ ├── test_assembly.py │ ├── test_assembly_reactivation.py │ ├── test_ensemble_dynamics.py │ ├── test_ensemble_geometry.py │ ├── test_explained_variance.py │ ├── test_replay.py │ ├── test_similarity_index.py │ └── test_weighted_corr.py ├── lfp │ ├── __init__.py │ ├── test_clean_lfp.py │ └── test_filter_signal.py ├── plotting │ ├── __init__.py │ └── test_plot_peth_fast.py ├── process │ ├── __init__.py │ ├── test_batch_analysis.py │ ├── test_compute_image_spread.py │ ├── test_count_events.py │ ├── test_deconvolve_peth.py │ ├── test_event_triggered_average.py │ ├── test_event_triggered_average_fast.py │ ├── test_event_triggered_cross_correlation.py │ ├── test_event_triggered_wavelet.py │ ├── test_find_intervals.py │ ├── test_get_rank_order.py │ ├── test_in_intervals.py │ ├── test_nearest_event_delay.py │ ├── test_pychronux.py │ ├── test_relative_times.py │ ├── test_shift_epoch_array.py │ └── test_truncate_epoch.py ├── raw │ ├── __init__.py │ ├── test_cut_artifacts.py │ ├── test_cut_artifacts_intan.py │ ├── test_fill_missing_channels.py │ ├── test_remove_artifacts.py │ └── test_reorder_channels.py ├── session │ ├── __init__.py │ └── test_find_multitask_pre_post.py ├── spikes │ ├── __init__.py │ └── test_spike_tools.py ├── stats │ ├── __init__.py │ ├── test_get_significant_events.py │ └── test_stats.py ├── test_io │ ├── __init__.py │ └── test_loading.py ├── tuning │ ├── __init__.py │ └── test_SpatialMap.py └── util │ ├── __init__.py │ ├── test_check_dependency.py │ ├── test_lazy_loading.py │ └── test_util_array.py └── tutorials ├── attractor_landscape.ipynb ├── batch_analysis.ipynb ├── bias_correlation.ipynb ├── decoding.ipynb ├── explained_variance.ipynb ├── neural_geodynamics.ipynb ├── reactivation.ipynb └── spatial_map.ipynb /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.github/workflows/deploy-docs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/.github/workflows/deploy-docs.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/README.md -------------------------------------------------------------------------------- /docs/copy_tutorials.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/docs/copy_tutorials.py -------------------------------------------------------------------------------- /docs/gen_ref_pages.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/docs/gen_ref_pages.py -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/stylesheets/extra.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/docs/stylesheets/extra.css -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/mkdocs.yml -------------------------------------------------------------------------------- /neuro_py/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/__init__.py -------------------------------------------------------------------------------- /neuro_py/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/behavior/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/behavior/__init__.py -------------------------------------------------------------------------------- /neuro_py/behavior/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/behavior/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/behavior/cheeseboard.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/behavior/cheeseboard.py -------------------------------------------------------------------------------- /neuro_py/behavior/circle_maze.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/behavior/circle_maze.py -------------------------------------------------------------------------------- /neuro_py/behavior/get_trials.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/behavior/get_trials.py -------------------------------------------------------------------------------- /neuro_py/behavior/kinematics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/behavior/kinematics.py -------------------------------------------------------------------------------- /neuro_py/behavior/linear_positions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/behavior/linear_positions.py -------------------------------------------------------------------------------- /neuro_py/behavior/linearization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/behavior/linearization.py -------------------------------------------------------------------------------- /neuro_py/behavior/linearization_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/behavior/linearization_pipeline.py -------------------------------------------------------------------------------- /neuro_py/behavior/preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/behavior/preprocessing.py -------------------------------------------------------------------------------- /neuro_py/behavior/well_traversal_classification.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/behavior/well_traversal_classification.py -------------------------------------------------------------------------------- /neuro_py/detectors/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/detectors/__init__.py -------------------------------------------------------------------------------- /neuro_py/detectors/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/detectors/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/detectors/dentate_spike.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/detectors/dentate_spike.py -------------------------------------------------------------------------------- /neuro_py/detectors/up_down_state.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/detectors/up_down_state.py -------------------------------------------------------------------------------- /neuro_py/ensemble/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/__init__.py -------------------------------------------------------------------------------- /neuro_py/ensemble/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/ensemble/assembly.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/assembly.py -------------------------------------------------------------------------------- /neuro_py/ensemble/assembly_reactivation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/assembly_reactivation.py -------------------------------------------------------------------------------- /neuro_py/ensemble/decoding/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/decoding/__init__.py -------------------------------------------------------------------------------- /neuro_py/ensemble/decoding/bayesian.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/decoding/bayesian.py -------------------------------------------------------------------------------- /neuro_py/ensemble/decoding/lstm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/decoding/lstm.py -------------------------------------------------------------------------------- /neuro_py/ensemble/decoding/m2mlstm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/decoding/m2mlstm.py -------------------------------------------------------------------------------- /neuro_py/ensemble/decoding/mlp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/decoding/mlp.py -------------------------------------------------------------------------------- /neuro_py/ensemble/decoding/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/decoding/pipeline.py -------------------------------------------------------------------------------- /neuro_py/ensemble/decoding/preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/decoding/preprocess.py -------------------------------------------------------------------------------- /neuro_py/ensemble/decoding/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/decoding/transformer.py -------------------------------------------------------------------------------- /neuro_py/ensemble/dynamics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/dynamics.py -------------------------------------------------------------------------------- /neuro_py/ensemble/explained_variance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/explained_variance.py -------------------------------------------------------------------------------- /neuro_py/ensemble/geometry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/geometry.py -------------------------------------------------------------------------------- /neuro_py/ensemble/pairwise_bias_correlation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/pairwise_bias_correlation.py -------------------------------------------------------------------------------- /neuro_py/ensemble/replay.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/replay.py -------------------------------------------------------------------------------- /neuro_py/ensemble/similarity_index.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/similarity_index.py -------------------------------------------------------------------------------- /neuro_py/ensemble/similaritymat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/ensemble/similaritymat.py -------------------------------------------------------------------------------- /neuro_py/io/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/io/__init__.py -------------------------------------------------------------------------------- /neuro_py/io/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/io/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/io/loading.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/io/loading.py -------------------------------------------------------------------------------- /neuro_py/io/saving.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/io/saving.py -------------------------------------------------------------------------------- /neuro_py/lfp/CSD.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/lfp/CSD.py -------------------------------------------------------------------------------- /neuro_py/lfp/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/lfp/__init__.py -------------------------------------------------------------------------------- /neuro_py/lfp/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/lfp/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/lfp/preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/lfp/preprocessing.py -------------------------------------------------------------------------------- /neuro_py/lfp/spectral.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/lfp/spectral.py -------------------------------------------------------------------------------- /neuro_py/lfp/theta_cycles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/lfp/theta_cycles.py -------------------------------------------------------------------------------- /neuro_py/plotting/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/plotting/__init__.py -------------------------------------------------------------------------------- /neuro_py/plotting/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/plotting/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/plotting/decorators.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/plotting/decorators.py -------------------------------------------------------------------------------- /neuro_py/plotting/events.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/plotting/events.py -------------------------------------------------------------------------------- /neuro_py/plotting/figure_helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/plotting/figure_helpers.py -------------------------------------------------------------------------------- /neuro_py/process/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/process/__init__.py -------------------------------------------------------------------------------- /neuro_py/process/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/process/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/process/batch_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/process/batch_analysis.py -------------------------------------------------------------------------------- /neuro_py/process/correlations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/process/correlations.py -------------------------------------------------------------------------------- /neuro_py/process/intervals.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/process/intervals.py -------------------------------------------------------------------------------- /neuro_py/process/peri_event.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/process/peri_event.py -------------------------------------------------------------------------------- /neuro_py/process/precession_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/process/precession_utils.py -------------------------------------------------------------------------------- /neuro_py/process/pychronux.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/process/pychronux.py -------------------------------------------------------------------------------- /neuro_py/process/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/process/utils.py -------------------------------------------------------------------------------- /neuro_py/raw/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/raw/__init__.py -------------------------------------------------------------------------------- /neuro_py/raw/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/raw/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/raw/preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/raw/preprocessing.py -------------------------------------------------------------------------------- /neuro_py/raw/spike_sorting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/raw/spike_sorting.py -------------------------------------------------------------------------------- /neuro_py/session/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/session/__init__.py -------------------------------------------------------------------------------- /neuro_py/session/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/session/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/session/locate_epochs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/session/locate_epochs.py -------------------------------------------------------------------------------- /neuro_py/spikes/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/spikes/__init__.py -------------------------------------------------------------------------------- /neuro_py/spikes/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/spikes/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/spikes/spike_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/spikes/spike_tools.py -------------------------------------------------------------------------------- /neuro_py/stats/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/stats/__init__.py -------------------------------------------------------------------------------- /neuro_py/stats/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/stats/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/stats/circ_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/stats/circ_stats.py -------------------------------------------------------------------------------- /neuro_py/stats/regression.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/stats/regression.py -------------------------------------------------------------------------------- /neuro_py/stats/stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/stats/stats.py -------------------------------------------------------------------------------- /neuro_py/stats/system_identifier.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/stats/system_identifier.py -------------------------------------------------------------------------------- /neuro_py/tuning/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/tuning/__init__.py -------------------------------------------------------------------------------- /neuro_py/tuning/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/tuning/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/tuning/fields.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/tuning/fields.py -------------------------------------------------------------------------------- /neuro_py/tuning/maps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/tuning/maps.py -------------------------------------------------------------------------------- /neuro_py/util/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/util/__init__.py -------------------------------------------------------------------------------- /neuro_py/util/__init__.pyi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/util/__init__.pyi -------------------------------------------------------------------------------- /neuro_py/util/_dependencies.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/util/_dependencies.py -------------------------------------------------------------------------------- /neuro_py/util/array.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/neuro_py/util/array.py -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/pyproject.toml -------------------------------------------------------------------------------- /tests/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/README.md -------------------------------------------------------------------------------- /tests/behavior/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/behavior/test_behavior_preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/behavior/test_behavior_preprocessing.py -------------------------------------------------------------------------------- /tests/behavior/test_circle_maze.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/behavior/test_circle_maze.py -------------------------------------------------------------------------------- /tests/behavior/test_linear_positions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/behavior/test_linear_positions.py -------------------------------------------------------------------------------- /tests/behavior/test_linearization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/behavior/test_linearization.py -------------------------------------------------------------------------------- /tests/behavior/test_position_estimator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/behavior/test_position_estimator.py -------------------------------------------------------------------------------- /tests/detectors/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/detectors/test_up_down_state.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/detectors/test_up_down_state.py -------------------------------------------------------------------------------- /tests/ensemble/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/ensemble/decoding/test_bayesian_decode.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/ensemble/decoding/test_bayesian_decode.py -------------------------------------------------------------------------------- /tests/ensemble/decoding/test_dnn_decoders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/ensemble/decoding/test_dnn_decoders.py -------------------------------------------------------------------------------- /tests/ensemble/test_assembly.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/ensemble/test_assembly.py -------------------------------------------------------------------------------- /tests/ensemble/test_assembly_reactivation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/ensemble/test_assembly_reactivation.py -------------------------------------------------------------------------------- /tests/ensemble/test_ensemble_dynamics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/ensemble/test_ensemble_dynamics.py -------------------------------------------------------------------------------- /tests/ensemble/test_ensemble_geometry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/ensemble/test_ensemble_geometry.py -------------------------------------------------------------------------------- /tests/ensemble/test_explained_variance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/ensemble/test_explained_variance.py -------------------------------------------------------------------------------- /tests/ensemble/test_replay.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/ensemble/test_replay.py -------------------------------------------------------------------------------- /tests/ensemble/test_similarity_index.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/ensemble/test_similarity_index.py -------------------------------------------------------------------------------- /tests/ensemble/test_weighted_corr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/ensemble/test_weighted_corr.py -------------------------------------------------------------------------------- /tests/lfp/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/lfp/test_clean_lfp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/lfp/test_clean_lfp.py -------------------------------------------------------------------------------- /tests/lfp/test_filter_signal.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/lfp/test_filter_signal.py -------------------------------------------------------------------------------- /tests/plotting/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/plotting/test_plot_peth_fast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/plotting/test_plot_peth_fast.py -------------------------------------------------------------------------------- /tests/process/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/process/test_batch_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_batch_analysis.py -------------------------------------------------------------------------------- /tests/process/test_compute_image_spread.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_compute_image_spread.py -------------------------------------------------------------------------------- /tests/process/test_count_events.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_count_events.py -------------------------------------------------------------------------------- /tests/process/test_deconvolve_peth.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_deconvolve_peth.py -------------------------------------------------------------------------------- /tests/process/test_event_triggered_average.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_event_triggered_average.py -------------------------------------------------------------------------------- /tests/process/test_event_triggered_average_fast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_event_triggered_average_fast.py -------------------------------------------------------------------------------- /tests/process/test_event_triggered_cross_correlation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_event_triggered_cross_correlation.py -------------------------------------------------------------------------------- /tests/process/test_event_triggered_wavelet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_event_triggered_wavelet.py -------------------------------------------------------------------------------- /tests/process/test_find_intervals.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_find_intervals.py -------------------------------------------------------------------------------- /tests/process/test_get_rank_order.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_get_rank_order.py -------------------------------------------------------------------------------- /tests/process/test_in_intervals.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_in_intervals.py -------------------------------------------------------------------------------- /tests/process/test_nearest_event_delay.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_nearest_event_delay.py -------------------------------------------------------------------------------- /tests/process/test_pychronux.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_pychronux.py -------------------------------------------------------------------------------- /tests/process/test_relative_times.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_relative_times.py -------------------------------------------------------------------------------- /tests/process/test_shift_epoch_array.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_shift_epoch_array.py -------------------------------------------------------------------------------- /tests/process/test_truncate_epoch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/process/test_truncate_epoch.py -------------------------------------------------------------------------------- /tests/raw/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/raw/test_cut_artifacts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/raw/test_cut_artifacts.py -------------------------------------------------------------------------------- /tests/raw/test_cut_artifacts_intan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/raw/test_cut_artifacts_intan.py -------------------------------------------------------------------------------- /tests/raw/test_fill_missing_channels.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/raw/test_fill_missing_channels.py -------------------------------------------------------------------------------- /tests/raw/test_remove_artifacts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/raw/test_remove_artifacts.py -------------------------------------------------------------------------------- /tests/raw/test_reorder_channels.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/raw/test_reorder_channels.py -------------------------------------------------------------------------------- /tests/session/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/session/test_find_multitask_pre_post.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/session/test_find_multitask_pre_post.py -------------------------------------------------------------------------------- /tests/spikes/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/spikes/test_spike_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/spikes/test_spike_tools.py -------------------------------------------------------------------------------- /tests/stats/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/stats/test_get_significant_events.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/stats/test_get_significant_events.py -------------------------------------------------------------------------------- /tests/stats/test_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/stats/test_stats.py -------------------------------------------------------------------------------- /tests/test_io/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/test_io/test_loading.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/test_io/test_loading.py -------------------------------------------------------------------------------- /tests/tuning/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/tuning/test_SpatialMap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/tuning/test_SpatialMap.py -------------------------------------------------------------------------------- /tests/util/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/util/test_check_dependency.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/util/test_check_dependency.py -------------------------------------------------------------------------------- /tests/util/test_lazy_loading.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/util/test_lazy_loading.py -------------------------------------------------------------------------------- /tests/util/test_util_array.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tests/util/test_util_array.py -------------------------------------------------------------------------------- /tutorials/attractor_landscape.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tutorials/attractor_landscape.ipynb -------------------------------------------------------------------------------- /tutorials/batch_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tutorials/batch_analysis.ipynb -------------------------------------------------------------------------------- /tutorials/bias_correlation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tutorials/bias_correlation.ipynb -------------------------------------------------------------------------------- /tutorials/decoding.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tutorials/decoding.ipynb -------------------------------------------------------------------------------- /tutorials/explained_variance.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tutorials/explained_variance.ipynb -------------------------------------------------------------------------------- /tutorials/neural_geodynamics.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tutorials/neural_geodynamics.ipynb -------------------------------------------------------------------------------- /tutorials/reactivation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tutorials/reactivation.ipynb -------------------------------------------------------------------------------- /tutorials/spatial_map.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ryanharvey1/neuro_py/HEAD/tutorials/spatial_map.ipynb --------------------------------------------------------------------------------