Index

A

atleast_2d() (in module replay_trajectory_classification.core)

C

check_converged() (in module replay_trajectory_classification.core) ClusterlessClassifier (class in replay_trajectory_classification.classifier) ClusterlessDecoder (class in replay_trajectory_classification.decoder) combined_likelihood() (in module replay_trajectory_classification.likelihoods.calcium_likelihood) (in module replay_trajectory_classification.likelihoods.spiking_likelihood_glm) (in module replay_trajectory_classification.likelihoods.spiking_likelihood_kde) convert_2D_to_1D_results() (ClusterlessClassifier static method) (SortedSpikesClassifier static method)

convert_polar_to_slope_intercept() (in module replay_trajectory_classification.standard_decoder) convert_results_to_xarray() (ClusterlessDecoder method) (SortedSpikesDecoder method) copy() (ClusterlessClassifier method) (ClusterlessDecoder method) (SortedSpikesClassifier method) (SortedSpikesDecoder method)

D

detect_line_with_radon() (in module replay_trajectory_classification.standard_decoder) diagonal_value (DiagonalDiscrete attribute)

DiagonalDiscrete (class in replay_trajectory_classification.discrete_state_transitions) diffuse() (in module replay_trajectory_classification.environments) diffuse_each_bin() (in module replay_trajectory_classification.environments)

E

EmpiricalMovement (class in replay_trajectory_classification.continuous_state_transitions) encoding_group (EmpiricalMovement attribute) (ObservationModel attribute) Environment (class in replay_trajectory_classification.environments) environment_name (EmpiricalMovement attribute) (Identity attribute) (ObservationModel attribute) (RandomWalk attribute) (RandomWalkDirection1 attribute) (RandomWalkDirection2 attribute) (Uniform attribute) environment_name2 (Uniform attribute) estimate_calcium_likelihood() (in module replay_trajectory_classification.likelihoods.calcium_likelihood) estimate_calcium_place_fields() (in module replay_trajectory_classification.likelihoods.calcium_likelihood) estimate_diffusion_position_density() (in module replay_trajectory_classification.likelihoods.diffusion) estimate_diffusion_position_distance() (in module replay_trajectory_classification.likelihoods.diffusion) estimate_discrete_state_transition() (in module replay_trajectory_classification.discrete_state_transitions) estimate_intensity() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood) (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer) estimate_log_intensity() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood) (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer) estimate_log_joint_mark_intensity() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood) (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer)

estimate_movement_var() (in module replay_trajectory_classification.continuous_state_transitions) estimate_multiunit_likelihood() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood) estimate_multiunit_likelihood_gpu() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_gpu) estimate_multiunit_likelihood_integer() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer) estimate_multiunit_likelihood_integer_gpu() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer_gpu) estimate_parameters() (ClusterlessClassifier method) (SortedSpikesClassifier method) estimate_place_fields() (in module replay_trajectory_classification.likelihoods.spiking_likelihood_glm) estimate_place_fields_kde() (in module replay_trajectory_classification.likelihoods.spiking_likelihood_kde) estimate_place_fields_kde_gpu() (in module replay_trajectory_classification.likelihoods.spiking_likelihood_kde_gpu) estimate_position_density() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood) (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer) (in module replay_trajectory_classification.likelihoods.spiking_likelihood_kde) estimate_position_distance() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood) (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer) (in module replay_trajectory_classification.likelihoods.spiking_likelihood_kde) estimate_spiking_likelihood() (in module replay_trajectory_classification.likelihoods.spiking_likelihood_glm) estimate_spiking_likelihood_kde() (in module replay_trajectory_classification.likelihoods.spiking_likelihood_kde) estimate_spiking_likelihood_kde_gpu() (in module replay_trajectory_classification.likelihoods.spiking_likelihood_kde_gpu) expected_duration() (in module replay_trajectory_classification.discrete_state_transitions) extract_bin_info_from_track_graph() (in module replay_trajectory_classification.environments)

F

fit() (ClusterlessClassifier method) (ClusterlessDecoder method) (SortedSpikesClassifier method) (SortedSpikesDecoder method) fit_continuous_state_transition() (ClusterlessClassifier method) (SortedSpikesClassifier method) fit_discrete_state_transition() (ClusterlessClassifier method) (SortedSpikesClassifier method) fit_environment() (ClusterlessDecoder method) (SortedSpikesDecoder method) fit_environments() (ClusterlessClassifier method) (SortedSpikesClassifier method)

fit_initial_conditions() (ClusterlessClassifier method) (ClusterlessDecoder method) (SortedSpikesClassifier method) (SortedSpikesDecoder method) fit_multiunit_likelihood() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood) fit_multiunit_likelihood_gpu() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_gpu) fit_multiunit_likelihood_integer() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer) fit_multiunit_likelihood_integer_gpu() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer_gpu) fit_multiunits() (ClusterlessClassifier method) (ClusterlessDecoder method) fit_place_fields() (SortedSpikesClassifier method) (SortedSpikesDecoder method) fit_place_grid() (Environment method)

G

gamma_log_likelihood() (in module replay_trajectory_classification.likelihoods.calcium_likelihood) gaussian_pdf() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood) (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer) (in module replay_trajectory_classification.likelihoods.spiking_likelihood_kde) get_activity_rate() (in module replay_trajectory_classification.likelihoods.calcium_likelihood) get_bin_ind() (in module replay_trajectory_classification.environments) get_centers() (in module replay_trajectory_classification.core) get_diffusion_firing_rate() (in module replay_trajectory_classification.likelihoods.spiking_likelihood_kde) get_firing_rate() (in module replay_trajectory_classification.likelihoods.spiking_likelihood_glm) (in module replay_trajectory_classification.likelihoods.spiking_likelihood_kde) get_grid() (in module replay_trajectory_classification.environments) get_metadata_routing() (ClusterlessClassifier method) (ClusterlessDecoder method) (SortedSpikesClassifier method) (SortedSpikesDecoder method)

get_n_bins() (in module replay_trajectory_classification.environments) get_params() (ClusterlessClassifier method) (ClusterlessDecoder method) (SortedSpikesClassifier method) (SortedSpikesDecoder method) get_track_boundary() (in module replay_trajectory_classification.environments) get_track_boundary_points() (in module replay_trajectory_classification.environments) get_track_grid() (in module replay_trajectory_classification.environments) get_track_interior() (in module replay_trajectory_classification.environments) get_track_segments_from_graph() (in module replay_trajectory_classification.environments) get_trajectory_direction() (in module replay_trajectory_classification.simulate)

I

Identity (class in replay_trajectory_classification.continuous_state_transitions)

isotonic_regression() (in module replay_trajectory_classification.standard_decoder)

L

linear_regression() (in module replay_trajectory_classification.standard_decoder) load_environment() (Environment static method) load_model() (ClusterlessClassifier static method) (ClusterlessDecoder static method) (SortedSpikesClassifier static method) (SortedSpikesDecoder static method)

M

make_continuous_replay() (in module replay_trajectory_classification.clusterless_simulation) (in module replay_trajectory_classification.sorted_spikes_simulation) make_fragmented_continuous_fragmented_replay() (in module replay_trajectory_classification.clusterless_simulation) (in module replay_trajectory_classification.sorted_spikes_simulation) make_fragmented_hover_fragmented_replay() (in module replay_trajectory_classification.clusterless_simulation) (in module replay_trajectory_classification.sorted_spikes_simulation) make_fragmented_replay() (in module replay_trajectory_classification.clusterless_simulation) (in module replay_trajectory_classification.sorted_spikes_simulation) make_hover_continuous_hover_replay() (in module replay_trajectory_classification.clusterless_simulation) (in module replay_trajectory_classification.sorted_spikes_simulation) make_hover_replay() (in module replay_trajectory_classification.clusterless_simulation) (in module replay_trajectory_classification.sorted_spikes_simulation) make_initial_conditions() (UniformInitialConditions method) (UniformOneEnvironmentInitialConditions method) make_simulated_run_data() (in module replay_trajectory_classification.clusterless_simulation) (in module replay_trajectory_classification.sorted_spikes_simulation) make_spline_design_matrix() (in module replay_trajectory_classification.likelihoods.calcium_likelihood) (in module replay_trajectory_classification.likelihoods.spiking_likelihood_glm) make_spline_predict_matrix() (in module replay_trajectory_classification.likelihoods.calcium_likelihood) (in module replay_trajectory_classification.likelihoods.spiking_likelihood_glm) make_state_transition() (DiagonalDiscrete method) (EmpiricalMovement method) (Identity method) (RandomDiscrete method) (RandomWalk method) (RandomWalkDirection1 method) (RandomWalkDirection2 method) (Uniform method) (UniformDiscrete method) (UserDefinedDiscrete method)

make_theta_sweep() (in module replay_trajectory_classification.sorted_spikes_simulation) make_track_graph_with_bin_centers_edges() (in module replay_trajectory_classification.environments) map_estimate() (in module replay_trajectory_classification.standard_decoder) mask() (in module replay_trajectory_classification.core) module replay_trajectory_classification replay_trajectory_classification.classifier replay_trajectory_classification.clusterless_simulation replay_trajectory_classification.continuous_state_transitions replay_trajectory_classification.core replay_trajectory_classification.decoder replay_trajectory_classification.discrete_state_transitions replay_trajectory_classification.environments replay_trajectory_classification.initial_conditions replay_trajectory_classification.likelihoods.calcium_likelihood replay_trajectory_classification.likelihoods.diffusion replay_trajectory_classification.likelihoods.multiunit_likelihood replay_trajectory_classification.likelihoods.multiunit_likelihood_gpu replay_trajectory_classification.likelihoods.multiunit_likelihood_integer replay_trajectory_classification.likelihoods.multiunit_likelihood_integer_gpu replay_trajectory_classification.likelihoods.spiking_likelihood_glm replay_trajectory_classification.likelihoods.spiking_likelihood_kde replay_trajectory_classification.likelihoods.spiking_likelihood_kde_gpu replay_trajectory_classification.observation_model replay_trajectory_classification.simulate replay_trajectory_classification.sorted_spikes_simulation replay_trajectory_classification.standard_decoder movement_mean (RandomWalk attribute) movement_var (RandomWalk attribute) (RandomWalkDirection1 attribute) (RandomWalkDirection2 attribute)

N

normal_pdf_integer_lookup() (in module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer)

normalize_to_posterior() (in module replay_trajectory_classification.standard_decoder) normalize_to_probability() (in module replay_trajectory_classification.core)

O

ObservationModel (class in replay_trajectory_classification.observation_model)

order_boundary() (in module replay_trajectory_classification.environments)

P

plot_discrete_state_transition() (ClusterlessClassifier method) (SortedSpikesClassifier method) plot_grid() (Environment method) plot_place_fields() (SortedSpikesClassifier method) (SortedSpikesDecoder method) poisson_log_likelihood() (in module replay_trajectory_classification.likelihoods.spiking_likelihood_glm) (in module replay_trajectory_classification.likelihoods.spiking_likelihood_kde) poisson_mark_log_likelihood() (in module replay_trajectory_classification.standard_decoder) predict() (ClusterlessClassifier method) (ClusterlessDecoder method) (SortedSpikesClassifier method) (SortedSpikesDecoder method)

predict_mark_likelihood() (in module replay_trajectory_classification.standard_decoder) predict_poisson_likelihood() (in module replay_trajectory_classification.standard_decoder) predict_proba() (ClusterlessClassifier static method) (SortedSpikesClassifier static method) project_1D_position_to_2D() (ClusterlessClassifier method) (ClusterlessDecoder method) (SortedSpikesClassifier method) (SortedSpikesDecoder method) project_points_to_segment() (in module replay_trajectory_classification.environments)

R

RandomDiscrete (class in replay_trajectory_classification.discrete_state_transitions) RandomWalk (class in replay_trajectory_classification.continuous_state_transitions) RandomWalkDirection1 (class in replay_trajectory_classification.continuous_state_transitions) RandomWalkDirection2 (class in replay_trajectory_classification.continuous_state_transitions) replay_trajectory_classification module replay_trajectory_classification.classifier module replay_trajectory_classification.clusterless_simulation module replay_trajectory_classification.continuous_state_transitions module replay_trajectory_classification.core module replay_trajectory_classification.decoder module replay_trajectory_classification.discrete_state_transitions module replay_trajectory_classification.environments module replay_trajectory_classification.initial_conditions module replay_trajectory_classification.likelihoods.calcium_likelihood module

replay_trajectory_classification.likelihoods.diffusion module replay_trajectory_classification.likelihoods.multiunit_likelihood module replay_trajectory_classification.likelihoods.multiunit_likelihood_gpu module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer module replay_trajectory_classification.likelihoods.multiunit_likelihood_integer_gpu module replay_trajectory_classification.likelihoods.spiking_likelihood_glm module replay_trajectory_classification.likelihoods.spiking_likelihood_kde module replay_trajectory_classification.likelihoods.spiking_likelihood_kde_gpu module replay_trajectory_classification.observation_model module replay_trajectory_classification.simulate module replay_trajectory_classification.sorted_spikes_simulation module replay_trajectory_classification.standard_decoder module run_diffusion() (in module replay_trajectory_classification.environments)

S

save_environment() (Environment method) save_model() (ClusterlessClassifier method) (ClusterlessDecoder method) (SortedSpikesClassifier method) (SortedSpikesDecoder method) scaled_likelihood() (in module replay_trajectory_classification.core) set_fit_request() (ClusterlessClassifier method) (ClusterlessDecoder method) (SortedSpikesClassifier method) (SortedSpikesDecoder method) set_params() (ClusterlessClassifier method) (ClusterlessDecoder method) (SortedSpikesClassifier method) (SortedSpikesDecoder method)

set_predict_request() (ClusterlessClassifier method) (ClusterlessDecoder method) (SortedSpikesClassifier method) (SortedSpikesDecoder method) simulate_multiunit_with_place_fields() (in module replay_trajectory_classification.simulate) simulate_neuron_with_place_field() (in module replay_trajectory_classification.simulate) simulate_place_field_firing_rate() (in module replay_trajectory_classification.simulate) simulate_poisson_spikes() (in module replay_trajectory_classification.simulate) simulate_position() (in module replay_trajectory_classification.simulate) simulate_position_with_pauses() (in module replay_trajectory_classification.simulate) simulate_time() (in module replay_trajectory_classification.simulate) SortedSpikesClassifier (class in replay_trajectory_classification.classifier) SortedSpikesDecoder (class in replay_trajectory_classification.decoder) speedup (EmpiricalMovement attribute) state_transition (UserDefinedDiscrete attribute)

U

Uniform (class in replay_trajectory_classification.continuous_state_transitions) UniformDiscrete (class in replay_trajectory_classification.discrete_state_transitions) UniformInitialConditions (class in replay_trajectory_classification.initial_conditions)

UniformOneEnvironmentInitialConditions (class in replay_trajectory_classification.initial_conditions) use_diffusion (RandomWalk attribute) UserDefinedDiscrete (class in replay_trajectory_classification.discrete_state_transitions)

W

weighted_correlation() (in module replay_trajectory_classification.standard_decoder)