Index

_

__add__() (hdnet.patterns.Counter method) __call__() (hdnet.hopfield.HopfieldNet method)

__len__() (hdnet.patterns.Counter method)

A

add_key() (hdnet.patterns.Counter method) (hdnet.patterns.PatternsHopfield method) apply_dynamics() (hdnet.patterns.PatternsHopfield method)

approximate_basin_size() (hdnet.patterns.PatternsHopfield method)

B

BernoulliHomogeneous (class in hdnet.spikes_model) BernoulliInhomogeneous (class in hdnet.spikes_model) bin_size (hdnet.spikes.Spikes attribute)

bin_spike_times() (hdnet.data.Binner static method) Binner (class in hdnet.data) bits_recalled() (hdnet.hopfield.HopfieldNet method)

C

calculate_cycles_entropy_scores() (hdnet.stats.SequenceAnalyzer method) calculate_paths_entropy_scores() (hdnet.stats.SequenceAnalyzer method) chomp() (hdnet.patterns.Counter method) (hdnet.patterns.PatternsHopfield method) (hdnet.spikes_model.SpikeModel method) chomp_spikes() (hdnet.patterns.Counter method) chomp_vector() (hdnet.patterns.Counter method) (hdnet.patterns.PatternsHopfield method) close() (hdnet.data.MatlabReaderHDF5 method) combine_windows() (in module hdnet.visualization) compute_kappa() (hdnet.hopfield.HopfieldNet method) compute_label_markov_entropies() (hdnet.stats.SequenceAnalyzer method) compute_label_markov_probabilities() (hdnet.stats.SequenceAnalyzer method)

compute_label_occurrences() (hdnet.stats.SequenceAnalyzer method) compute_label_probabilities() (hdnet.stats.SequenceAnalyzer method) compute_markov_graph() (hdnet.stats.SequenceAnalyzer method) Counter (class in hdnet.patterns) counter (hdnet.stats.SequenceAnalyzer attribute) counts (hdnet.patterns.Counter attribute) counts_by_label (hdnet.patterns.Counter attribute) coupling_matrix (hdnet.hopfield.HopfieldNet attribute) covariance() (hdnet.spikes.Spikes method)

D

dg_second_moment() (in module hdnet.sampling) DichotomizedGaussian (class in hdnet.spikes_model)

DichotomizedGaussianPoisson (class in hdnet.spikes_model) distinct_patterns_over_windows() (hdnet.spikes_model.SpikeModel method)

E

energy() (hdnet.hopfield.HopfieldNet method) (in module hdnet.sampling) entropy() (hdnet.stats.SequenceAnalyzer method)

exact_recalled() (hdnet.hopfield.HopfieldNet method)

F

filter_sequence_repeating_labels() (hdnet.stats.SequenceAnalyzer method) filter_sequence_threshold() (hdnet.stats.SequenceAnalyzer method) filter_sequence_top_occurring() (hdnet.stats.SequenceAnalyzer method) find_dg_any_marginal() (in module hdnet.sampling)

find_latent_gaussian() (in module hdnet.sampling) find_subsequences() (hdnet.stats.SequenceAnalyzer method) find_subsequences_positions() (hdnet.stats.SequenceAnalyzer method) fit() (hdnet.spikes_model.SpikeModel method)

G

get_hdf5() (hdnet.data.MatlabReaderHDF5 method) get_keys() (hdnet.data.MatlabReaderLegacy method) get_object() (hdnet.data.MatlabReaderLegacy method) get_object_numpy() (hdnet.data.MatlabReaderHDF5 method)

get_object_raw() (hdnet.data.MatlabReaderHDF5 method) get_objects() (hdnet.data.MatlabReaderLegacy method) get_spike_sequence() (hdnet.data.SequenceEncoder static method)

H

hdnet.data (module) hdnet.hopfield (module) hdnet.learner (module) hdnet.maths (module) hdnet.patterns (module) hdnet.sampling (module) hdnet.spikes (module) hdnet.spikes_model (module) hdnet.stats (module)

hdnet.stimulus (module) hdnet.util (module) hdnet.visualization (module) heaviside() (in module hdnet.maths) hopfield_binary_dynamics() (hdnet.hopfield.HopfieldNet method) hopfield_patterns (hdnet.spikes_model.SpikeModel attribute) hopfield_spikes (hdnet.spikes_model.SpikeModel attribute) HopfieldNet (class in hdnet.hopfield) HopfieldNetMPF (class in hdnet.hopfield)

I

integer_to_binary() (in module hdnet.sampling)

Ising (class in hdnet.spikes_model)

J

J (hdnet.hopfield.HopfieldNet attribute)

J_norm() (hdnet.hopfield.HopfieldNet method)

K

key_for_pattern() (hdnet.patterns.Counter static method) keys() (hdnet.data.MatlabReaderHDF5 method)

KlustaKwickReader (class in hdnet.data)

L

label_markov_entropies (hdnet.stats.SequenceAnalyzer attribute) label_markov_probabilities (hdnet.stats.SequenceAnalyzer attribute) label_probabilities (hdnet.stats.SequenceAnalyzer attribute) learn_all() (hdnet.hopfield.HopfieldNet method) (hdnet.hopfield.HopfieldNetMPF method) learn_from_binary() (hdnet.learner.Learner method) learn_from_sampler() (hdnet.hopfield.HopfieldNetMPF method) learn_from_spikes() (hdnet.learner.Learner method) learn_from_spikes_rot() (hdnet.learner.Learner method) learn_iterations (hdnet.hopfield.HopfieldNet attribute)

learn_time (hdnet.spikes_model.SpikeModel attribute) Learner (class in hdnet.learner) learner (hdnet.spikes_model.SpikeModel attribute) load() (hdnet.hopfield.HopfieldNet class method) (hdnet.learner.Learner class method) (hdnet.patterns.Counter class method) (hdnet.patterns.PatternsHopfield class method) (hdnet.patterns.PatternsRaw class method) (hdnet.spikes.Spikes class method) (hdnet.spikes_model.SpikeModel class method) (hdnet.stimulus.Stimulus class method) load_from_spikes_times() (hdnet.data.SpkReader static method) load_legacy() (hdnet.patterns.Counter class method) (hdnet.patterns.PatternsHopfield class method) lookup_patterns (hdnet.patterns.Counter attribute) ltqnorm() (in module hdnet.sampling) ltqnorm_nd() (in module hdnet.sampling)

M

M (hdnet.spikes.Spikes attribute) (hdnet.stimulus.Stimulus attribute) markov_graph (hdnet.stats.SequenceAnalyzer attribute) MatlabReaderHDF5 (class in hdnet.data) MatlabReaderLegacy (class in hdnet.data) mean_activity() (hdnet.spikes.Spikes method)

mean_activity_hz() (hdnet.spikes.Spikes method) mem_triggered_stim_avgs() (hdnet.patterns.Counter method) merge_counts() (hdnet.patterns.Counter method) (hdnet.patterns.PatternsHopfield method) mtas (hdnet.patterns.PatternsHopfield attribute) mtas_raw (hdnet.patterns.PatternsHopfield attribute)

N

N (hdnet.hopfield.HopfieldNet attribute) (hdnet.spikes.Spikes attribute) network (hdnet.learner.Learner attribute) neuron_order (hdnet.hopfield.HopfieldNet attribute) num_bins (hdnet.spikes.Spikes attribute) num_hopfield_iter() (hdnet.hopfield.HopfieldNet method)

num_neurons (hdnet.spikes.Spikes attribute) num_nodes (hdnet.hopfield.HopfieldNet attribute) num_patterns (hdnet.patterns.Counter attribute) num_trials (hdnet.spikes.Spikes attribute)

O

objective_function() (hdnet.hopfield.HopfieldNetMPF method) objective_function_batched() (hdnet.hopfield.HopfieldNetMPF method) objective_gradient() (hdnet.hopfield.HopfieldNetMPF method) objective_gradient_batched() (hdnet.hopfield.HopfieldNetMPF method) objective_gradient_minfunc() (hdnet.hopfield.HopfieldNetMPF method)

objective_gradient_minfunc_batched() (hdnet.hopfield.HopfieldNetMPF method) open() (hdnet.data.MatlabReaderHDF5 method) optcallback() (hdnet.hopfield.HopfieldNetMPF method) original_spikes (hdnet.spikes_model.SpikeModel attribute)

P

params (hdnet.learner.Learner attribute) pattern_correlation_coefficients() (hdnet.patterns.Counter method) pattern_distance_hamming() (hdnet.patterns.Counter static method) pattern_distance_jaccard() (hdnet.patterns.Counter static method) pattern_for_key() (hdnet.patterns.Counter static method) pattern_rank_plot() (in module hdnet.visualization) pattern_to_binary_matrix() (hdnet.patterns.Counter method) pattern_to_mta_matrix() (hdnet.patterns.PatternsHopfield method) pattern_to_mtv() (hdnet.patterns.PatternsHopfield method) pattern_to_raw_patterns() (hdnet.patterns.PatternsHopfield method)

pattern_to_trial_raster() (hdnet.patterns.PatternsHopfield method) patterns (hdnet.patterns.Counter attribute) PatternsHopfield (class in hdnet.patterns) PatternsRaw (class in hdnet.patterns) plot_all_matrices() (in module hdnet.visualization) plot_graph() (in module hdnet.visualization) plot_matrix_whole_canvas() (in module hdnet.visualization) plot_memories_distribution_matrix() (in module hdnet.visualization) poisson_marginals() (in module hdnet.sampling) preprocess() (hdnet.stimulus.Stimulus method)

R

raster_plot_psth() (in module hdnet.visualization) rasterize() (hdnet.spikes.Spikes method) raw_patterns (hdnet.spikes_model.SpikeModel attribute) read() (hdnet.data.MatlabReaderLegacy method) read_spikes() (hdnet.data.KlustaKwickReader static method) read_spk_files() (hdnet.data.SpkReader static method) read_spk_folder() (hdnet.data.SpkReader static method) Reader (class in hdnet.data) reduce_graph_bridge() (hdnet.stats.SequenceAnalyzer method) reduce_graph_brute() (hdnet.stats.SequenceAnalyzer method) reduce_graph_cycle() (hdnet.stats.SequenceAnalyzer method)

reduce_graph_ncycle() (hdnet.stats.SequenceAnalyzer method) reduce_graph_out_degree() (hdnet.stats.SequenceAnalyzer method) reduce_graph_self_cycles() (hdnet.stats.SequenceAnalyzer method) reduce_graph_stub() (hdnet.stats.SequenceAnalyzer method) reduce_graph_triangles() (hdnet.stats.SequenceAnalyzer method) reset() (hdnet.hopfield.HopfieldNet method) Restoreable (class in hdnet.util) restrict_to_indices() (hdnet.spikes.Spikes method) restrict_to_most_active_neurons() (hdnet.spikes.Spikes method) restricted_neurons_indices (hdnet.spikes.Spikes attribute)

S

sample_dg_any_marginal() (in module hdnet.sampling) sample_from_bernoulli() (in module hdnet.sampling) sample_from_dichotomized_gaussian() (in module hdnet.sampling) sample_from_ising() (in module hdnet.sampling) sample_from_model() (hdnet.spikes_model.BernoulliHomogeneous method) (hdnet.spikes_model.BernoulliInhomogeneous method) (hdnet.spikes_model.DichotomizedGaussian method) (hdnet.spikes_model.DichotomizedGaussianPoisson method) (hdnet.spikes_model.Ising method) (hdnet.spikes_model.Shuffled method) (hdnet.spikes_model.SpikeModel method) sample_from_prob_vector() (in module hdnet.sampling) sample_spikes (hdnet.spikes_model.SpikeModel attribute) save() (hdnet.hopfield.HopfieldNet method) (hdnet.learner.Learner method) (hdnet.patterns.Counter method) (hdnet.patterns.PatternsHopfield method) (hdnet.patterns.PatternsRaw method) (hdnet.spikes.Spikes method) (hdnet.spikes_model.SpikeModel method) (hdnet.stimulus.Stimulus method) save_matrix_whole_canvas() (in module hdnet.visualization) seen_sequence (hdnet.patterns.Counter attribute) sequence (hdnet.patterns.Counter attribute) (hdnet.stats.SequenceAnalyzer attribute) SequenceAnalyzer (class in hdnet.stats) SequenceEncoder (class in hdnet.data) Shuffled (class in hdnet.spikes_model)

skipped_patterns (hdnet.patterns.Counter attribute) snapshot() (hdnet.stimulus.Stimulus method) SpikeModel (class in hdnet.spikes_model) Spikes (class in hdnet.spikes) spikes (hdnet.learner.Learner attribute) (hdnet.spikes.Spikes attribute) spikes_file (hdnet.learner.Learner attribute) SpkReader (class in hdnet.data) Stimulus (class in hdnet.stimulus) stimulus (hdnet.spikes_model.SpikeModel attribute) stimulus_arr (hdnet.stimulus.Stimulus attribute) store_patterns_using_mpf() (hdnet.hopfield.HopfieldNetMPF method) store_patterns_using_outer_products() (hdnet.hopfield.HopfieldNet method) subseqs() (hdnet.stats.SequenceAnalyzer static method) symmetric (hdnet.hopfield.HopfieldNet attribute)

T

T (hdnet.spikes.Spikes attribute) theta (hdnet.hopfield.HopfieldNet attribute) thresholds (hdnet.hopfield.HopfieldNet attribute) to_windowed() (hdnet.spikes.Spikes method)

top_binary_matrices() (hdnet.patterns.Counter method) top_mta_matrices() (hdnet.patterns.PatternsHopfield method) trials_average() (hdnet.spikes.Spikes method)

U

update (hdnet.hopfield.HopfieldNet attribute)

W

window_size (hdnet.learner.Learner attribute) (hdnet.spikes_model.SpikeModel attribute)

X

X (hdnet.stimulus.Stimulus attribute)