Index

_

__eq__() (flowstab.state_tracking.OrderedEnum method) __hash__() (flowstab.state_tracking.OrderedEnum method) __lt__() (flowstab.state_tracking.OrderedEnum method) __repr__() (flowstab.flow_stability.FlowStability method) (flowstab.FlowStability method) (flowstab.network_clustering.Partition method)

__str__() (flowstab.network_clustering.Partition method) (flowstab.state_tracking.OrderedEnum method) __version__ (in module flowstab)

A

all_files (in module flowstab.scripts.run_cov_integrals) ap (in module flowstab.scripts.run_clusterings) (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats)

args (in module flowstab.scripts.run_laplacians_transmats) attach_state() (flowstab.state_tracking.StateMeta method) attributes_list_to_save (in module flowstab.scripts.run_laplacians_transmats) avg_norm_var_information() (in module flowstab.network_clustering)

B

BaseClustering (class in flowstab.network_clustering) batch (in module flowstab.scripts.run_laplacians_transmats), [1]

batch_num (in module flowstab.scripts.run_laplacians_transmats) batch_size (in module flowstab.scripts.run_laplacians_transmats)

C

check_integrity() (flowstab.network_clustering.Partition method) clust_verbose (in module flowstab.scripts.run_clusterings) Clustering (class in flowstab.network_clustering) CLUSTERING (flowstab.flow_stability.States attribute) clustering (flowstab.network_clustering.FlowIntegralClustering attribute) compress_inter_T (in module flowstab.scripts.run_laplacians_transmats) compress_slice_trans (in module flowstab.scripts.run_laplacians_transmats) compression (in module flowstab.scripts.run_cov_integrals) compute_clustering (in module flowstab.scripts.run_clusterings) compute_expm_transmat (in module flowstab.scripts.run_laplacians_transmats) compute_inter_transition_matrices() (flowstab.flow_stability.FlowStability method) (flowstab.FlowStability method) compute_intermediate (in module flowstab.scripts.run_laplacians_transmats)

compute_laplacian_matrices() (flowstab.flow_stability.FlowStability method) (flowstab.FlowStability method) compute_lin_transmat (in module flowstab.scripts.run_laplacians_transmats) compute_nvarinf (in module flowstab.scripts.run_clusterings) compute_nvi_sample() (in module flowstab.scripts.run_clusterings) compute_parallel_clustering() (in module flowstab.parallel_clustering) compute_parallel_nvi() (in module flowstab.parallel_clustering) compute_stability() (flowstab.network_clustering.BaseClustering method) (flowstab.network_clustering.Clustering method) (flowstab.network_clustering.SparseClustering method) compute_static_clustering (in module flowstab.scripts.run_clusterings) compute_static_clustering_fct() (in module flowstab.scripts.run_clusterings) current (flowstab.state_tracking.State attribute) CustomPathnameFilter (class in flowstab.logger)

D

datadir (in module flowstab.scripts.run_clusterings) (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats)

direction (in module flowstab.scripts.run_clusterings)

F

files (in module flowstab.scripts.run_clusterings), [1] filter() (flowstab.logger.CustomPathnameFilter method) FINAL (flowstab.flow_stability.States attribute) find_louvain_clustering() (flowstab.flow_stability.FlowStability method) (flowstab.FlowStability method) (flowstab.network_clustering.BaseClustering method) (flowstab.network_clustering.Clustering method) (flowstab.network_clustering.FlowIntegralClustering method) flow_clustering_backward (flowstab.flow_stability.FlowStability property) (flowstab.FlowStability property) flow_clustering_forward (flowstab.flow_stability.FlowStability property) (flowstab.FlowStability property) FlowIntegralClustering (class in flowstab.network_clustering) flowstab module flowstab.flow_stability module flowstab.helpers module

flowstab.logger module flowstab.network_clustering module flowstab.parallel_clustering module flowstab.scripts module flowstab.scripts.run_clusterings module flowstab.scripts.run_cov_integrals module flowstab.scripts.run_laplacians_transmats module flowstab.state_tracking module FlowStability (class in flowstab) (class in flowstab.flow_stability) force_csr (in module flowstab.scripts.run_laplacians_transmats) full_batch (in module flowstab.scripts.run_laplacians_transmats)

G

get_indicator() (flowstab.network_clustering.Partition method) get_logger() (in module flowstab) (in module flowstab.logger)

get_num_clusters() (flowstab.network_clustering.Partition method)

H

help() (flowstab.flow_stability.FlowStability method) (flowstab.FlowStability method)

I

i (in module flowstab.scripts.run_cov_integrals) inargs (in module flowstab.scripts.run_clusterings) (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats) include_doc_from() (in module flowstab.helpers) init_p1 (in module flowstab.scripts.run_clusterings) init_state() (flowstab.state_tracking.StateMeta class method) INITIAL (flowstab.flow_stability.States attribute) int_length (in module flowstab.scripts.run_cov_integrals), [1] int_list (in module flowstab.scripts.run_cov_integrals)

integral_rtol (in module flowstab.scripts.run_clusterings) (in module flowstab.scripts.run_cov_integrals) INTER_T (flowstab.flow_stability.States attribute) intervals (in module flowstab.scripts.run_cov_integrals), [1] intervals_to_skip (in module flowstab.scripts.run_laplacians_transmats) inverted_iterator() (in module flowstab.helpers) is_nparray (flowstab.network_clustering.FlowIntegralClustering attribute) is_sparse (flowstab.network_clustering.FlowIntegralClustering attribute) is_sparse_stoch (flowstab.network_clustering.FlowIntegralClustering attribute) iter_cluster_node_index() (flowstab.network_clustering.Partition method)

J

jaccard_distance() (in module flowstab.network_clustering)

L

lamda (flowstab.flow_stability.FlowStability property) (flowstab.FlowStability property) LAPLAC (flowstab.flow_stability.States attribute) load_autocov_int() (in module flowstab.scripts.run_clusterings)

load_trans_mat() (in module flowstab.scripts.run_cov_integrals) logger (in module flowstab.flow_stability) (in module flowstab.logger) (in module flowstab.network_clustering)

M

main() (in module flowstab.scripts.run_clusterings) (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats) max_num_varinf_samples (in module flowstab.scripts.run_clusterings) methods_required (flowstab.state_tracking.State attribute) missing_parameters (flowstab.state_tracking.State property) module flowstab flowstab.flow_stability flowstab.helpers flowstab.logger flowstab.network_clustering flowstab.parallel_clustering flowstab.scripts flowstab.scripts.run_clusterings flowstab.scripts.run_cov_integrals flowstab.scripts.run_laplacians_transmats flowstab.state_tracking

move_node() (flowstab.network_clustering.Partition method)

N

n_meta_iter_max (in module flowstab.scripts.run_clusterings) n_random_seeds() (in module flowstab.network_clustering) (in module flowstab.parallel_clustering) (in module flowstab.scripts.run_clusterings) n_sub_iter_max (in module flowstab.scripts.run_clusterings) ncpu (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats) net (in module flowstab.scripts.run_laplacians_transmats) net_filename (in module flowstab.scripts.run_laplacians_transmats) net_name (in module flowstab.scripts.run_clusterings) (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats) next (flowstab.state_tracking.State property)

norm_mutual_information() (in module flowstab.network_clustering) norm_var_information() (in module flowstab.network_clustering) normalize_cov_mat (in module flowstab.scripts.run_clusterings) nproc_clustering (in module flowstab.scripts.run_clusterings) nproc_files (in module flowstab.scripts.run_clusterings) num_nodes (flowstab.network_clustering.FlowIntegralClustering attribute) (flowstab.network_clustering.Partition attribute) (in module flowstab.scripts.run_cov_integrals) num_norm_iter (in module flowstab.scripts.run_clusterings) num_points (in module flowstab.scripts.run_cov_integrals) num_repeat (in module flowstab.scripts.run_clusterings) num_slices (in module flowstab.scripts.run_laplacians_transmats) num_small_grid_points (in module flowstab.scripts.run_cov_integrals) num_varinf_samples (in module flowstab.scripts.run_clusterings), [1]

O

only_expm_transmats (in module flowstab.scripts.run_cov_integrals) only_from_finish (in module flowstab.scripts.run_cov_integrals) only_from_start (in module flowstab.scripts.run_cov_integrals) only_from_start_and_finish (in module flowstab.scripts.run_cov_integrals) only_largest_comp (in module flowstab.scripts.run_clusterings)

only_lin_transmats (in module flowstab.scripts.run_cov_integrals) only_one_interval (in module flowstab.scripts.run_cov_integrals) optional (in module flowstab.scripts.run_clusterings) (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats) OrderedEnum (class in flowstab.state_tracking)

P

p1 (flowstab.network_clustering.BaseClustering attribute) (flowstab.network_clustering.FlowIntegralClustering attribute) (flowstab.network_clustering.SparseClustering attribute) p2 (flowstab.network_clustering.BaseClustering attribute) (flowstab.network_clustering.SparseClustering attribute) Partition (class in flowstab.network_clustering) partition (flowstab.network_clustering.Clustering attribute) (flowstab.network_clustering.FlowIntegralClustering attribute) (flowstab.network_clustering.SparseClustering attribute)

print_interval (in module flowstab.scripts.run_cov_integrals) print_mem_usage (in module flowstab.scripts.run_cov_integrals) print_num_loops (in module flowstab.scripts.run_clusterings) ProcessException properties_required (flowstab.state_tracking.State attribute) properties_set (flowstab.state_tracking.State attribute)

R

register (in module flowstab.flow_stability) register() (flowstab.state_tracking.StateMeta static method) remove_empty_clusters() (flowstab.network_clustering.Partition method) required (in module flowstab.scripts.run_clusterings) (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats)

rev_time_list (in module flowstab.scripts.run_cov_integrals) reverse_time_list (in module flowstab.scripts.run_laplacians_transmats) reversed_time (flowstab.network_clustering.FlowIntegralClustering attribute) run_multi_louvain() (in module flowstab.network_clustering)

S

S_threshold (flowstab.network_clustering.BaseClustering attribute) save_clustering_before_nvarinf (in module flowstab.scripts.run_clusterings) save_delta_inter_T (in module flowstab.scripts.run_laplacians_transmats) save_flow_int (in module flowstab.scripts.run_laplacians_transmats) save_inter_T (in module flowstab.scripts.run_laplacians_transmats) save_intermediate (in module flowstab.scripts.run_cov_integrals) save_slice_trans (in module flowstab.scripts.run_laplacians_transmats) save_static_adjacencies (in module flowstab.scripts.run_laplacians_transmats) savedir (in module flowstab.scripts.run_clusterings) (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats) separate_comps (in module flowstab.scripts.run_clusterings) set_flow_clustering() (flowstab.flow_stability.FlowStability method) (flowstab.FlowStability method) set_log_level() (in module flowstab)

set_temporal_network() (flowstab.flow_stability.FlowStability method) (flowstab.FlowStability method) set_time_scale() (flowstab.flow_stability.FlowStability method) (flowstab.FlowStability method) setup_logger() (in module flowstab) (in module flowstab.logger) slice_length (in module flowstab.scripts.run_laplacians_transmats) sort_clusters() (in module flowstab.network_clustering) source_part (flowstab.network_clustering.BaseClustering attribute) (flowstab.network_clustering.SparseClustering attribute) SparseClustering (class in flowstab.network_clustering) State (class in flowstab.state_tracking) StateMeta (class in flowstab.state_tracking) States (class in flowstab.flow_stability) static_clustering() (in module flowstab.network_clustering)

T

t0 (in module flowstab.scripts.run_laplacians_transmats) t_s (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats) t_start (flowstab.flow_stability.FlowStability property) (flowstab.FlowStability property) t_starts (in module flowstab.scripts.run_laplacians_transmats) t_stop (flowstab.flow_stability.FlowStability property) (flowstab.FlowStability property) t_stops (in module flowstab.scripts.run_laplacians_transmats) target_part (flowstab.network_clustering.BaseClustering attribute) (flowstab.network_clustering.Clustering attribute) (flowstab.network_clustering.SparseClustering attribute) tau_ws (in module flowstab.scripts.run_cov_integrals), [1] (in module flowstab.scripts.run_laplacians_transmats)

TEMP_NW (flowstab.flow_stability.States attribute) temporal_network (flowstab.flow_stability.FlowStability property) (flowstab.FlowStability property) tend (in module flowstab.scripts.run_laplacians_transmats) time_direction (flowstab.flow_stability.FlowStability property) (flowstab.FlowStability property) (in module flowstab.scripts.run_cov_integrals) time_list (flowstab.network_clustering.FlowIntegralClustering attribute) time_scale (flowstab.flow_stability.FlowStability property) (flowstab.FlowStability property) time_slices (in module flowstab.scripts.run_laplacians_transmats) time_slices_from_net_file (in module flowstab.scripts.run_laplacians_transmats) tol (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats) total_num_batches (in module flowstab.scripts.run_laplacians_transmats)

U

use_dense_expm (in module flowstab.scripts.run_laplacians_transmats) use_expm_transmats (in module flowstab.scripts.run_cov_integrals), [1]

use_lin_transmats (in module flowstab.scripts.run_cov_integrals), [1] use_sparse_stoch (in module flowstab.scripts.run_laplacians_transmats)

V

var_dict (in module flowstab.parallel_clustering) (in module flowstab.scripts.run_clusterings) verbose (in module flowstab.scripts.run_clusterings) (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats)

verbose_sparse_matmul (in module flowstab.scripts.run_cov_integrals)

W

worker() (in module flowstab.scripts.run_clusterings) (in module flowstab.scripts.run_cov_integrals) (in module flowstab.scripts.run_laplacians_transmats)