Index

A

AH_glob() (pyDNMFk.dist_nmf.nmf_algorithms_2D method)

ATW_glob() (pyDNMFk.dist_nmf.nmf_algorithms_2D method)

B

box_plot() (in module pyDNMFk.plot_results)

C

calc_norm() (pyDNMFk.dist_svd.DistSVD method) cart_1d_column() (pyDNMFk.dist_comm.MPI_comm method) cart_1d_row() (pyDNMFk.dist_comm.MPI_comm method) cart_2d_collect_factors() (pyDNMFk.pyDNMF.PyNMF method) change_order() (pyDNMFk.dist_clustering.custom_clustering method) column_err() (pyDNMFk.pyDNMF.PyNMF method) comm_timing (class in pyDNMFk.utils)

commonFactors() (pyDNMFk.utils.data_operations method) compute_global_dim() (pyDNMFk.pyDNMF.PyNMF method) create_folder_dir() (pyDNMFk.data_generator.data_generator method) (pyDNMFk.data_io.data_write method) custom_clustering (class in pyDNMFk.dist_clustering) custom_read_npy() (pyDNMFk.data_io.read_factors method) cutZero() (pyDNMFk.utils.data_operations method)

D

data_generator (class in pyDNMFk.data_generator) data_operations (class in pyDNMFk.utils) data_partition() (pyDNMFk.data_io.data_read method) data_read (class in pyDNMFk.data_io) data_write (class in pyDNMFk.data_io) desampleT() (pyDNMFk.utils.data_operations method) determine_block_index_range_asymm() (pyDNMFk.data_generator.data_generator method) (pyDNMFk.utils.determine_block_params method)

determine_block_params (class in pyDNMFk.utils) determine_block_shape_asymm() (pyDNMFk.data_generator.data_generator method) (pyDNMFk.utils.determine_block_params method) dist_custom_clustering() (pyDNMFk.dist_clustering.custom_clustering method) dist_feature_ordering() (pyDNMFk.dist_clustering.custom_clustering method) dist_fromfunction() (pyDNMFk.data_generator.data_generator method) dist_norm() (pyDNMFk.pyDNMF.PyNMF method) dist_silhouettes() (pyDNMFk.dist_clustering.custom_clustering method) DistSVD (class in pyDNMFk.dist_svd)

F

fit() (pyDNMFk.data_generator.data_generator method) (pyDNMFk.dist_clustering.custom_clustering method) (pyDNMFk.pyDNMF.PyNMF method) (pyDNMFk.pyDNMFk.PyNMFk method) (pyDNMFk.pyDNMFk.sample method) Free() (pyDNMFk.dist_comm.MPI_comm method) FRO_BCD_update() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method) FRO_HALS_update() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method)

FRO_HALS_update_H() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method) FRO_HALS_update_W() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method) Fro_MU_update() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method) Fro_MU_update_H() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method) Fro_MU_update_W() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method)

G

gather_W_H() (pyDNMFk.dist_nmf.nmf_algorithms_2D method) gauss_matrix_generator() (pyDNMFk.data_generator.data_generator method) generate_factors_data() (pyDNMFk.data_generator.data_generator method) glob_UX() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) global_gram() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method)

global_mm() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method) globalGram() (pyDNMFk.dist_svd.DistSVD method) globalSqNorm() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method) greedy_lsa() (pyDNMFk.dist_clustering.custom_clustering method)

I

init() (in module pyDNMFk.config) init_factors() (pyDNMFk.pyDNMF.PyNMF method)

initWandH() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method)

K

KL_MU_update() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method) KL_MU_update_H() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method)

KL_MU_update_W() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method)

L

load_factors() (pyDNMFk.data_io.read_factors method)

M

mad() (pyDNMFk.dist_clustering.custom_clustering method) matSplit() (pyDNMFk.utils.data_operations method) module pyDNMFk pyDNMFk.config pyDNMFk.data_generator pyDNMFk.data_io pyDNMFk.dist_clustering pyDNMFk.dist_comm pyDNMFk.dist_nmf pyDNMFk.dist_svd pyDNMFk.plot_results pyDNMFk.pyDNMF pyDNMFk.pyDNMFk pyDNMFk.utils

MPI_comm (class in pyDNMFk.dist_comm)

N

nmf_algorithms_1D (class in pyDNMFk.dist_nmf) nmf_algorithms_2D (class in pyDNMFk.dist_nmf) nnsvd() (pyDNMFk.dist_svd.DistSVD method)

norm() (in module pyDNMFk.utils) normalize_by_W() (pyDNMFk.dist_clustering.custom_clustering method) (pyDNMFk.dist_svd.DistSVD method) normalize_features() (pyDNMFk.pyDNMF.PyNMF method)

P

parse (class in pyDNMFk.utils) parser() (in module pyDNMFk.data_generator) plot_err() (in module pyDNMFk.plot_results) plot_results() (in module pyDNMFk.plot_results) plot_timing_stats() (in module pyDNMFk.plot_results) plot_W() (in module pyDNMFk.plot_results) poisson() (pyDNMFk.pyDNMFk.sample method) primeFactors() (pyDNMFk.utils.data_operations method) pvalueAnalysis() (pyDNMFk.pyDNMFk.PyNMFk method) pyDNMFk module pyDNMFk.config module pyDNMFk.data_generator module pyDNMFk.data_io module pyDNMFk.dist_clustering module

pyDNMFk.dist_comm module pyDNMFk.dist_nmf module pyDNMFk.dist_svd module pyDNMFk.plot_results module pyDNMFk.pyDNMF module pyDNMFk.pyDNMFk module pyDNMFk.utils module PyNMF (class in pyDNMFk.pyDNMF) PyNMFk (class in pyDNMFk.pyDNMFk) pynmfk_per_k() (pyDNMFk.pyDNMFk.PyNMFk method)

R

randM() (pyDNMFk.pyDNMFk.sample method) random_matrix_generator() (pyDNMFk.data_generator.data_generator method) randomUnitVector() (pyDNMFk.dist_svd.DistSVD method) rankidx2blkidx() (pyDNMFk.utils.transform_H_index method) read() (pyDNMFk.data_io.data_read method) read_dat() (pyDNMFk.data_io.data_read method) read_factor() (pyDNMFk.data_io.read_factors method) read_factors (class in pyDNMFk.data_io)

read_file_csv() (pyDNMFk.data_io.data_read method) read_file_mat() (pyDNMFk.data_io.data_read method) read_file_npy() (pyDNMFk.data_io.data_read method) read_plot_factors() (in module pyDNMFk.plot_results) recZero() (pyDNMFk.utils.data_operations method) rel_error() (pyDNMFk.dist_svd.DistSVD method) relative_err() (pyDNMFk.pyDNMF.PyNMF method) remove_bad_factors() (pyDNMFk.utils.data_operations method)

S

sample (class in pyDNMFk.pyDNMFk) save_cluster_results() (pyDNMFk.data_io.data_write method) save_data_to_file() (pyDNMFk.data_io.data_read method) (pyDNMFk.data_io.split_files_save method) save_factors() (pyDNMFk.data_io.data_write method) split_files() (pyDNMFk.data_io.split_files_save method)

split_files_save (class in pyDNMFk.data_io) str2bool() (in module pyDNMFk.utils) sum_along_axis() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) sum_axis() (pyDNMFk.dist_nmf.nmf_algorithms_2D method) svd() (pyDNMFk.dist_svd.DistSVD method) svd1D() (pyDNMFk.dist_svd.DistSVD method)

T

timing_stats() (in module pyDNMFk.plot_results)

transform_H_idx() (pyDNMFk.utils.transform_H_index method) transform_H_index (class in pyDNMFk.utils)

U

UHT_glob() (pyDNMFk.dist_nmf.nmf_algorithms_2D method) unravel_column() (pyDNMFk.data_generator.data_generator method)

unravel_row() (pyDNMFk.data_generator.data_generator method) update() (pyDNMFk.dist_nmf.nmf_algorithms_1D method) (pyDNMFk.dist_nmf.nmf_algorithms_2D method)

V

var_init() (in module pyDNMFk.utils)

W

WTU_glob() (pyDNMFk.dist_nmf.nmf_algorithms_2D method)