Index

_

__init__() (Bold method), [1] (BoldParams method) (BoldStephan2008 method) (BoldTVB method) (BoxUniform method) (Data_F method) (DO method), [1] (GHB_sde method) (JR_sdde method) (JR_sde method), [1], [2] (KM_sde method), [1] (LoadSample method) (MPR_sde method), [1], [2], [3] (VEP_sde method), [1] (WC_ode method) (WC_sde method) (WC_sde_numba method) (WW_sde method), [1]

A

abs_energy() (in module vbi.feature_extraction.features) add_feature() (in module vbi.feature_extraction.features_settings) add_features_from_json() (in module vbi.feature_extraction.features_settings) allocate_memory() (Bold method), [1]

auc() (in module vbi.feature_extraction.features) auc_lim() (in module vbi.feature_extraction.features) autocorr_norm() (in module vbi.feature_extraction.features_utils) average_power() (in module vbi.feature_extraction.features)

B

band_pass_filter() (in module vbi.feature_extraction.features_utils) Bold (class in vbi.models.cupy.bold) (class in vbi.models.cupy.mpr) bold_step() (BoldStephan2008 method)

BoldParams (class in vbi.models.cpp.mpr) BoldStephan2008 (class in vbi.models.cupy.bold) BoldTVB (class in vbi.models.cupy.bold) BoxUniform (class in vbi.utils) burstiness() (in module vbi.feature_extraction.features)

C

calc_centroid() (in module vbi.feature_extraction.features) calc_ecdf() (in module vbi.feature_extraction.features_utils) calc_entropy() (in module vbi.feature_extraction.features) calc_entropy_bin() (in module vbi.feature_extraction.features) calc_envelope() (in module vbi.feature_extraction.features) calc_features() (in module vbi.feature_extraction.calc_features) calc_fft() (in module vbi.feature_extraction.features_utils) calc_kurtosis() (in module vbi.feature_extraction.features) calc_max() (in module vbi.feature_extraction.features) calc_mean() (in module vbi.feature_extraction.features) calc_median() (in module vbi.feature_extraction.features) calc_mi() (in module vbi.feature_extraction.features) calc_min() (in module vbi.feature_extraction.features) calc_moments() (in module vbi.feature_extraction.features) calc_skewness() (in module vbi.feature_extraction.features) calc_std() (in module vbi.feature_extraction.features) calc_te() (in module vbi.feature_extraction.features) calc_var() (in module vbi.feature_extraction.features) calculate_plv() (in module vbi.feature_extraction.features_utils) catch22() (in module vbi.feature_extraction.features) cdf() (BoxUniform method) check_cupy_available() (in module vbi.optional_deps) check_input() (GHB_sde method) (JR_sde method) (MPR_sde method) (WC_sde_numba method) check_parameters() (Bold method), [1] (BoldParams method) (BoldStephan2008 method) (DO method), [1] (GHB_sde method) (JR_sdde method) (JR_sde method), [1], [2] (KM_sde method), [1] (MPR_sde method), [1], [2], [3] (VEP_sde method) (WC_ode method) (WC_sde method) (WC_sde_numba method) (WW_sde method), [1]

check_sbi_available() (in module vbi.optional_deps) check_sequence() (in module vbi.models.cpp.jansen_rit) (in module vbi.models.cpp.mpr) (in module vbi.models.cpp.vep) (in module vbi.models.cpp.wc) check_torch_available() (in module vbi.optional_deps) check_vec_size() (in module vbi.models.numba.mpr) (in module vbi.models.numba.wilson_cowan) check_vec_size_1d() (in module vbi.models.numba.ww) coactivation_degree() (in module vbi.feature_extraction.features) coactivation_phase() (in module vbi.feature_extraction.features) compute_time() (in module vbi.feature_extraction.features_utils) count_depth() (in module vbi.feature_extraction.utility) create_symmetric_matrix() (in module vbi.feature_extraction.features_utils) create_xx() (in module vbi.feature_extraction.features_utils)

D

Data_F (class in vbi.feature_extraction.features_settings) derivative() (WC_sde method) display_time() (in module vbi.utils) DO (class in vbi.models.cpp.damp_oscillator) (class in vbi.models.numba.damp_oscillator) do_bold_step() (Bold method), [1] (in module vbi.models.numba.mpr) (in module vbi.models.numba.ww) (WW_sde method)

DO_nb_numba (in module vbi.models.numba.damp_oscillator) do_step() (WW_sde method) do_step_EI() (WC_sde method) dtype_convert() (in module vbi.models.cupy.utils)

E

euler() (in module vbi.models.numba.damp_oscillator) (JR_sde method) (KM_sde method) euler_maruyama() (WC_sde method)

euler_step() (in module vbi.models.numba.vep) extract_features() (in module vbi.feature_extraction.calc_features) extract_features_df() (in module vbi.feature_extraction.calc_features) extract_features_list() (in module vbi.feature_extraction.calc_features)

F

f_jr() (in module vbi.models.numba.jansen_rit) f_mpr() (in module vbi.models.numba.mpr) (MPR_sde method), [1] f_sys() (JR_sde method) (KM_sde method) f_vep() (in module vbi.models.numba.vep) f_wc() (in module vbi.models.numba.wilson_cowan) f_ww() (in module vbi.models.numba.ww) (WW_sde method)

fc_homotopic() (in module vbi.feature_extraction.features) fc_stat() (in module vbi.feature_extraction.features) fc_sum() (in module vbi.feature_extraction.features) fcd_stat() (in module vbi.feature_extraction.features) filter() (in module vbi.feature_extraction.utility) filterbank() (in module vbi.feature_extraction.features_utils) firing_rate() (in module vbi.models.numba.ww) fundamental_frequency() (in module vbi.feature_extraction.features_utils)

G

gaussian() (in module vbi.feature_extraction.features_utils) get_() (in module vbi.models.cupy.utils) get_bold() (LoadSample method) get_cuda_info() (in module vbi.utils) get_default_parameters() (Bold method), [1] (BoldParams method) (BoldStephan2008 method) (DO method) (JR_sdde method) (JR_sde method), [1] (KM_sde method), [1] (MPR_sde method), [1], [2] (VEP_sde method) (WC_ode method) (WC_sde method) (WW_sde method) get_fc() (in module vbi.feature_extraction.features_utils) get_fcd() (in module vbi.feature_extraction.features_utils) get_fcd2() (in module vbi.feature_extraction.features_utils)

get_features_by_domain() (in module vbi.feature_extraction.features_settings) get_features_by_given_names() (in module vbi.feature_extraction.features_settings) get_features_by_tag() (in module vbi.feature_extraction.features_settings) get_firing_rate() (WW_sde method) get_interh_mask() (in module vbi.feature_extraction.utility) get_intrah_mask() (in module vbi.feature_extraction.utility) get_jar_location() (in module vbi.feature_extraction.features_utils) get_lengths() (LoadSample method) get_limits() (in module vbi.utils) get_limits_numpy() (in module vbi.utils) get_masks() (in module vbi.feature_extraction.utility) get_module() (in module vbi.models.cupy.utils) get_par_mpr() (MPR_sde method) get_par_obj() (GHB_sde method) get_params() (BoldParams method) get_parobj() (DO method) get_weights() (LoadSample method) GHB_sde (class in vbi.models.numba.ghb) GHB_sde_numba (in module vbi.models.numba.ghb)

H

heun() (in module vbi.models.numba.damp_oscillator) (JR_sde method) (KM_sde method) heun_sde() (in module vbi.models.numba.jansen_rit) (in module vbi.models.numba.mpr) (in module vbi.models.numba.wilson_cowan) (in module vbi.models.numba.ww)

heun_step() (in module vbi.models.numba.vep) heunStochastic() (MPR_sde method), [1] (WC_sde method) (WW_sde method) hmm_stat() (in module vbi.feature_extraction.features)

I

if_symmetric() (in module vbi.feature_extraction.utility) init_jvm() (in module vbi.feature_extraction.features_utils) initialize_random_state() (in module vbi.models.numba.ww) integrate() (in module vbi.models.numba.jansen_rit) (in module vbi.models.numba.mpr) (in module vbi.models.numba.wilson_cowan) (KM_sde method)

interq_range() (in module vbi.feature_extraction.features) is_on_cpu() (in module vbi.models.cupy.utils) is_on_gpu() (in module vbi.models.cupy.utils) is_seq() (in module vbi.models.cupy.utils) is_sequence() (in module vbi.feature_extraction.utility)

J

j2p() (in module vbi.utils) JR_sdde (class in vbi.models.cpp.jansen_rit) JR_sde (class in vbi.models.cpp.jansen_rit) (class in vbi.models.cupy.jansen_rit) (class in vbi.models.numba.jansen_rit)

JR_sde_numba (in module vbi.models.numba.jansen_rit)

K

kde() (in module vbi.feature_extraction.features_utils) km_order() (in module vbi.feature_extraction.features_utils)

KM_sde (class in vbi.models.cpp.km) (class in vbi.models.cupy.km) kop() (in module vbi.feature_extraction.features)

L

load_json() (in module vbi.feature_extraction.features_settings) LoadSample (class in vbi.utils)

log_prob() (BoxUniform method) lpc() (in module vbi.feature_extraction.features_utils)

M

make_mask() (in module vbi.feature_extraction.utility) matrix_stat() (in module vbi.feature_extraction.features_utils) max_frequency() (in module vbi.feature_extraction.features_utils) max_psd() (in module vbi.feature_extraction.features_utils) mean() (BoxUniform method) mean_abs_dev() (in module vbi.feature_extraction.features) median_abs_dev() (in module vbi.feature_extraction.features) median_frequency() (in module vbi.feature_extraction.features_utils) module vbi.dataset vbi.feature_extraction.calc_features vbi.feature_extraction.features vbi.feature_extraction.features_settings vbi.feature_extraction.features_utils vbi.feature_extraction.utility vbi.models.cpp.damp_oscillator vbi.models.cpp.jansen_rit vbi.models.cpp.km vbi.models.cpp.mpr vbi.models.cpp.vep vbi.models.cpp.wc vbi.models.cupy.bold vbi.models.cupy.jansen_rit vbi.models.cupy.km vbi.models.cupy.mpr vbi.models.cupy.mpr_modified_bold vbi.models.cupy.utils vbi.models.cupy.wilson_cowan vbi.models.cupy.ww vbi.models.numba.damp_oscillator vbi.models.numba.ghb vbi.models.numba.jansen_rit vbi.models.numba.mpr vbi.models.numba.vep vbi.models.numba.wilson_cowan vbi.models.numba.ww vbi.optional_deps vbi.utils

move_data() (in module vbi.models.cupy.utils) MPR_sde (class in vbi.models.cpp.mpr) (class in vbi.models.cupy.mpr) (class in vbi.models.cupy.mpr_modified_bold) (class in vbi.models.numba.mpr) MPR_sde_numba (in module vbi.models.numba.mpr)

N

nat2bit() (in module vbi.feature_extraction.features_utils)

normalize_signal() (in module vbi.feature_extraction.features_utils)

O

optional_import() (in module vbi.optional_deps)

OptionalDependencyError

P

p2j() (in module vbi.utils) Param (class in vbi.models.numba.damp_oscillator) ParBold (class in vbi.models.numba.mpr) (class in vbi.models.numba.ww) ParGHB (class in vbi.models.numba.ghb) ParJR (class in vbi.models.numba.jansen_rit) ParMPR (class in vbi.models.numba.mpr) ParVEP (class in vbi.models.numba.vep) ParWC (class in vbi.models.numba.wilson_cowan) ParWW (class in vbi.models.numba.ww) posterior_peaks() (in module vbi.utils) posterior_peaks_numpy() (in module vbi.utils) posterior_shrinkage() (in module vbi.feature_extraction.utility) (in module vbi.utils) posterior_shrinkage_numpy() (in module vbi.utils) posterior_zscore() (in module vbi.feature_extraction.utility) (in module vbi.utils) posterior_zscore_numpy() (in module vbi.utils) prepare_input() (DO method) (in module vbi.feature_extraction.utility) (JR_sdde method) (JR_sde method), [1] (KM_sde method), [1] (MPR_sde method), [1], [2] (VEP_sde method) (WC_ode method) (WC_sde method) (WW_sde method)

prepare_input_ts() (in module vbi.feature_extraction.utility) prepare_stimulus() (JR_sdde method) prepare_vec() (in module vbi.models.cupy.utils) prepare_vec_1d() (in module vbi.models.cupy.utils) prepare_vec_2d() (in module vbi.models.cupy.utils) preprocess() (in module vbi.feature_extraction.features_utils) pretty_dtype() (in module vbi.utils) print_valid_parameters() (in module vbi.utils) (JR_sde method) prob() (BoxUniform method) psd_raw() (in module vbi.feature_extraction.features)

R

remove_strong_artefacts() (in module vbi.feature_extraction.features_utils) repmat_vec() (in module vbi.models.cupy.utils) report_cfg() (in module vbi.feature_extraction.features_utils) require_optional() (in module vbi.optional_deps) requires_optional() (in module vbi.optional_deps) rk4() (in module vbi.models.numba.damp_oscillator) rms() (in module vbi.feature_extraction.features) run() (DO method), [1] (GHB_sde method) (in module vbi.models.numba.ghb) (JR_sdde method) (JR_sde method), [1], [2] (KM_sde method), [1] (MPR_sde method), [1], [2], [3] (VEP_sde method), [1] (WC_ode method) (WC_sde method) (WC_sde_numba method) (WW_sde method), [1]

S

S_() (JR_sde method) S_sigmoid() (in module vbi.models.numba.jansen_rit) sample() (BoxUniform method) scipy_iir_filter_data() (in module vbi.feature_extraction.utility) seed_rng() (in module vbi.models.numba.vep) seizure_onset() (in module vbi.feature_extraction.features) seizure_onset_indicator() (in module vbi.feature_extraction.features_utils) select_features_by_domain() (in module vbi.feature_extraction.features_settings) select_functions_by_domain_and_tag() (in module vbi.feature_extraction.features_settings) select_functions_by_tag() (in module vbi.feature_extraction.features_settings) set_attribute() (in module vbi.feature_extraction.features_utils) set_diag() (in module vbi.utils) set_initial_state() (GHB_sde method) (in module vbi.models.cpp.jansen_rit) (in module vbi.models.cpp.km) (in module vbi.models.cpp.mpr) (in module vbi.models.cpp.vep) (in module vbi.models.cupy.jansen_rit) (in module vbi.models.cupy.km) (in module vbi.models.cupy.mpr) (in module vbi.models.cupy.wilson_cowan) (in module vbi.models.cupy.ww) (in module vbi.models.numba.mpr) (in module vbi.models.numba.wilson_cowan) (in module vbi.models.numba.ww) (JR_sdde method) (JR_sde method), [1], [2] (KM_sde method), [1] (MPR_sde method), [1], [2], [3] (VEP_sde method), [1] (WC_ode method) (WC_sde method) (WC_sde_numba method) (WW_sde method)

set_initial_state_jit() (in module vbi.models.numba.vep) set_initial_state_jr() (in module vbi.models.numba.jansen_rit) set_k_diagonals() (in module vbi.feature_extraction.utility) set_seed() (BoxUniform method) set_seed_compat() (in module vbi.models.numba.jansen_rit) (in module vbi.models.numba.mpr) (in module vbi.models.numba.wilson_cowan) sigmoid() (WC_sde method) sigmoid_vec() (in module vbi.models.numba.wilson_cowan) slice_features() (in module vbi.feature_extraction.features_utils) spectral_centroid() (in module vbi.feature_extraction.features_utils) spectral_distance() (in module vbi.feature_extraction.features_utils) spectral_kurtosis() (in module vbi.feature_extraction.features_utils) spectral_spread() (in module vbi.feature_extraction.features_utils) spectral_variation() (in module vbi.feature_extraction.features_utils) spectrum_auc() (in module vbi.feature_extraction.features) spectrum_moments() (in module vbi.feature_extraction.features) spectrum_stats() (in module vbi.feature_extraction.features) state_duration() (in module vbi.feature_extraction.features_utils) std() (BoxUniform method) step() (KM_sde method) support() (BoxUniform method) sync_() (MPR_sde method), [1]

T

Tensor (torch attribute) test_imports() (in module vbi.utils) timer() (in module vbi.utils)

todevice() (in module vbi.models.cupy.utils) tohost() (in module vbi.models.cupy.utils) torch (class in vbi.feature_extraction.features_utils)

U

update_cfg() (in module vbi.feature_extraction.features_settings) update_dependent_parameters() (Bold method), [1] (MPR_sde method), [1] (WC_sde method)

update_par() (DO method), [1]

V

valid_parameters (KM_sde attribute) valid_params (DO attribute) (JR_sdde attribute) (JR_sde attribute) variance() (BoxUniform method) vbi.dataset module vbi.feature_extraction.calc_features module vbi.feature_extraction.features module vbi.feature_extraction.features_settings module vbi.feature_extraction.features_utils module vbi.feature_extraction.utility module vbi.models.cpp.damp_oscillator module vbi.models.cpp.jansen_rit module vbi.models.cpp.km module vbi.models.cpp.mpr module vbi.models.cpp.vep module vbi.models.cpp.wc module vbi.models.cupy.bold module vbi.models.cupy.jansen_rit module

vbi.models.cupy.km module vbi.models.cupy.mpr module vbi.models.cupy.mpr_modified_bold module vbi.models.cupy.utils module vbi.models.cupy.wilson_cowan module vbi.models.cupy.ww module vbi.models.numba.damp_oscillator module vbi.models.numba.ghb module vbi.models.numba.jansen_rit module vbi.models.numba.mpr module vbi.models.numba.vep module vbi.models.numba.wilson_cowan module vbi.models.numba.ww module vbi.optional_deps module vbi.utils module VEP_sde (class in vbi.models.cpp.vep) (class in vbi.models.numba.vep)

W

wavelet() (in module vbi.feature_extraction.features_utils) wavelet_abs_mean() (in module vbi.feature_extraction.features) wavelet_abs_mean_1d() (in module vbi.feature_extraction.features) wavelet_energy() (in module vbi.feature_extraction.features) wavelet_energy_1d() (in module vbi.feature_extraction.features) wavelet_std() (in module vbi.feature_extraction.features)

WC_ode (class in vbi.models.cpp.wc) WC_sde (class in vbi.models.cupy.wilson_cowan) (in module vbi.models.numba.wilson_cowan) WC_sde_numba (class in vbi.models.numba.wilson_cowan) WW_sde (class in vbi.models.cupy.ww) (class in vbi.models.numba.ww)

Z

zero_crossing() (in module vbi.feature_extraction.features)