pynibs gitlab
pynibs
index
modules
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
A
add_center() (in module pynibs.util.util)
add_experiment_info() (pynibs.subject.Subject method)
add_mesh_info() (pynibs.subject.Subject method)
add_mri_info() (pynibs.subject.Subject method)
add_plotsettings() (pynibs.subject.Subject method)
add_roi_info() (pynibs.subject.Subject method)
add_sigmoidal_bestfit() (in module pynibs.exp.exp)
arrays_similar() (in module pynibs.exp.tmsnav)
B
b2rcw() (in module pynibs.para)
bash() (in module pynibs.util.util)
bash_call() (in module pynibs.util.util)
biphasic_pulse() (in module pynibs.tms_pulse)
butter_lowpass() (in module pynibs.exp.Mep)
butter_lowpass_filter() (in module pynibs.exp.Mep)
C
c_map_comparison() (in module pynibs.util.quality_measures)
calc_coil_position_pdf() (in module pynibs.coil)
calc_coil_transformation_matrix() (in module pynibs.coil)
calc_E() (pynibs.main.TetrahedraLinear method)
calc_e_in_midlayer_roi() (in module pynibs.simnibs)
calc_E_normal_tangential_surface() (pynibs.main.TetrahedraLinear method)
calc_E_on_GM_WM_surface() (pynibs.main.TetrahedraLinear method)
calc_E_on_GM_WM_surface3() (pynibs.main.TetrahedraLinear method)
calc_E_on_GM_WM_surface_simnibs() (pynibs.main.TetrahedraLinear method)
calc_E_on_GM_WM_surface_simnibs_KW() (pynibs.main.TetrahedraLinear method)
calc_gradient() (pynibs.main.TetrahedraLinear method)
calc_gradient_surface() (in module pynibs.main)
calc_J() (pynibs.main.TetrahedraLinear method)
calc_mep_wilson() (in module pynibs.muap)
calc_motor_threshold() (pynibs.exp.Mep.Mep method)
calc_n_network_combs() (in module pynibs.util.util)
calc_outlier() (in module pynibs.exp.exp)
calc_p2p() (in module pynibs.exp.Mep)
calc_p2p_old_exp0() (in module pynibs.exp.Mep)
calc_p2p_old_exp1() (in module pynibs.exp.Mep)
calc_QOI_in_points() (pynibs.main.TetrahedraLinear method)
calc_QOI_in_points_tet_idx() (pynibs.main.TetrahedraLinear method)
calc_score() (pynibs.regression.Element method)
calc_surface_adjacent_tetrahedra_idx_list() (pynibs.main.TetrahedraLinear method)
calc_tet_volume() (in module pynibs.util.util)
calc_tetrahedra_volume_cross() (in module pynibs.main)
calc_tetrahedra_volume_det() (in module pynibs.main)
calc_tri_surface() (in module pynibs.util.util)
cell_data_to_point_data() (in module pynibs.util.util)
center (pynibs.roi.RegionOfInterestSurface attribute)
cfs2hdf5() (in module pynibs.exp.exp)
check_coil_position() (in module pynibs.coil)
check_file_and_format() (in module pynibs.subject)
check_mesh() (in module pynibs.simnibs)
clean_roi() (in module pynibs.roi)
coil_distance_correction() (in module pynibs.exp.exp)
coil_distance_correction_matsimnibs() (in module pynibs.exp.exp)
coil_outlier_correction_cond() (in module pynibs.exp.exp)
compute_chunks() (in module pynibs.util.util)
compute_signal() (in module pynibs.muap)
congruence_factor_curveshift_kernel() (in module pynibs.postproc)
congruence_factor_curveshift_workhorse() (in module pynibs.postproc)
congruence_factor_curveshift_workhorse_stretch_correction() (in module pynibs.postproc)
congruence_factor_curveshift_workhorse_stretch_correction_new() (in module pynibs.postproc)
congruence_factor_curveshift_workhorse_stretch_correction_sign_new() (in module pynibs.postproc)
congruence_factor_curveshift_workhorse_stretch_correction_variance() (in module pynibs.postproc)
congruence_factor_variance_sign_workhorse() (in module pynibs.postproc)
congruence_factor_variance_workhorse() (in module pynibs.postproc)
convert_csv_to_hdf5() (in module pynibs.exp.exp)
copt (pynibs.exp.Mep.Mep attribute)
create_dictionary() (in module pynibs.exp.exp)
create_electrode() (in module pynibs.muap)
create_muscle_coords() (in module pynibs.muap)
create_muscle_fibre() (in module pynibs.muap)
create_plot_settings_dict() (in module pynibs.para)
create_position_path_xdmf() (in module pynibs.hdf5_io)
create_refine_spherical_roi() (in module pynibs.roi)
create_sensor_matrix() (in module pynibs.muap)
create_signal_matrix() (in module pynibs.muap)
create_stimsite_from_exp_hdf5() (in module pynibs.coil)
create_stimsite_from_list() (in module pynibs.coil)
create_stimsite_from_matsimnibs() (in module pynibs.coil)
create_stimsite_from_tmslist() (in module pynibs.coil)
create_stimsite_hdf5() (in module pynibs.coil)
crop_data_hdf5_to_datarange() (in module pynibs.para)
crop_image() (in module pynibs.para)
cross_product() (in module pynibs.main)
cross_product_einsum2() (in module pynibs.main)
D
data_elements2nodes() (in module pynibs.main)
(pynibs.main.TetrahedraLinear method)
data_nodes2elements() (in module pynibs.main)
(pynibs.main.TetrahedraLinear method)
data_sub2avg() (in module pynibs.freesurfer)
data_superimpose() (in module pynibs.main)
delta (pynibs.roi.RegionOfInterestSurface attribute)
determine_e_midlayer() (in module pynibs.main)
determine_e_midlayer_workhorse() (in module pynibs.main)
determine_element_idx_in_mesh() (in module pynibs.roi)
(pynibs.roi.RegionOfInterestSurface method)
differential_evolution() (in module pynibs.util.util)
dipole_potential() (in module pynibs.muap)
dummy_fun() (in module pynibs.exp.Mep)
dvs_likelihood() (in module pynibs.postproc)
E
e_cog_workhorse() (in module pynibs.postproc)
e_focal_workhorse() (in module pynibs.postproc)
elem_workhorse() (in module pynibs.roi)
Element (class in pynibs.regression)
ellipse_eccentricity() (in module pynibs.tensor_scaling)
euclidean_dist() (in module pynibs.util.quality_measures)
euler_angles_to_rotation_matrix() (in module pynibs.util.util)
eval() (pynibs.exp.Mep.Mep method)
eval_fun_sig() (pynibs.exp.Mep.Mep method)
eval_opt() (pynibs.exp.Mep.Mep method)
eval_uncertainties() (pynibs.exp.Mep.Mep method)
exp() (in module pynibs.exp.Mep)
exp0() (in module pynibs.exp.Mep)
exp0_log() (in module pynibs.exp.Mep)
exp_log() (in module pynibs.exp.Mep)
extract_condition_combination() (in module pynibs.postproc)
F
fill_defaults() (pynibs.subject.Mesh method)
fill_from_dict() (in module pynibs.subject)
filter_emg() (in module pynibs.exp.visor)
find_element_idx_by_points() (in module pynibs.main)
find_nearest() (in module pynibs.util.util)
fit (pynibs.exp.Mep.Mep attribute)
fit_elms() (in module pynibs.regression)
fit_mep_to_function() (pynibs.exp.Mep.Mep method)
fit_mep_to_function_multistart() (pynibs.exp.Mep.Mep method)
fix_mesh() (in module pynibs.simnibs)
fn_mask (pynibs.roi.RegionOfInterestSurface attribute)
fn_mask_avg (pynibs.roi.RegionOfInterestSurface attribute)
fn_mask_nii (pynibs.roi.RegionOfInterestSurface attribute)
fun (pynibs.exp.Mep.Mep attribute)
fun_sig (pynibs.exp.Mep.Mep attribute)
G
generalized_extreme_value_distribution() (in module pynibs.util.util)
geodesic_dist() (in module pynibs.util.quality_measures)
get_bad_elms() (in module pynibs.regression)
get_cartesian_product() (in module pynibs.util.util)
get_cnt_data() (in module pynibs.exp.visor)
get_cnt_infos() (in module pynibs.exp.exp)
get_coil_dipole_pos() (in module pynibs.coil)
get_coil_flip_m() (in module pynibs.exp.exp)
get_coil_sn_lst() (in module pynibs.exp.exp)
get_csv_matrix() (in module pynibs.exp.exp)
get_det_fim() (in module pynibs.opt)
get_faces() (pynibs.main.TetrahedraLinear method)
get_fim_sample() (in module pynibs.opt)
get_indices_discontinuous_data() (in module pynibs.util.util)
get_instrument_marker() (in module pynibs.exp.tmsnav)
(in module pynibs.exp.visor)
get_intensity_e() (in module pynibs.exp.exp)
get_intensity_e_old() (in module pynibs.exp.exp)
get_intensity_stokes() (in module pynibs.exp.exp)
get_invalid_coil_parameters() (in module pynibs.coil)
get_marker() (in module pynibs.exp.tmsnav)
get_mask() (in module pynibs.roi)
get_mep_elements() (in module pynibs.exp.Mep)
get_mep_sampling_rate() (in module pynibs.exp.Mep)
get_mep_virtual_subject_DVS() (in module pynibs.exp.Mep)
get_mep_virtual_subject_TVS() (in module pynibs.exp.Mep)
get_model_init_values() (in module pynibs.regression)
get_optimal_coil_positions() (in module pynibs.opt)
get_optimal_sample_fim() (in module pynibs.opt)
get_outside_faces() (pynibs.main.TetrahedraLinear method)
get_patient_id() (in module pynibs.exp.exp)
get_single_marker_file() (in module pynibs.exp.tmsnav)
get_sphere() (in module pynibs.util.util)
get_sphere_in_nii() (in module pynibs.roi)
get_time_date() (in module pynibs.exp.Mep)
get_tms_elements() (in module pynibs.exp.tmsnav)
gm_surf_fname (pynibs.roi.RegionOfInterestSurface attribute)
H
hdf_2_ascii() (in module pynibs.hdf5_io)
hermite_rodriguez_1st() (in module pynibs.muap)
I
id (pynibs.subject.Subject.self attribute)
in_hull() (in module pynibs.util.util)
init() (in module pynibs.regression)
init_fim_matrix() (in module pynibs.opt)
invert() (in module pynibs.util.util)
L
layer (pynibs.roi.RegionOfInterestSurface attribute)
likelihood_posterior() (in module pynibs.util.util)
linear() (in module pynibs.exp.Mep)
linear_log() (in module pynibs.exp.Mep)
list2dict() (in module pynibs.util.util)
load_matsimnibs_txt() (in module pynibs.exp.exp)
load_mepobj() (in module pynibs.exp.Mep)
load_mesh_hdf5() (in module pynibs.hdf5_io)
load_mesh_msh() (in module pynibs.hdf5_io)
load_muaps() (in module pynibs.util.util)
load_roi_surface_obj_from_hdf5() (in module pynibs.roi)
load_subject() (in module pynibs.subject)
load_subject_hdf5() (in module pynibs.subject)
load_subject_pkl() (in module pynibs.subject)
logistic_regression() (in module pynibs.regression)
M
make_average_subject() (in module pynibs.freesurfer)
make_GM_WM_surface() (in module pynibs.roi)
(pynibs.roi.RegionOfInterestSurface method)
make_group_average() (in module pynibs.freesurfer)
make_roi_volume_from_msh() (pynibs.roi.RegionOfInterestVolume method)
map_data_to_surface() (in module pynibs.main)
marker_is_empty() (in module pynibs.exp.tmsnav)
markers_are_empty() (in module pynibs.exp.tmsnav)
match_instrument_marker_file() (in module pynibs.exp.tmsnav)
match_instrument_marker_string() (in module pynibs.exp.tmsnav)
match_mep_and_triggermarker_timestamps() (in module pynibs.exp.exp)
match_tm_to_im() (in module pynibs.exp.tmsnav)
Mep (class in pynibs.exp.Mep)
merge_exp_data_brainsight() (in module pynibs.exp.exp)
merge_exp_data_localite() (in module pynibs.exp.exp)
merge_exp_data_visor() (in module pynibs.exp.exp)
Mesh (class in pynibs.subject)
module
pynibs
pynibs.coil
pynibs.exp
pynibs.exp.brainsight
pynibs.exp.brainvis
pynibs.exp.exp
pynibs.exp.Mep
pynibs.exp.tmsnav
pynibs.exp.visor
pynibs.freesurfer
pynibs.hdf5_io
pynibs.main
pynibs.models
pynibs.muap
pynibs.opt
pynibs.para
pynibs.postproc
pynibs.regression
pynibs.roi
pynibs.simnibs
pynibs.subject
pynibs.tensor_scaling
pynibs.tms_pulse
pynibs.util
pynibs.util.quality_measures
pynibs.util.util
msh2hdf5() (in module pynibs.hdf5_io)
mt (pynibs.exp.Mep.Mep attribute)
mutual_coherence() (in module pynibs.util.util)
N
N_points (pynibs.main.TetrahedraLinear attribute)
N_region (pynibs.main.TetrahedraLinear attribute)
N_tet (pynibs.main.TetrahedraLinear attribute)
N_tri (pynibs.main.TetrahedraLinear attribute)
nii2msh() (in module pynibs.roi)
nl_hdf5() (in module pynibs.regression)
nl_hdf5_single_core() (in module pynibs.regression)
nl_hdf5_single_core_write() (in module pynibs.regression)
nnav2simnibs() (in module pynibs.exp.exp)
node_coord (pynibs.roi.RegionOfInterestVolume attribute)
node_coord_low (pynibs.roi.RegionOfInterestSurface attribute)
node_coord_mid (pynibs.roi.RegionOfInterestSurface attribute)
node_coord_up (pynibs.roi.RegionOfInterestSurface attribute)
node_number_list (pynibs.roi.RegionOfInterestSurface attribute)
norm_percentile() (in module pynibs.util.util)
normalize_rot() (in module pynibs.util.util)
nrmsd() (in module pynibs.util.quality_measures)
O
online_optimization() (in module pynibs.opt)
outliers_mask() (in module pynibs.exp.exp)
P
plot() (pynibs.exp.Mep.Mep method)
popt (pynibs.exp.Mep.Mep attribute)
popt_sig (pynibs.exp.Mep.Mep attribute)
print() (pynibs.subject.Mesh method)
(pynibs.subject.ROI method)
print_attrs() (in module pynibs.hdf5_io)
print_time() (in module pynibs.exp.exp)
project_on_midlayer() (pynibs.roi.RegionOfInterestSurface method)
project_on_scalp() (in module pynibs.main)
project_on_scalp_hdf5() (in module pynibs.main)
pstd (pynibs.exp.Mep.Mep attribute)
pynibs
module
pynibs.coil
module
pynibs.exp
module
pynibs.exp.brainsight
module
pynibs.exp.brainvis
module
pynibs.exp.exp
module
pynibs.exp.Mep
module
pynibs.exp.tmsnav
module
pynibs.exp.visor
module
pynibs.freesurfer
module
pynibs.hdf5_io
module
pynibs.main
module
pynibs.models
module
pynibs.muap
module
pynibs.opt
module
pynibs.para
module
pynibs.postproc
module
pynibs.regression
module
pynibs.roi
module
pynibs.simnibs
module
pynibs.subject
module
pynibs.tensor_scaling
module
pynibs.tms_pulse
module
pynibs.util
module
pynibs.util.quality_measures
module
pynibs.util.util
module
Q
quat_rotation_angle() (in module pynibs.util.util)
quat_to_rot() (in module pynibs.util.util)
quaternion_conjugate() (in module pynibs.util.util)
quaternion_diff() (in module pynibs.util.util)
quaternion_inverse() (in module pynibs.util.util)
R
radius (pynibs.roi.RegionOfInterestSurface attribute)
rd() (in module pynibs.util.util)
read_arr_from_hdf5() (in module pynibs.hdf5_io)
read_channel_names() (in module pynibs.exp.brainvis)
read_coil() (in module pynibs.exp.tmsnav)
read_coil_geo() (in module pynibs.simnibs)
read_csv() (in module pynibs.exp.exp)
read_curv_data() (in module pynibs.freesurfer)
read_data_hdf5() (in module pynibs.hdf5_io)
read_dict_from_hdf5() (in module pynibs.hdf5_io)
read_exp_stimulations() (in module pynibs.exp.exp)
read_nlr() (in module pynibs.exp.visor)
read_sampling_frequency() (in module pynibs.exp.brainvis)
read_targets_brainsight() (in module pynibs.exp.brainsight)
read_triggermarker_localite() (in module pynibs.exp.tmsnav)
recursive_len() (in module pynibs.util.util)
refine_surface() (in module pynibs.main)
region (pynibs.main.TetrahedraLinear attribute)
RegionOfInterestSurface (class in pynibs.roi)
RegionOfInterestVolume (class in pynibs.roi)
regress_data() (in module pynibs.regression)
rescale_lambda_centerized() (in module pynibs.tensor_scaling)
rescale_lambda_centerized_workhorse() (in module pynibs.tensor_scaling)
ResetSession() (in module pynibs.para)
ridge_from_hdf5() (in module pynibs.regression)
ROI (class in pynibs.subject)
rot_to_quat() (in module pynibs.util.util)
rotation_matrix_to_euler_angles() (in module pynibs.util.util)
rsd_inverse_workhorse() (in module pynibs.postproc)
run_fit() (pynibs.regression.Element method)
run_fit_multistart() (pynibs.exp.Mep.Mep method)
run_select_signed_data() (pynibs.regression.Element method)
S
sample_sphere() (in module pynibs.util.util)
save_matsimnibs_txt() (in module pynibs.exp.exp)
save_mepobj() (in module pynibs.exp.Mep)
save_subject() (in module pynibs.subject)
save_subject_hdf5() (in module pynibs.subject)
save_subject_pkl() (in module pynibs.subject)
set_constants() (pynibs.regression.Element method)
set_init_vals() (pynibs.regression.Element method)
set_limits() (pynibs.regression.Element method)
set_random_init_vals() (pynibs.regression.Element method)
setup_model() (pynibs.regression.Element method)
sfap() (in module pynibs.muap)
sfap_dip() (in module pynibs.muap)
sigmoid() (in module pynibs.exp.Mep)
sigmoid4() (in module pynibs.exp.Mep)
sigmoid4_log() (in module pynibs.exp.Mep)
sigmoid_log() (in module pynibs.exp.Mep)
sigmoid_log_p() (in module pynibs.util.util)
simnibs_results_msh2hdf5() (in module pynibs.hdf5_io)
simnibs_results_msh2hdf5_workhorse() (in module pynibs.hdf5_io)
sing_elm_fitted() (in module pynibs.regression)
sing_elm_raw() (in module pynibs.regression)
single_fit() (in module pynibs.postproc)
smooth_mesh() (in module pynibs.simnibs)
sort_by_condition() (in module pynibs.exp.exp)
sort_data_by_condition() (in module pynibs.exp.exp)
sort_opt_coil_positions() (in module pynibs.coil)
split_hdf5() (in module pynibs.hdf5_io)
splitext_niigz() (in module pynibs.exp.exp)
square() (in module pynibs.exp.exp)
stepdown_approach() (in module pynibs.regression)
stimulation_threshold() (in module pynibs.postproc)
stimulation_threshold_intensity() (in module pynibs.postproc)
stimulation_threshold_mean_mep_threshold() (in module pynibs.postproc)
stimulation_threshold_sigmoid() (in module pynibs.postproc)
Subject (class in pynibs.subject)
subsample() (pynibs.roi.RegionOfInterestSurface method)
surface_vector_plot() (in module pynibs.para)
surface_vector_plot_vtu() (in module pynibs.para)
T
template (pynibs.roi.RegionOfInterestSurface attribute)
test_coil_position_gpc() (in module pynibs.coil)
tet_idx_node_coord (pynibs.roi.RegionOfInterestVolume attribute)
tet_idx_node_coord_mid (pynibs.roi.RegionOfInterestSurface attribute)
tet_idx_tetrahedra_center (pynibs.roi.RegionOfInterestVolume attribute)
tet_idx_tri_center_low (pynibs.roi.RegionOfInterestSurface attribute)
tet_idx_tri_center_mid (pynibs.roi.RegionOfInterestSurface attribute)
tet_idx_tri_center_up (pynibs.roi.RegionOfInterestSurface attribute)
tet_idx_triangle_center (pynibs.roi.RegionOfInterestVolume attribute)
tet_node_number_list (pynibs.roi.RegionOfInterestVolume attribute)
tetrahedra_center (pynibs.main.TetrahedraLinear attribute)
tetrahedra_volume (pynibs.main.TetrahedraLinear attribute)
TetrahedraLinear (class in pynibs.main)
tets_in_sphere() (in module pynibs.util.util)
toRAS() (in module pynibs.exp.exp)
tri_center_coord_low (pynibs.roi.RegionOfInterestSurface attribute)
tri_center_coord_mid (pynibs.roi.RegionOfInterestSurface attribute)
tri_center_coord_up (pynibs.roi.RegionOfInterestSurface attribute)
tri_node_number_list (pynibs.roi.RegionOfInterestVolume attribute)
triangles_center (pynibs.main.TetrahedraLinear attribute)
triangles_normal (pynibs.main.TetrahedraLinear attribute)
tris_in_sphere() (in module pynibs.util.util)
U
unique_rows() (in module pynibs.util.util)
V
volume_plot() (in module pynibs.para)
volume_plot_vtu() (in module pynibs.para)
W
weight_signal_matrix() (in module pynibs.muap)
wm_surf_fname (pynibs.roi.RegionOfInterestSurface attribute)
workhorse_corr() (in module pynibs.opt)
workhorse_coverage() (in module pynibs.opt)
workhorse_coverage_prepare() (in module pynibs.opt)
workhorse_dist() (in module pynibs.opt)
workhorse_dist_mc() (in module pynibs.opt)
workhorse_dist_svd() (in module pynibs.opt)
workhorse_element_init() (in module pynibs.regression)
workhorse_element_run_fit() (in module pynibs.regression)
workhorse_fim() (in module pynibs.opt)
workhorse_fim_mc() (in module pynibs.opt)
workhorse_fim_svd() (in module pynibs.opt)
workhorse_mc() (in module pynibs.opt)
workhorse_smooth() (in module pynibs.opt)
workhorse_svd() (in module pynibs.opt)
workhorse_var() (in module pynibs.opt)
workhorse_variability() (in module pynibs.opt)
write_arr_to_hdf5() (in module pynibs.hdf5_io)
write_coil_pos_hdf5() (in module pynibs.coil)
write_csv() (in module pynibs.exp.exp)
write_data_hdf5() (in module pynibs.hdf5_io)
write_data_hdf5_surf() (in module pynibs.hdf5_io)
write_dict_to_hdf5() (in module pynibs.hdf5_io)
write_geo_hdf5() (in module pynibs.hdf5_io)
write_geo_hdf5_surf() (in module pynibs.hdf5_io)
write_regression_hdf5() (in module pynibs.regression)
write_targets_brainsight() (in module pynibs.exp.brainsight)
write_temporal_xdmf() (in module pynibs.hdf5_io)
write_to_hdf5() (pynibs.subject.Mesh method)
(pynibs.subject.ROI method)
write_triggermarker_stats() (in module pynibs.exp.exp)
write_vtu() (in module pynibs.para)
write_vtu_coilpos() (in module pynibs.para)
write_vtu_mult() (in module pynibs.para)
write_xdmf() (in module pynibs.hdf5_io)
X
x_limits (pynibs.exp.Mep.Mep attribute)
X_ROI (pynibs.roi.RegionOfInterestSurface attribute)
Y
y_limits (pynibs.exp.Mep.Mep attribute)
Y_ROI (pynibs.roi.RegionOfInterestSurface attribute)
Z
Z_ROI (pynibs.roi.RegionOfInterestSurface attribute)