Index

A

active_brownian_2d() (in module genepy3d.util.geo) active_brownian_3d() (in module genepy3d.util.geo) add_noise() (genepy3d.obj.curves.SimuIntrinsic method)

align() (in module genepy3d.obj.curves) angle2vectors() (in module genepy3d.util.geo) angle3points() (in module genepy3d.util.geo) append() (genepy3d.obj.points.Points method)

B

build_scales_from_radius() (genepy3d.obj.curves.RadiusScaleTable method)

build_treenodes() (genepy3d.obj.trees.Tree static method)

C

Catmaid (class in genepy3d.io.catmaid) CatmaidApiTokenAuth (class in genepy3d.io.base) center() (genepy3d.obj.points.Points method) compute_curvature() (genepy3d.obj.curves.Curve method) compute_derivative() (genepy3d.obj.curves.Curve method) compute_length() (genepy3d.obj.curves.Curve method) (genepy3d.obj.trees.Tree method) compute_local_3d_scale() (genepy3d.obj.curves.Curve method) (genepy3d.obj.trees.Tree method) compute_local_3d_scale_radius() (genepy3d.obj.curves.Curve method) (genepy3d.obj.trees.Tree method) compute_local_3d_scale_sigma() (genepy3d.obj.curves.Curve method) (genepy3d.obj.trees.Tree method) compute_orientation() (genepy3d.obj.curves.Curve method) (genepy3d.obj.trees.Tree method)

compute_scales_from_radius() (genepy3d.obj.curves.RadiusScaleTable method) compute_spine() (genepy3d.obj.trees.Tree method) compute_strahler_order() (genepy3d.obj.trees.Tree method) compute_torsion() (genepy3d.obj.curves.Curve method) compute_tortuosity() (genepy3d.obj.curves.Curve method) compute_wiggliness() (genepy3d.obj.curves.Curve method) convolve_gaussian() (genepy3d.obj.curves.Curve method) coors (genepy3d.obj.curves.Curve attribute) (genepy3d.obj.points.Points attribute) copy() (genepy3d.obj.trees.Tree method) crv (genepy3d.obj.curves.RadiusScaleTable attribute) Curve (class in genepy3d.obj.curves) curve_id (genepy3d.obj.curves.Curve attribute) curve_name (genepy3d.obj.curves.Curve attribute)

D

decompose_intrinsicdim() (genepy3d.obj.curves.Curve method) decompose_intrinsicdim_sequential() (in module genepy3d.obj.curves) decompose_leaves() (genepy3d.obj.trees.Tree method) decompose_segments() (genepy3d.obj.trees.Tree method)

decompose_spines() (genepy3d.obj.trees.Tree method) denoise() (genepy3d.obj.curves.Curve method) dfcon (genepy3d.io.catmaid.Catmaid attribute) dfneu (genepy3d.io.catmaid.Catmaid attribute)

E

emd() (in module genepy3d.obj.points) (in module genepy3d.util.geo) evaluate() (genepy3d.obj.curves.SimuIntrinsic method)

export_to_VTK() (genepy3d.obj.points.Points method) (genepy3d.obj.surfaces.Surface method) extract_subtrees() (genepy3d.obj.trees.Tree method)

F

faces (genepy3d.obj.surfaces.Surface attribute) filepath (genepy3d.io.swc.SWC attribute) fit_plane() (genepy3d.obj.points.Points method) fix_equal_axis() (in module genepy3d.util.plot) from_catmaid_server() (genepy3d.obj.trees.Tree class method) from_csv() (genepy3d.io.catmaid.Catmaid class method) (genepy3d.obj.curves.Curve class method) (genepy3d.obj.points.Points class method) from_eswc() (genepy3d.obj.trees.Tree class method)

from_points_alpha_shape() (genepy3d.obj.surfaces.Surface class method) from_points_qhull() (genepy3d.obj.surfaces.Surface class method) from_server() (genepy3d.io.catmaid.Catmaid class method) from_STL() (genepy3d.obj.surfaces.Surface class method) from_swc() (genepy3d.obj.trees.Tree class method) from_table() (genepy3d.obj.trees.Tree class method) from_text() (genepy3d.obj.curves.Curve class method) (genepy3d.obj.points.Points class method) from_volume() (genepy3d.obj.surfaces.Surface class method)

G

gen() (genepy3d.obj.curves.SimuIntrinsic method) gen_blobs() (in module genepy3d.obj.points) gen_ellipsoid() (in module genepy3d.obj.points) gen_gaussian_points() (in module genepy3d.obj.points) gen_sphere() (in module genepy3d.obj.points) genepy3d module genepy3d.io module genepy3d.io.base module genepy3d.io.catmaid module genepy3d.io.swc module genepy3d.obj module genepy3d.obj.curves module genepy3d.obj.points module genepy3d.obj.surfaces module genepy3d.obj.trees module

genepy3d.util module genepy3d.util.geo module genepy3d.util.plot module geo_len() (in module genepy3d.util.geo) get_branchingnodes() (genepy3d.obj.trees.Tree method) get_children() (genepy3d.obj.trees.Tree method) get_connectors() (genepy3d.obj.trees.Tree method) get_coordinates() (genepy3d.obj.trees.Tree method) get_curve() (genepy3d.obj.curves.SimuIntrinsic method) get_innervation_relation() (genepy3d.io.catmaid.Catmaid method) get_leaves() (genepy3d.obj.trees.Tree method) get_neuron_id() (genepy3d.io.catmaid.Catmaid method) (genepy3d.io.swc.SWC method) get_neuron_id_from_server() (genepy3d.io.catmaid.Catmaid static method) get_neuron_name() (genepy3d.io.catmaid.Catmaid method) get_neurons() (genepy3d.io.catmaid.Catmaid method) (genepy3d.io.swc.SWC method) get_nodes_number() (genepy3d.obj.trees.Tree method) get_parent() (genepy3d.obj.trees.Tree method) get_preorder_nodes() (genepy3d.obj.trees.Tree method) get_root() (genepy3d.obj.trees.Tree method) get_scale() (genepy3d.obj.curves.RadiusScaleMap method) get_synaptic_relation() (genepy3d.io.catmaid.Catmaid method)

I

id (genepy3d.obj.trees.Tree attribute)

K

kerlen (genepy3d.obj.curves.RadiusScaleMap attribute) (genepy3d.obj.curves.RadiusScaleTable attribute)

kmeans() (genepy3d.obj.points.Points method)

L

l (genepy3d.obj.curves.RadiusScaleMap attribute)

l2() (in module genepy3d.util.geo)

M

main_turns() (genepy3d.obj.curves.Curve method) max_seg (genepy3d.obj.curves.SimuIntrinsic attribute) mo (genepy3d.obj.curves.RadiusScaleMap attribute) (genepy3d.obj.curves.RadiusScaleTable attribute) module genepy3d genepy3d.io genepy3d.io.base genepy3d.io.catmaid genepy3d.io.swc genepy3d.obj genepy3d.obj.curves genepy3d.obj.points genepy3d.obj.surfaces genepy3d.obj.trees genepy3d.util genepy3d.util.geo genepy3d.util.plot

N

name (genepy3d.obj.trees.Tree attribute) nb_seg (genepy3d.obj.curves.SimuIntrinsic attribute)

nodes (genepy3d.obj.trees.Tree attribute) norm() (in module genepy3d.util.geo) npoints (genepy3d.obj.curves.SimuIntrinsic attribute)

P

params (genepy3d.obj.curves.SimuIntrinsic attribute) path() (genepy3d.obj.trees.Tree method) pca() (genepy3d.obj.points.Points method) plot() (genepy3d.obj.curves.Curve method) (genepy3d.obj.curves.SimuIntrinsic method) (genepy3d.obj.points.Points method) (genepy3d.obj.surfaces.Surface method) (genepy3d.obj.trees.Tree method)

plot_decomposed_table() (genepy3d.obj.curves.Curve method) plot_intrinsicdim() (genepy3d.obj.curves.Curve method) plot_line() (in module genepy3d.util.plot) plot_point() (in module genepy3d.util.plot) plot_ridge_map() (genepy3d.obj.curves.Curve method) Points (class in genepy3d.obj.points) prune_leaves() (genepy3d.obj.trees.Tree method)

R

r (genepy3d.obj.curves.RadiusScaleTable attribute) RadiusScaleMap (class in genepy3d.obj.curves) RadiusScaleTable (class in genepy3d.obj.curves) random_state (genepy3d.obj.curves.SimuIntrinsic attribute) recursive (genepy3d.io.swc.SWC attribute)

remove_zero_replica (genepy3d.obj.curves.SimuIntrinsic attribute) resample() (genepy3d.obj.curves.Curve method) (genepy3d.obj.trees.Tree method) rmax (genepy3d.obj.curves.RadiusScaleMap attribute) rmin (genepy3d.obj.curves.RadiusScaleMap attribute) rotation_matrix() (in module genepy3d.util.geo)

S

save_circles (genepy3d.obj.curves.RadiusScaleMap attribute) scale_space() (genepy3d.obj.curves.Curve method) seg_lbl (genepy3d.obj.curves.SimuIntrinsic attribute) sigma (genepy3d.obj.curves.SimuIntrinsic attribute) SimuIntrinsic (class in genepy3d.obj.curves) size (genepy3d.obj.points.Points attribute) (genepy3d.obj.points.Points property)

smax (genepy3d.obj.curves.RadiusScaleMap attribute) smin (genepy3d.obj.curves.RadiusScaleMap attribute) split() (genepy3d.obj.surfaces.Surface method) summary() (genepy3d.obj.trees.Tree method) Surface (class in genepy3d.obj.surfaces) SWC (class in genepy3d.io.swc)

T

test_isotropy() (genepy3d.obj.points.Points method) to_csv() (genepy3d.io.catmaid.Catmaid method) to_curve() (genepy3d.obj.points.Points method) (genepy3d.obj.trees.Tree method) to_points() (genepy3d.obj.curves.Curve method) (genepy3d.obj.surfaces.Surface method) (genepy3d.obj.trees.Tree method)

to_surface_alphashape() (genepy3d.obj.points.Points method) to_surface_qhull() (genepy3d.obj.points.Points method) token (genepy3d.io.base.CatmaidApiTokenAuth attribute) transform() (genepy3d.obj.curves.Curve method) (genepy3d.obj.points.Points method) Tree (class in genepy3d.obj.trees)

V

vector2points() (in module genepy3d.util.geo) vector_axes_angles() (in module genepy3d.util.geo)

vector_spherical_angles() (in module genepy3d.util.geo) vertices (genepy3d.obj.surfaces.Surface attribute)