Index

_

__init__() (neurom.core.neuron.BaseSoma method) (neurom.core.neuron.Neuron method) (neurom.core.neuron.SomaA method) (neurom.core.neuron.SomaB method) (neurom.core.neuron.SomaC method) (neurom.core.tree.Tree method) (neurom.ezy.Neuron method) (neurom.ezy.Population method) (neurom.ezy.neuron.Neuron method) (neurom.ezy.population.Population method) (neurom.io.readers.RawDataWrapper method)

A

A (neurom.core.neuron.SOMA_TYPE attribute) add_child() (neurom.core.tree.Tree method) all (neurom.core.types.TreeType attribute) angle_3points() (in module neurom.analysis.morphmath) APICAL_DENDRITE (neurom.core.dataformat.POINT_TYPE attribute)

apical_dendrite (neurom.core.types.TreeType attribute) as_point() (in module neurom.core.point) average_points_dist() (in module neurom.analysis.morphmath) AXON (neurom.core.dataformat.POINT_TYPE attribute) axon (neurom.core.types.TreeType attribute)

B

B (neurom.core.neuron.SOMA_TYPE attribute) BASAL_DENDRITE (neurom.core.dataformat.POINT_TYPE attribute) basal_dendrite (neurom.core.types.TreeType attribute)

BaseSoma (class in neurom.core.neuron) bounding_box() (neurom.core.neuron.Neuron method) (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) branch_order() (in module neurom.analysis.morphtree)

C

C (neurom.core.neuron.SOMA_TYPE attribute) center (neurom.core.neuron.BaseSoma attribute) (neurom.core.neuron.SomaA attribute) (neurom.core.neuron.SomaB attribute) (neurom.core.neuron.SomaC attribute) checkTreeType() (in module neurom.core.types) COLS (class in neurom.core.dataformat)

compare_trees() (in module neurom.analysis.morphtree) copy() (neurom.core.neuron.Neuron method) (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) count() (neurom.core.point.Point method) (neurom.stats.FitResults method) CUSTOM (neurom.core.dataformat.POINT_TYPE attribute)

D

dendrogram() (in module neurom.view.view)

E

END_POINT (neurom.core.dataformat.POINT_TYPE attribute)

errs (neurom.stats.FitResults attribute)

F

figure_naming() (in module neurom.view.common) find_tree_type() (in module neurom.analysis.morphtree) fit() (in module neurom.stats)

fit_results_to_dict() (in module neurom.stats) FitResults (class in neurom.stats) FORK_POINT (neurom.core.dataformat.POINT_TYPE attribute)

G

get_bounding_box() (in module neurom.analysis.morphtree) get_children() (neurom.io.readers.RawDataWrapper method) get_col() (neurom.io.readers.RawDataWrapper method) get_color() (in module neurom.view.common) get_default() (in module neurom.view.view) get_end_points() (neurom.io.readers.RawDataWrapper method) get_figure() (in module neurom.view.common) get_fork_points() (neurom.io.readers.RawDataWrapper method) get_ids() (neurom.io.readers.RawDataWrapper method) get_initial_segment_ids() (in module neurom.io.utils) get_local_bifurcation_angles() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_morph_files() (in module neurom.io.utils) get_n_neurites() (neurom.ezy.Neuron method) (neurom.ezy.Population method) (neurom.ezy.neuron.Neuron method) (neurom.ezy.population.Population method) get_n_sections() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_n_sections_per_neurite() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_parent() (neurom.io.readers.RawDataWrapper method)

get_point() (neurom.io.readers.RawDataWrapper method) get_remote_bifurcation_angles() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_row() (neurom.io.readers.RawDataWrapper method) get_section_lengths() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_section_path_distances() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_section_radial_distances() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_segment_lengths() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_soma_ids() (in module neurom.io.utils) get_soma_radius() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_soma_surface_area() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_tree_type() (in module neurom.analysis.morphtree) get_trunk_origin_radii() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_trunk_section_lengths() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_type() (neurom.core.neuron.SOMA_TYPE static method) get_version() (in module neurom.io.hdf5)

H

H5 (class in neurom.io.hdf5) has_all_finite_length_segments() (in module neurom.io.check) has_all_finite_radius_neurites() (in module neurom.io.check)

has_increasing_ids() (in module neurom.io.check) has_sequential_ids() (in module neurom.io.check) has_soma_points() (in module neurom.io.check)

I

i_branch_end_points() (in module neurom.core.tree) i_chain() (in module neurom.core.tree) i_local_bifurcation_angle() (in module neurom.analysis.morphtree) i_neurites() (neurom.core.neuron.Neuron method) (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) i_remote_bifurcation_angle() (in module neurom.analysis.morphtree) i_section_length() (in module neurom.analysis.morphtree) i_section_path_length() (in module neurom.analysis.morphtree) i_section_radial_dist() (in module neurom.analysis.morphtree) i_segment_area() (in module neurom.analysis.morphtree) i_segment_length() (in module neurom.analysis.morphtree) i_segment_meander_angle() (in module neurom.analysis.morphtree) i_segment_radial_dist() (in module neurom.analysis.morphtree) i_segment_radius() (in module neurom.analysis.morphtree) i_segment_volume() (in module neurom.analysis.morphtree) ibifurcation_point() (in module neurom.core.tree) ID (neurom.core.dataformat.COLS attribute) (neurom.io.swc.SWC attribute) IDSequenceError iforking_point() (in module neurom.core.tree) ileaf() (in module neurom.core.tree) imap_val() (in module neurom.core.tree) index() (neurom.core.point.Point method) (neurom.stats.FitResults method)

INVALID (neurom.core.neuron.SOMA_TYPE attribute) ipostorder() (in module neurom.core.tree) ipreorder() (in module neurom.core.tree) is_bifurcation_point() (in module neurom.core.tree) is_forking_point() (in module neurom.core.tree) is_leaf() (in module neurom.core.tree) is_neurite_segment() (in module neurom.io.check) is_root() (in module neurom.core.tree) isection() (in module neurom.core.tree) isegment() (in module neurom.core.tree) iter() (neurom.core.neuron.BaseSoma method) (neurom.core.neuron.SomaA method) (neurom.core.neuron.SomaB method) (neurom.core.neuron.SomaC method) iter_neurites() (neurom.ezy.Neuron method) (neurom.ezy.Population method) (neurom.ezy.neuron.Neuron method) (neurom.ezy.population.Population method) iter_neurons() (neurom.ezy.Population method) (neurom.ezy.population.Population method) iter_points() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) iter_row() (neurom.io.readers.RawDataWrapper method) iter_sections() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) iter_segments() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) iter_somata() (neurom.ezy.Population method) (neurom.ezy.population.Population method) itriplet() (in module neurom.core.tree) iupstream() (in module neurom.core.tree)

L

load_data() (in module neurom.io) (in module neurom.io.readers) load_neuron() (in module neurom.ezy) (in module neurom.io.utils) load_neurons() (in module neurom.ezy)

load_population() (in module neurom.ezy) local_bifurcation_angle() (in module neurom.analysis.morphtree)

M

make_copy() (in module neurom.core.tree) make_neuron() (in module neurom.io.utils)

make_soma() (in module neurom.core.neuron) make_tree() (in module neurom.io.utils)

N

n_bifurcations() (in module neurom.analysis.morphtree) n_sections() (in module neurom.analysis.morphtree) n_segments() (in module neurom.analysis.morphtree) n_terminations() (in module neurom.analysis.morphtree) neurite_loop() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) NEURITES (neurom.core.dataformat.POINT_TYPE attribute) neurom.analysis (module) neurom.analysis.morphmath (module) neurom.analysis.morphtree (module) neurom.core (module) neurom.core.dataformat (module) neurom.core.neuron (module) neurom.core.point (module) neurom.core.tree (module) neurom.core.types (module) neurom.exceptions (module) neurom.ezy (module)

neurom.ezy.neuron (module) neurom.ezy.population (module) neurom.io (module) neurom.io.check (module) neurom.io.hdf5 (module) neurom.io.readers (module) neurom.io.swc (module) neurom.io.utils (module) neurom.stats (module) neurom.view (module) neurom.view.common (module) neurom.view.view (module) NeuroMError Neuron (class in neurom.core.neuron) (class in neurom.ezy) (class in neurom.ezy.neuron) neuron() (in module neurom.view.view) neuron3d() (in module neurom.view.view)

O

optimal_distribution() (in module neurom.stats)

P

P (neurom.core.dataformat.COLS attribute) (neurom.io.swc.SWC attribute) params (neurom.stats.FitResults attribute) partition() (in module neurom.analysis.morphtree) path_distance() (in module neurom.analysis.morphmath) path_length() (in module neurom.analysis.morphtree) pca() (in module neurom.analysis.morphmath) plot_labels() (in module neurom.view.common) plot_legend() (in module neurom.view.common) plot_limits() (in module neurom.view.common) plot_sphere() (in module neurom.view.common)

plot_style() (in module neurom.view.common) plot_ticks() (in module neurom.view.common) plot_title() (in module neurom.view.common) Point (class in neurom.core.point) point_dist() (in module neurom.analysis.morphmath) point_dist2() (in module neurom.analysis.morphmath) POINT_TYPE (class in neurom.core.dataformat) polygon_diameter() (in module neurom.analysis.morphmath) Population (class in neurom.ezy) (class in neurom.ezy.population) principal_direction_extent() (in module neurom.analysis.morphtree)

R

R (neurom.core.dataformat.COLS attribute) r (neurom.core.point.Point attribute) R (neurom.io.swc.SWC attribute) RawDataWrapper (class in neurom.io.readers)

read() (neurom.io.hdf5.H5 static method) (neurom.io.swc.SWC static method) read_v1() (neurom.io.hdf5.H5 static method) read_v2() (neurom.io.hdf5.H5 static method) remove_duplicate_points() (neurom.io.hdf5.H5 static method)

S

save_plot() (in module neurom.view.common) section_length() (in module neurom.analysis.morphmath) segment_area() (in module neurom.analysis.morphmath) segment_length() (in module neurom.analysis.morphmath) segment_radial_dist() (in module neurom.analysis.morphmath) segment_radius() (in module neurom.analysis.morphmath) segment_taper_rate() (in module neurom.analysis.morphmath) segment_volume() (in module neurom.analysis.morphmath) set_tree_type() (in module neurom.analysis.morphtree) SOMA (neurom.core.dataformat.POINT_TYPE attribute)

soma (neurom.core.types.TreeType attribute) soma() (in module neurom.view.view) soma3d() (in module neurom.view.view) SOMA_TYPE (class in neurom.core.neuron) SomaA (class in neurom.core.neuron) SomaB (class in neurom.core.neuron) SomaC (class in neurom.core.neuron) SomaError SWC (class in neurom.io.swc)

T

t (neurom.core.point.Point attribute) taper_rate() (in module neurom.analysis.morphmath) Tree (class in neurom.core.tree) tree() (in module neurom.view.view) tree3d() (in module neurom.view.view) TreeType (class in neurom.core.types) trunk_origin_azimuth() (in module neurom.analysis.morphtree)

trunk_origin_direction() (in module neurom.analysis.morphtree) trunk_origin_elevation() (in module neurom.analysis.morphtree) trunk_origin_radius() (in module neurom.analysis.morphtree) trunk_section_length() (in module neurom.analysis.morphtree) TYPE (neurom.core.dataformat.COLS attribute) (neurom.io.swc.SWC attribute) type (neurom.stats.FitResults attribute)

U

UNDEFINED (neurom.core.dataformat.POINT_TYPE attribute) undefined (neurom.core.types.TreeType attribute)

unpack_data() (neurom.io.hdf5.H5 static method)

V

val_iter() (in module neurom.core.tree)

vector() (in module neurom.analysis.morphmath)

X

X (neurom.core.dataformat.COLS attribute) x (neurom.core.point.Point attribute)

X (neurom.io.swc.SWC attribute)

Y

Y (neurom.core.dataformat.COLS attribute) y (neurom.core.point.Point attribute)

Y (neurom.io.swc.SWC attribute)

Z

Z (neurom.core.dataformat.COLS attribute) z (neurom.core.point.Point attribute)

Z (neurom.io.swc.SWC attribute)