Index

_ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z

_

__init__() (neurom.check.CheckResult method)
(neurom.core.neuron.BaseSoma method)
(neurom.core.neuron.Neuron method)
(neurom.core.neuron.SomaSimpleContour method)
(neurom.core.neuron.SomaSinglePoint method)
(neurom.core.neuron.SomaThreePoint method)
(neurom.core.tree.BaseTree method)
(neurom.core.tree.Tree method)
(neurom.fst.Neurite method)
(neurom.fst.Neuron method)
(neurom.fst.Section method)
(neurom.io.swc.SWCRawDataWrapper method)

A

add_child() (neurom.core.tree.BaseTree method)
(neurom.core.tree.Tree method)
(neurom.fst.Section method)
all (neurom.core.types.NeuriteType attribute)
(neurom.NeuriteType attribute)
angle_3points() (in module neurom.analysis.morphmath)
APICAL_DENDRITE (neurom.core.dataformat.POINT_TYPE attribute)
apical_dendrite (neurom.core.types.NeuriteType attribute)
(neurom.NeuriteType attribute)
as_elements() (in module neurom.core.tree)
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.NeuriteType attribute)
(neurom.NeuriteType attribute)

B

BASAL_DENDRITE (neurom.core.dataformat.POINT_TYPE attribute)
basal_dendrite (neurom.core.types.NeuriteType attribute)
(neurom.NeuriteType attribute)
BaseSoma (class in neurom.core.neuron)
BaseTree (class in neurom.core.tree)
bounding_box() (neurom.core.neuron.Neuron method)
branch_order() (in module neurom.analysis.morphtree)
(in module neurom.fst.sectionfunc)

C

center (neurom.core.neuron.BaseSoma attribute)
(neurom.core.neuron.SomaSimpleContour attribute)
(neurom.core.neuron.SomaSinglePoint attribute)
(neurom.core.neuron.SomaThreePoint attribute)
check_wrapper() (in module neurom.check)
CheckResult (class in neurom.check)
COLS (class in neurom.core.dataformat)
compare_trees() (in module neurom.analysis.morphtree)
compare_two() (in module neurom.stats)
copy() (neurom.core.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)
dist_point_line() (in module neurom.analysis.morphmath)
draw() (in module neurom.viewer)

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() (in module neurom)
(in module neurom.fst)
get_bounding_box() (in module neurom.analysis.morphtree)
get_children() (neurom.io.swc.SWCRawDataWrapper method)
get_col() (neurom.io.swc.SWCRawDataWrapper method)
get_color() (in module neurom.view.common)
get_default() (in module neurom.view.view)
get_end_points() (neurom.io.swc.SWCRawDataWrapper method)
get_figure() (in module neurom.view.common)
get_fork_points() (neurom.io.swc.SWCRawDataWrapper method)
get_ids() (neurom.io.swc.SWCRawDataWrapper method)
get_initial_neurite_segment_ids() (in module neurom.io.utils)
get_morph_files() (in module neurom.io.utils)
get_parent() (neurom.io.swc.SWCRawDataWrapper method)
get_point() (neurom.io.swc.SWCRawDataWrapper method)
get_row() (neurom.io.swc.SWCRawDataWrapper method)
get_soma_ids() (in module neurom.io.utils)
get_test() (in module neurom.stats)
get_tree_type() (in module neurom.analysis.morphtree)
get_type() (neurom.core.neuron.SOMA_TYPE static method)
get_version() (in module neurom.io.hdf5)
GPFIRST (neurom.io.hdf5.H5 attribute)
GPID (neurom.io.hdf5.H5 attribute)
GTYPE (neurom.io.hdf5.H5 attribute)

H

H5 (class in neurom.io.hdf5)
has_all_finite_radius_neurites() (in module neurom.check.structural_checks)
has_increasing_ids() (in module neurom.check.structural_checks)
has_sequential_ids() (in module neurom.check.structural_checks)
has_soma_points() (in module neurom.check.structural_checks)
has_valid_neurites() (in module neurom.check.structural_checks)
has_valid_soma() (in module neurom.check.structural_checks)

I

i_branch_end_points() (in module neurom.core.tree)
i_chain() (in module neurom.core.tree)
i_chain2() (in module neurom.core.tree)
i_neurites() (neurom.core.neuron.Neuron method)
i_section_radial_dist() (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)
interpolate_radius() (in module neurom.analysis.morphmath)
INVALID (neurom.core.neuron.SOMA_TYPE attribute)
InvalidDrawModeError
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_root() (in module neurom.core.tree)
is_single_tree() (in module neurom.check.structural_checks)
isection() (in module neurom.core.tree)
isegment() (in module neurom.core.tree)
iter() (neurom.core.neuron.BaseSoma method)
(neurom.core.neuron.SomaSimpleContour method)
(neurom.core.neuron.SomaSinglePoint method)
(neurom.core.neuron.SomaThreePoint method)
iter_neurites() (in module neurom)
(in module neurom.core)
iter_row() (neurom.io.swc.SWCRawDataWrapper method)
iter_sections() (in module neurom.fst)
(neurom.fst.Neurite method)
iter_segments() (in module neurom.fst)
itriplet() (in module neurom.core.tree)
iupstream() (in module neurom.core.tree)

K

ks (neurom.stats.StatTests attribute)

L

linear_interpolate() (in module neurom.analysis.morphmath)
load_data() (in module neurom.io)
(in module neurom.io.readers)
load_neuron() (in module neurom)
(in module neurom.fst)
(in module neurom.io.utils)
load_neurons() (in module neurom.io.utils)
load_trees() (in module neurom.io.utils)
local_bifurcation_angle() (in module neurom.analysis.morphtree)

M

make_neuron() (in module neurom.io.utils)
make_soma() (in module neurom.core.neuron)
make_tree() (in module neurom.io.utils)
map_sum_segments() (in module neurom.fst.sectionfunc)
MissingParentError
MultipleTrees

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 (class in neurom.fst)
NEURITES (neurom.core.dataformat.POINT_TYPE attribute)
NeuriteType (class in neurom)
(class in neurom.core.types)
neurom (module)
neurom.analysis (module)
neurom.analysis.morphmath (module)
neurom.analysis.morphtree (module)
neurom.check (module)
neurom.check.structural_checks (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.fst (module)
neurom.fst.sectionfunc (module)
neurom.io (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)
neurom.viewer (module)
NeuroMError
Neuron (class in neurom.core.neuron)
(class in neurom.fst)
neuron() (in module neurom.view.view)
neuron3d() (in module neurom.view.view)
no_missing_parents() (in module neurom.check.structural_checks)
NotDrawableError

O

ok() (in module neurom.check)
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_fraction_point() (in module neurom.analysis.morphmath)
path_length() (in module neurom.analysis.morphtree)
pca() (in module neurom.analysis.morphmath)
PD (neurom.io.hdf5.H5 attribute)
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)
points (neurom.core.neuron.BaseSoma attribute)
(neurom.core.neuron.SomaSimpleContour attribute)
(neurom.core.neuron.SomaSinglePoint attribute)
(neurom.core.neuron.SomaThreePoint attribute)
(neurom.fst.Neurite attribute)
(neurom.fst.Neuron attribute)
polygon_diameter() (in module neurom.analysis.morphmath)
principal_direction_extent() (in module neurom.analysis.morphmath)
(in module neurom.analysis.morphtree)
PX (neurom.io.hdf5.H5 attribute)
PY (neurom.io.hdf5.H5 attribute)
PZ (neurom.io.hdf5.H5 attribute)

R

R (neurom.core.dataformat.COLS attribute)
r (neurom.core.point.Point attribute)
R (neurom.io.swc.SWC attribute)
read() (neurom.io.hdf5.H5 static method)
(neurom.io.swc.SWC static method)
remove_duplicate_points() (neurom.io.hdf5.H5 static method)

S

save_plot() (in module neurom.view.common)
scalar_projection() (in module neurom.analysis.morphmath)
scalar_stats() (in module neurom.stats)
Section (class in neurom.fst)
section_area() (in module neurom.fst.sectionfunc)
section_fun() (in module neurom.fst.sectionfunc)
section_length() (in module neurom.analysis.morphmath)
section_meander_angles() (in module neurom.fst.sectionfunc)
section_path_length() (in module neurom.fst.sectionfunc)
section_radial_distance() (in module neurom.fst.sectionfunc)
section_tortuosity() (in module neurom.fst.sectionfunc)
section_volume() (in module neurom.fst.sectionfunc)
segment_area() (in module neurom.analysis.morphmath)
segment_length() (in module neurom.analysis.morphmath)
segment_length2() (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)
segment_x_coordinate() (in module neurom.analysis.morphmath)
segment_y_coordinate() (in module neurom.analysis.morphmath)
segment_z_coordinate() (in module neurom.analysis.morphmath)
set_tree_type() (in module neurom.analysis.morphtree)
SimpleContour (neurom.core.neuron.SOMA_TYPE attribute)
SinglePoint (neurom.core.neuron.SOMA_TYPE attribute)
SOMA (neurom.core.dataformat.POINT_TYPE attribute)
soma (neurom.core.types.NeuriteType attribute)
(neurom.NeuriteType attribute)
soma() (in module neurom.view.view)
soma3d() (in module neurom.view.view)
soma_points() (neurom.io.swc.SWCRawDataWrapper method)
SOMA_TYPE (class in neurom.core.neuron)
SomaError
SomaSimpleContour (class in neurom.core.neuron)
SomaSinglePoint (class in neurom.core.neuron)
SomaThreePoint (class in neurom.core.neuron)
sphere_area() (in module neurom.analysis.morphmath)
StatTests (class in neurom.stats)
SWC (class in neurom.io.swc)
SWCRawDataWrapper (class in neurom.io.swc)

T

t (neurom.core.point.Point attribute)
taper_rate() (in module neurom.analysis.morphmath)
ThreePoint (neurom.core.neuron.SOMA_TYPE attribute)
total_score() (in module neurom.stats)
transform() (neurom.fst.Neurite method)
(neurom.fst.Neuron method)
Tree (class in neurom.core.tree)
tree() (in module neurom.view.view)
tree3d() (in module neurom.view.view)
tree_type_checker() (in module 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)
ttest (neurom.stats.StatTests attribute)
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.NeuriteType attribute)
(neurom.NeuriteType attribute)
unpack_data() (neurom.io.hdf5.H5 static method)

V

val_iter() (in module neurom.core.tree)
vector() (in module neurom.analysis.morphmath)
vector_projection() (in module neurom.analysis.morphmath)
ViewerError

W

wilcoxon (neurom.stats.StatTests attribute)

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)