bmtk.builder.bionet package

Submodules

bmtk.builder.bionet.swc_reader module

class bmtk.builder.bionet.swc_reader.SWCReader(swc_path, rng_seed=None)

Bases: object

choose_sections(section_names, distance_range, n_sections=1)

Similar to find_sections, but will only N=n_section number of sections_ids/x values randomly selected (may return less if there aren’t as many sections

Parameters:

• section_names – ‘soma’, ‘dend’, ‘apic’, ‘axon’

• distance_range – [float, float]: distance range of sections from the soma, in um.

• n_sections – int: maximum number of sections to select

Returns:

[int], [float]: A list of all section_ids and a list of all segment_x values (as defined by NEURON) that meet the given critera.

delete_axon()

find_sections(section_names, distance_range)

Retrieves a list of sections ids and section x’s given a section name/type (eg axon, soma, apic, dend) and the distance from the soma.

Parameters:

• section_names – ‘soma’, ‘dend’, ‘apic’, ‘axon’

• distance_range – [float, float]: distance range of sections from the soma, in um.

Returns:

[float], [float]: A list of all section_ids and a list of all segment_x values (as defined by NEURON) that meet the given critera.

fix_axon()

Removes and refixes axon

get_coords(sec_id, sec_x)

get_section(section_idx)

get_swc_id(sec_id, sec_x)

move_and_rotate(soma_coords=None, rotation_angles=None, inplace=False)

property n_sections

property nseg

sec_type_swc = {'apic': 4, 'apical': 4, 'axon': 2, 'axonal': 2, 'basal': 3, 'dend': 3, 'soma': 1, 'somatic': 1}

property sections

property seg_coords

property seg_props

set_segment_dl(dl)

Define number of segments in a cell

property soma_position

property swc_map

class bmtk.builder.bionet.swc_reader.SegmentCoords(p0, p1, p05)

Bases: tuple

p0

Alias for field number 0

p05

Alias for field number 2

p1

Alias for field number 1

class bmtk.builder.bionet.swc_reader.SegmentProps(type, area, x, dist, length, dist0, dist1, sec_id)

Bases: tuple

area

Alias for field number 1

dist

Alias for field number 3

dist0

Alias for field number 5

dist1

Alias for field number 6

length

Alias for field number 4

sec_id

Alias for field number 7

type

Alias for field number 0

x

Alias for field number 2

bmtk.builder.bionet.swc_reader.get_swc(cell, morphology_dir=None, use_cache=False, dL=None)

bmtk.builder.bionet.swc_reader.rotation_matrix(axis, theta)

Return the rotation matrix associated with counterclockwise rotation about the given axis by theta radians.

Module contents

bmtk.builder.bionet.rand_syn_locations(src, trg, sections=('soma', 'apical', 'basal'), distance_range=(0.0, 1e+20), morphology_dir='./components/morphologies', return_coords=False, dL=None)