bmtk.builder.bionet package#

Submodules#

bmtk.builder.bionet.swc_reader module#

class bmtk.builder.bionet.swc_reader.SWCReader(swc_path, rng_seed=None)[source]#

Bases: object

choose_sections(section_names, distance_range, n_sections=1)[source]#

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()[source]#
find_sections(section_names, distance_range)[source]#

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()[source]#

Removes and refixes axon

get_coords(sec_id, sec_x)[source]#
get_section(section_idx)[source]#
get_swc_id(sec_id, sec_x)[source]#
move_and_rotate(soma_coords=None, rotation_angles=None, inplace=False)[source]#
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)[source]#

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)[source]#
bmtk.builder.bionet.swc_reader.rotation_matrix(axis, theta)[source]#

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)[source]#