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.
- 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.
- 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#
- 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