bmtk.builder.bionet package¶
Submodules¶
bmtk.builder.bionet.swc_reader module¶
- class bmtk.builder.bionet.swc_reader.SWCReader(swc_file, random_seed=10, fix_axon=True)[source]¶
Bases:
object
A class for pulling out section id, section locations, coordinates from a SWC file. Useful when building a network that requires exact locations of pre- or post-synaptic locations. Requires NEURON.
- Attributes
- swc_file - path to a SWC morphology file
- fix_axon - If set to true, the axon will be removed and replaced with a 30 um stub, as defined for all Allen
Cell-Type models (default: True).
- random_seed - integer value to seed the random genator, used by choose_sections method.
- 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
[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.
- 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.
- get_coord(sec_ids, sec_xs, soma_center=(0.0, 0.0, 0.0), rotations=None)[source]¶
Takes in a list of section_ids and section_x values and returns a list of coordinates, assuming the soma is at the center of the system.
- Parameters
sec_ids – [float]: list of N section_ids
sec_xs – [float]: list of N cooresponding section_x’s
soma_center – location of soma in respect to the coordinate system. (default (0, 0, 0)).
rotations – List of rotations (not yet implemented)
- Returns
[(float, float, float)]: for seach sec_ids/sec_xs returna the x,y,z coordinates as a tuple