bmtk.builder.bionet package¶
Submodules¶
bmtk.builder.bionet.swc_reader module¶
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class
bmtk.builder.bionet.swc_reader.
SWCReader
(swc_path, rng_seed=None)[source]¶ Bases:
object
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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.
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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.
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n_sections
¶
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nseg
¶
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sec_type_swc
= {'apic': 4, 'apical': 4, 'axon': 2, 'axonal': 2, 'basal': 3, 'dend': 3, 'soma': 1, 'somatic': 1}¶
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sections
¶
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seg_coords
¶
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seg_props
¶
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soma_position
¶
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swc_map
¶
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class
bmtk.builder.bionet.swc_reader.
SegmentCoords
(p0, p1, p05)¶ Bases:
tuple
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p0
¶ Alias for field number 0
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p05
¶ Alias for field number 2
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p1
¶ Alias for field number 1
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class
bmtk.builder.bionet.swc_reader.
SegmentProps
(type, area, x, dist, length, dist0, dist1, sec_id)¶ Bases:
tuple
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area
¶ Alias for field number 1
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dist
¶ Alias for field number 3
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dist0
¶ Alias for field number 5
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dist1
¶ Alias for field number 6
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length
¶ Alias for field number 4
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sec_id
¶ Alias for field number 7
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type
¶ Alias for field number 0
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x
¶ Alias for field number 2
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