netpyne.conversion.sonataImport

Module with functions to import from and export to SONATA format

Functions:

load_csv_props(info_file)	Load a generic csv file as used in Sonata
ascii_encode_dict(data)
load_json(filename)
fix_axon_peri(hobj)	Replace reconstructed axon with a stub :param hobj: hoc object
fix_axon_peri_v2(hobj)	Replace reconstructed axon with a stub (keep order); BBP version :param hobj: hoc object
fix_sec_nseg(secs, dL)	Set nseg of sections based on dL param: section.nseg = 1 + 2 * int(section.L / (2*dL)) :param secs: netpyne dictionary with all sections :param dL: dL from config file
swap_soma_xy(secs)	Swap soma x and y coords so cylinder is vertical instead of horizontal

Classes:

EmptyCell()
SONATAImporter(**parameters)

netpyne.conversion.sonataImport.load_csv_props(info_file)

Load a generic csv file as used in Sonata

netpyne.conversion.sonataImport.ascii_encode_dict(data)

netpyne.conversion.sonataImport.load_json(filename)

class netpyne.conversion.sonataImport.EmptyCell

Bases: object

netpyne.conversion.sonataImport.fix_axon_peri(hobj)

Replace reconstructed axon with a stub :param hobj: hoc object

netpyne.conversion.sonataImport.fix_axon_peri_v2(hobj)

Replace reconstructed axon with a stub (keep order); BBP version :param hobj: hoc object

netpyne.conversion.sonataImport.fix_sec_nseg(secs, dL)

Set nseg of sections based on dL param: section.nseg = 1 + 2 * int(section.L / (2*dL)) :param secs: netpyne dictionary with all sections :param dL: dL from config file

netpyne.conversion.sonataImport.swap_soma_xy(secs)

Swap soma x and y coords so cylinder is vertical instead of horizontal

class netpyne.conversion.sonataImport.SONATAImporter(**parameters)

Bases: object

Methods:

importNet(configFile[, replaceAxon, ...])
createSimulationConfig()
createPops()
createCells()
createConns()	SONATA method - works but same results as NeuroMLlite
createNetStims()
createIClamps()
setCellRuleDynamicParamsFromNeuroml(...)
setCellRuleDynamicParamsFromNeuroml_old(...)
setCellRuleDynamicParamsFromJson(...)
parse_group(g)
parse_dataset(d)
subs(path)	Search the strings in a config file for a substitutable value, e.g. "morphologies_dir": "$COMPONENT_DIR/morphologies",.

importNet(configFile, replaceAxon=True, setdLNseg=True, swapSomaXY=True)

createSimulationConfig()

createPops()

createCells()

createConns()

SONATA method - works but same results as NeuroMLlite

createNetStims()

createIClamps()

setCellRuleDynamicParamsFromNeuroml(nml_params, cellRule)

setCellRuleDynamicParamsFromNeuroml_old(cell, cellRule)

setCellRuleDynamicParamsFromJson(cell_dynamic_params, cellRule)

parse_group(g)

parse_dataset(d)

subs(path)

Search the strings in a config file for a substitutable value, e.g. “morphologies_dir”: “$COMPONENT_DIR/morphologies”,