def write_nmodl(nineml_file, weight_variables={}, hierarchical_mode=False):
from nineml.abstraction_layer.readers import XMLReader
components = XMLReader.read_components(nineml_file)
if len(components) == 0:
print 'No components found in file!'
elif len(components) == 1:
output_filename = nineml_file.replace(".xml", ".mod").replace("-", "_")
print "Converting %s to %s" % (nineml_file, output_filename)
write_nmodldirect(component=component, mod_filename=output_filename, weight_variables=weight_variables, hierarchical_mode=hierarchical_mode)
else:
for c in components:
output_filename = nineml_file.replace(".xml", "_%s.mod"%c.name).replace("-", "_")
print "Converting %s to %s" % (nineml_file, output_filename)
write_nmodldirect(component=component, mod_filename=output_filename, weight_variables=weight_variables, hierarchical_mode=hierarchical_mode)
Andrew Davison, May 2012
"""
# Example 1
import pyNN.neuron as sim
from neuroml import load_morphology, load_lems, Section
from pyramidal.spatial_distributions import uniform, by_distance
from nineml.abstraction_layer.readers import XMLReader
from quantities import S, cm, um
from pyNN.space import Grid2D, RandomStructure, Sphere
pkj_morph = load_morphology("http://neuromorpho.org/...") # smart inference of morphology file format
# support ion channel models defined in NineML, LEMS, or from built-in library
na_channel = XMLReader.read("na.xml")
kdr_channel = load_lems("kd.xml")
ka_channel = XMLReader.read("ka.xml")
ampa = XMLReader.read("ampa.xml")
gabaa = sim.ExpSynCond
# first we define cell types (templates)
# ... declarative style
purkinje_cell = sim.MultiCompartmentNeuron(
morphology=pkj_morph,
ion_channels={'na': na_channel, 'kdr': kdr_channel, 'kA': kA_channel},
channel_distribution={'na': uniform('all', 0.1*S/cm**2),
'kdr': by_distance(lambda d: 0.05*S/cm**2*d/200.0*um),
'kA': uniform('soma', 0.02*S/cm**2)},
# need to specify cm, Ra (possibly with spatial variation) somewhere here
def alConnectionRuleFromURI(uri):
component = XMLReader.read(uri)
return CgClosure(component.parameters, component.connection_rule)
def parse(filename):
"""Left over from orignal Version. This will be deprecated"""
from nineml.abstraction_layer.readers import XMLReader
return XMLReader.read_component(filename)
