def _compile_nmodl(nineml_component,
weight_variables,
hierarchical_mode=None
): # weight variables should really be within component
"""
Generate NMODL code for the 9ML component, run "nrnivmodl" and then load
the mechanisms into NEURON.
"""
wdir = os.path.join(NMODL_DIR, nineml_component.name)
if not os.path.exists(wdir):
os.makedirs(wdir)
cwd = os.getcwd()
os.chdir(wdir)
xml_file = "%s.xml" % nineml_component.name
logger.debug("Writing NineML component to %s" % xml_file)
nineml_component.write(xml_file)
mod_filename = nineml_component.name + ".mod"
write_nmodldirect(component=nineml_component,
mod_filename=mod_filename,
weight_variables=weight_variables)
#write_nmodl(xml_file, weight_variables) # weight variables should really come from xml file
print("Running 'nrnivmodl' from %s" % wdir)
import nineml2nmodl
call_nrnivmodl()
os.chdir(cwd)
neuron.load_mechanisms(wdir)
def _compile_nmodl(nineml_component, weight_variables, hierarchical_mode=None): # weight variables should really be within component
"""
Generate NMODL code for the 9ML component, run "nrnivmodl" and then load
the mechanisms into NEURON.
"""
if not os.path.exists(NMODL_DIR):
os.makedirs(NMODL_DIR)
cwd = os.getcwd()
os.chdir(NMODL_DIR)
xml_file = "%s.xml" % nineml_component.name
logger.debug("Writing NineML component to %s" % xml_file)
nineml_component.write(xml_file)
from nineml2nmodl import write_nmodl, write_nmodldirect
mod_filename = nineml_component.name + ".mod"
write_nmodldirect(component=nineml_component, mod_filename=mod_filename, weight_variables=weight_variables)
#write_nmodl(xml_file, weight_variables) # weight variables should really come from xml file
print "Running 'nrnivmodl' from %s"%NMODL_DIR
import nineml2nmodl
nineml2nmodl.call_nrnivmodl()
os.chdir(cwd)
neuron.load_mechanisms(NMODL_DIR)
def write_and_compile_nmodl(component):
build_dir = os.path.join(BUILD_DIR, component.name.replace('-', '_'))
clear_and_recreate_dir(build_dir)
if not component.is_flat():
component = flatten(component)
ComponentModifier.close_all_reduce_ports(component=component)
print ' -- Writing Component to .mod'
modfilename = os.path.join(build_dir, component.name + '.mod').replace('-', '_')
write_nmodldirect(component=component, mod_filename=modfilename, weight_variables={})
compile_nmodl(build_dir)
def write_and_compile_nmodl(component):
build_dir = os.path.join(BUILD_DIR, component.name.replace('-', '_'))
clear_and_recreate_dir(build_dir)
if not component.is_flat():
component = flatten(component)
ComponentModifier.close_all_reduce_ports(component=component)
print ' -- Writing Component to .mod'
modfilename = os.path.join(build_dir,
component.name + '.mod').replace('-', '_')
write_nmodldirect(component=component,
mod_filename=modfilename,
weight_variables={})
compile_nmodl(build_dir)
return build_dir
def write(cls, component, filename):
from nineml2nmodl import write_nmodl, write_nmodldirect
write_nmodldirect(component=component, mod_filename=filename, weight_variables={})
