forked from openworm/sibernetic
/
sibernetic_c302.py
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/
sibernetic_c302.py
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from pyneuroml import pynml
import argparse
import re
import os
import sys
import time
import pprint
pp = pprint.PrettyPrinter(indent=4)
DEFAULTS = {'duration': 1.0,
'dt': 0.005,
'dtNrn': 0.05,
'reference': 'Muscles',
'c302params': 'C1',
'verbose': False}
def process_args():
"""
Parse command-line arguments.
"""
parser = argparse.ArgumentParser(
description=("A script which can run Sibernetic, controlled by a "+
"neuronal network in c302"))
parser.add_argument('-duration',
type=float,
metavar='<duration>',
default=DEFAULTS['duration'],
help="Duration of simulation in ms, default: %sms"%DEFAULTS['duration'])
parser.add_argument('-dt',
type=float,
metavar='<dt>',
default=DEFAULTS['dt'],
help="Time step for SIBERNETIC in ms, default: %sms"%DEFAULTS['dt'])
parser.add_argument('-dtNrn',
type=float,
metavar='<dtNrn>',
default=DEFAULTS['dtNrn'],
help="Time step for NEURON in ms, default: %sms"%DEFAULTS['dtNrn'])
parser.add_argument('-reference',
type=str,
metavar='<reference>',
default=DEFAULTS['reference'],
help="Reference for network subset (Muscles, Full, etc.), default: %s"%DEFAULTS['reference'])
parser.add_argument('-c302params',
type=str,
metavar='<c302params>',
default=DEFAULTS['c302params'],
help="Parameter set from c302 (A, B, C, C1), default: %s"%DEFAULTS['c302params'])
return parser.parse_args()
def print_(msg):
pre = "Sib_c302 >>>"
print('%s %s'%(pre,msg.replace('\n','\n'+pre+' ')))
def main(args=None):
if args is None:
args = process_args()
run(a=args)
def build_namespace(a=None,**kwargs):
if a is None:
a = argparse.Namespace()
# Add arguments passed in by keyword.
for key,value in kwargs.items():
setattr(a,key,value)
# Add defaults for arguments not provided.
for key,value in DEFAULTS.items():
if not hasattr(a,key):
setattr(a,key,value)
# Change all values to under_score from camelCase.
for key,value in a.__dict__.items():
new_key = convert_case(key)
if new_key != key:
setattr(a,new_key,value)
delattr(a,key)
return a
def convert_case(name):
"""Converts from camelCase to under_score"""
s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower()
def announce(message):
print_("\n************************************************************************\n*")
print_("* %s"%message.replace('\n','\n* '))
print_("*\n************************************************************************")
def run(a=None,**kwargs):
try:
import neuroml
import pyneuroml
import xlrd
except Exception as e:
print_("Cannot import one of the required packages. Please install!\n"
"Exception: %s\n"%e)
try:
if os.environ.has_key('C302_HOME'):
os.environ['C302_HOME']
sys.path.append(os.environ['C302_HOME'])
print_('Python path now: %s'%sys.path)
import c302
import c302_utils
except Exception as e:
print_("Cannot import c302!\n"
"Exception: %s\n"%e
+"Please set environment variable C302_HOME to point to the directory: CElegansNeuroML/CElegans/pythonScripts/c302!\n")
exit()
a = build_namespace(a,**kwargs)
gen_start = time.time()
ref = a.reference
if not os.path.isdir('simulations'):
os.mkdir('simulations')
sim_ref = "%s_%s_%s"%(a.c302params,ref, time.ctime().replace(' ','_' ).replace(':','.' ))
sim_dir = "simulations/%s"%(sim_ref)
os.mkdir(sim_dir)
#exec('from %s import ParameterisedModel'%a.c302params)
#params = ParameterisedModel()
id = '%s_%s'%(a.c302params,ref)
exec('from c302_%s import setup'%ref)
setup(a.c302params,
generate=True,
duration = a.duration,
dt = a.dt,
target_directory=sim_dir)
lems_file0 = '%s/LEMS_c302_%s.xml'%(sim_dir,id)
lems_file = '%s/LEMS_c302.xml'%(sim_dir)
print_("Renaming %s -> %s"%(lems_file0,lems_file))
os.rename(lems_file0,lems_file)
announce("Generating NEURON files from: %s..."%lems_file)
pynml.run_lems_with_jneuroml_neuron(lems_file,
only_generate_scripts=True,
nogui=True,
load_saved_data=False,
verbose=True)
main_nrn_py = open('%s/LEMS_c302_nrn.py'%(sim_dir),'r')
updated =''
for line in main_nrn_py:
line = line.replace('GenericCell.hoc','%s/GenericCell.hoc'%sim_dir)
line = line.replace('GenericNeuronCell.hoc','%s/GenericNeuronCell.hoc'%sim_dir)
line = line.replace('GenericMuscleCell.hoc','%s/GenericMuscleCell.hoc'%sim_dir)
line = line.replace("open('time.dat","open('%s/time.dat"%sim_dir)
line = line.replace("open('c302_","open('%s/c302_"%sim_dir)
updated += line
main_nrn_py.close()
main_nrn_py = open('%s/LEMS_c302_nrn.py'%(sim_dir),'w')
main_nrn_py.write(updated)
main_nrn_py.close()
run_dir = '.'
command = 'nrnivmodl %s'%sim_dir
announce("Compiling NMODL files for NEURON...")
pynml.execute_command_in_dir(command, run_dir, prefix="nrnivmodl: ")
command = './Release/Sibernetic -c302 -f worm -no_g -l_to lpath=%s timelimit=%s timestep=%s'%(sim_dir,a.duration/1000.0,a.dt/1000)
env={"PYTHONPATH":"./src:./%s"%sim_dir}
sim_start = time.time()
announce("Executing main Sibernetic simulation of %sms using: \n\n %s \n\n in %s with %s"%(a.duration, command, run_dir, env))
#pynml.execute_command_in_dir('env', run_dir, prefix="Sibernetic: ",env=env,verbose=True)
pynml.execute_command_in_dir(command, run_dir, prefix="Sibernetic: ",env=env,verbose=True)
sim_end = time.time()
reportj = {}
reportj['duration'] = '%s ms'%a.duration
reportj['dt'] = '%s ms'%a.dt
reportj['sim_ref'] = sim_ref
reportj['reference'] = a.reference
reportj['c302params'] = a.c302params
reportj['generation_time'] = '%s s'%(sim_start-gen_start)
reportj['run_time'] = '%s s'%(sim_end-sim_start)
reportj['command'] = '%s'%(command)
report_file = open("%s/report.json"%sim_dir,'w')
report_file.write(pp.pformat(reportj))
report_file.close()
announce("Generating images for neuronal activity...")
results = pynml.reload_saved_data(lems_file,
plot=False,
show_plot_already=False,
simulator=None,
verbose=True)
c302_utils.plot_c302_results(results,
config=a.reference,
parameter_set=a.c302params,
directory=sim_dir,
save=True,
show_plot_already=False)
pos_file_name = os.path.abspath('%s/position_buffer.txt'%sim_dir)
announce("Plotting positions of worm body particles in %s..."%pos_file_name)
from plot_positions import plot_positions
if not os.path.isfile(pos_file_name):
time.sleep(2)
plot_positions(pos_file_name,rate_to_plot = int(a.duration/5))
announce("Finished in %s sec!\n\nSimulation saved in: %s\n\n"%((sim_end-sim_start),sim_dir) + \
"Report of simulation at: %s/report.json\n\n"%(sim_dir)+ \
"Rerun simulation with: ./Release/Sibernetic -l_from lpath=%s\n"%(sim_dir))
if __name__ == '__main__':
main()