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))
import sys
from pyneuroml import pynml
example_lems_file = 'LEMS_NML2_Ex5_DetCell.xml'
pynml.reload_saved_data(example_lems_file,
plot=True,
show_plot_already=False)
example_lems_file = 'LEMS_NML2_Ex9_FN.xml'
pynml.reload_saved_data(example_lems_file,
plot=True,
show_plot_already=False)
if not '-nogui' in sys.argv:
from matplotlib import pyplot as plt
plt.show()
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))
def main (argv):
args = process_args()
#for v in range(int(args.minV),int(args.maxV)+5,5): print get_rainbow_color_for_volts(v, args)
#exit()
results = pynml.reload_saved_data(args.lems_file_name,
plot=False)
times = [t*1000 for t in results['t']]
dt = times[1]-times[0]
#stepTime = (args.skip+1)*dt
t = 0
times_used = []
frame_indices = []
to_skip = 0
index = 0
while t<=args.endTime:
if to_skip == 0:
times_used.append(t)
frame_indices.append(index)
to_skip = args.skip
else:
to_skip -=1
index+=1
t = times[index]
print_comment_v("There are %i time points total, max: %f ms, dt: %f ms"%(len(times),times[-1], dt))
print_comment_v("times_used: %s; frame_indices %s"%(times_used, frame_indices))
print_comment_v("All refs: %s"%results.keys())
volt_colors = {}
for ref in results.keys():
if ref!='t':
pathBits = ref.split('/')
pop = pathBits[0]
index = pathBits[1]
seg = pathBits[3]
ref2 = '%s_%s'%(pop, index)
if seg == '0' or seg == 'v':
volt_color =[]
for i in frame_indices:
v = results[ref][i]*1000
colour = get_rainbow_color_for_volts(v, args) if args.rainbow else get_color_for_volts(v, args)
volt_color.append(colour)
volt_colors[ref2] = volt_color
print_comment_v("All refs: %s"%volt_colors.keys())
print_comment_v("All volt_colors: %s"%volt_colors)
t=args.startTime
index = 0
#give the single frames an alphabetical order
maxind = "00000"
ind = "00000"
bat_file_name = "%s_pov.bat"%(args.prefix)
bat_file = open(bat_file_name, 'w')
sh_file_name = "%s_pov.sh"%(args.prefix)
sh_file = open(sh_file_name, 'w')
for fi in frame_indices:
t = times[fi]
print_comment_v("\n---- Exporting for time: %f, index %i frame index %i ----\n"%(t, index, fi))
if not args.singlecell:
in_file_name = args.prefix+"_net.inc"
in_file = open(in_file_name)
out_file_name = args.prefix+"_net.inc"+str(index)
out_file = open(out_file_name, 'w')
print_comment_v("in_file_name %s; out_file_name: %s"%(in_file_name,out_file_name))
for line in in_file:
if line.strip().startswith("//"):
ref = line.strip()[2:]
if ref in volt_colors.keys():
vs = volt_colors[ref]
#print_comment_v(('-- %s: %s '%(ref,len(vs)))
out_file.write(" %s // %s t= %s\n" %(vs[index], ref, t))
elif ref+".0" in volt_colors.keys():
vs = volt_colors[ref+".0"]
out_file.write(" "+vs[index]+" //"+ref+" t= "+str(t)+"\n")
else:
out_file.write("// No ref there: "+ref+"\n")
print_comment_v("Missing ref: "+ref)
else:
out_file.write(line)
in_file.close()
out_file.close()
print_comment_v("Written file: %s for time: %f"%(out_file_name, t))
in_file = open(args.prefix+".pov")
out_file_name = "%s_T%i.pov"%(args.prefix, index)
out_file = open(out_file_name, 'w')
clock = args.rotations * (t-args.startTime)/(args.endTime-args.startTime)
pre = '%s_net.inc'%args.prefix
pre = pre.split('/')[-1]
post = '%s_net.inc%i'%(args.prefix,index)
post = post.split('/')[-1]
print_comment_v("Swapping %s for %s"%(pre, post))
for line in in_file:
if line.find(pre)>=0:
out_file.write(line.replace(pre,post))
else:
out_file.write(line.replace("clock", str(clock)))
print_comment_v("Written file: %s for time: %f"%(out_file_name, t))
in_file.close()
out_file.close()
toEx = os.path.realpath(out_file_name)
bat_file.write("C:\\Users\\Padraig\\AppData\\Local\\Programs\\POV-Ray\\v3.7\\bin\\pvengine.exe %s /nr /exit\n"%toEx)
sh_file.write("povray %s %s\n"%(args.povrayOptions,toEx) )
else:
ind = maxind[0:len(maxind)-len(str(index))] #compute index indentation
in_file = open(args.prefix+"_cells.inc")
out_file_name = args.prefix+"_cells.inc"+ind+str(index)
out_file = open(out_file_name, 'w')
dummy_ref = 'CELL_GROUP_NAME_0'
for line in in_file:
if line.strip().startswith("//"):
ref = line.strip()[2:]
ref = ref.replace(dummy_ref, args.singlecell)
if ref in volts.keys():
vs = volts[ref]
out_file.write(" "+vs[index]+"\n//"+ref+" t= "+ind+str(t)+"\n")
else:
out_file.write("//No ref found: "+ref+", was looking for "+dummy_ref+"\n")
else:
out_file.write(line)
in_file.close()
out_file.close()
print_comment_v("Written file: %s for time: %f"%(out_file_name, t))
in_file = open(args.prefix+".pov")
out_file_name = "%s_T%s%i.pov"%(args.prefix, ind, index)
out_file = open(out_file_name, 'w')
for line in in_file:
pre = '%s_cells.inc'%args.prefix
post = '%s_cells.inc%s%i'%(args.prefix, ind, index)
if line.find(pre)>=0:
out_file.write(line.replace(pre,post))
else:
clock = args.rotations * (t-args.startTime)/(args.endTime-args.startTime)
out_file.write(line.replace("clock", str(clock)))
print_comment_v("Written file: %s for time: %f"%(out_file_name, t))
in_file.close()
out_file.close()
toEx = os.path.realpath(out_file_name)
bat_file.write("C:\\Users\\Padraig\\AppData\\Local\\Programs\\POV-Ray\\v3.7\\bin\\pvengine.exe %s /nr /exit\n"%toEx)
sh_file.write("povray %s %s\n"%(args.povrayOptions,toEx) )
index=index+1
print_comment_v("Done!: ")
print_comment_v("\nTo generate images type:\n\n bash %s_pov.sh\n\n"%args.prefix)
def main(argv):
args = process_args()
#for v in range(int(args.minV),int(args.maxV)+5,5): print get_rainbow_color_for_volts(v, args)
#exit()
results = pynml.reload_saved_data(args.lems_file_name, plot=False)
times = [t * 1000 for t in results['t']]
dt = times[1] - times[0]
#stepTime = (args.skip+1)*dt
t = 0
times_used = []
frame_indices = []
to_skip = 0
index = 0
while t <= args.endTime:
if to_skip == 0:
times_used.append(t)
frame_indices.append(index)
to_skip = args.skip
else:
to_skip -= 1
index += 1
t = times[index]
print_comment_v("There are %i time points total, max: %f ms, dt: %f ms" %
(len(times), times[-1], dt))
print_comment_v("times_used: %s; frame_indices %s" %
(times_used, frame_indices))
print_comment_v("All refs: %s" % results.keys())
volt_colors = {}
for ref in results.keys():
if ref != 't':
pathBits = ref.split('/')
pop = pathBits[0]
index = pathBits[1]
seg = pathBits[3]
ref2 = '%s_%s' % (pop, index)
if seg == '0' or seg == 'v':
volt_color = []
for i in frame_indices:
v = results[ref][i] * 1000
colour = get_rainbow_color_for_volts(
v, args) if args.rainbow else get_color_for_volts(
v, args)
volt_color.append(colour)
volt_colors[ref2] = volt_color
print_comment_v("All refs: %s" % volt_colors.keys())
print_comment_v("All volt_colors: %s" % volt_colors)
t = args.startTime
index = 0
#give the single frames an alphabetical order
maxind = "00000"
ind = "00000"
bat_file_name = "%s_pov.bat" % (args.prefix)
bat_file = open(bat_file_name, 'w')
sh_file_name = "%s_pov.sh" % (args.prefix)
sh_file = open(sh_file_name, 'w')
for fi in frame_indices:
t = times[fi]
print_comment_v(
"\n---- Exporting for time: %f, index %i frame index %i ----\n" %
(t, index, fi))
if not args.singlecell:
in_file_name = args.prefix + "_net.inc"
in_file = open(in_file_name)
out_file_name = args.prefix + "_net.inc" + str(index)
out_file = open(out_file_name, 'w')
print_comment_v("in_file_name %s; out_file_name: %s" %
(in_file_name, out_file_name))
for line in in_file:
if line.strip().startswith("//"):
ref = line.strip()[2:]
if ref in volt_colors.keys():
vs = volt_colors[ref]
#print_comment_v(('-- %s: %s '%(ref,len(vs)))
out_file.write(" %s // %s t= %s\n" %
(vs[index], ref, t))
elif ref + ".0" in volt_colors.keys():
vs = volt_colors[ref + ".0"]
out_file.write(" " + vs[index] + " //" + ref +
" t= " + str(t) + "\n")
else:
out_file.write("// No ref there: " + ref + "\n")
print_comment_v("Missing ref: " + ref)
else:
out_file.write(line)
in_file.close()
out_file.close()
print_comment_v("Written file: %s for time: %f" %
(out_file_name, t))
in_file = open(args.prefix + ".pov")
out_file_name = "%s_T%i.pov" % (args.prefix, index)
out_file = open(out_file_name, 'w')
clock = args.rotations * (t - args.startTime) / (args.endTime -
args.startTime)
pre = '%s_net.inc' % args.prefix
pre = pre.split('/')[-1]
post = '%s_net.inc%i' % (args.prefix, index)
post = post.split('/')[-1]
print_comment_v("Swapping %s for %s" % (pre, post))
for line in in_file:
if line.find(pre) >= 0:
out_file.write(line.replace(pre, post))
else:
out_file.write(line.replace("clock", str(clock)))
print_comment_v("Written file: %s for time: %f" %
(out_file_name, t))
in_file.close()
out_file.close()
toEx = os.path.realpath(out_file_name)
bat_file.write(
"C:\\Users\\Padraig\\AppData\\Local\\Programs\\POV-Ray\\v3.7\\bin\\pvengine.exe %s /nr /exit\n"
% toEx)
sh_file.write("povray %s %s\n" % (args.povrayOptions, toEx))
else:
ind = maxind[0:len(maxind) -
len(str(index))] #compute index indentation
in_file = open(args.prefix + "_cells.inc")
out_file_name = args.prefix + "_cells.inc" + ind + str(index)
out_file = open(out_file_name, 'w')
dummy_ref = 'CELL_GROUP_NAME_0'
for line in in_file:
if line.strip().startswith("//"):
ref = line.strip()[2:]
ref = ref.replace(dummy_ref, args.singlecell)
if ref in volts.keys():
vs = volts[ref]
out_file.write(" " + vs[index] + "\n//" + ref +
" t= " + ind + str(t) + "\n")
else:
out_file.write("//No ref found: " + ref +
", was looking for " + dummy_ref + "\n")
else:
out_file.write(line)
in_file.close()
out_file.close()
print_comment_v("Written file: %s for time: %f" %
(out_file_name, t))
in_file = open(args.prefix + ".pov")
out_file_name = "%s_T%s%i.pov" % (args.prefix, ind, index)
out_file = open(out_file_name, 'w')
for line in in_file:
pre = '%s_cells.inc' % args.prefix
post = '%s_cells.inc%s%i' % (args.prefix, ind, index)
if line.find(pre) >= 0:
out_file.write(line.replace(pre, post))
else:
clock = args.rotations * (t - args.startTime) / (
args.endTime - args.startTime)
out_file.write(line.replace("clock", str(clock)))
print_comment_v("Written file: %s for time: %f" %
(out_file_name, t))
in_file.close()
out_file.close()
toEx = os.path.realpath(out_file_name)
bat_file.write(
"C:\\Users\\Padraig\\AppData\\Local\\Programs\\POV-Ray\\v3.7\\bin\\pvengine.exe %s /nr /exit\n"
% toEx)
sh_file.write("povray %s %s\n" % (args.povrayOptions, toEx))
index = index + 1
print_comment_v("Done!: ")
print_comment_v("\nTo generate images type:\n\n bash %s_pov.sh\n\n" %
args.prefix)
import sys
from pyneuroml import pynml
example_lems_file = 'LEMS_NML2_Ex5_DetCell.xml'
pynml.reload_saved_data(example_lems_file, plot=True, show_plot_already=False)
example_lems_file = 'LEMS_NML2_Ex9_FN.xml'
pynml.reload_saved_data(example_lems_file, plot=True, show_plot_already=False)
if '-nogui' not in sys.argv:
from matplotlib import pyplot as plt
plt.show()
