# -*- coding: utf-8 -*-
# ALL SI UNITS
# milliMolar is same as mol/m^3
## USAGE: nohup python2.6 odor_pulses_repeats.py &> nohup_pulses.out < /dev/null &
## if running multiple of these, change pulses to pulses1, pulses2, etc above,
## change loop lists to result in largely non-overlapping runs or opposite order,
## change the morphproc command far below to have pulses1, pulses2, etc unique str.
import os,sys
import os.path
import pickle
import subprocess
cwd = os.getcwd() # current working directory
from pylab import *
from lock_utils import *
IN_VIVO = True
directed = True
frac_directed = 0.01
NONLINEAR_ORNS = False
NONLINEAR_TYPE = 'P' # P for primary glom non-linear, L for lateral gloms non-linear
## inh_options = [ (no_singles,no_joints,no_lat,no_PGs,varyRMP), ... ]
## in order,below options are: all cells; no lat; no joints;
## no PGs; no singles + no joints; only mitrals
inh_options = [ \
(False,False,False,False,False), (False,False,True,False,False), (False,True,False,False,False),\
(False,False,False,True,False), (True,True,False,False,False), (True,True,False,True,False) ]
inh_options = [ (True,True,False,False,False) ]
FORCE_SALIENT = False#True
if FORCE_SALIENT:
stim_seed_list = [-10]#,-10,-19,-28]#[-1,-2,-3,-4,-5,-6,-7,-8,-9]
else:
#stim_seed_list = [802.0,853.0,753.0,751.0]#arange(800.0,805.0,1.0)#[157.0,160.0,190.0,191.0,212.0,441.0]
stim_seed_list = arange(765.0,780.0,1.0)#[157.0,160.0,190.0,191.0,212.0,441.0]
net_seed_list = [200.0]#[100.0,200.0,300.0]
print "Starting automated pulses simulations ..."
morphs = []
for num_gloms in [3]:
morphs_stimseeds = []
for stimseed in stim_seed_list:
morphs_netseeds = []
## for the non-salient stimuli, change the network also each time
if stimseed>0: net_seed_list = [stimseed]
for netseed in net_seed_list:
morphs_inh = []
for inh in inh_options:
files_locked = True # files have started to be opened for this iteration
# made False, once simulation is loaded and files closed
## a special lock file to keep track of locking,
## since portalocker didn't work properly with multiple files
print "Acquiring Lock for odor pulses."
sys.stdout.flush()
#mylock('locksimfile.txt','pulses\n')
lock_file = portalock_open('locksimfile.txt')
print "Locked files for odor pulses."
sys.stdout.flush()
## generate the stimuli params file
gen_file = open('../generators/stimuliConstantsMinimal.py','w')
gen_file.write('## This file is programmatically generated.\n')
gen_file.write('\n')
gen_file.write('## used by generate_firerates.py\n')
gen_file.write('stim_rate_seednum = '+str(stimseed)+'\n')
gen_file.write('## used by generate_neuroml.py\n')
gen_file.write('stim_net_seed = '+str(netseed)+'\n')
gen_file.write('## distance between 2 mitrals for activity dependent inhibition\n')
gen_file.write('mit_distance = 0 # microns ## irrelevant for odor responses\n')
gen_file.write('## use thresholded erf() on ORN firing rate?\n')
gen_file.write('NONLINEAR_ORNS = '+str(NONLINEAR_ORNS)+'\n')
gen_file.write('NONLINEAR_TYPE = "'+ NONLINEAR_TYPE \
+'" # P for primary glom non-linear, L for lateral gloms non-linear\n')
gen_file.write('scaledWidth = 0.2 # s # width of scaled pulses\n')
gen_file.close()
## generate the network params file
net_file = open('../networks/networkConstantsMinimal.py','w')
net_file.write('## actual number of modelled gloms could be 10 (for odor testing)\n')
net_file.write('## or 2 (for inhibition testing) decided during neuroml generation.\n')
net_file.write('## can set number of modelled glom to whatever you like.\n')
net_file.write('## Randomly half of them will lie on central glom\'s mit0 or mit1.\n')
net_file.write('## First half will receive odor A. Rest will receive odor B.\n')
net_file.write('NUM_GLOMS = '+str(num_gloms)+'\n')
net_file.write('\n')
net_file.write('## Whether FRAC_DIRECTED of mits_per_syns will be\n')
net_file.write('## connected between pairs listed in DIRECTED_CONNS.\n')
net_file.write('## Keep directed True for simulating odors,\n')
net_file.write('## Even for ADI, choose two connected mitrals.\n')
net_file.write('directed = '+str(directed)+'\n')
net_file.write('\n')
net_file.write('## ensure that FRAC_DIRECTED * num of mitrals directed < 1.\n')
net_file.write('## For NUM_GLOMS=10, 20mits all connected to mit0, FRAC_DIRECTED < 0.05.\n')
net_file.write('## Can set FRAC_DIRECTED to 0.0 keeping DIRECTED=True. This will ensure that\n')
net_file.write('## other mits lat dends are over directed centralmit\'s soma, if PROXIMAL_CONNECTION = True\n')
net_file.write('frac_directed = '+str(frac_directed))
net_file.write(' # I think you need to set this to 0.05 to get reasonable phase separation?\n')
net_file.close()
## generate the neuroML netfile, don't if exists
OBNet_file = '../netfiles/syn_conn_array_10000'
OBNet_file += '_singlesclubbed100_jointsclubbed1'+\
'_numgloms'+str(num_gloms)+'_seed'+str(netseed)
if directed: OBNet_file += '_directed'+str(frac_directed)+'_proximal'
OBNet_file += '.xml'
if not os.path.exists(OBNet_file):
print "Generating netfile",OBNet_file
gen_command = 'python2.6 '+cwd+'/../generators/generate_neuroML.py'
subprocess.check_call(gen_command,shell=True)
else:
print "Netfile",OBNet_file,"already exists."
## Generate the odor frates, don't if exists
stim_frate_filename = '../generators/firerates/firerates_2sgm_'+str(stimseed)
stim_frate_filename += '.pickle'
if not os.path.exists(stim_frate_filename):
print "Generating firerate file",stim_frate_filename
gen_command = 'python2.6 '+cwd+'/../generators/generate_firerates_odors.py NOSHOW'
subprocess.check_call(gen_command,shell=True)
else:
print "Firerate file",stim_frate_filename,"already exists."
## generate the odor morph firefiles (spiketimes),
## don't if an exemplary firefile exists
stim_firefiles_dirname = '../firefiles/firefiles'+str(stimseed)
if NONLINEAR_ORNS: stim_firefiles_dirname += '_NL'+NONLINEAR_TYPE
if not os.path.exists(stim_firefiles_dirname):
print "Creating firefiles directory ",stim_firefiles_dirname
subprocess.check_call('mkdir '+stim_firefiles_dirname,shell=True)
if not os.path.exists(stim_firefiles_dirname+\
'/firetimes_rndpulse_glom_'+str(num_gloms-1)+\
'_pulse_0_avgnum0.txt'):
print "Generating firefiles in",stim_firefiles_dirname
## number of processes is numpulses*num_gloms+1
## numpulses is RANDOM_PULSE_NUMS*2 = 6
gen_command = 'mpiexec -machinefile ~/hostfile -n '+str(6*num_gloms+1)+\
' ~/Python-2.6.4/bin/python2.6 '+\
cwd+'/../generators/generate_firefiles_odors.py NOSHOW'
subprocess.check_call(gen_command,shell=True)
else:
print "Exemplary firefile in",stim_firefiles_dirname,"already exists."
## no need to presently generate baseline anew: I instead need to shuffle for trials!
## generate baseline firefiles also anew with this stimseed*netseed combo.
#print "Generating baseline firefiles."
#gen_command = 'python2.6 '+cwd+'/../generators/generate_firefiles_gran_baseline.py'
#subprocess.check_call(gen_command,shell=True)
## generate the odor simulation params file
simset_file = open('simset_odor_minimal.py','w')
simset_file.write('## This file is programmatically generated.\n')
simset_file.write('\n')
simset_file.write('netseedstr = "'+str(netseed)+'"\n')
simset_file.write('rateseedstr = "'+str(stimseed)+'"\n')
simset_file.write('\n')
simset_file.write('OBNet_file = "'+OBNet_file+'"\n')
simset_file.write('ORNpathseedstr = "'+stim_firefiles_dirname+'/"\n')
## inh = (no_singles,no_joints,no_lat,no_PGs,varyRMP)
simset_file.write('NO_SINGLES = '+str(inh[0])+'\n')
simset_file.write('## spine inhibition and singles are self-inh\n')
simset_file.write('## toggle them on/off together\n')
simset_file.write('NO_SPINE_INH = NO_SINGLES\n')
simset_file.write('NO_JOINTS = '+str(inh[1])+'\n')
simset_file.write('NO_MULTIS = NO_JOINTS\n')
simset_file.write('NO_PGS = '+str(inh[3])+'\n')
simset_file.write('NO_LATERAL = '+str(inh[2])+'\n')
simset_file.write('\n')
simset_file.write('VARY_MITS_RMP = '+str(inh[4])+'\n')
simset_file.close()
## odor_pulses.py checks if the output files exists
## if there is already an output file, it quits.
morphproc = subprocess.Popen('mpiexec -machinefile ~/hostfile -n 55'\
' ~/Python-2.6.4/bin/python2.6 odor_pulses.py NOSHOW pulses4',\
shell=True,stdout=subprocess.PIPE)
while True:
next_line = morphproc.stdout.readline()
if not next_line:
break
sys.stdout.write(next_line)
if files_locked and ('Loading' in next_line):
## now that the simulation has loaded,
## unlock files for the other process.
## only if files are locked still,
## else redundant since 'Loading' appears multiple times
#myunlock('locksimfile.txt')
portalocker.unlock(lock_file)
lock_file.close()
files_locked = False # files are closed now
print "UnLocked files for odor pulses."
if 'Wrote' in next_line:
morphfilename = next_line.split()[1]
morphs_inh.append(morphfilename)
break
print morphproc.communicate()[0]
## unlock in case files are locked even after odor_morphs quits.
if files_locked:
#myunlock('locksimfile.txt')
portalocker.unlock(lock_file)
lock_file.close()
print "UnLocked files for odor pulses after quit."
morphs_netseeds.append(morphs_inh)
morphs_stimseeds.append(morphs_netseeds)
morphs.append(morphs_stimseeds)
print morphs
fullfilename = '../results/odor_pulses/pulses_random'
if NONLINEAR_ORNS: fullfilename += 'NL'+NONLINEAR_TYPE
fullfilename += '.pickle'
fullfile = open(fullfilename,'w')
pickle.dump(morphs, fullfile)
fullfile.close()
print "Wrote",fullfilename
