def run(self):
if self.parser.options is None:
self.parser.parse_args()
o = self.parser.options
for noise_sigma in self.parser.noise_sigmas:
p = self._dp.copy()
p['noise_sigma'] = noise_sigma # pA
p['time'] = 10e3 if o.time is None else o.time # ms
p['nthreads'] = 1
p['ntrials'] = o.ntrials
p['verbosity'] = o.verbosity
p.update(self._up)
# Submitting
ac = ArgumentCreator(p, printout=True)
simLabel = '{0}pA'.format(int(p['noise_sigma']))
numRepeat = 1
submitter = SubmitterFactory.getSubmitter(ac,
self._app_name,
envType=o.env,
rtLimit=o.rtLimit,
output_dir=o.where,
label=simLabel,
blocking=True,
timePrefix=False,
numCPU=o.nCPU)
ac.setOption('output_dir', submitter.outputDir())
startJobNum = 0
submitter.submitAll(startJobNum, numRepeat, dry_run=o.dry_run)
def run(self):
if self.parser.options is None:
self.parser.parse_args()
o = self.parser.options
for noise_sigma in self.parser.noise_sigmas:
p = self._dp.copy()
p["noise_sigma"] = noise_sigma # pA
p["time"] = 10e3 if o.time is None else o.time # ms
p["nthreads"] = 1
p["ntrials"] = o.ntrials
p["verbosity"] = o.verbosity
p.update(self._up)
# Submitting
ac = ArgumentCreator(p, printout=True)
simLabel = "{0}pA".format(int(p["noise_sigma"]))
numRepeat = 1
submitter = SubmitterFactory.getSubmitter(
ac,
self._app_name,
envType=o.env,
rtLimit=o.rtLimit,
output_dir=o.where,
label=simLabel,
blocking=True,
timePrefix=False,
numCPU=o.nCPU,
)
ac.setOption("output_dir", submitter.outputDir())
startJobNum = 0
submitter.submitAll(startJobNum, numRepeat, dry_run=o.dry_run)
def run(self):
"""Run the parameter sweep."""
if self.parser.options is None:
self.parser.parse_args()
o = self.parser.options
for noise_sigma in self.parser.noise_sigmas:
p = self._dp.copy()
p["noise_sigma"] = noise_sigma # pA
p["time"] = 10e3 if o.time is None else o.time # ms
p["nthreads"] = 1
p["ntrials"] = o.ntrials
p["verbosity"] = o.verbosity
p.update(self._up)
# Submitting
iterparams = self.parser.iter_params
if self._slope_selector is not None:
iterparams.update({"bumpCurrentSlope": self._slope_selector.get_slopes(noise_sigma)})
ac = ArgumentCreator(p, printout=True)
ac.insertDict(iterparams, mult=False)
###################################################################
simLabel = "{0}pA".format(int(p["noise_sigma"]))
numRepeat = 1
submitter = SubmitterFactory.getSubmitter(
ac,
self._app_name,
envType=o.env,
rtLimit=o.rtLimit,
output_dir=o.where,
label=simLabel,
blocking=True,
timePrefix=False,
numCPU=o.nCPU,
)
ac.setOption("output_dir", submitter.outputDir())
startJobNum = 0
submitter.submitAll(startJobNum, numRepeat, dry_run=o.dry_run, filter=self.parser.flat_filter)
submitter.saveIterParams(
iterparams, self.parser.options.param_list, self.parser.dimensions, dry_run=o.dry_run
)
def submitNoiseSweep(p, gEp, gIp, noisep,
ENV, simRootDir, simLabel, appName, rtLimit, numCPU,
blocking, timePrefix, numRepeat, dry_run,
extraIterparams=None):
'''
Submit a parameter sweep with an extra dimension: noise_sigma.
'''
if extraIterparams is None:
extraIterparams = {}
noise_sigma_arr = []
g_AMPA_total_arr = []
g_GABA_total_arr = []
for n in noisep.values():
for E_coupling in gEp.values():
for I_coupling in gIp.values():
noise_sigma_arr.append(n)
g_AMPA_total_arr.append(E_coupling)
g_GABA_total_arr.append(I_coupling)
iterparams = {
'noise_sigma' : np.array(noise_sigma_arr),
'g_AMPA_total' : np.array(g_AMPA_total_arr),
'g_GABA_total' : np.array(g_GABA_total_arr),
#'noise_sigma' : [150],
#'g_AMPA_total' : [1020],
#'g_GABA_total' : [3060]
}
iterparams.update(extraIterparams)
ac = ArgumentCreator(p, printout=True)
ac.insertDict(iterparams, mult=False)
###############################################################################
submitter = SubmitterFactory.getSubmitter(ac, appName, envType=ENV,
rtLimit=rtLimit,
output_dir=simRootDir,
label=simLabel,
blocking=blocking,
timePrefix=timePrefix,
numCPU=numCPU)
ac.setOption('output_dir', submitter.outputDir())
startJobNum = 0
submitter.submitAll(startJobNum, numRepeat, dry_run=dry_run)
submitter.saveIterParams(iterparams, None, None, dry_run=dry_run)
def submitNoiseSweep(p,
gEp,
gIp,
noisep,
ENV,
simRootDir,
simLabel,
appName,
rtLimit,
numCPU,
blocking,
timePrefix,
numRepeat,
dry_run,
extraIterparams=None):
'''
Submit a parameter sweep with an extra dimension: noise_sigma.
'''
if extraIterparams is None:
extraIterparams = {}
noise_sigma_arr = []
g_AMPA_total_arr = []
g_GABA_total_arr = []
for n in noisep.values():
for E_coupling in gEp.values():
for I_coupling in gIp.values():
noise_sigma_arr.append(n)
g_AMPA_total_arr.append(E_coupling)
g_GABA_total_arr.append(I_coupling)
iterparams = {
'noise_sigma': np.array(noise_sigma_arr),
'g_AMPA_total': np.array(g_AMPA_total_arr),
'g_GABA_total': np.array(g_GABA_total_arr),
#'noise_sigma' : [150],
#'g_AMPA_total' : [1020],
#'g_GABA_total' : [3060]
}
iterparams.update(extraIterparams)
ac = ArgumentCreator(p, printout=True)
ac.insertDict(iterparams, mult=False)
###############################################################################
submitter = SubmitterFactory.getSubmitter(ac,
appName,
envType=ENV,
rtLimit=rtLimit,
output_dir=simRootDir,
label=simLabel,
blocking=blocking,
timePrefix=timePrefix,
numCPU=numCPU)
ac.setOption('output_dir', submitter.outputDir())
startJobNum = 0
submitter.submitAll(startJobNum, numRepeat, dry_run=dry_run)
submitter.saveIterParams(iterparams, None, None, dry_run=dry_run)
def run(self):
'''Run the parameter sweep.'''
if self.parser.options is None:
self.parser.parse_args()
o = self.parser.options
for noise_sigma in self.parser.noise_sigmas:
p = self._dp.copy()
p['noise_sigma'] = noise_sigma # pA
p['time'] = 10e3 if o.time is None else o.time # ms
p['nthreads'] = 1
p['ntrials'] = o.ntrials
p['verbosity'] = o.verbosity
p.update(self._up)
# Submitting
iterparams = self.parser.iter_params
if self._slope_selector is not None:
iterparams.update({
'bumpCurrentSlope':
self._slope_selector.get_slopes(noise_sigma)
})
ac = ArgumentCreator(p, printout=True)
ac.insertDict(iterparams, mult=False)
###################################################################
simLabel = '{0}pA'.format(int(p['noise_sigma']))
numRepeat = 1
submitter = SubmitterFactory.getSubmitter(ac,
self._app_name,
envType=o.env,
rtLimit=o.rtLimit,
output_dir=o.where,
label=simLabel,
blocking=True,
timePrefix=False,
numCPU=o.nCPU)
ac.setOption('output_dir', submitter.outputDir())
startJobNum = 0
submitter.submitAll(startJobNum,
numRepeat,
dry_run=o.dry_run,
filter=self.parser.flat_filter)
submitter.saveIterParams(iterparams,
self.parser.options.param_list,
self.parser.dimensions,
dry_run=o.dry_run)
rowN = shape[0]
colN = shape[1]
p["type"] = o.type
p["shapeRows"] = rowN
p["shapeCols"] = colN
p["verbosity"] = o.verbosity
p["forceUpdate"] = int(o.forceUpdate)
if p["type"] == common.velocityType:
percentile = 99.0
p["bumpSpeedMax"] = getSpeedPercentile(percentile, dp["ratVelFName"], dp["gridSep"], dp["Ne"])
###############################################################################
ac = ArgumentCreator(p, printout=True)
iterparams = {
"row": np.arange(rowN) if o.row is None else [o.row],
"col": np.arange(colN) if o.col is None else [o.col],
}
ac.insertDict(iterparams, mult=True)
###############################################################################
submitter = SubmitterFactory.getSubmitter(
ac,
appName,
envType=ENV,
rtLimit=rtLimit,
output_dir=simRootDir,
label=simLabel,
p['ntrials'] = o.ntrials
p['verbosity'] = o.verbosity
p['Ivel'] = 50. if o.Ivel is None else o.Ivel # mA
p['g_AMPA_total'] = 25. # nS
p['g_GABA_total'] = 8. # nS
# No theta parameters
p['Iext_e_const'] = 400.0 # pA
p['Iext_i_const'] = 175.0 # pA
p['Iext_e_theta'] = 0 # pA
p['Iext_i_theta'] = 0 # pA
# Here, no PC inputs
p['pc_start_max_rate'] = .0 # Hz
p['prefDirC_e'] = 0.
p = set_up_connection_params(o, p)
###########################################################################
ac = ArgumentCreator(p, printout=True)
submitter = SubmitterFactory.getSubmitter(
ac, appName, envType=ENV, rtLimit=rtLimit, output_dir=simRootDir,
label=simLabel, blocking=blocking, timePrefix=timePrefix,
numCPU=numCPU)
ac.setOption('output_dir', submitter.outputDir())
startJobNum = 0
submitter.submitAll(startJobNum, numRepeat, dry_run=dry_run)
p['Iext_e_theta'] = 0 # pA
p['Iext_i_theta'] = 0 # pA
# Here, no PC inputs
p['pc_start_max_rate'] = .0 # Hz
p['prefDirC_e'] = 0.
explored_param = np.arange(o.param_start, o.param_stop + o.param_step,
o.param_step)
dummy = explored_param * 0. + p['prefDirC_e']
iterparams = {
'prefDirC_e': dummy,
o.explored_param: explored_param
}
dimension_labels = ['prefDirC_e', o.explored_param]
dimensions = [1, len(explored_param)]
ac = ArgumentCreator(p, printout=True)
ac.insertDict(iterparams, mult=False)
###########################################################################
submitter = SubmitterFactory.getSubmitter(
ac, appName, envType=ENV, rtLimit=rtLimit, output_dir=simRootDir,
label=simLabel, blocking=blocking, timePrefix=timePrefix,
numCPU=numCPU)
ac.setOption('output_dir', submitter.outputDir())
startJobNum = 0
submitter.submitAll(startJobNum, numRepeat, dry_run=dry_run)
submitter.saveIterParams(iterparams, dimension_labels, dimensions,
dry_run=dry_run)
p['master_seed'] = 123456
p['time'] = 0.1 # unused
p['nthreads'] = 1
p['ntrials'] = 1
p['verbosity'] = o.verbosity
p['probabilistic_synapses'] = o.probabilistic_synapses
# Range of E/I synaptic conductances
Nvals = 31 # Number of values (these will be equivalent to go through the
# diagonal of the parameter space
startG = 0.0 # nS
endG = 6120.0 # nS
###############################################################################
ac = ArgumentCreator(p, printout=True)
GArr = np.linspace(startG, endG, Nvals)
g_AMPA_total_arr = []
g_GABA_total_arr = []
for coupling in GArr:
g_AMPA_total_arr.append(coupling)
g_GABA_total_arr.append(coupling)
iterparams = {
'g_AMPA_total': np.array(g_AMPA_total_arr),
'g_GABA_total': np.array(g_GABA_total_arr),
}
ac.insertDict(iterparams, mult=False)
###############################################################################
def submitParamSweep(p,
startG,
endG,
Nvals,
ENV,
simRootDir,
simLabel,
appName,
rtLimit,
numCPU,
blocking,
timePrefix,
numRepeat,
dry_run,
extraIterparams=None,
rc=None,
**kwargs):
'''Submit and save metadata for the gE vs gI parameter sweep.'''
printout = kwargs.pop('printout', True)
if extraIterparams is None:
extraIterparams = {}
ac = ArgumentCreator(p, printout=printout)
GArr = np.linspace(startG, endG, Nvals)
print(GArr)
g_AMPA_total_arr = []
g_GABA_total_arr = []
for E_coupling in GArr:
for I_coupling in GArr:
g_AMPA_total_arr.append(E_coupling)
g_GABA_total_arr.append(I_coupling)
iterparams = {
'g_AMPA_total': np.array(g_AMPA_total_arr),
'g_GABA_total': np.array(g_GABA_total_arr),
}
dimension_labels = ['g_AMPA_total', 'g_GABA_total']
dimensions = [Nvals, Nvals]
iterparams.update(extraIterparams)
ac.insertDict(iterparams, mult=False)
###############################################################################
submitter = SubmitterFactory.getSubmitter(ac,
appName,
envType=ENV,
rtLimit=rtLimit,
output_dir=simRootDir,
label=simLabel,
blocking=blocking,
timePrefix=timePrefix,
numCPU=numCPU,
**kwargs)
ac.setOption('output_dir', submitter.outputDir())
startJobNum = 0
filter = rc[0] * len(GArr) + rc[1] if rc is not None else None
submitter.submitAll(startJobNum, numRepeat, dry_run=dry_run, filter=filter)
submitter.saveIterParams(iterparams,
dimension_labels,
dimensions,
dry_run=dry_run)
p['g_AMPA_total'] = 25. # nS
p['g_GABA_total'] = 8. # nS
# No theta parameters
p['Iext_e_const'] = 400.0 # pA
p['Iext_i_const'] = 175.0 # pA
p['Iext_e_theta'] = 0 # pA
p['Iext_i_theta'] = 0 # pA
# Here, no PC inputs
p['pc_start_max_rate'] = .0 # Hz
p['prefDirC_e'] = 0.
p = set_up_connection_params(o, p)
###########################################################################
ac = ArgumentCreator(p, printout=True)
submitter = SubmitterFactory.getSubmitter(ac,
appName,
envType=ENV,
rtLimit=rtLimit,
output_dir=simRootDir,
label=simLabel,
blocking=blocking,
timePrefix=timePrefix,
numCPU=numCPU)
ac.setOption('output_dir', submitter.outputDir())
startJobNum = 0
submitter.submitAll(startJobNum, numRepeat, dry_run=dry_run)