def run_recs_fifos(pardir, outdir, ttime, recnames, fifonames, fifo_trange):
stimpar = jspar.load(os.path.join(pardir, 'stimpar.json'))
cellpar = jspar.load(os.path.join(pardir, 'cellpar.json'))
spkthr = jspar.load(os.path.join(pardir, 'spkthr.json'))
if not os.path.exists(outdir):
os.makedirs(outdir)
simfunc = run.cellpar_wrapper(run.simulation, cellpar, spkthr)
spkt, stimvec, recs, fifos = simfunc(ttime,
'OU',
stimpar,
None,
retstim=True,
recnames=recnames,
fifonames=fifonames,
fifo_trange=fifo_trange)
with open(os.path.join(outdir, 'fifos.p'), 'w') as f:
pickle.dump(fifos, f)
with open(os.path.join(outdir, 'recs.p'), 'w') as f:
pickle.dump(recs, f)
runpar = dict(hpar=run.hpar,
ttime=ttime,
stimpar=stimpar,
cellpar=cellpar,
spkthr=spkthr,
fifo_trange=fifo_trange)
rpfile = os.path.join(outdir, 'runpar.json')
jspar.save(rpfile, runpar)
def run_contours(outdir_base,
cellpar,
spkthr,
bracket,
statname,
targ_list,
fxvec,
xname,
tau,
ttime,
fvsplit=None):
spkthrfile = os.path.join(outdir_base, 'spkthr.json')
jspar.save(spkthrfile, spkthr)
cpfile = os.path.join(outdir_base, 'cellpar.json')
jspar.save(cpfile, cellpar)
for targ in targ_list:
outdir = os.path.join(outdir_base, targ_lab(statname,
targ,
dirlab=True))
if not os.path.exists(outdir):
os.mkdir(outdir)
if fvsplit:
spfxvec = np.split(fxvec, fvsplit)
for i, fxv in enumerate(spfxvec):
subdir = os.path.join(outdir, '%.2d' % i)
if not os.path.exists(subdir):
os.mkdir(subdir)
run_contour(fxv, bracket, xname, tau, statname, targ, ttime,
cpfile, spkthr, subdir)
else:
jobname = 'ctg{:.0f}t{:.0f}'.format(cellpar['gkbar'] * 1e3, targ)
run_contour(fxvec, bracket, xname, tau, statname, targ, ttime,
cpfile, spkthr, outdir, jobname)
def run_fifos(ttime, pardir, outdir):
stimpar = jspar.load(os.path.join(pardir, 'stimpar.json'))
cellpar = jspar.load(os.path.join(pardir, 'cellpar.json'))
spkthr = jspar.load(os.path.join(pardir, 'spkthr.json'))
if not os.path.exists(outdir):
os.makedirs(outdir)
simfunc = run.cellpar_wrapper(run.simulation, cellpar, spkthr)
fifonames = ('time', 'v_ais', 'icap_ais', 'nav_m')
fifo_trange = (-40, 0)
spkt, fifos = simfunc(ttime,
'OU',
stimpar,
None,
fifonames=fifonames,
fifo_trange=fifo_trange)
pff.save_fifos(fifos, outdir)
runpar = dict(hpar=run.hpar,
ttime=ttime,
stimpar=stimpar,
cellpar=cellpar,
spkthr=spkthr,
fifo_trange=fifo_trange)
rpfile = os.path.join(outdir, 'runpar.json')
jspar.save(rpfile, runpar)
def run_optstimpar(outdir, cellpar, spkthr, x0, *optmargs):
spkthrfile = os.path.join(outdir, 'spkthr.json')
jspar.save(spkthrfile, spkthr)
cpfile = os.path.join(outdir, 'cellpar.json')
jspar.save(cpfile, cellpar)
args = [outdir, cpfile, spkthr, x0[0], x0[1]]
args.extend(optmargs)
submit_to_cluster('optstm', '../../run/run_optstimpar.py', args)
def run_ficurve(curtvec, cellpar, outdir, noise=0, tau=0):
cpfile = os.path.join(outdir, 'cellpar.json')
jspar.save(cpfile, cellpar)
ctvfile = os.path.join(outdir, 'curtvec.npy')
np.save(ctvfile, curtvec)
args = [ctvfile, cpfile, spkthr, outdir, '--noise', noise, '--tau', tau]
submit_to_cluster('ficurve', '../../run/run_ficurve.py', args)
def run_optstimpar(qname, outdir, cellpar, spkthr, x0, *optmargs):
spkthrfile = os.path.join(outdir, 'spkthr.json')
jspar.save(spkthrfile, spkthr)
cpfile = os.path.join(outdir, 'cellpar.json')
jspar.save(cpfile, cellpar)
args = [outdir, cpfile, spkthr, x0[0], x0[1]]
args.extend(optmargs)
scpath = os.path.join(rjpath, 'run_optstimpar.py')
submit_to_cluster(qname, 'optstm', scpath, args)
def run_ficurve(qname, curtvec, cellpar, spkthr, outdir, noise=0, tau=0):
cpfile = os.path.join(outdir, 'cellpar.json')
jspar.save(cpfile, cellpar)
ctvfile = os.path.join(outdir, 'curtvec.npy')
np.save(ctvfile, curtvec)
args = [ctvfile, cpfile, spkthr, outdir, '--noise', noise, '--tau', tau]
scpath = os.path.join(rjpath, 'run_ficurve.py')
submit_to_cluster(qname, 'ficurve', scpath, args)
moddir = '.'
run = imp.load_source('run', os.path.join(moddir, 'run.py'))
stimpar = jspar.load(args.spfile)
cellpar = jspar.load(args.cpfile)
outdir = args.outdir
if not os.path.exists(outdir):
raise OSError('No such directory: {}'.format(outdir))
spktimes, stimvec = run.simulation(cellpar,
args.spkthr,
args.ttime,
args.stimtyp,
stimpar,
retstim=True)
runpar = dict(hpar=run.hpar,
ttime=args.ttime,
stimpar=stimpar,
cellpar=cellpar,
spkthr=args.spkthr)
rpfile = os.path.join(outdir, 'runpar.json')
jspar.save(rpfile, runpar)
with open(os.path.join(outdir, 'stimvec.npy'), 'w') as f:
np.save(f, stimvec)
with open(os.path.join(outdir, 'spktimes.npy'), 'w') as f:
np.save(f, spktimes)
parser.add_argument('spkthr',
type=float,
help='voltage thresh for spike detection')
parser.add_argument('outdir', help='output directory')
parser.add_argument('--moddir', help='path for model definition')
parser.add_argument(
'--noise',
type=float,
help='0: no noise, non-0: standard deviation of OU process')
parser.add_argument('--tau', type=float, help='tau for OU process')
args = parser.parse_args()
if args.moddir:
moddir = args.moddir
else:
moddir = '.'
run = imp.load_source('run', os.path.join(moddir, 'run.py'))
curtvec = np.load(args.ctvfile)
cellpar = jspar.load(args.cpfile)
outdir = args.outdir
if not os.path.exists(outdir):
raise Exception('No such directory: %s' % outdir)
simfunc = run.cellpar_wrapper(run.simulation, cellpar, args.spkthr)
frtvec = ficurve.get_frtvec(simfunc, curtvec, noise=args.noise, tau=args.tau)
np.save(os.path.join(outdir, 'frtvec.npy'), frtvec)
jspar.save(os.path.join(outdir, 'fipar.json'), vars(args))
type=float,
help='total simulation time for one evaluation')
parser.add_argument('frttarg', type=float, help='target firing rate')
parser.add_argument('cvtarg', type=float, help='target cv')
parser.add_argument('--moddir', help='path for model definition')
args = parser.parse_args()
if args.moddir:
moddir = args.moddir
else:
moddir = '.'
run = imp.load_source('run', os.path.join(moddir, 'run.py'))
outdir = args.outdir
if not os.path.exists(outdir):
raise Exception('No such output directory: %s' % outdir)
cellpar = jspar.load(args.cpfile)
x0 = (args.mean0, args.std0)
logfile = os.path.join(outdir, 'optstimpar.log')
logging.basicConfig(filename=logfile, level=logging.INFO)
simfunc = run.cellpar_wrapper(run.simulation, cellpar, args.spkthr)
ostimpar, res = optstimpar.optstimpar(simfunc, x0, args.tau, args.ttime,
args.frttarg, args.cvtarg)
spfile = os.path.join(outdir, 'stimpar.json')
jspar.save(spfile, ostimpar)
parser.add_argument('statname', help='spike statistic variable for contour')
parser.add_argument('targ', type=float, help='value of statistic variable for contour')
parser.add_argument('ttime', type=float, help='total simulation time')
parser.add_argument('--rseed', type=int, default=3, help='random number seed for OU')
parser.add_argument('--moddir', help='path for model definition')
args = parser.parse_args()
if args.moddir:
moddir = args.moddir
else:
moddir = '.'
run = imp.load_source('run', os.path.join(moddir, 'run.py'))
outdir = args.outdir
if not os.path.exists(outdir):
raise OSError('No such output directory: %s' % outdir)
cellpar = jspar.load(args.cpfile)
fxvec = np.load(args.fxvfile)
logfile = os.path.join(outdir, 'contour.log')
logging.basicConfig(filename=logfile, level=logging.INFO)
simfunc = run.cellpar_wrapper(run.simulation, cellpar, args.spkthr)
targfunc = contour.targfunc_wrapper(simfunc, args.xname, args.tau, args.statname, args.targ, args.ttime, rseed=args.rseed)
xvec = contour.get_contour(targfunc, fxvec, args.bracket)
logging.info(str(xvec))
np.save(os.path.join(args.outdir, 'xvec.npy'), xvec)
jspar.save(os.path.join(args.outdir, 'ctpar.json'), vars(args))