def setUp(self):
from core.network.default_params import Perturbation_list as pl
from_disk=2
import oscillation_perturbations4 as op
rep=2
sim_time=rep*1000.0
local_num_threads=20
l=op.get()
p=pl({'simu':{'sim_time':sim_time,
'sim_stop':sim_time,
'local_num_threads':local_num_threads}},
'=')
p+=l[7]
self.setup=Setup(**{'local_num_threads':local_num_threads,
'repetition':rep})
v=simulate(builder=Builder,
from_disk=from_disk,
perturbation_list=p,
script_name=(__file__.split('/')[-1][0:-3]
+'/data'),
setup=self.setup)
file_name, file_name_figs, from_disks, d, models= v
self.file_name_figs=file_name_figs
self.from_disks=from_disks
self.d=d
self.models=models
def perturbations(rep, res):
threads = 4
l = []
# l.append(op.get()[0])
# l.append(op3.get()[3])
l = op.get()[4::3]
ll = []
p_sizes = [
0.1989460102,
# 0.1608005821,
# 0.122655154,
# 0.0845097259
]
p_sizes = [p / p_sizes[0] for p in p_sizes]
max_size = 4000
for ss, p_size in zip(
[
6.25,
#8.3 ,
#12.5,
# 25
],
p_sizes):
for i, _l in enumerate(l):
_l = deepcopy(_l)
per = pl(
{
'netw': {
'size': int(p_size * max_size),
'sub_sampling': {
'M1': ss,
'M2': ss
},
}
}, '=', **{'name': 'ss-' + str(ss)})
_l += per
_l += pl({'simu': {'threads': threads}}, '=')
ll.append(_l)
for _l in ll:
_l += pl(
{
'conn': {
'FS_M1_gaba': {
'rule': 'set-not_set'
},
'FS_M2_gaba': {
'rule': 'set-not_set'
}
}
}, '=')
return ll, threads
def perturbations(rep, res):
threads = 20
l = []
# l.append(op.get()[0])
# l.append(op.get()[4::3])
l.append(op.get()[4 + 3])
ll = []
# w=0.4
p_sizes = [0.1989460102, 0.1608005821, 0.122655154, 0.0845097259]
p_sizes = [p / p_sizes[0] for p in p_sizes]
max_size = 4000
for ss, p_size in zip([6.25, 8.3, 12.5, 25], p_sizes):
for i, _l in enumerate(l):
_l = deepcopy(_l)
per = pl(
{
'netw': {
'size': int(p_size * max_size),
'sub_sampling': {
'M1': ss,
'M2': ss
},
}
}, '=', **{'name': 'ss-' + str(ss)})
_l += per
_l += pl({'simu': {'threads': threads}}, '=')
ll.append(_l)
# for _l in deepcopy([ll[0]]):
# _lr=deepcopy(_l)
# _lr.update_list(
# pl({'nest':{'GA_M1_gaba':{'weight':5*2.*w},
# # 'GA_FS_gaba':{'weight':0.1}
# }},'*', **{'name':'GA-XX-equal'}))
# ll.append(_lr)
#
# _lr=deepcopy(_l)
# _lr.update_list(
# pl({'nest':{'GA_M1_gaba':{'weight':5*4.*w},
# # 'GA_FS_gaba':{'weight':0.1}
# }},'*', **{'name':'GA-XX-equal'}))
# ll.append(_lr)
#
# _lr=deepcopy(_l)
# _lr.update_list(
# pl({'nest':{'GA_M1_gaba':{'weight':5*0.5*w},
# # 'GA_FS_gaba':{'weight':0.1}
# }},'*', **{'name':'GA-XX-equal'}))
# ll.append(_lr)
return ll, threads
def perturbations():
sim_time = 10000.0
size = 20000.0
threads = 1
freqs = [1., 2.0]
path = ('/home/mikael/results/papers/inhibition' +
'/network/simulate_inhibition_ZZZ4/')
l = op.get()[-3:]
for i in range(len(l)):
l[i] += pl(
{
'simu': {
'sim_time': sim_time,
'sim_stop': sim_time,
'threads': threads
},
'netw': {
'size': size
}
}, '=')
damp = process(path, freqs)
for key in sorted(damp.keys()):
val = damp[key]
print numpy.round(val, 2), key
ll = []
for i, _l in enumerate(l):
for j, _ in enumerate(freqs):
amp = [numpy.round(damp[_l.name][j], 2), 1]
d = {
'type': 'oscillation2',
'params': {
'p_amplitude_mod': amp[0],
'p_amplitude0': amp[1],
'freq': 20.
}
}
_ll = deepcopy(_l)
dd = {}
for key in ['C1', 'C2', 'CF', 'CS']:
dd = misc.dict_update(dd, {'netw': {'input': {key: d}}})
_ll += pl(dd, '=', **{'name': 'amp_{0}-{1}'.format(*amp)})
ll.append(_ll)
return ll, threads
def perturbations():
threads = 8
l = []
# l.append(op.get()[0])
l.append(op.get()[7])
ll = []
l[-1] += pl({'simu': {'threads': threads}}, '=')
return l, threads
def perturbations(rep, res):
threads = 16
l = []
# l.append(op.get()[0])
# l.append(op.get()[4::3])
l.append(op.get()[4 + 3])
ll = []
p_sizes = [
# 0.1989460102,
0.1608005821,
# 0.122655154,
# 0.0845097259
]
p_sizes = [p / p_sizes[0] for p in p_sizes]
max_size = 4000
for ss, p_size in zip(
[
# 6.25,
8.3,
# 12.5,
# 25
],
p_sizes):
for i, _l in enumerate(l):
_l = deepcopy(_l)
per = pl(
{
'netw': {
'size': int(p_size * max_size),
'sub_sampling': {
'M1': ss,
'M2': ss
},
}
}, '=', **{'name': 'ss-' + str(ss)})
_l += per
_l += pl({'simu': {'threads': threads}}, '=')
ll.append(_l)
return ll, threads
def perturbations(rep, res):
sim_time = rep * res * 1000.0
size = 3000.0
threads = 8
l = op.get()
for i in range(len(l)):
l[i] += pl(
{
'simu': {
'sim_time': sim_time,
'sim_stop': sim_time,
'threads': threads
},
'netw': {
'size': size
}
}, '=')
return l, threads
def perturbations(rep,res, sizes):
threads=40
l=[]
# l.append(op.get()[0])
# l.append(op.get()[4::3])
l.append(op.get()[4+3])
ll=[]
for size in sizes:
for i, _l in enumerate(l):
_lt=deepcopy(_l)
per=pl({'netw':{'size':size,
'sub_sampling':{'M1':1,
'M2':1},}},
'=',
**{'name':''})
_lt+=per
_lt+=pl({'simu':{'threads':threads}},'=')
ll.append(_lt)
for l in ll[:]:
for beta in [0, 0.9375, 0.3125]:
_lb=deepcopy(l)
per=pl({'nest':{'M1_low':{'beta_I_GABAA_2':beta },
'M2_low':{'beta_I_GABAA_2':beta },
}},
'=',
**{'name':'beta-'+str(beta)})
_lb+=per
ll.append(_lb)
return ll, threads
def get():
ll = [op.get()[7]]
for l in ll[:]:
for beta in [0., -0.9375, -0.3125]:
_lb = deepcopy(l)
per = pl(
{
'nest': {
'M1_low': {
'beta_I_GABAA_2': beta
},
'M2_low': {
'beta_I_GABAA_2': beta
},
}
}, '=', **{'name': 'beta-' + str(beta)})
_lb += per
ll.append(_lb)
return ll
'do_runs': range(NUM_NETS / 2), #A run for each perturbation
'do_obj': False,
'i0': FROM_DISK_0,
'job_name': 'inh_YYY',
'l_hours': ['00', '00', '00'],
'l_minutes': ['15', '10', '5'],
'l_seconds': ['00', '00', '00'],
'lower': 1,
'local_threads_milner': 20,
'local_threads_superm': 5,
'module': module,
'nets': ['Net_{}'.format(i) for i in range(NUM_RUNS)],
'repetitions': 5,
'path_code': default_params.HOME_CODE,
'path_results': get_path_logs(LOAD_MILNER_ON_SUPERMICRO, FILE_NAME),
'perturbation_list': [op.get()[7]],
'size': 3000,
'upper': 1.5
}
d_process_and_thread = par_process_and_thread(**kwargs)
pp(d_process_and_thread)
kwargs.update(d_process_and_thread)
p_list = pert_add_MSN_cluster_compete(**kwargs)
p_list = pert_set_data_path_to_milner_on_supermicro(p_list,
LOAD_MILNER_ON_SUPERMICRO)
for i, p in enumerate(p_list):
print i, p
'laptime':
1000.0,
'local_threads_milner':
20,
'local_threads_superm':
4,
'max_size':
5000,
'module':
module,
'nets': ['Net_0', 'Net_1', 'Net_2', 'Net_3', 'Net_4'],
'path_code':
default_params.HOME_CODE,
'path_results':
get_path_logs(LOAD_MILNER_ON_SUPERMICRO, FILE_NAME),
'perturbation_list': [op.get()[4 + 3]],
'p_sizes': [
1,
0.523,
0.4278185787,
],
'p_subsamp': [
1.,
2.5,
5.,
],
'res':
10,
'rep':
10,
'time_bin':
'freqs': [1.5],
'freq_oscillation': 20.,
'from_disk_0': FROM_DISK_0,
'i0': FROM_DISK_0,
'job_name': 'beta_final',
'l_hours': ['00', '00', '00'],
'l_minutes': ['15', '10', '5'],
'l_seconds': ['00', '00', '00'],
'local_threads_milner': 20,
'local_threads_superm': 5,
'module': module,
'nets': ['Net_0', 'Net_1'], #The nets for each run
'path_code': default_params.HOME_CODE,
'path_rate_runs': get_path_rate_runs('simulate_inhibition_ZZZ4/'),
'path_results': get_path_logs(LOAD_MILNER_ON_SUPERMICRO, FILE_NAME),
'perturbation_list': op.get(),
'sim_time': 10000.0,
'size': 20000.0,
}
d_process_and_thread = par_process_and_thread(**kwargs)
pp(d_process_and_thread)
kwargs.update(d_process_and_thread)
p_list = pert_add_oscillations(**kwargs)
p_list = pert_set_data_path_to_milner_on_supermicro(p_list,
LOAD_MILNER_ON_SUPERMICRO)
for i, p in enumerate(p_list):
print i, p
'GPe TA lesioned (D1,D2)'],
'laptime':1000.0,
'local_threads_milner':40,
'local_threads_superm':4,
'max_size':20000.,
'module':module,
'nets':['Net_0', 'Net_1', 'Net_2', 'Net_3', 'Net_4'],
'other_scenario':True,
'path_code':default_params.HOME_CODE,
'path_results':get_path_logs(LOAD_MILNER_ON_SUPERMICRO,
FILE_NAME),
'perturbation_list':[op.get()[4+3]],
'proportion_connected':[0.2]*1, #related to toal number fo runs
'p_sizes':[
1.
],
'p_subsamp':[
1.
],
'res':10,
'rep':80,
'time_bin':100,
}
d_process_and_thread=par_process_and_thread(**kwargs)
kwargs.update(d_process_and_thread)
from scripts_inhibition.base_simulate import (
get_path_logs, get_args_list_inhibition, get_kwargs_list_indv_nets,
par_process_and_thread, pert_set_data_path_to_milner_on_supermicro,
pert_add_inhibition)
import scripts_inhibition.base_inhibition_striatum as module
import oscillation_perturbations4 as op
import pprint
pp = pprint.pprint
FILE_NAME = __file__.split('/')[-1][0:-3]
FROM_DISK_0 = 0
LOAD_MILNER_ON_SUPERMICRO = False
NUM_NETS = 1
NUM_RUNS = len(op.get()) #A run for each perturbation
num_sim = NUM_NETS * NUM_RUNS
kwargs = {
'Builder': Builder,
'cores_milner': 40 * 1,
'cores_superm': 20,
'file_name': FILE_NAME,
'from_disk': 0,
'debug': False,
'do_runs': [0], #range(NUM_RUNS), #A run for each perturbation
'do_obj': False,
'i0': FROM_DISK_0,
'job_name': 'inh_YYY',
'l_hours': ['00', '00', '00'],
'l_minutes': ['15', '10', '5'],
