def create_dir(name):
'''Creates a directory relative to the MIIND_ROOT/build/jobs.'''
sep = os.path.sep
directories.initialize_global_variables()
miind_root = directories.miind_root()
abspath = os.path.join(miind_root,'build', 'jobs', name)
return abspath
def create_dir(name):
'''Creates a directory relative to the MIIND_ROOT/build/jobs.'''
sep = os.path.sep
directories.initialize_global_variables()
miind_root = directories.miind_root()
abspath = os.path.join(miind_root, 'build', 'jobs', name)
return abspath
def write_out_jobs(base_name, job_names):
''' A directory with job names will be added.'''
abspath=create_dir(base_name)
try:
os.makedirs(abspath)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
joblistname = os.path.join(abspath,'joblist')
with open(joblistname,'w') as f:
for name in job_names:
name = directories.check_and_strip_name(name)
path = os.path.join(directories.miind_root(), 'build' ,'apps', base_name, name, name)
f.write(path + '\n')
return abspath
def write_out_jobs(base_name, job_names):
''' A directory with job names will be added.'''
abspath = create_dir(base_name)
try:
os.makedirs(abspath)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
joblistname = os.path.join(abspath, 'joblist')
with open(joblistname, 'w') as f:
for name in job_names:
name = directories.check_and_strip_name(name)
path = os.path.join(directories.miind_root(), 'build', 'apps',
base_name, name, name)
f.write(path + '\n')
return abspath
def write_out_job(job_name):
''' Just a single job needs to be added.'''
dirname=job_name[:-4]
if job_name[-4:] != '.xml':
raise NameError
abspath=create_dir(dirname)
try:
os.makedirs(abspath)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
joblistname = os.path.join(abspath,'joblist')
with open(joblistname,'w') as f:
path = os.path.join(directories.miind_root(), 'build' ,'apps', job_name)
f.write(path + '\n')
return
def write_out_job(job_name):
''' Just a single job needs to be added.'''
dirname = job_name[:-4]
if job_name[-4:] != '.xml':
raise NameError
abspath = create_dir(dirname)
try:
os.makedirs(abspath)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
joblistname = os.path.join(abspath, 'joblist')
with open(joblistname, 'w') as f:
path = os.path.join(directories.miind_root(), 'build', 'apps',
job_name)
f.write(path + '\n')
return
#!/usr/bin/env python
import subprocess
import submit
import sys
import os
import directories
dir = sys.argv[1]
build = os.path.join(directories.miind_root(), 'build')
path = os.path.join(build, 'jobs', dir)
with submit.cd(os.path.join(directories.miind_root(), 'python')):
subprocess.call(["cp", "sub.sh", path])
with submit.cd(build):
subprocess.call(['make'])
with submit.cd(path):
f = open('joblist')
lines = f.readlines()
for line in lines:
name = line.strip()
subprocess.call(['qsub', './sub.sh', name])
import ROOT
import sys
import os
import directories
import numpy as np
'''Analyse the response curve data.'''
# Don't want flashing canvasses.
ROOT.gROOT.SetBatch(True)
ROOT.gStyle.SetOptStat(0)
jobpath = os.path.join(directories.miind_root(),'build','jobs','single','joblist')
def nodecay():
filepath = os.path.split(jobpath)[0]
path = os.path.join(filepath,'no_decay_0.root')
f=ROOT.TFile(path)
c=ROOT.TCanvas('c')
c.SetGrayscale()
h = ROOT.TH2F("h","No leakage",500,0.01,1.,500,0.,40.)
h.SetXTitle('V')
h.SetYTitle('#rho')
h.GetYaxis().SetLabelOffset(0.02)
h.Draw()
g2=f.Get('grid_0_1.1513041e-05')
g2.SetLineColor(ROOT.kYellow+4)
g2.SetFillColor(ROOT.kYellow+4)
g2.SetFillStyle(1001)
import ROOT
import sys
import os
import directories
'''Analyse the response curve data.'''
# Don't want flashing canvasses.
ROOT.gROOT.SetBatch(True)
jobpath = os.path.join(directories.miind_root(),'build','jobs','response','joblist')
f = open(jobpath)
lines = f.readlines()
for line in lines:
path = os.path.split(line.strip())
print path[-1]
f=ROOT.TFile(os.path.join(os.path.split(jobpath)[0] , path[-1] + '_0.root'))
# Get the firing rate response of the LIF population
g=f.Get('rate_0')
# Fit and write out
fun=ROOT.TF1('func1','pol1',0.8,1.0)
g.Fit('func1','R')
p = fun.GetParameters()
with open('response.dat','a') as f:
items= path[-1].split('_')
print items[2], items[1]
def __init__(self, newPath):
self.newPath = os.path.expanduser(newPath)
def __enter__(self):
self.savedPath = os.getcwd()
os.chdir(self.newPath)
def __exit__(self, etype, value, traceback):
os.chdir(self.savedPath)
if __name__ == "__main__":
if len(sys.argv) != 2:
print 'submit requirs exactly one argument: the subdirectory under which the jobs are organized.'
sys.exit()
dir = sys.argv[1]
build = os.path.join(directories.miind_root(), 'build')
path = os.path.join(build, 'jobs', dir)
with cd(build):
subprocess.call(['make'])
with open(os.path.join(path, 'joblist')) as f:
lines = f.readlines()
with cd(path):
for line in lines:
name = line.split()[0]
subprocess.call([name, '>&log&'])
import numpy as np
import ROOT
import sys
import os
import directories
"""Analyse the response curve data."""
# Don't want flashing canvasses.
ANALYTIC_DATAFILE = "analytic.dat"
POPULATION_DATAFILE = "pop.dat"
ROOT.gROOT.SetBatch(True)
jobpath = os.path.join(directories.miind_root(), "build", "jobs", "rate", "joblist")
f = open(jobpath)
lines = f.readlines()
def ExtractPopulationResults():
with open(POPULATION_DATAFILE, "w") as fpop:
fpop.close()
for line in lines:
path = os.path.split(line.strip())
print path[-1]
f = ROOT.TFile(os.path.join(os.path.split(jobpath)[0], path[-1] + "_0.root"))
# Get the firing rate response of the LIF population
import imp
import os
import directories
libmiindwc = imp.load_dynamic(
"libmiindwc",
os.path.join(directories.miind_root(), 'build', 'apps', 'TvbModels',
'wilsoncowan', 'libmiindwc.so'))
import ROOT
import sys
import os
import directories
'''Analyse the response curve data.'''
# Don't want flashing canvasses.
ROOT.gROOT.SetBatch(True)
jobpath = os.path.join(directories.miind_root(), 'build', 'jobs', 'response',
'joblist')
f = open(jobpath)
lines = f.readlines()
for line in lines:
path = os.path.split(line.strip())
print path[-1]
f = ROOT.TFile(
os.path.join(os.path.split(jobpath)[0], path[-1] + '_0.root'))
# Get the firing rate response of the LIF population
g = f.Get('rate_0')
# Fit and write out
fun = ROOT.TF1('func1', 'pol1', 0.8, 1.0)
g.Fit('func1', 'R')
p = fun.GetParameters()
with open('response.dat', 'a') as f:
self.newPath = os.path.expanduser(newPath)
def __enter__(self):
self.savedPath = os.getcwd()
os.chdir(self.newPath)
def __exit__(self, etype, value, traceback):
os.chdir(self.savedPath)
if __name__ == "__main__":
if len(sys.argv) != 2:
print 'submit requirs exactly one argument: the subdirectory under which the jobs are organized.'
sys.exit()
dir=sys.argv[1]
build = os.path.join(directories.miind_root(),'build')
path = os.path.join(build,'jobs',dir)
with cd(build):
subprocess.call(['make'])
with open(os.path.join(path,'joblist')) as f:
lines = f.readlines()
with cd(path):
for line in lines:
name = line.split()[0]
subprocess.call([name, '>&log&'])
#!/usr/bin/env python
import subprocess
import submit
import sys
import os
import directories
dir=sys.argv[1]
build = os.path.join(directories.miind_root(),'build')
path = os.path.join(build,'jobs',dir)
with submit.cd(os.path.join(directories.miind_root(),'python')):
subprocess.call(["cp","sub.sh",path])
with submit.cd(build):
subprocess.call(['make'])
with submit.cd(path):
f=open('joblist')
lines=f.readlines()
for line in lines:
name=line.strip()
subprocess.call(['qsub','./sub.sh',name])
