def main():
global SPEM, gleam_path
if not gleam_path:
gleam_path = os.getcwd()
SPEM = os.path.join(gleam_path, SPEM)
sim_dir = os.path.join(os.getcwd(),argv[1])
if not os.path.exists(sim_dir):
print >> stderr, "Can't open simulation directory", sim_dir
exit(1)
print >> stderr, "Running in", sim_dir
input_file = os.path.join(sim_dir, "simul.in")
model_file = os.path.join(sim_dir, "simul.mdl")
cfg_file = os.path.join(sim_dir, "req.cfg")
run_end_file = os.path.join(sim_dir, "run.end")
frames_dir = os.path.join(sim_dir, "frames")
output_dir = os.path.join(sim_dir,"output")
if not os.path.exists(SPEM):
print >> stderr, "ExactEM not found!"
exit(1)
if not os.path.exists(input_file) or not os.path.exists(model_file):
print >> stderr, "Invalid simulation directory."
exit(2)
nruns = 0
comps = []
outVal = "I"
input.infections(input_file, sim_dir, False)
input.initial(input_file, sim_dir)
os.chdir(sim_dir)
aggregate = []
aggregate.append("basins")
args = [SPEM, "simul.in", "-outVal", input.quoteString(outVal), "-infections", "infections.txt", "-initial", "initial.txt", "-output", input.quoteString(output_dir)]
run.runSingle(args, 0, outVal, output_dir)
time.sleep(2)
stats.extract_compartments(os.path.join(output_dir,"ExactEM.0.out"), output_dir)
# Signal successful termination and exit
if not os.path.exists(run_end_file):
open(run_end_file, 'w').close()
else:
print >> stderr, "Run was already over???"
def main():
global SPEM, gleam_path
if not gleam_path:
gleam_path = os.getcwd()
SPEM = os.path.join(gleam_path, SPEM)
sim_dir = os.path.join(os.getcwd(), argv[1])
if not os.path.exists(sim_dir):
print >> stderr, "Can't open simulation directory", sim_dir
exit(1)
print >> stderr, "Running in", sim_dir
input_file = os.path.join(sim_dir, "simul.in")
model_file = os.path.join(sim_dir, "simul.mdl")
cfg_file = os.path.join(sim_dir, "req.cfg")
run_end_file = os.path.join(sim_dir, "run.end")
frames_dir = os.path.join(sim_dir, "frames")
output_dir = os.path.join(sim_dir, "output")
if not os.path.exists(SPEM):
print >> stderr, "ExactEM not found!"
exit(1)
if not os.path.exists(input_file) or not os.path.exists(model_file):
print >> stderr, "Invalid simulation directory."
exit(2)
nruns = 0
comps = []
outVal = "I"
input.infections(input_file, sim_dir, False)
input.initial(input_file, sim_dir)
os.chdir(sim_dir)
aggregate = []
aggregate.append("basins")
args = [
SPEM, "simul.in", "-outVal",
input.quoteString(outVal), "-infections", "infections.txt", "-initial",
"initial.txt", "-output",
input.quoteString(output_dir)
]
run.runSingle(args, 0, outVal, output_dir)
time.sleep(2)
stats.extract_compartments(os.path.join(output_dir, "ExactEM.0.out"),
output_dir)
# Signal successful termination and exit
if not os.path.exists(run_end_file):
open(run_end_file, 'w').close()
else:
print >> stderr, "Run was already over???"
def main():
global SPEM, gleam_path
if not gleam_path:
gleam_path = os.getcwd()
SPEM = os.path.join(gleam_path, SPEM)
sim_dir = os.path.join(os.getcwd(), argv[1])
if not os.path.exists(sim_dir):
print >> stderr, "Can't open simulation directory", sim_dir
exit(1)
print >> stderr, "Running in", sim_dir
input_file = os.path.join(sim_dir, "simul.in")
model_file = os.path.join(sim_dir, "simul.mdl")
cfg_file = os.path.join(sim_dir, "req.cfg")
run_end_file = os.path.join(sim_dir, "run.end")
frames_dir = os.path.join(sim_dir, "frames")
output_dir = os.path.join(sim_dir, "output")
print input_file
print model_file
print cfg_file
if not os.path.exists(SPEM):
print >> stderr, "SPEM not found!"
exit(1)
if not os.path.exists(input_file) or not os.path.exists(
model_file) or not os.path.exists(cfg_file):
print >> stderr, "Invalid simulation directory."
exit(2)
nruns = 0
comps = []
outVal = ""
for line in open(cfg_file):
if len(line) == 0 or line[0] == "#":
continue
fields = line.split(":")
if fields[0].strip() == "RUNS":
nruns = int(fields[1].strip())
elif fields[0].strip() == "OUTVAL":
comps = fields[1].strip()
outVal = fields[1].strip()
if comps[-1] == ";":
comps = comps[:-1]
comps = comps.split(";")
if nruns == 0 or len(comps) == 0:
print >> stderr, "Invalid configuration file: Zero runs or no output compartments"
exit(3)
print >> stderr, "Running", nruns, "runs for", len(comps), "compartments"
input.infections(input_file, sim_dir, False)
input.initial(input_file, sim_dir)
runTime, startDate = input.parameters(input_file)
os.chdir(sim_dir)
for line in open(input_file):
fields = line.strip().split()
if len(fields) == 2 and fields[0] == "alphamin":
alphamin = float(fields[1])
input.seasonality(1.1, alphamin)
print >> stderr, "Found seasonal factor", alphamin
break
aggregate = []
aggregate.append("basins")
args = [
SPEM, "simul.in", "-outVal",
input.quoteString(outVal), "-infections", "infections.txt", "-initial",
"initial.txt", "-output",
input.quoteString(output_dir)
]
if nruns == 1:
run.runSingle(args, 0, outVal, output_dir)
fp = open(os.path.join(output_dir, "outVal.dat"), "w")
for time in xrange(runTime + 1):
filename = os.path.join(
output_dir, "sum." + aggregate[0] + "." + str(time) + ".dat")
for line in open(filename):
fields = line.strip()
print >> fp, time, fields[1:]
stats.extract_compartments(os.path.join(output_dir, "SPEM.0.out"),
output_dir)
else:
run.runSequential(args, nruns, outVal, output_dir)
print >> stderr, "Running aggregation"
for a in xrange(len(aggregate)):
agg = aggregate[a]
file = os.path.join(sim_dir, "output/")
for time in xrange(runTime + 1):
# for comp in comps:
filename = file + "sum." + agg + "." + str(time) + ".dat"
stats.stats(startDate, time, nruns, filename, "sum", agg,
a + 1, output_dir)
list = glob.glob(os.path.join(output_dir, "step-*.1.sum.dat"))
filename = os.path.join(output_dir, "outVal.dat")
fp = open(filename, "w")
count = 0
for file in list:
for line in open(file):
fields = line.strip()
print >> fp, count, fields[1:]
count += 1
stats.compartments(os.path.join(output_dir, "list.out.dat"),
output_dir)
# Signal successful termination and exit
if not os.path.exists(run_end_file):
open(run_end_file, 'w').close()
else:
print >> stderr, "Run was already over???"
def main():
global NetEM, gleam_path
if not gleam_path:
gleam_path = os.getcwd()
NetEM = os.path.join(gleam_path, NetEM)
sim_dir = os.path.join(os.getcwd(),argv[1])
if not os.path.exists(sim_dir):
print >> stderr, "Can't open simulation directory", sim_dir
exit(1)
print >> stderr, "Running in", sim_dir
input_file = os.path.join(sim_dir, "simul.in")
model_file = os.path.join(sim_dir, "simul.mdl")
cfg_file = os.path.join(sim_dir, "req.cfg")
run_end_file = os.path.join(sim_dir, "run.end")
frames_dir = os.path.join(sim_dir, "frames")
output_dir = os.path.join(sim_dir,"output")
if not os.path.exists(NetEM):
print >> stderr, "NetEM.x not found!"
exit(1)
if not os.path.exists(input_file) or not os.path.exists(model_file) or not os.path.exists(cfg_file):
print >> stderr, "Invalid simulation directory."
exit(2)
nruns = 0
comps = []
outVal = ""
for line in open(cfg_file):
if len(line) == 0 or line[0] == "#":
continue
fields = line.split(":")
if fields[0].strip() == "RUNS":
nruns = int(fields[1].strip())
elif fields[0].strip() == "OUTVAL":
comps = fields[1].strip()
outVal = fields[1].strip()
if comps[-1] == ";":
comps = comps[:-1]
comps = comps.split(";")
if nruns == 0 or len(comps) == 0:
print >> stderr, "Invalid configuration file: Zero runs or no output compartments"
exit(3)
print >> stderr, "Running", nruns, "runs for", len(comps), "compartments"
input.infections(input_file, sim_dir, False)
input.initial(input_file, sim_dir)
runTime, startDate = input.parameters(input_file)
os.chdir(sim_dir)
for line in open(input_file):
fields = line.strip().split()
if len(fields) == 2 and fields[0] == "alphamin":
alphamin = float(fields[1])
input.seasonality(1.1, alphamin)
print >> stderr, "Found seasonal factor",alphamin
break
aggregate = []
aggregate.append("basins")
if nruns == 1:
args = [NetEM, "simul.in", "-outVal", input.quoteString(outVal), "-infections", "infections.txt", "-initial", "initial.txt", "-output", input.quoteString(output_dir), "-frames", input.quoteString(output_dir)]
run.runSingle(args, 0, outVal, output_dir)
fp = open(os.path.join(output_dir, "outVal.dat"), "w")
for time in xrange(runTime+1):
filename = os.path.join(output_dir, "sum." + aggregate[0] + "." + str(time) + ".dat")
for line in open(filename):
fields = line.strip()
print >> fp, time, fields[1:]
stats.extract_compartments(os.path.join(output_dir,"NetEM.0.out"), output_dir)
else:
args = [NetEM, "simul.in", "-outVal", input.quoteString(outVal), "-infections", "infections.txt", "-initial", "initial.txt", "-output", input.quoteString(output_dir)]
run.runSequential(args, nruns, outVal, output_dir)
print >> stderr, "Running aggregation"
for a in xrange(len(aggregate)):
agg = aggregate[a]
file = os.path.join(sim_dir, "output")
for time in xrange(runTime+1):
# for comp in comps:
filename = os.path.join(file, "sum." + agg + "." + str(time) + ".dat")
stats.stats(startDate, time, nruns, filename, "sum", agg, a+1, output_dir)
list = glob.glob(os.path.join(output_dir,"step-*.1.sum.dat"))
filename = os.path.join(output_dir, "outVal.dat")
fp = open(filename, "w")
count = 0
for file in list:
for line in open(file):
fields = line.strip()
print >> fp, count, fields[1:]
count += 1
stats.compartments(os.path.join(output_dir,"list.out.dat"), output_dir)
# Signal successful termination and exit
if not os.path.exists(run_end_file):
open(run_end_file, 'w').close()
else:
print >> stderr, "Run was already over???"