elif ext == ".csv":
flatchainList.append(utils.csvread(file, args.burn, args.thin))
except OSError as e:
print("{} does not exist, skipping. Or error {}".format(file, e))
print("Using a total of {} flatchains".format(len(flatchainList)))
if args.cat:
assert len(flatchainList) > 1, "If concatenating samples, must provide more than one flatchain"
utils.cat_list(args.output, flatchainList)
# Assume that if we are using either args.chain, or args.triangle, we are only suppling one
# chain, since these commands don't make sense otherwise.
if args.chain:
assert len(flatchainList) == 1, "If plotting Markov Chain, only specify one flatchain"
utils.plot_walkers(flatchainList[0], base=args.outdir)
if args.triangle:
assert len(flatchainList) == 1, "If making Triangle, only specify one flatchain"
utils.plot(flatchainList[0], base=args.outdir)
if args.paper:
assert len(flatchainList) == 1, "If making Triangle, only specify one flatchain"
utils.paper_plot(flatchainList[0], base=args.outdir)
if args.cov:
assert len(flatchainList) == 1, "If estimating covariance, only specify one flatchain"
utils.estimate_covariance(flatchainList[0], base=args.outdir, ndim=args.ndim)
if args.gelman:
assert len(flatchainList) > 1, "If running Gelman-Rubin test, must provide more than one flatchain"
paths = glob("s*o*/mc.hdf5")
if args.triangle:
flatchain = utils.h5read("mc.hdf5", args.burn)
utils.plot(flatchain, base="")
cmd = ["chain.py", "--files", "mc.hdf5", "-t", "--burn", "{}".format(args.burn)]
for path in paths:
dirname, fname = path.split("/")
# CD to this directory using context managers
with chdir(dirname):
subprocess.call(cmd)
if args.chain:
flatchain = utils.h5read("mc.hdf5", args.burn)
utils.plot_walkers(flatchain, base="")
cmd = ["chain.py", "--files", "mc.hdf5", "--chain", "--burn", "{}".format(args.burn)]
print(cmd)
for path in paths:
dirname, fname = path.split("/")
# CD to this directory using context managers
with chdir(dirname):
subprocess.call("ls")
subprocess.call(cmd)
utils.plot(flatchain, base="")
cmd = [
"chain.py", "--files", "mc.hdf5", "-t", "--burn",
"{}".format(args.burn)
]
for path in paths:
dirname, fname = path.split("/")
# CD to this directory using context managers
with chdir(dirname):
subprocess.call(cmd)
if args.chain:
flatchain = utils.h5read("mc.hdf5", args.burn)
utils.plot_walkers(flatchain, base="")
cmd = [
"chain.py", "--files", "mc.hdf5", "--chain", "--burn",
"{}".format(args.burn)
]
print(cmd)
for path in paths:
dirname, fname = path.split("/")
# CD to this directory using context managers
with chdir(dirname):
subprocess.call("ls")
subprocess.call(cmd)
print("{} does not exist, skipping. Or error {}".format(file, e))
print("Using a total of {} flatchains".format(len(flatchainList)))
if args.cat:
assert len(
flatchainList
) > 1, "If concatenating samples, must provide more than one flatchain"
utils.cat_list(args.output, flatchainList)
# Assume that if we are using either args.chain, or args.triangle, we are only suppling one
# chain, since these commands don't make sense otherwise.
if args.chain:
assert len(flatchainList
) == 1, "If plotting Markov Chain, only specify one flatchain"
utils.plot_walkers(flatchainList[0], base=args.outdir)
if args.triangle:
assert len(
flatchainList) == 1, "If making Triangle, only specify one flatchain"
utils.plot(flatchainList[0], base=args.outdir)
if args.paper:
assert len(
flatchainList) == 1, "If making Triangle, only specify one flatchain"
utils.paper_plot(flatchainList[0], base=args.outdir)
if args.cov:
assert len(flatchainList
) == 1, "If estimating covariance, only specify one flatchain"
utils.estimate_covariance(flatchainList[0],
