def process_exp_argv(argv):
"""Process pos arguments for python programs with a invocation like:
$ python ./script.py name data roifile cond [, filtfile]
"""
if len(argv) == 6:
basename = argv[1] ## name
dataname = argv[2] ## data
_, rois = load_roifile(argv[3]) ## roifile
cond = argv[4] ## cond
tr = argv[5]
filtfile = None
elif len(argv) == 7:
basename = argv[1]
dataname = argv[2]
_, rois = load_roifile(argv[3])
cond = argv[4]
tr = argv[5]
filtfile = argv[6]
else:
raise ValueError("Wrong number of arguments")
return basename, dataname, rois, cond, tr, filtfile
parser.add_argument(
"filtfile",
help="Name of this exp",
nargs='?',
default=None
)
args = parser.parse_args()
# ---------------------------------------------------------------------------
# Process argv
# ---------------------------------------------------------------------------
# Replace this with good arg processing....
# basename, dataname, rois, cond, tr, filtfile = process_exp_argv(sys.argv)
data = get_data(args.data)
_, rois = load_roifile(args.roifile) ## roifile
# ---------------------------------------------------------------------------
# Setup exp
# ---------------------------------------------------------------------------
spacetime = SelectSpace(PCA(6, whiten=True), fir, mode="decompose")
exp = DecomposeExp(
spacetime, data, window=args.window, nsig=3, tr=args.tr
)
# ---------------------------------------------------------------------------
# And run each roi
# ---------------------------------------------------------------------------
for n, roi in enumerate(rois):
print("{3}: {0} ({1}/{2})".format(roi, n+1, len(rois), args.data))
exp.run(
# ----
# Create a place for
# the roi data to
# live if necessary.
try:
os.mkdir("./roinii")
except OSError:
pass
# ----
# Process argv
if len(sys.argv[1:]) != 1:
raise ValueError("One arguments are required.")
# ----
# Go!
rois, names = load_roifile(sys.argv[1])
# Build up arguements lists
# creates needs
# (roi, path, niipartial, name, restart)
arglist = []
for roi, name in zip(rois, names):
print("Creating ROI data for {0} as {1}.".format(roi, name))
arglist.append((roi, path, niipartial, name, restart))
# Parallelize using the arglist and Pool
pool = Pool(ncore)
pool.map(create, arglist)
# Log success
f = open("{0}_roinii.log".format(expname), "a")
f.write("{0}:{1}\n".format(maskname, newname))
f.close()
if __name__ == '__main__':
"""Command line invocation setup."""
ncore = 1
overwrite = False
# Process argv
if len(sys.argv[1:]) != 2:
raise ValueError("Two arguments are required.")
roinames, newnames = load_roifile(sys.argv[1])
expname = sys.argv[2]
# Cleaup success log from previous runs
try:
os.remove("{0}_roinii.log".format(expname))
except OSError:
pass
# Go, multpprocess on request
if ncore == 1:
[
create(roiname, newname, expname, overwrite)
for roiname, newname in zip(roinames, newnames)
]
elif ncore > 1:
# ----
# Create a place for
# the roi data to
# live if necessary.
try:
os.mkdir("./roinii")
except OSError:
pass
# ----
# Process argv
if len(sys.argv[1:]) != 1:
raise ValueError("One arguments are required.")
# ----
# Go!
rois, names = load_roifile(sys.argv[1])
# Build up arguements lists
# creates needs
# (roi, path, niipartial, name, restart)
arglist = []
for roi, name in zip(rois, names):
print("Creating ROI data for {0} as {1}.".format(roi, name))
arglist.append((roi, path, niipartial, name, restart))
# Parallelize using the arglist and Pool
pool = Pool(ncore)
pool.map(create, arglist)
# Log success
f = open("{0}_roinii.log".format(expname), "a")
f.write("{0}:{1}\n".format(maskname, newname))
f.close()
if __name__ == '__main__':
"""Command line invocation setup."""
ncore = 1
overwrite = False
# Process argv
if len(sys.argv[1:]) != 2:
raise ValueError("Two arguments are required.")
roinames, newnames = load_roifile(sys.argv[1])
expname = sys.argv[2]
# Cleaup success log from previous runs
try:
os.remove("{0}_roinii.log".format(expname))
except OSError:
pass
# Go, multpprocess on request
if ncore == 1:
[create(roiname, newname, expname, overwrite) for
roiname, newname in zip(roinames, newnames)]
elif ncore > 1:
p = Pool(ncore)
for roiname, newname in zip(roinames, newnames):
