def main():
"""
Entry point for BASIL command line application
"""
try:
parser = AslOptionParser(usage="basil -i <ASL input file> [options...]", version=__version__)
parser.add_category(image.AslImageOptions())
parser.add_category(BasilOptions())
parser.add_category(GenericOptions())
options, _ = parser.parse_args()
if not options.output:
options.output = "basil"
if not options.asldata:
sys.stderr.write("Input file not specified\n")
parser.print_help()
sys.exit(1)
wsp = Workspace(savedir=options.output, separate_input=True, auto_asldata=True, **vars(options))
# Deal with --artonly
if wsp.artonly:
wsp.infertiss = False
wsp.inferart = True
# Adjust number of iterations based on fast option
if not wsp.fast:
num_iter, num_trials, onestep = 20, 10, False
elif wsp.fast == 1:
num_iter, num_trials, onestep = 5, 2, False
elif wsp.fast == 2:
num_iter, num_trials, onestep = 10, 5, True
else:
raise ValueError("Not a valid option for fast: %s" % str(wsp.fast))
wsp.max_iterations = num_iter
wsp.max_trials = num_trials
wsp.onestep = onestep
# Read in additional model options from a file
wsp.model_options = {}
if wsp.model_options:
with open(wsp.model_options) as optfile:
for line in optfile:
keyval = line.strip().rstrip("\n").lstrip("--").split("=", 1)
key = keyval[0].strip().replace("-", "_")
if key != "":
if len(keyval) == 1:
wsp.model_options[key] = True
else:
wsp.model_options[key] = keyval[1].strip()
# Run BASIL processing
basil(wsp)
except ValueError as exc:
sys.stderr.write("\nERROR: " + str(exc) + "\n")
sys.stderr.write("Use --help for usage information\n")
sys.exit(1)
def main():
"""
Entry point for BASIL command line application
"""
try:
parser = AslOptionParser(
usage="basil -i <ASL input file> [options...]",
version=__version__)
parser.add_category(image.AslImageOptions())
parser.add_category(BasilOptions())
parser.add_category(GenericOptions())
options, _ = parser.parse_args(sys.argv)
if not options.output:
options.output = "basil"
if not options.asldata:
sys.stderr.write("Input file not specified\n")
parser.print_help()
sys.exit(1)
asldata = AslImage(options.asldata, **parser.filter(options, "image"))
wsp = Workspace(savedir=options.output, **vars(options))
wsp.asldata = asldata
# Deal with --artonly
if wsp.artonly:
wsp.infertiss = False
wsp.inferart = True
# Adjust number of iterations based on fast option
if not wsp.fast:
num_iter, num_trials, onestep = 20, 10, False
elif wsp.fast == 1:
num_iter, num_trials, onestep = 5, 2, False
elif wsp.fast == 2:
num_iter, num_trials, onestep = 10, 5, True
else:
raise ValueError("Not a valid option for fast: %s" % str(wsp.fast))
wsp.max_iterations = num_iter
wsp.max_trials = num_trials
wsp.onestep = onestep
# Run BASIL processing, passing options as keyword arguments using **
basil(wsp)
except ValueError as exc:
sys.stderr.write("\nERROR: " + str(exc) + "\n")
sys.stderr.write("Use --help for usage information\n")
sys.exit(1)
