def main():
"""
Entry point for command line tool
"""
try:
parser = AslOptionParser(usage="asl_mask -i <asl_image> [options...]",
version=__version__)
parser.add_option("--calib",
"-c",
help="Calibration image",
default=None)
parser.add_option(
"--use-pwi",
help=
"Use the perfusion weighted average rather than the timeseries mean",
action="store_true",
default=False)
parser.add_category(image.AslImageOptions())
parser.add_category(struc.StructuralImageOptions())
parser.add_category(GenericOptions())
options, _ = parser.parse_args(sys.argv)
options.mask = None # No point in using command line tool if you already have a mask!
wsp = Workspace(**vars(options))
if not options.asldata:
sys.stderr.write("Input file not specified\n")
parser.print_help()
sys.exit(1)
wsp.asldata = AslImage(wsp.asldata,
**parser.filter(vars(options), "image"))
wsp.asldata.summary()
wsp.generate_mask()
if wsp.output is None:
wsp.output = wsp.asldata.name + "_mask"
wsp.rois.mask.save(wsp.output)
except ValueError as exc:
sys.stderr.write("ERROR: " + str(exc) + "\n")
sys.exit(1)
def main():
"""
Entry point for oxasl_calib command line program
"""
debug = False
try:
parser = AslOptionParser(
usage=
"oxasl_calib -i <perfusion image> -c <calibration image> --calib-method <voxelwise|refregion> -o <output filename> [options]"
)
parser.add_category(CalibOptions())
parser.add_category(GenericOptions(output_type="file"))
options, _ = parser.parse_args(sys.argv)
if not options.perf:
sys.stderr.write("Perfusion input file not specified\n")
parser.print_help()
sys.exit(1)
if not options.calib:
sys.stderr.write("Calibration input file not specified\n")
parser.print_help()
sys.exit(1)
wsp = Workspace(**vars(options))
summary(wsp.perf)
summary(wsp.calib)
if wsp.output is None:
wsp.output = "%s_calib" % wsp.perf.name
calibrated_img = calibrate(wsp, wsp.perf)
summary(calibrated_img)
calibrated_img.save(wsp.output)
except ValueError as exc:
sys.stderr.write("ERROR: " + str(exc) + "\n")
if debug:
traceback.print_exc()
sys.exit(1)
