def main():
parser = ArgumentParser(description=DESCRIP,
epilog=EPILOG,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('filename', type=str,
help='4D image filename')
parser.add_argument('--out-path', type=str,
help='path for output image files')
parser.add_argument('--out-fname-label', type=str,
help='mid part of output image filenames')
parser.add_argument('--ncomponents', type=int, default=10,
help='number of PCA components to write')
# parse the command line
args = parser.parse_args()
# process inputs
filename = args.filename
out_path = args.out_path
out_root = args.out_fname_label
ncomps = args.ncomponents
# collect extension for output images
froot, ext, gz = splitext_addext(filename)
pth, fname = os.path.split(froot)
if out_path is None:
out_path = pth
if out_root is None:
out_root = fname
img = nipy.load_image(filename)
res = nads.screen(img, ncomps)
nads.write_screen_res(res, out_path, out_root, ext + gz)
def main():
parser = ArgumentParser(description=DESCRIP,
epilog=EPILOG,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('examples_path', type=str,
help='filename of example or directory containing '
'examples to run')
parser.add_argument('--log-path', type=str, default='',
help='path for output logs (default is cwd)')
parser.add_argument('--excludex', type=str, action='append', default=[],
help='regex for files to exclude (add more than one '
'--excludex option for more than one regex filter')
args = parser.parse_args()
# Proc runner
eg_path = abspath(expanduser(args.examples_path))
if args.log_path == '':
log_path = abspath(os.getcwd())
else:
log_path = abspath(expanduser(args.log_path))
excludexes = [re.compile(s) for s in args.excludex]
if isfile(eg_path): # example was a file
proc_logger = PyProcLogger(log_path=log_path,
working_path=dirname(eg_path))
print("Running " + eg_path)
stdout, stderr, code = proc_logger.run_pipes(eg_path)
print('==== Stdout ====')
print(stdout)
print('==== Stderr ====')
print(stderr)
sys.exit(code)
# Multi-run with logging to file
proc_logger = PyProcLogger(log_path=log_path,
working_path=eg_path)
fails = 0
with open(pjoin(log_path, 'summary.txt'), 'wt') as f:
for dirpath, dirnames, filenames in os.walk(eg_path):
for fname in filenames:
full_fname = pjoin(dirpath, fname)
if fname.endswith(".py"):
print(fname, end=': ')
sys.stdout.flush()
for excludex in excludexes:
if excludex.search(fname):
_record('SKIP', fname, f)
break
else: # run test
cmd_name = full_fname.replace(eg_path + psep, '')
cmd_name = cmd_name.replace(psep, '-')
code = proc_logger(cmd_name, full_fname, cwd=dirpath)
if code == 0:
_record('OK', fname, f)
else:
fails += 1
_record('FAIL', fname, f)
sys.exit(fails if fails < 255 else 255)
parser = ArgumentParser(description=description)
parser.add_argument('img', metavar='img', nargs='+', help='input image')
parser.add_argument('--mask', dest='mask', help='mask image')
parser.add_argument('--niters', dest='niters',
help='number of iterations (default=%d)' % 25)
parser.add_argument('--beta', dest='beta',
help='Markov random field beta parameter (default=%f)' % 0.5)
parser.add_argument('--ngb_size', dest='ngb_size',
help='Markov random field neighborhood system (default=%d)' % 6)
parser.add_argument('--probc', dest='probc', help='csf probability map')
parser.add_argument('--probg', dest='probg',
help='gray matter probability map')
parser.add_argument('--probw', dest='probw',
help='white matter probability map')
args = parser.parse_args()
def get_argument(dest, default):
val = args.__getattribute__(dest)
if val is None:
return default
else:
return val
# Input image
img = load_image(args.img[0])
# Input mask image
mask_img = get_argument('mask', None)
if mask_img is None:
parser.add_argument('--beta',
dest='beta',
help='Markov random field beta parameter (default=%f)' %
0.5)
parser.add_argument(
'--ngb_size',
dest='ngb_size',
help='Markov random field neighborhood system (default=%d)' % 6)
parser.add_argument('--probc', dest='probc', help='csf probability map')
parser.add_argument('--probg',
dest='probg',
help='gray matter probability map')
parser.add_argument('--probw',
dest='probw',
help='white matter probability map')
args = parser.parse_args()
def get_argument(dest, default):
val = args.__getattribute__(dest)
if val is None:
return default
else:
return val
# Input image
img = load_image(args.img[0])
# Input mask image
mask_img = get_argument('mask', None)
