def test_citation():
from sys import stdout
t = mh.citation(False)
assert len(stdout.getvalue()) == 0
t2 = mh.citation(True)
assert len(stdout.getvalue()) != 0
assert t == t2
def test_citation():
from sys import stdout
t = mh.citation(False)
assert len(stdout.getvalue()) == 0
t2 = mh.citation(True)
assert len(stdout.getvalue()) != 0
assert t == t2
def main():
sys.stderr.write(mh.citation(print_out=False, short=True))
sys.stderr.write('\n\n')
parser = argparse.ArgumentParser(
description='Compute features using mahotas')
parser.add_argument('fnames',
metavar='input_file_name',
nargs='+',
type=str,
help='Image files names')
parser.add_argument('--output',
default='features.tsv',
type=str,
help='Output file for feature files')
parser.add_argument('--clobber',
default=False,
action='store_true',
help='Overwrite output file (if it exists)')
parser.add_argument(
'--convert-to-bw',
default='no',
help=
'Convert color images to greyscale.\nAcceptable values:\n\tno: raises an error (default)'
+ '\n\tmax: use max projection' + '\n\tyes: use rgb2gray')
parser.add_argument(
'--no-color',
default=False,
action='store_true',
help='Do not print in color (for error and warning messages)')
parser.add_argument('--haralick',
default=False,
action='store_true',
help='Compute Haralick features')
parser.add_argument('--lbp',
default=False,
action='store_true',
help='Compute LBP (linear binary patterns) features')
parser.add_argument('--lbp-radius',
default=8,
action='store',
type=int,
help='Radius to use for LBP features')
parser.add_argument('--lbp-points',
default=6,
action='store',
type=int,
help='Nr of points to use for LBP features')
args = parser.parse_args()
if not (args.haralick or args.lbp):
sys.stderr.write('''\
No features selected. Doing nothing.
For example, use --haralick switch to compute Haralick features\n''')
sys.exit(1)
if not args.clobber and path.exists(args.output):
print_error(
'Output file ({}) already exists. Refusing to overwrite results without --clobber argument.'
.format(args.output))
sys.exit(2)
output = open(args.output, 'w')
colnames = []
if args.haralick:
hlabels = mh.features.texture.haralick_labels[:-1]
colnames.extend(["mean:{}".format(ell) for ell in hlabels])
colnames.extend(["ptp:{}".format(ell) for ell in hlabels])
if args.lbp:
from mahotas.features.lbp import lbp_names
colnames.extend(lbp_names(args.lbp_radius, args.lbp_points))
_write_row(output, colnames)
for fname in args.fnames:
cur = []
im = read_bw(fname, args)
if args.haralick:
har = mh.features.haralick(im, return_mean_ptp=True)
cur.append(har)
if args.lbp:
cur.append(mh.features.lbp(im, args.lbp_radius, args.lbp_points))
_write_row(output, chain.from_iterable(cur), fname)
output.close()
def main():
sys.stderr.write(mh.citation(print_out=False, short=True))
sys.stderr.write('\n\n')
parser = argparse.ArgumentParser(
description='Compute features using mahotas')
parser.add_argument(
'fnames', metavar='input_file_name', nargs='+', type=str,
help='Image files names')
parser.add_argument(
'--output', default='features.tsv', type=str,
help='Output file for feature files')
parser.add_argument(
'--clobber', default=False, action='store_true',
help='Overwrite output file (if it exists)')
parser.add_argument(
'--convert-to-bw', default='no',
help='Convert color images to greyscale.\nAcceptable values:\n\tno: raises an error (default)' +
'\n\tmax: use max projection' +
'\n\tyes: use rgb2gray')
parser.add_argument(
'--no-color', default=False, action='store_true',
help='Do not print in color (for error and warning messages)')
parser.add_argument(
'--haralick', default=False, action='store_true',
help='Compute Haralick features')
parser.add_argument(
'--lbp', default=False, action='store_true',
help='Compute LBP (linear binary patterns) features')
parser.add_argument(
'--lbp-radius', default=8, action='store', type=int,
help='Radius to use for LBP features')
parser.add_argument(
'--lbp-points', default=6, action='store', type=int,
help='Nr of points to use for LBP features')
args = parser.parse_args()
if not (args.haralick or args.lbp):
sys.stderr.write('''\
No features selected. Doing nothing.
For example, use --haralick switch to compute Haralick features\n''')
sys.exit(1)
if not args.clobber and path.exists(args.output):
print_error('Output file ({}) already exists. Refusing to overwrite results without --clobber argument.'.format(args.output))
sys.exit(2)
output = open(args.output, 'w')
colnames = []
if args.haralick:
hlabels = mh.features.texture.haralick_labels[:-1]
colnames.extend(["mean:{}".format(ell) for ell in hlabels])
colnames.extend(["ptp:{}".format(ell) for ell in hlabels])
if args.lbp:
from mahotas.features.lbp import lbp_names
colnames.extend(lbp_names(args.lbp_radius, args.lbp_points))
_write_row(output, colnames)
for fname in args.fnames:
cur = []
im = read_bw(fname, args)
if args.haralick:
har = mh.features.haralick(im, return_mean_ptp=True)
cur.append(har)
if args.lbp:
cur.append(mh.features.lbp(im, args.lbp_radius, args.lbp_points))
_write_row(output, chain.from_iterable(cur), fname)
output.close()
