def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(filenames, show_progress = options.show_progress)
if options.first_point is not None:
options.first_point -= 1
if options.scale is not None or options.rotate is not None or options.units is not None or options.first_point is not None:
in_radians = False
if options.units is not None and options.units.lower() in ('um', 'micron', 'microns'):
options.units = '\N{MICRO SIGN}m'
contours = simple_interface.transform_contours(contours, options.scale, options.rotate, in_radians,
options.units, options.first_point, options.show_progress, title = 'Modifying Contours')
if options.weights is not None:
contours = simple_interface.reweight_landmarks(contours, options.weights, options.show_progress)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(
filenames, show_progress=options.show_progress)
if options.reference is not None:
reference = contour_class.from_file(options.reference)
contours = simple_interface.align_contours_to(
contours,
reference,
align_steps=options.alignment_steps,
allow_reflection=options.allow_reflection,
show_progress=options.show_progress)
else:
contours = simple_interface.align_contours(
contours,
options.alignment_steps,
options.allow_reflection,
max_iters=options.max_iterations,
show_progress=options.show_progress)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour and image files must be specified!')
intensity_ranges = []
for r in options.intensity_ranges:
try:
low, high = r
except:
low = high = r
intensity_ranges.append([low, high])
if options.weights is None or len(options.weights) == 0:
options.weights = [0.5]
elif len(options.weights) != 1 and len(options.weights) != len(intensity_ranges):
raise optparse.OptionValueError("Either one or %d weights are required; %d sepcified."%(len(intensity_ranges), len(options.weights)))
elif sum(options.weights) > 1:
raise optparse.OptionValueError("The sum of the weights must be <= 1.")
matches = match_files.match_contours_and_images(args, options.match_by_name, options.show_progress)
contours, image_names, unmatched_contours, unmatched_image_names = matches
filenames = [path.path(contour._filename) for contour in contours]
contours = simple_interface.add_image_landmarks_to_contours(contours, image_names,
intensity_ranges, options.weights, options.image_type, options.show_progress)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some image files must be specified!')
filenames = [path.path(arg) for arg in args]
contours_groups = simple_interface.extract_contours(
filenames, options.contour_value, options.min_area, options.max_area,
options.show_progress)
contours = []
names = []
destination = path.path(options.destination)
destination.makedirs_p()
for contour_group, image_name in zip(contours_groups, filenames):
num_contours = len(contour_group)
if num_contours == 1:
contours.append(contour_group[0])
# note that with path objects, the '/' operator means 'join path components.'
names.append(destination / image_name.namebase + '.contour')
contour_group[0]._filename = image_name.namebase
else:
width = len(str(num_contours))
for i, contour in enumerate(contour_group):
contours.append(contour)
names.append(destination / image_name.namebase +
'-%.*d.contour' % (width, i + 1))
contour._filename = image_name.namebase + '-%.*d' % (width,
i + 1)
if options.scale is not None:
# if not rescaling, contours are already denominated in pixels, so do nothing.
units = options.units
if units.lower() in ('um', 'micron', 'microns'):
units = '\N{MICRO SIGN}m'
contours = simple_interface.transform_contours(
contours,
scale_factor=options.scale,
units=units,
show_progress=options.show_progress,
title='Rescaling Contours')
if options.resample:
contours = simple_interface.resample_contours(contours,
options.resample_points,
options.smoothing_factor,
options.show_progress)
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(filenames, show_progress = options.show_progress)
if options.endpoints is None:
endpoints = options.endpoint_method
else:
endpoints = options.endpoints
contours = simple_interface.find_centerlines(contours, options.axis_points, endpoints, options.show_progress)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(filenames, show_progress = options.show_progress)
if options.reference is not None:
reference = contour_class.from_file(options.reference)
contours = simple_interface.align_contours_to(contours, reference, align_steps=options.alignment_steps,
allow_reflection=options.allow_reflection, show_progress=options.show_progress)
else:
contours = simple_interface.align_contours(contours, options.alignment_steps, options.allow_reflection,
max_iters=options.max_iterations, show_progress = options.show_progress)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(
filenames, show_progress=options.show_progress)
if options.first_point is not None:
options.first_point -= 1
if options.scale is not None or options.rotate is not None or options.units is not None or options.first_point is not None:
in_radians = False
if options.units is not None and options.units.lower() in ('um',
'micron',
'microns'):
options.units = u'\N{MICRO SIGN}m'
contours = simple_interface.transform_contours(
contours,
options.scale,
options.rotate,
in_radians,
options.units,
options.first_point,
options.show_progress,
title='Modifying Contours')
if options.weights is not None:
contours = simple_interface.reweight_landmarks(contours,
options.weights,
options.show_progress)
destination = path.path(options.destination)
if not destination.exists():
destination.makedirs()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour and image files must be specified!')
intensity_ranges = []
for r in options.intensity_ranges:
try:
low, high = r
except:
low = high = r
intensity_ranges.append([low, high])
if options.weights is None or len(options.weights) == 0:
options.weights = [0.5]
elif len(options.weights) != 1 and len(
options.weights) != len(intensity_ranges):
raise optparse.OptionValueError(
"Either one or %d weights are required; %d sepcified." %
(len(intensity_ranges), len(options.weights)))
elif sum(options.weights) > 1:
raise optparse.OptionValueError("The sum of the weights must be <= 1.")
matches = match_files.match_contours_and_images(args,
options.match_by_name,
options.show_progress)
contours, image_names, unmatched_contours, unmatched_image_names = matches
filenames = [path.path(contour._filename) for contour in contours]
contours = simple_interface.add_image_landmarks_to_contours(
contours, image_names, intensity_ranges, options.weights,
options.image_type, options.show_progress)
destination = path.path(options.destination)
if not destination.exists():
destination.makedirs()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some image files must be specified!')
filenames = [path.path(arg) for arg in args]
contours_groups = simple_interface.extract_contours(filenames, options.contour_value,
options.min_area, options.max_area, options.show_progress)
contours = []
names = []
destination = path.path(options.destination)
destination.makedirs_p()
for contour_group, image_name in zip(contours_groups, filenames):
num_contours = len(contour_group)
if num_contours == 1:
contours.append(contour_group[0])
# note that with path objects, the '/' operator means 'join path components.'
names.append(destination / image_name.namebase + '.contour')
contour_group[0]._filename = image_name.namebase
else:
width = len(str(num_contours))
for i, contour in enumerate(contour_group):
contours.append(contour)
names.append(destination / image_name.namebase + '-%.*d.contour'%(width, i+1))
contour._filename = image_name.namebase + '-%.*d'%(width, i+1)
if options.scale is not None:
# if not rescaling, contours are already denominated in pixels, so do nothing.
units = options.units
if units.lower() in ('um', 'micron', 'microns'):
units = '\N{MICRO SIGN}m'
contours = simple_interface.transform_contours(contours, scale_factor=options.scale,
units=units, show_progress=options.show_progress, title='Rescaling Contours')
if options.resample:
contours = simple_interface.resample_contours(contours, options.resample_points, options.smoothing_factor, options.show_progress)
simple_interface.save_contours(contours, names, options.show_progress)
