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!')
contours = simple_interface.load_contours(args, show_progress = options.show_progress)
if options.grid:
contours = simple_interface.grid_contours(contours)
# Transform (begin, end) from a one-indexed, inclusive range (normal for humans)
# to a zero-indexed inclusive range.
if options.begin is not None:
options.begin -= 1
if options.end is not None:
options.end -= 1
if options.color_by == 'none':
gradient_factory = None
else:
gradient_factory = plot_tools.default_gradient
if options.color_by == 'points' or options.begin or options.end or options.label_points:
# do point ordering plot
colorbar = options.color_by == 'points'
color_by_point = options.color_by == 'points'
# use a color bar if we're doing a gradient
plot_tools.point_order_plot(contours, options.output_file, plot_title=options.title,
label_points=options.label_points, colorbar=colorbar, begin=options.begin,
end=options.end, gradient_factory=gradient_factory, color_by_point=color_by_point,
scale=options.scale, show_progress=options.show_progress)
else:
plot_tools.contour_plot(contours, options.output_file, plot_title=options.title,
gradient_factory=gradient_factory, scale=options.scale, show_progress=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 = '\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 options.help:
print_help()
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
contours = simple_interface.load_contours(args, show_progress = options.show_progress)
measurements = [m(**kws) for m, kws in options.measurements]
header, rows = simple_interface.measure_contours(contours, options.show_progress, *measurements)
datafile.write_data_file([header]+rows, options.output_file)
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!')
contours = simple_interface.load_contours(args, show_progress = options.show_progress)
shape_model, header, rows, norm_header, norm_rows = simple_interface.make_shape_model(contours, options.variance_explained)
shape_model.to_file(options.output_prefix + '.contour')
if options.write_data:
datafile.write_data_file([header]+rows, options.output_prefix + '-positions.csv')
datafile.write_data_file([norm_header]+norm_rows, options.output_prefix + '-normalized-positions.csv')
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)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.namebase + '.mat' for filename in filenames]
simple_interface.save_contour_data_for_matlab(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 options.help:
print_help()
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
contours = simple_interface.load_contours(
args, show_progress=options.show_progress)
measurements = [m(**kws) for m, kws in options.measurements]
header, rows = simple_interface.measure_contours(contours,
options.show_progress,
*measurements)
datafile.write_data_file([header] + rows, options.output_file)
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)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [
destination / filename.namebase + '.mat' for filename in filenames
]
simple_interface.save_contour_data_for_matlab(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!')
contours = simple_interface.load_contours(
args, show_progress=options.show_progress)
if options.grid:
contours = simple_interface.grid_contours(contours)
# Transform (begin, end) from a one-indexed, inclusive range (normal for humans)
# to a zero-indexed inclusive range.
if options.begin is not None:
options.begin -= 1
if options.end is not None:
options.end -= 1
if options.color_by == 'none':
gradient_factory = None
else:
gradient_factory = plot_tools.default_gradient
if options.color_by == 'points' or options.begin or options.end or options.label_points:
# do point ordering plot
colorbar = options.color_by == 'points'
color_by_point = options.color_by == 'points'
# use a color bar if we're doing a gradient
plot_tools.point_order_plot(contours,
options.output_file,
plot_title=options.title,
label_points=options.label_points,
colorbar=colorbar,
begin=options.begin,
end=options.end,
gradient_factory=gradient_factory,
color_by_point=color_by_point,
scale=options.scale,
show_progress=options.show_progress)
else:
plot_tools.contour_plot(contours,
options.output_file,
plot_title=options.title,
gradient_factory=gradient_factory,
scale=options.scale,
show_progress=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)
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 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)
