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) != 1:
raise ValueError('Only a single PCA contour can be plotted at a time -- please specify only one model file on the command line.')
pca_contour = contour_class.from_file(args[0], contour_class.PCAContour)
if not options.output_file:
output_file = pca_contour.simple_name()+'.svg'
else:
output_file = options.output_file
plot_tools.pca_modes_plot(pca_contour, output_file, modes=options.modes,
positions=options.positions, scale=options.scale)
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 _get_contours_and_images(filenames, show_progress = True):
contours = []
image_names = []
if show_progress:
filenames = terminal_tools.progress_list(filenames, 'Loading Contours and Images')
for filename in filenames:
filename = path.path(filename)
if not filename.exists():
raise ValueError('File "%s" does not exist.'%filename)
try:
freeimage.read_metadata(filename)
image_names.append(filename)
except IOError as e:
# print e
# print Image.ID
try:
contours.append(contour_class.from_file(filename))
except IOError as e:
# print e
raise ValueError('Could not open file "%s" as an image or a contour.'%filename)
return contours, image_names
def _get_contours_and_images(filenames, show_progress=True):
contours = []
image_names = []
if show_progress:
filenames = terminal_tools.progress_list(
filenames, 'Loading Contours and Images')
for filename in filenames:
filename = path.path(filename)
if not filename.exists():
raise ValueError('File "%s" does not exist.' % filename)
try:
Image.open(filename)
image_names.append(filename)
except IOError, e:
# print e
# print Image.ID
try:
contours.append(contour_class.from_file(filename))
except IOError, e:
# print e
raise ValueError(
'Could not open file "%s" as an image or a contour.' %
filename)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
data_files = []
new_args = []
for arg in args:
if type(arg) == list:
data_files.append(arg)
else:
new_args.append(arg)
args = cli_tools.glob_args(new_args)
if len(args) + len(data_files) == 0:
raise ValueError('Some data files (and optionally contour files, for 2D plots) must be specified!')
# if the x, y, and name columns are convertible to integers, do so and
# then convert them from 1-indexed to 0-indexed
try:
options.name_column = int(options.name_column)
options.name_column -= 1
except:
pass
try:
options.x_column = int(options.x_column)
options.x_column -= 1
except:
pass
try:
options.y_column = int(options.y_column)
options.y_column -= 1
except:
pass
contours = {}
if options.show_progress:
args = terminal_tools.progress_list(args, "Reading input data and contours")
for arg in args:
contour = None
try:
contour = contour_class.from_file(arg)
except:
data_files.append(arg)
if contour is not None:
contours[contour.simple_name()] = contour
if len(data_files) == 0:
raise ValueError('No data files were specified!')
headers, data_ranges, data_names, data_files, row_ranges = get_data(data_files)
if not options.x_title:
if isinstance(options.x_column, int):
try: options.x_title = headers[0][options.x_column]
except: pass
else:
options.x_title = options.x_column
if options.y_column is not None:
# make scatterplot
if not options.y_title:
if isinstance(options.y_column, int):
try: options.y_title = headers[0][options.y_column]
except: pass
else:
options.y_title = options.y_column
contour_groups = get_contour_groups(data_ranges, contours, data_files, row_ranges, options.name_column, options.x_column, options.y_column)
if numpy.alltrue([len(cg)==0 for cg in contour_groups]):
raise RuntimeError('No contours found for data rows specified (perhaps the names mismatch or there were no data rows?).')
plot_tools.contour_scatterplot(contour_groups, options.output_file, options.scale,
(options.x_title, options.y_title), options.title, names=data_names,
axes_at_origin=options.axes_at_origin, fix_xrange=(options.x_min, options.x_max),
fix_yrange=(options.y_min, options.y_max), show_contour_axes=options.contour_axes,
show_progress=options.show_progress)
else:
data_groups = [[row[options.x_column] for row in data_range] for data_range in data_ranges]
plot_tools.distribution_plot(data_groups, options.output_file, options.x_title,
options.title, names=data_names, axes_at_origin=options.axes_at_origin,
fix_xrange=(options.x_min, options.x_max))
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
data_files = []
new_args = []
for arg in args:
if type(arg) == list:
data_files.append(arg)
else:
new_args.append(arg)
args = cli_tools.glob_args(new_args)
if len(args) + len(data_files) == 0:
raise ValueError(
'Some data files (and optionally contour files, for 2D plots) must be specified!'
)
# if the x, y, and name columns are convertible to integers, do so and
# then convert them from 1-indexed to 0-indexed
try:
options.name_column = int(options.name_column)
options.name_column -= 1
except:
pass
try:
options.x_column = int(options.x_column)
options.x_column -= 1
except:
pass
try:
options.y_column = int(options.y_column)
options.y_column -= 1
except:
pass
contours = {}
if options.show_progress:
args = terminal_tools.progress_list(args,
"Reading input data and contours")
for arg in args:
contour = None
try:
contour = contour_class.from_file(arg)
except:
data_files.append(arg)
if contour is not None:
contours[contour.simple_name()] = contour
if len(data_files) == 0:
raise ValueError('No data files were specified!')
headers, data_ranges, data_names, data_files, row_ranges = get_data(
data_files)
if not options.x_title:
if isinstance(options.x_column, int):
try:
options.x_title = headers[0][options.x_column]
except:
pass
else:
options.x_title = options.x_column
if options.y_column is not None:
# make scatterplot
if not options.y_title:
if isinstance(options.y_column, int):
try:
options.y_title = headers[0][options.y_column]
except:
pass
else:
options.y_title = options.y_column
contour_groups = get_contour_groups(data_ranges, contours, data_files,
row_ranges, options.name_column,
options.x_column, options.y_column)
if numpy.alltrue([len(cg) == 0 for cg in contour_groups]):
raise RuntimeError(
'No contours found for data rows specified (perhaps the names mismatch or there were no data rows?).'
)
plot_tools.contour_scatterplot(contour_groups,
options.output_file,
options.scale,
(options.x_title, options.y_title),
options.title,
names=data_names,
axes_at_origin=options.axes_at_origin,
fix_xrange=(options.x_min,
options.x_max),
fix_yrange=(options.y_min,
options.y_max),
show_contour_axes=options.contour_axes,
show_progress=options.show_progress)
else:
data_groups = [[row[options.x_column] for row in data_range]
for data_range in data_ranges]
plot_tools.distribution_plot(data_groups,
options.output_file,
options.x_title,
options.title,
names=data_names,
axes_at_origin=options.axes_at_origin,
fix_xrange=(options.x_min, options.x_max))
