def define_pixel_sizes(args):
"""
Defines the pixel sizes based on metadata file, or CLI flags
:param args: amap argument object
:return: args updated
"""
if None in [args.x_pixel_um, args.y_pixel_um, args.z_pixel_um]:
if args.metadata is None:
raise CommandLineInputError(
"Not all pixel sizes are defined on the command line, but "
"no metadata file has been supplied")
try:
metadata = get_acquisition_metadata(args.metadata)
except NotImplementedError:
raise CommandLineInputError(
"Not all pixel sizes are defined on the command line, but the"
" metadata file cannot be read.")
for dim in ["x", "y", "z"]:
dim_attribute = "{}_pixel_um".format(dim)
if getattr(args, dim_attribute) is None:
try:
setattr(args, dim_attribute, getattr(metadata, dim_attribute))
except ArgumentTypeError:
raise CommandLineInputError(
"No {} pixel size was defined on the command line, and it "
"cannot be parsed from the metadata".format(dim))
return args
def check_signal_overlap(signal_ids):
signal_unique, repeated_signal_ch = tools.check_unique_list(signal_ids)
if not signal_unique:
logging.error(
"Non-unique values for '--signal-channel-ids' ({}) given. ID:"
" {} given more than once.".format(signal_ids, repeated_signal_ch))
raise CommandLineInputError(
"Non-unique values for '--signal-channel-ids' ({}) given. ID:"
" {} given more than once.".format(signal_ids, repeated_signal_ch))
def check_correct_number_signal_channels(signal_ids, num_signal_channels):
num_signal_ids = len(signal_ids)
if num_signal_channels != num_signal_ids:
logging.error(
"Number of signal channel IDs ({}) does not match the number of "
"signal channels ({})".format(num_signal_ids, num_signal_channels))
raise CommandLineInputError(
"Number of signal channel IDs ({}) does not match the number of "
"signal channels ({})".format(num_signal_ids, num_signal_channels))
def xml_scale(
xml_file,
x_scale=1,
y_scale=1,
z_scale=1,
output_directory=None,
integer=True,
):
# TODO: add a csv option
"""
To rescale the cell positions within an XML file. For compatibility with
other software, or if data has been scaled after cell detection.
:param xml_file: Any cellfinder xml file
:param x_scale: Rescaling factor in the first dimension
:param y_scale: Rescaling factor in the second dimension
:param z_scale: Rescaling factor in the third dimension
:param output_directory: Directory to save the rescaled XML file.
Defaults to the same directory as the input XML file
:param integer: Force integer cell positions (default: True)
:return:
"""
if x_scale == y_scale == z_scale == 1:
raise CommandLineInputError(
"All rescaling factors are 1, " "please check the input."
)
else:
input_file = Path(xml_file)
start_time = datetime.now()
cells = cell_io.get_cells(xml_file)
for cell in cells:
cell.transform(
x_scale=x_scale,
y_scale=y_scale,
z_scale=z_scale,
integer=integer,
)
if output_directory:
output_directory = Path(output_directory)
else:
output_directory = input_file.parent
ensure_directory_exists(output_directory)
output_filename = output_directory / (input_file.stem + "_rescaled")
output_filename = output_filename.with_suffix(input_file.suffix)
cell_io.save_cells(cells, output_filename)
print(
"Finished. Total time taken: {}".format(
datetime.now() - start_time
)
)
def catch_input_file_error(path):
"""
Catches if an input path doesn't exist, and returns an informative error
:param path: Input file path
default)
"""
try:
check_path_exists(path)
except FileNotFoundError:
message = ("File path: '{}' cannot be found. Please check your input "
"arguments.".format(path))
raise CommandLineInputError(message)
def check_sig_bg_id_overlap(signal_ids, background_id):
common_id_result, intersection = tools.common_member(
signal_ids, background_id)
if common_id_result:
logging.error(
"Non-unique values for '--signal-channel-ids' ({}) and for "
"'--background-channel-id' ({}) given. ID: {} was given in"
" both.".format(signal_ids, background_id, intersection))
raise CommandLineInputError(
"Non-unique values for '--signal-channel-ids' ({}) and for "
"'--background-channel-id' ({}) given. ID: {} was given in"
" both.".format(signal_ids, background_id, intersection))