def main(args=sys.argv[1:]):
args = parse_args(args)
if args.output is None:
get_tiff_dims(input_glob_or_list=args.input,
print_out=True)
else:
if args.x_pixels or args.y_pixels or args.z_pixels:
x_dim, y_dim, z_dim = get_tiff_dims(args.input, print_out=False)
crop_xyz = parse_crop_dims_str(args.crop_x, args.crop_y, args.crop_z)
crop_x, crop_y, crop_z = validate_tiff_crop_dims(x_dim, y_dim, z_dim, *crop_xyz)
if args.x_pixels:
args.scale_x = float(args.x_pixels) / (crop_x[1] - crop_x[0] + 1)
if args.y_pixels:
args.scale_y = float(args.y_pixels) / (crop_y[1] - crop_y[0] + 1)
if args.z_pixels:
args.scale_z = float(args.z_pixels) / (crop_z[1] - crop_z[0] + 1)
transform_tiff(input_glob_or_list=args.input,
output_path=args.output,
crop_x=args.crop_x,
crop_y=args.crop_y,
crop_z=args.crop_z,
flip_x=args.flip_x,
flip_y=args.flip_y,
flip_z=args.flip_z,
scale_x=args.scale_x,
scale_y=args.scale_y,
scale_z=args.scale_z,
split_output=args.split_output,
start_num=args.start_num,
num_digits=args.num_digits)
def main(args=sys.argv[1:]):
args = parse_args(args)
if args.output is None:
num_tuples = get_num_coords(input_path=args.input)
print("JSON file at {} has {} coordinate tuples".format(
args.input, num_tuples))
else:
if args.x_pixels or args.y_pixels or args.z_pixels:
x_dim, y_dim, z_dim = get_tiff_dims(args.original_tiff,
print_out=False)
crop_xyz = parse_crop_dims_str(args.crop_x, args.crop_y,
args.crop_z)
crop_x, crop_y, crop_z = validate_tiff_crop_dims(
x_dim, y_dim, z_dim, *crop_xyz)
if args.x_pixels:
args.scale_x = float(
args.x_pixels) / (crop_x[1] - crop_x[0] + 1)
if args.y_pixels:
args.scale_y = float(
args.y_pixels) / (crop_y[1] - crop_y[0] + 1)
if args.z_pixels:
args.scale_z = float(
args.z_pixels) / (crop_z[1] - crop_z[0] + 1)
transform_json(input_path=args.input,
output_path=args.output,
crop_x=args.crop_x,
crop_y=args.crop_y,
crop_z=args.crop_z,
flip_x=args.flip_x,
flip_y=args.flip_y,
flip_z=args.flip_z,
scale_x=args.scale_x,
scale_y=args.scale_y,
scale_z=args.scale_z,
original_tiff=args.original_tiff)
def transform_tiff(input_glob_or_list: Union[str, List[str]],
output_path: str,
crop_x: Union[str, List[int], Tuple[int, int]] = None,
crop_y: Union[str, List[int], Tuple[int, int]] = None,
crop_z: Union[str, List[int], Tuple[int, int]] = None,
flip_x: bool = False,
flip_y: bool = False,
flip_z: bool = False,
scale_x: float = 1,
scale_y: float = 1,
scale_z: float = 1,
split_output: bool = False,
start_num: int = 0,
num_digits: int = None) -> None:
"""Main function for cropping tiffs
Note: progress bars not particularly accurate for inputs with very large tiff files due to
IO-limited multiprocessing and how the jobs are queued
Parameters
----------
input_glob_or_list : Union[str, List[str]]
String containing input glob or list of file paths to individual tiffs
output_path : str
Output file path, should either be a directory or tiff file, depending on the value of split_output
crop_x : Union[str, List[int], Tuple[int, int]]
String in format "[x_min,x_max]" or Sequence of ints in format [x_min, x_max] specifying the minimum
and maximum x-values (inclusive) to include in the outputted cropped tiff
crop_y : Union[str, List[int], Tuple[int, int]]
String in format "[y_min,y_max]" or Sequence of ints in format [y_min, y_max] specifying the minimum
and maximum y-values (inclusive) to include in the outputted cropped tiff
crop_z : Union[str, List[int], Tuple[int, int]]
String in format "[z_min,z_max]" or Sequence of ints in format [z_min, z_max] specifying the minimum
and maximum x-values (inclusive) to include in the outputted cropped tiff
flip_x : bool
Specify whether or not the output image should have its x-axis reversed after cropping
flip_y : bool
Specify whether or not the output image should have its y-axis reversed after cropping
flip_z : bool
Specify whether or not the output image should have its z-axis reversed after cropping
scale_x : float
Specify the scaling factor along the x-axis after cropping
scale_y : float
Specify the scaling factor along the y-axis after cropping
scale_z : float
Specify the scaling factor along the z-axis after cropping
split_output : bool
True if output should be a directory of 2D tiffs, False if output should be single multi-page tiff file
start_num : int
Number from which to start outputting in output TIFF stack
num_digits : int
Number of digits in output TIFF stack file names
Returns
-------
None
"""
tiff_paths = glob_to_list(input_glob_or_list)
# Ensures TIFF stack is outputted into a directory
if split_output:
if platform.system() == "Windows":
if output_path[-1] != "\\":
output_path += "\\"
elif platform.system() == "Linux" or platform.system == "Darwin":
if output_path[-1] != "/":
output_path += "/"
x_dim, y_dim, z_dim = get_tiff_dims(input_glob_or_list)
crop_x, crop_y, crop_z = parse_crop_dims_str(crop_x, crop_y, crop_z)
crop_x, crop_y, crop_z = validate_tiff_crop_dims(x_dim, y_dim, z_dim,
crop_x, crop_y, crop_z)
if num_digits is None:
num_digits = int(np.floor(np.log10(crop_z[1] - crop_z[0] + 1)) + 1)
if len(tiff_paths) == 1:
tiff_ndarray_reshape = reshape_single_tiff(tiff_paths[0])
transform_single_tiff(tiff_ndarray_reshape,
output_filepath=output_path,
output_tiff_stack=split_output,
crop_x=crop_x,
crop_y=crop_y,
crop_z=crop_z,
flip_x=flip_x,
flip_y=flip_y,
flip_z=flip_z,
scale_x=scale_x,
scale_y=scale_y,
scale_z=scale_z,
start_num=start_num,
num_digits=num_digits)
else:
transform_multi_tiff(tiff_paths,
output_filepath=output_path,
output_tiff_stack=split_output,
crop_x=crop_x,
crop_y=crop_y,
crop_z=crop_z,
flip_x=flip_x,
flip_y=flip_y,
flip_z=flip_z,
scale_x=scale_x,
scale_y=scale_y,
scale_z=scale_z,
start_num=start_num,
num_digits=num_digits)