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# pylint: disable=import-outside-toplevel |
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"""Console script for torchio.""" |
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import sys |
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import click |
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@click.command() |
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@click.argument('input-path', type=click.Path(exists=True)) |
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@click.argument('transform-name', type=str) |
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@click.argument('output-path', type=click.Path()) |
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@click.option( |
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'--kwargs', '-k', |
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type=str, |
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help='String of kwargs, e.g. "degrees=(-5,15) num_transforms=3".', |
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) |
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@click.option( |
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'--seed', '-s', |
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type=int, |
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help='Seed for PyTorch random number generator.', |
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) |
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@click.option( |
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'--verbose/--no-verbose', '-v', |
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type=bool, |
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default=False, |
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help='Print random transform parameters.', |
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) |
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def main( |
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input_path, |
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transform_name, |
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output_path, |
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kwargs, |
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seed, |
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verbose, |
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): |
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"""Apply transform to an image. |
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\b |
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Example: |
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$ torchio-transform -k "degrees=(-5,15) num_transforms=3" input.nrrd RandomMotion output.nii |
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""" |
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# Imports are placed here so that the tool loads faster if not being run |
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import torch |
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import torchio.transforms as transforms |
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from torchio.utils import apply_transform_to_file |
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try: |
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transform_class = getattr(transforms, transform_name) |
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except AttributeError as error: |
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message = f'Transform "{transform_name}" not found in torchio' |
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raise ValueError(message) from error |
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params_dict = get_params_dict_from_kwargs(kwargs) |
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transform = transform_class(**params_dict) |
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if seed is not None: |
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torch.manual_seed(seed) |
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apply_transform_to_file( |
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input_path, |
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transform, |
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output_path, |
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verbose=verbose, |
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) |
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return 0 |
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def get_params_dict_from_kwargs(kwargs): |
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from torchio.utils import guess_type |
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params_dict = {} |
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if kwargs is not None: |
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for substring in kwargs.split(): |
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try: |
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key, value_string = substring.split('=') |
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except ValueError as error: |
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message = f'Arguments string "{kwargs}" not valid' |
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raise ValueError(message) from error |
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value = guess_type(value_string) |
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params_dict[key] = value |
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return params_dict |
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if __name__ == '__main__': |
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# pylint: disable=no-value-for-parameter |
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sys.exit(main()) # pragma: no cover |
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fepegar /
torchio
