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from typing import Union, Sequence, List, Optional |
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import torch |
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import torchio |
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import numpy as np |
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from torchvision.transforms import Compose as PyTorchCompose |
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from ...data.subject import Subject |
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from ...utils import gen_seed |
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from .. import Transform |
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from . import RandomTransform |
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class Compose(Transform): |
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"""Compose several transforms together. |
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Args: |
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transforms: Sequence of instances of |
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:py:class:`~torchio.transforms.transform.Transform`. |
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p: Probability that this transform will be applied. |
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.. note:: |
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This is a thin wrapper of :py:class:`torchvision.transforms.Compose`. |
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""" |
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def __init__( |
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self, |
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transforms: Optional[Sequence[Transform]] = None, |
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p: float = 1, |
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): |
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super().__init__(p=p) |
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transforms = [] if transforms is None else transforms |
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self.transform = PyTorchCompose(transforms) |
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def __call__(self, data: Union[Subject, torch.Tensor, np.ndarray], seeds: List = None): |
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if not self.transform.transforms: |
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return data |
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if not seeds: |
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seeds = [gen_seed() for _ in range(len(self.transform.transforms))] |
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self.seeds = seeds |
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return super().__call__(data, seeds) |
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def apply_transform(self, sample: Subject): |
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for t, s in zip(self.transform.transforms, self.seeds): |
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sample = t(sample, s) |
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return sample |
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class OneOf(RandomTransform): |
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"""Apply only one of the given transforms. |
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Args: |
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transforms: Dictionary with instances of |
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:py:class:`~torchio.transforms.transform.Transform` as keys and |
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probabilities as values. Probabilities are normalized so they sum |
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to one. If a sequence is given, the same probability will be |
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assigned to each transform. |
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p: Probability that this transform will be applied. |
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Example: |
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>>> import torchio as tio |
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>>> colin = tio.datasets.Colin27() |
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>>> transforms_dict = { |
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... tio.RandomAffine(): 0.75, |
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... tio.RandomElasticDeformation(): 0.25, |
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... } # Using 3 and 1 as probabilities would have the same effect |
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>>> transform = torchio.transforms.OneOf(transforms_dict) |
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>>> transformed = transform(colin) |
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""" |
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def __init__( |
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self, |
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transforms: Union[dict, Sequence[Transform]], |
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p: float = 1, |
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): |
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super().__init__(p=p) |
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self.transforms_dict = self._get_transforms_dict(transforms) |
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def apply_transform(self, subject: Subject): |
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weights = torch.Tensor(list(self.transforms_dict.values())) |
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index = torch.multinomial(weights, 1) |
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transforms = list(self.transforms_dict.keys()) |
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transform = transforms[index] |
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transformed = transform(subject) |
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return transformed |
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def _get_transforms_dict(self, transforms: Union[dict, Sequence]): |
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if isinstance(transforms, dict): |
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transforms_dict = dict(transforms) |
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self._normalize_probabilities(transforms_dict) |
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else: |
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try: |
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p = 1 / len(transforms) |
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except TypeError as e: |
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message = ( |
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'Transforms argument must be a dictionary or a sequence,' |
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f' not {type(transforms)}' |
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) |
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raise ValueError(message) from e |
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transforms_dict = {transform: p for transform in transforms} |
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for transform in transforms_dict: |
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if not isinstance(transform, Transform): |
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message = ( |
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'All keys in transform_dict must be instances of' |
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f'torchio.Transform, not "{type(transform)}"' |
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) |
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raise ValueError(message) |
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return transforms_dict |
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@staticmethod |
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def _normalize_probabilities(transforms_dict: dict): |
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probabilities = np.array(list(transforms_dict.values()), dtype=float) |
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if np.any(probabilities < 0): |
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message = ( |
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'Probabilities must be greater or equal to zero,' |
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f' not "{probabilities}"' |
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) |
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raise ValueError(message) |
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if np.all(probabilities == 0): |
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message = ( |
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'At least one probability must be greater than zero,' |
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f' but they are "{probabilities}"' |
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) |
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raise ValueError(message) |
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for transform, probability in transforms_dict.items(): |
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transforms_dict[transform] = probability / probabilities.sum() |
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def compose_from_history(history: List): |
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""" |
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Builds a composition of transformations from a given subject history |
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:param history: subject history given as a list of tuples containing (transformation_name, transformation_parameters) |
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:return: Tuple (Compose of transforms, list of seeds to reproduce the transforms from the history) |
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""" |
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trsfm_list = [] |
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seed_list = [] |
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for trsfm_history in history: |
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trsfm_name, trsfm_params = trsfm_history[0], (trsfm_history[1]) |
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seed_list.append(trsfm_params['seed']) |
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trsfm_no_seed = {key: value for key, value in trsfm_params.items() if key != 'seed'} |
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trsfm_func = getattr(torchio, trsfm_name)() |
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trsfm_func.__dict__ = trsfm_no_seed |
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trsfm_list.append(trsfm_func) |
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return Compose(trsfm_list), seed_list |
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fepegar /
torchio
