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from typing import Union, Sequence, List |
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import json |
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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 .. import Transform |
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from . import RandomTransform, Interpolation |
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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__(self, transforms: Sequence[Transform], p: float = 1): |
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super().__init__(p=p) |
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self.transform = PyTorchCompose(transforms) |
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def apply_transform(self, subject: Subject): |
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return self.transform(subject) |
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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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"""Builds a list of transformations and seeds to reproduce a given subject's transformations from its history |
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Args: |
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history: subject history given as a list of tuples containing (transformation_name, transformation_parameters) |
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Returns: |
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Tuple (List 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_name, trsfm_params in history: |
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# No need to add the RandomDownsample since its Resampling operation is taken into account in the history |
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if trsfm_name == 'RandomDownsample': |
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continue |
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# Add the seed if there is one (if the transform is random) |
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if 'seed' in trsfm_params.keys(): |
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seed_list.append(trsfm_params['seed']) |
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else: |
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seed_list.append(None) |
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# Gather all available attributes from the transformations' history |
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# Ugly fix for RandomSwap's patch_size... |
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trsfm_no_seed = {key: json.loads(value) if type(value) == str and value.startswith('[') else value |
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for key, value in trsfm_params.items() if key != 'seed'} |
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# Special case for the interpolation as it is stored as a string in the history, a conversion is needed |
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if 'interpolation' in trsfm_no_seed.keys(): |
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trsfm_no_seed['interpolation'] = getattr(Interpolation, trsfm_no_seed['interpolation'].split('.')[1]) |
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# Special cases when an argument is needed in the __init__ |
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if trsfm_name == 'RandomLabelsToImage': |
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trsfm_func = getattr(torchio, trsfm_name)(label_key=trsfm_no_seed['label_key']) |
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elif trsfm_name == 'Resample': |
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if 'target' in trsfm_no_seed.keys(): |
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trsfm_func = getattr(torchio, trsfm_name)(target=trsfm_no_seed['target']) |
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elif 'target_spacing' in trsfm_no_seed.keys(): |
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trsfm_func = getattr(torchio, trsfm_name)(target=trsfm_no_seed['target_spacing']) |
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else: |
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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 trsfm_list, seed_list |
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fepegar /
torchio
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