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import warnings |
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from numbers import Number |
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from typing import Union |
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import numpy as np |
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import torch |
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from nibabel.affines import apply_affine |
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from ....data.image import LabelMap |
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from ....data.subject import Subject |
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from .bounds_transform import BoundsTransform |
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from .bounds_transform import TypeBounds |
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class Pad(BoundsTransform): |
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r"""Pad an image. |
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Args: |
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padding: Tuple |
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:math:`(w_{ini}, w_{fin}, h_{ini}, h_{fin}, d_{ini}, d_{fin})` |
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defining the number of values padded to the edges of each axis. |
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If the initial shape of the image is |
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:math:`W \times H \times D`, the final shape will be |
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:math:`(w_{ini} + W + w_{fin}) \times (h_{ini} + H + h_{fin}) |
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\times (d_{ini} + D + d_{fin})`. |
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If only three values :math:`(w, h, d)` are provided, then |
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:math:`w_{ini} = w_{fin} = w`, |
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:math:`h_{ini} = h_{fin} = h` and |
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:math:`d_{ini} = d_{fin} = d`. |
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If only one value :math:`n` is provided, then |
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:math:`w_{ini} = w_{fin} = h_{ini} = h_{fin} = |
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d_{ini} = d_{fin} = n`. |
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padding_mode: See possible modes in `NumPy docs`_. If it is a number, |
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the mode will be set to ``'constant'``. If it is ``'mean'``, |
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``'maximum'``, ``'median'`` or ``'minimum'``, the statistic will be |
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computed from the whole volume, unlike in NumPy, which computes it |
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along the padded axis. |
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**kwargs: See :class:`~torchio.transforms.Transform` for additional |
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keyword arguments. |
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.. seealso:: If you want to pass the output shape instead, please use |
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:class:`~torchio.transforms.CropOrPad` instead. |
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.. _NumPy docs: https://numpy.org/doc/stable/reference/generated/numpy.pad.html |
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""" |
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PADDING_MODES = ( |
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'empty', |
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'edge', |
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'wrap', |
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'constant', |
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'linear_ramp', |
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'maximum', |
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'mean', |
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'median', |
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'minimum', |
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'reflect', |
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'symmetric', |
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) |
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def __init__( |
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self, |
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padding: TypeBounds, |
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padding_mode: Union[str, float] = 0, |
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**kwargs, |
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): |
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super().__init__(padding, **kwargs) |
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self.padding = padding |
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self.check_padding_mode(padding_mode) |
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self.padding_mode = padding_mode |
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self.args_names = ['padding', 'padding_mode'] |
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@classmethod |
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def check_padding_mode(cls, padding_mode): |
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is_number = isinstance(padding_mode, Number) |
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is_callable = callable(padding_mode) |
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if not (padding_mode in cls.PADDING_MODES or is_number or is_callable): |
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message = ( |
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f'Padding mode "{padding_mode}" not valid. Valid options are' |
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f' {list(cls.PADDING_MODES)}, a number or a function' |
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) |
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raise KeyError(message) |
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def apply_transform(self, subject: Subject) -> Subject: |
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assert self.bounds_parameters is not None |
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low = self.bounds_parameters[::2] |
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for image in self.get_images(subject): |
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if isinstance(image, LabelMap) and self.padding_mode == 'mean': |
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message = ( |
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'Padding mode "mean" might create non-integer values in label maps' |
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) |
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warnings.warn(message, RuntimeWarning, stacklevel=2) |
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new_origin = apply_affine(image.affine, -np.array(low)) |
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new_affine = image.affine.copy() |
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new_affine[:3, 3] = new_origin |
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mode: str | float = 'constant' |
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constant: torch.Tensor | float | None = None |
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if isinstance(self.padding_mode, Number): |
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constant = self.padding_mode # type: ignore[assignment] |
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elif self.padding_mode == 'maximum': |
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constant = image.data.max() |
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elif self.padding_mode == 'mean': |
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constant = image.data.float().mean() |
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elif self.padding_mode == 'median': |
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constant = torch.quantile(image.data.float(), 0.5) |
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elif self.padding_mode == 'minimum': |
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constant = image.data.min() |
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else: |
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constant = None |
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mode = self.padding_mode |
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pad_params = self.bounds_parameters |
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paddings = (0, 0), pad_params[:2], pad_params[2:4], pad_params[4:] |
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padded = np.pad(image.data, paddings, mode=mode, constant_values=constant) # type: ignore[call-overload] |
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image.set_data(torch.as_tensor(padded)) |
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image.affine = new_affine |
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return subject |
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def inverse(self): |
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from .crop import Crop |
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return Crop(self.padding) |
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TorchIO-project /
torchio
