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""" |
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A collection of dictionary-based wrappers around the "vanilla" transforms for crop and pad operations |
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defined in :py:class:`monai.transforms.croppad.array`. |
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Class names are ended with 'd' to denote dictionary-based transforms. |
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""" |
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from __future__ import annotations |
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|
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from collections.abc import Callable, Hashable, Mapping, Sequence |
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from copy import deepcopy |
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from typing import Any |
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import numpy as np |
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import torch |
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from monai.config import IndexSelection, KeysCollection, SequenceStr |
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from monai.config.type_definitions import NdarrayOrTensor |
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from monai.data.meta_tensor import MetaTensor |
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from monai.transforms.croppad.array import ( |
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BorderPad, |
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BoundingRect, |
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CenterScaleCrop, |
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CenterSpatialCrop, |
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Crop, |
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CropForeground, |
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DivisiblePad, |
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Pad, |
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RandCropByLabelClasses, |
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RandCropByPosNegLabel, |
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RandScaleCrop, |
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RandSpatialCrop, |
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RandSpatialCropSamples, |
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RandWeightedCrop, |
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ResizeWithPadOrCrop, |
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SpatialCrop, |
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SpatialPad, |
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) |
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from monai.transforms.inverse import InvertibleTransform |
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from monai.transforms.traits import LazyTrait, MultiSampleTrait |
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from monai.transforms.transform import LazyTransform, MapTransform, Randomizable |
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from monai.transforms.utils import is_positive |
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from monai.utils import MAX_SEED, Method, PytorchPadMode, deprecated_arg_default, ensure_tuple_rep |
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__all__ = [ |
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"Padd", |
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"SpatialPadd", |
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"BorderPadd", |
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"DivisiblePadd", |
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"Cropd", |
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"RandCropd", |
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"SpatialCropd", |
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"CenterSpatialCropd", |
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"CenterScaleCropd", |
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"RandScaleCropd", |
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"RandSpatialCropd", |
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"RandSpatialCropSamplesd", |
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"CropForegroundd", |
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"RandWeightedCropd", |
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"RandCropByPosNegLabeld", |
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"ResizeWithPadOrCropd", |
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"BoundingRectd", |
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"RandCropByLabelClassesd", |
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"PadD", |
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"PadDict", |
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"SpatialPadD", |
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"SpatialPadDict", |
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"BorderPadD", |
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"BorderPadDict", |
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"DivisiblePadD", |
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"DivisiblePadDict", |
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"CropD", |
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"CropDict", |
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"RandCropD", |
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"RandCropDict", |
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"SpatialCropD", |
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"SpatialCropDict", |
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"CenterSpatialCropD", |
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"CenterSpatialCropDict", |
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"CenterScaleCropD", |
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"CenterScaleCropDict", |
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"RandScaleCropD", |
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"RandScaleCropDict", |
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"RandSpatialCropD", |
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"RandSpatialCropDict", |
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"RandSpatialCropSamplesD", |
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"RandSpatialCropSamplesDict", |
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"CropForegroundD", |
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"CropForegroundDict", |
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"RandWeightedCropD", |
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"RandWeightedCropDict", |
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"RandCropByPosNegLabelD", |
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"RandCropByPosNegLabelDict", |
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"ResizeWithPadOrCropD", |
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"ResizeWithPadOrCropDict", |
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"BoundingRectD", |
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"BoundingRectDict", |
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"RandCropByLabelClassesD", |
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"RandCropByLabelClassesDict", |
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] |
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class Padd(MapTransform, InvertibleTransform, LazyTransform): |
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""" |
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Dictionary-based wrapper of :py:class:`monai.transforms.Pad`. |
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This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
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for more information. |
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""" |
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backend = Pad.backend |
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def __init__( |
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self, |
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keys: KeysCollection, |
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padder: Pad, |
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mode: SequenceStr = PytorchPadMode.CONSTANT, |
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allow_missing_keys: bool = False, |
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lazy: bool = False, |
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) -> None: |
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""" |
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Args: |
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keys: keys of the corresponding items to be transformed. |
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See also: :py:class:`monai.transforms.compose.MapTransform` |
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padder: pad transform for the input image. |
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mode: available modes for numpy array:{``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, |
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``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``} |
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available modes for PyTorch Tensor: {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}. |
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One of the listed string values or a user supplied function. Defaults to ``"constant"``. |
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See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html |
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https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html |
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It also can be a sequence of string, each element corresponds to a key in ``keys``. |
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allow_missing_keys: don't raise exception if key is missing. |
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lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
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""" |
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MapTransform.__init__(self, keys, allow_missing_keys) |
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LazyTransform.__init__(self, lazy) |
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if lazy is True and not isinstance(padder, LazyTrait): |
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raise ValueError("'padder' must inherit LazyTrait if lazy is True " f"'padder' is of type({type(padder)})") |
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self.padder = padder |
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self.mode = ensure_tuple_rep(mode, len(self.keys)) |
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@LazyTransform.lazy.setter |
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def lazy(self, value: bool) -> None: |
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self._lazy = value |
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if isinstance(self.padder, LazyTransform): |
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self.padder.lazy = value |
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def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
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d = dict(data) |
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lazy_ = self.lazy if lazy is None else lazy |
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if lazy_ is True and not isinstance(self.padder, LazyTrait): |
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raise ValueError( |
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"'self.padder' must inherit LazyTrait if lazy is True " f"'self.padder' is of type({type(self.padder)}" |
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) |
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for key, m in self.key_iterator(d, self.mode): |
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if isinstance(self.padder, LazyTrait): |
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d[key] = self.padder(d[key], mode=m, lazy=lazy_) |
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else: |
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d[key] = self.padder(d[key], mode=m) |
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return d |
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def inverse(self, data: Mapping[Hashable, MetaTensor]) -> dict[Hashable, MetaTensor]: |
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d = dict(data) |
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for key in self.key_iterator(d): |
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d[key] = self.padder.inverse(d[key]) |
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return d |
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|
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class SpatialPadd(Padd): |
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""" |
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|
Dictionary-based wrapper of :py:class:`monai.transforms.SpatialPad`. |
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|
Performs padding to the data, symmetric for all sides or all on one side for each dimension. |
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This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
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|
for more information. |
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|
""" |
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def __init__( |
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|
self, |
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keys: KeysCollection, |
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|
spatial_size: Sequence[int] | int, |
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method: str = Method.SYMMETRIC, |
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mode: SequenceStr = PytorchPadMode.CONSTANT, |
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|
allow_missing_keys: bool = False, |
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|
lazy: bool = False, |
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|
**kwargs, |
|
|
) -> None: |
|
|
""" |
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|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: :py:class:`monai.transforms.compose.MapTransform` |
|
|
spatial_size: the spatial size of output data after padding, if a dimension of the input |
|
|
data size is larger than the pad size, will not pad that dimension. |
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|
If its components have non-positive values, the corresponding size of input image will be used. |
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|
for example: if the spatial size of input data is [30, 30, 30] and `spatial_size=[32, 25, -1]`, |
|
|
the spatial size of output data will be [32, 30, 30]. |
|
|
method: {``"symmetric"``, ``"end"``} |
|
|
Pad image symmetrically on every side or only pad at the end sides. Defaults to ``"symmetric"``. |
|
|
mode: available modes for numpy array:{``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, |
|
|
``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``} |
|
|
available modes for PyTorch Tensor: {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}. |
|
|
One of the listed string values or a user supplied function. Defaults to ``"constant"``. |
|
|
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html |
|
|
https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html |
|
|
It also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
kwargs: other arguments for the `np.pad` or `torch.pad` function. |
|
|
note that `np.pad` treats channel dimension as the first dimension. |
|
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|
|
|
""" |
|
|
padder = SpatialPad(spatial_size, method, lazy=lazy, **kwargs) |
|
|
Padd.__init__(self, keys, padder=padder, mode=mode, allow_missing_keys=allow_missing_keys, lazy=lazy) |
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|
|
|
|
|
class BorderPadd(Padd): |
|
|
""" |
|
|
Pad the input data by adding specified borders to every dimension. |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.BorderPad`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
""" |
|
|
|
|
|
backend = BorderPad.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
spatial_border: Sequence[int] | int, |
|
|
mode: SequenceStr = PytorchPadMode.CONSTANT, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
**kwargs, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: :py:class:`monai.transforms.compose.MapTransform` |
|
|
spatial_border: specified size for every spatial border. it can be 3 shapes: |
|
|
|
|
|
- single int number, pad all the borders with the same size. |
|
|
- length equals the length of image shape, pad every spatial dimension separately. |
|
|
for example, image shape(CHW) is [1, 4, 4], spatial_border is [2, 1], |
|
|
pad every border of H dim with 2, pad every border of W dim with 1, result shape is [1, 8, 6]. |
|
|
- length equals 2 x (length of image shape), pad every border of every dimension separately. |
|
|
for example, image shape(CHW) is [1, 4, 4], spatial_border is [1, 2, 3, 4], pad top of H dim with 1, |
|
|
pad bottom of H dim with 2, pad left of W dim with 3, pad right of W dim with 4. |
|
|
the result shape is [1, 7, 11]. |
|
|
|
|
|
mode: available modes for numpy array:{``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, |
|
|
``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``} |
|
|
available modes for PyTorch Tensor: {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}. |
|
|
One of the listed string values or a user supplied function. Defaults to ``"constant"``. |
|
|
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html |
|
|
https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html |
|
|
It also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
kwargs: other arguments for the `np.pad` or `torch.pad` function. |
|
|
note that `np.pad` treats channel dimension as the first dimension. |
|
|
|
|
|
""" |
|
|
padder = BorderPad(spatial_border=spatial_border, lazy=lazy, **kwargs) |
|
|
Padd.__init__(self, keys, padder=padder, mode=mode, allow_missing_keys=allow_missing_keys, lazy=lazy) |
|
|
|
|
|
|
|
|
class DivisiblePadd(Padd): |
|
|
""" |
|
|
Pad the input data, so that the spatial sizes are divisible by `k`. |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.DivisiblePad`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
""" |
|
|
|
|
|
backend = DivisiblePad.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
k: Sequence[int] | int, |
|
|
mode: SequenceStr = PytorchPadMode.CONSTANT, |
|
|
method: str = Method.SYMMETRIC, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
**kwargs, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: :py:class:`monai.transforms.compose.MapTransform` |
|
|
k: the target k for each spatial dimension. |
|
|
if `k` is negative or 0, the original size is preserved. |
|
|
if `k` is an int, the same `k` be applied to all the input spatial dimensions. |
|
|
mode: available modes for numpy array:{``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, |
|
|
``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``} |
|
|
available modes for PyTorch Tensor: {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}. |
|
|
One of the listed string values or a user supplied function. Defaults to ``"constant"``. |
|
|
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html |
|
|
https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html |
|
|
It also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
method: {``"symmetric"``, ``"end"``} |
|
|
Pad image symmetrically on every side or only pad at the end sides. Defaults to ``"symmetric"``. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
kwargs: other arguments for the `np.pad` or `torch.pad` function. |
|
|
note that `np.pad` treats channel dimension as the first dimension. |
|
|
|
|
|
See also :py:class:`monai.transforms.SpatialPad` |
|
|
|
|
|
""" |
|
|
padder = DivisiblePad(k=k, method=method, lazy=lazy, **kwargs) |
|
|
Padd.__init__(self, keys, padder=padder, mode=mode, allow_missing_keys=allow_missing_keys, lazy=lazy) |
|
|
|
|
|
|
|
|
class Cropd(MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of abstract class :py:class:`monai.transforms.Crop`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: :py:class:`monai.transforms.compose.MapTransform` |
|
|
cropper: crop transform for the input image. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
""" |
|
|
|
|
|
backend = Crop.backend |
|
|
|
|
|
def __init__(self, keys: KeysCollection, cropper: Crop, allow_missing_keys: bool = False, lazy: bool = False): |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy) |
|
|
self.cropper = cropper |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, value: bool) -> None: |
|
|
self._lazy = value |
|
|
if isinstance(self.cropper, LazyTransform): |
|
|
self.cropper.lazy = value |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.cropper(d[key], lazy=lazy_) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, MetaTensor]) -> dict[Hashable, MetaTensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.cropper.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class RandCropd(Cropd, Randomizable): |
|
|
""" |
|
|
Base class for random crop transform. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: :py:class:`monai.transforms.compose.MapTransform` |
|
|
cropper: random crop transform for the input image. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
""" |
|
|
|
|
|
backend = Crop.backend |
|
|
|
|
|
def __init__(self, keys: KeysCollection, cropper: Crop, allow_missing_keys: bool = False, lazy: bool = False): |
|
|
super().__init__(keys, cropper=cropper, allow_missing_keys=allow_missing_keys, lazy=lazy) |
|
|
|
|
|
def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = None) -> RandCropd: |
|
|
super().set_random_state(seed, state) |
|
|
if isinstance(self.cropper, Randomizable): |
|
|
self.cropper.set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def randomize(self, img_size: Sequence[int]) -> None: |
|
|
if isinstance(self.cropper, Randomizable): |
|
|
self.cropper.randomize(img_size) |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
|
|
|
first_item = d[self.first_key(d)] |
|
|
self.randomize(first_item.peek_pending_shape() if isinstance(first_item, MetaTensor) else first_item.shape[1:]) |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
if lazy_ is True and not isinstance(self.cropper, LazyTrait): |
|
|
raise ValueError( |
|
|
"'self.cropper' must inherit LazyTrait if lazy is True " |
|
|
f"'self.cropper' is of type({type(self.cropper)}" |
|
|
) |
|
|
for key in self.key_iterator(d): |
|
|
kwargs = {"randomize": False} if isinstance(self.cropper, Randomizable) else {} |
|
|
if isinstance(self.cropper, LazyTrait): |
|
|
kwargs["lazy"] = lazy_ |
|
|
d[key] = self.cropper(d[key], **kwargs) |
|
|
return d |
|
|
|
|
|
|
|
|
class SpatialCropd(Cropd): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.SpatialCrop`. |
|
|
General purpose cropper to produce sub-volume region of interest (ROI). |
|
|
If a dimension of the expected ROI size is larger than the input image size, will not crop that dimension. |
|
|
So the cropped result may be smaller than the expected ROI, and the cropped results of several images may |
|
|
not have exactly the same shape. |
|
|
It can support to crop ND spatial (channel-first) data. |
|
|
|
|
|
The cropped region can be parameterised in various ways: |
|
|
- a list of slices for each spatial dimension (allows for use of -ve indexing and `None`) |
|
|
- a spatial center and size |
|
|
- the start and end coordinates of the ROI |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
""" |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
roi_center: Sequence[int] | None = None, |
|
|
roi_size: Sequence[int] | None = None, |
|
|
roi_start: Sequence[int] | None = None, |
|
|
roi_end: Sequence[int] | None = None, |
|
|
roi_slices: Sequence[slice] | None = None, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: :py:class:`monai.transforms.compose.MapTransform` |
|
|
roi_center: voxel coordinates for center of the crop ROI. |
|
|
roi_size: size of the crop ROI, if a dimension of ROI size is larger than image size, |
|
|
will not crop that dimension of the image. |
|
|
roi_start: voxel coordinates for start of the crop ROI. |
|
|
roi_end: voxel coordinates for end of the crop ROI, if a coordinate is out of image, |
|
|
use the end coordinate of image. |
|
|
roi_slices: list of slices for each of the spatial dimensions. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
""" |
|
|
cropper = SpatialCrop(roi_center, roi_size, roi_start, roi_end, roi_slices, lazy=lazy) |
|
|
super().__init__(keys, cropper=cropper, allow_missing_keys=allow_missing_keys, lazy=lazy) |
|
|
|
|
|
|
|
|
class CenterSpatialCropd(Cropd): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.CenterSpatialCrop`. |
|
|
If a dimension of the expected ROI size is larger than the input image size, will not crop that dimension. |
|
|
So the cropped result may be smaller than the expected ROI, and the cropped results of several images may |
|
|
not have exactly the same shape. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: monai.transforms.MapTransform |
|
|
roi_size: the size of the crop region e.g. [224,224,128] |
|
|
if a dimension of ROI size is larger than image size, will not crop that dimension of the image. |
|
|
If its components have non-positive values, the corresponding size of input image will be used. |
|
|
for example: if the spatial size of input data is [40, 40, 40] and `roi_size=[32, 64, -1]`, |
|
|
the spatial size of output data will be [32, 40, 40]. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
""" |
|
|
|
|
|
def __init__( |
|
|
self, keys: KeysCollection, roi_size: Sequence[int] | int, allow_missing_keys: bool = False, lazy: bool = False |
|
|
) -> None: |
|
|
cropper = CenterSpatialCrop(roi_size, lazy=lazy) |
|
|
super().__init__(keys, cropper=cropper, allow_missing_keys=allow_missing_keys, lazy=lazy) |
|
|
|
|
|
|
|
|
class CenterScaleCropd(Cropd): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.CenterScaleCrop`. |
|
|
Note: as using the same scaled ROI to crop, all the input data specified by `keys` should have |
|
|
the same spatial shape. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: monai.transforms.MapTransform |
|
|
roi_scale: specifies the expected scale of image size to crop. e.g. [0.3, 0.4, 0.5] or a number for all dims. |
|
|
If its components have non-positive values, will use `1.0` instead, which means the input image size. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
""" |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
roi_scale: Sequence[float] | float, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
cropper = CenterScaleCrop(roi_scale, lazy=lazy) |
|
|
super().__init__(keys, cropper=cropper, allow_missing_keys=allow_missing_keys, lazy=lazy) |
|
|
|
|
|
|
|
|
class RandSpatialCropd(RandCropd): |
|
|
""" |
|
|
Dictionary-based version :py:class:`monai.transforms.RandSpatialCrop`. |
|
|
Crop image with random size or specific size ROI. It can crop at a random position as |
|
|
center or at the image center. And allows to set the minimum and maximum size to limit the randomly |
|
|
generated ROI. Suppose all the expected fields specified by `keys` have same shape. |
|
|
|
|
|
Note: even `random_size=False`, if a dimension of the expected ROI size is larger than the input image size, |
|
|
will not crop that dimension. So the cropped result may be smaller than the expected ROI, and the cropped |
|
|
results of several images may not have exactly the same shape. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: monai.transforms.MapTransform |
|
|
roi_size: if `random_size` is True, it specifies the minimum crop region. |
|
|
if `random_size` is False, it specifies the expected ROI size to crop. e.g. [224, 224, 128] |
|
|
if a dimension of ROI size is larger than image size, will not crop that dimension of the image. |
|
|
If its components have non-positive values, the corresponding size of input image will be used. |
|
|
for example: if the spatial size of input data is [40, 40, 40] and `roi_size=[32, 64, -1]`, |
|
|
the spatial size of output data will be [32, 40, 40]. |
|
|
max_roi_size: if `random_size` is True and `roi_size` specifies the min crop region size, `max_roi_size` |
|
|
can specify the max crop region size. if None, defaults to the input image size. |
|
|
if its components have non-positive values, the corresponding size of input image will be used. |
|
|
random_center: crop at random position as center or the image center. |
|
|
random_size: crop with random size or specific size ROI. |
|
|
if True, the actual size is sampled from: |
|
|
`randint(roi_scale * image spatial size, max_roi_scale * image spatial size + 1)`. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
""" |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
roi_size: Sequence[int] | int, |
|
|
max_roi_size: Sequence[int] | int | None = None, |
|
|
random_center: bool = True, |
|
|
random_size: bool = False, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
cropper = RandSpatialCrop(roi_size, max_roi_size, random_center, random_size, lazy=lazy) |
|
|
super().__init__(keys, cropper=cropper, allow_missing_keys=allow_missing_keys, lazy=lazy) |
|
|
|
|
|
|
|
|
class RandScaleCropd(RandCropd): |
|
|
""" |
|
|
Dictionary-based version :py:class:`monai.transforms.RandScaleCrop`. |
|
|
Crop image with random size or specific size ROI. |
|
|
It can crop at a random position as center or at the image center. |
|
|
And allows to set the minimum and maximum scale of image size to limit the randomly generated ROI. |
|
|
Suppose all the expected fields specified by `keys` have same shape. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: monai.transforms.MapTransform |
|
|
roi_scale: if `random_size` is True, it specifies the minimum crop size: `roi_scale * image spatial size`. |
|
|
if `random_size` is False, it specifies the expected scale of image size to crop. e.g. [0.3, 0.4, 0.5]. |
|
|
If its components have non-positive values, will use `1.0` instead, which means the input image size. |
|
|
max_roi_scale: if `random_size` is True and `roi_scale` specifies the min crop region size, `max_roi_scale` |
|
|
can specify the max crop region size: `max_roi_scale * image spatial size`. |
|
|
if None, defaults to the input image size. if its components have non-positive values, |
|
|
will use `1.0` instead, which means the input image size. |
|
|
random_center: crop at random position as center or the image center. |
|
|
random_size: crop with random size or specified size ROI by `roi_scale * image spatial size`. |
|
|
if True, the actual size is sampled from: |
|
|
`randint(roi_scale * image spatial size, max_roi_scale * image spatial size + 1)`. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
""" |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
roi_scale: Sequence[float] | float, |
|
|
max_roi_scale: Sequence[float] | float | None = None, |
|
|
random_center: bool = True, |
|
|
random_size: bool = False, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
cropper = RandScaleCrop(roi_scale, max_roi_scale, random_center, random_size, lazy=lazy) |
|
|
super().__init__(keys, cropper=cropper, allow_missing_keys=allow_missing_keys, lazy=lazy) |
|
|
|
|
|
|
|
|
class RandSpatialCropSamplesd(Randomizable, MapTransform, LazyTransform, MultiSampleTrait): |
|
|
""" |
|
|
Dictionary-based version :py:class:`monai.transforms.RandSpatialCropSamples`. |
|
|
Crop image with random size or specific size ROI to generate a list of N samples. |
|
|
It can crop at a random position as center or at the image center. And allows to set |
|
|
the minimum size to limit the randomly generated ROI. Suppose all the expected fields |
|
|
specified by `keys` have same shape, and add `patch_index` to the corresponding metadata. |
|
|
It will return a list of dictionaries for all the cropped images. |
|
|
|
|
|
Note: even `random_size=False`, if a dimension of the expected ROI size is larger than the input image size, |
|
|
will not crop that dimension. So the cropped result may be smaller than the expected ROI, and the cropped |
|
|
results of several images may not have exactly the same shape. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: monai.transforms.MapTransform |
|
|
roi_size: if `random_size` is True, it specifies the minimum crop region. |
|
|
if `random_size` is False, it specifies the expected ROI size to crop. e.g. [224, 224, 128] |
|
|
if a dimension of ROI size is larger than image size, will not crop that dimension of the image. |
|
|
If its components have non-positive values, the corresponding size of input image will be used. |
|
|
for example: if the spatial size of input data is [40, 40, 40] and `roi_size=[32, 64, -1]`, |
|
|
the spatial size of output data will be [32, 40, 40]. |
|
|
num_samples: number of samples (crop regions) to take in the returned list. |
|
|
max_roi_size: if `random_size` is True and `roi_size` specifies the min crop region size, `max_roi_size` |
|
|
can specify the max crop region size. if None, defaults to the input image size. |
|
|
if its components have non-positive values, the corresponding size of input image will be used. |
|
|
random_center: crop at random position as center or the image center. |
|
|
random_size: crop with random size or specific size ROI. |
|
|
The actual size is sampled from `randint(roi_size, img_size)`. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
|
|
|
Raises: |
|
|
ValueError: When ``num_samples`` is nonpositive. |
|
|
|
|
|
""" |
|
|
|
|
|
backend = RandSpatialCropSamples.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
roi_size: Sequence[int] | int, |
|
|
num_samples: int, |
|
|
max_roi_size: Sequence[int] | int | None = None, |
|
|
random_center: bool = True, |
|
|
random_size: bool = False, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy) |
|
|
self.cropper = RandSpatialCropSamples( |
|
|
roi_size, num_samples, max_roi_size, random_center, random_size, lazy=lazy |
|
|
) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, value: bool) -> None: |
|
|
self._lazy = value |
|
|
self.cropper.lazy = value |
|
|
|
|
|
def randomize(self, data: Any | None = None) -> None: |
|
|
self.sub_seed = self.R.randint(MAX_SEED, dtype="uint32") |
|
|
|
|
|
def __call__( |
|
|
self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None |
|
|
) -> list[dict[Hashable, torch.Tensor]]: |
|
|
ret: list[dict[Hashable, torch.Tensor]] = [dict(data) for _ in range(self.cropper.num_samples)] |
|
|
|
|
|
for i in range(self.cropper.num_samples): |
|
|
for key in set(data.keys()).difference(set(self.keys)): |
|
|
ret[i][key] = deepcopy(data[key]) |
|
|
|
|
|
|
|
|
self.randomize() |
|
|
|
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key in self.key_iterator(dict(data)): |
|
|
self.cropper.set_random_state(seed=self.sub_seed) |
|
|
for i, im in enumerate(self.cropper(data[key], lazy=lazy_)): |
|
|
ret[i][key] = im |
|
|
return ret |
|
|
|
|
|
|
|
|
class CropForegroundd(Cropd): |
|
|
""" |
|
|
Dictionary-based version :py:class:`monai.transforms.CropForeground`. |
|
|
Crop only the foreground object of the expected images. |
|
|
The typical usage is to help training and evaluation if the valid part is small in the whole medical image. |
|
|
The valid part can be determined by any field in the data with `source_key`, for example: |
|
|
- Select values > 0 in image field as the foreground and crop on all fields specified by `keys`. |
|
|
- Select label = 3 in label field as the foreground to crop on all fields specified by `keys`. |
|
|
- Select label > 0 in the third channel of a One-Hot label field as the foreground to crop all `keys` fields. |
|
|
Users can define arbitrary function to select expected foreground from the whole source image or specified |
|
|
channels. And it can also add margin to every dim of the bounding box of foreground object. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
""" |
|
|
|
|
|
@deprecated_arg_default("allow_smaller", old_default=True, new_default=False, since="1.2", replaced="1.5") |
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
source_key: str, |
|
|
select_fn: Callable = is_positive, |
|
|
channel_indices: IndexSelection | None = None, |
|
|
margin: Sequence[int] | int = 0, |
|
|
allow_smaller: bool = True, |
|
|
k_divisible: Sequence[int] | int = 1, |
|
|
mode: SequenceStr = PytorchPadMode.CONSTANT, |
|
|
start_coord_key: str | None = "foreground_start_coord", |
|
|
end_coord_key: str | None = "foreground_end_coord", |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
**pad_kwargs, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: :py:class:`monai.transforms.compose.MapTransform` |
|
|
source_key: data source to generate the bounding box of foreground, can be image or label, etc. |
|
|
select_fn: function to select expected foreground, default is to select values > 0. |
|
|
channel_indices: if defined, select foreground only on the specified channels |
|
|
of image. if None, select foreground on the whole image. |
|
|
margin: add margin value to spatial dims of the bounding box, if only 1 value provided, use it for all dims. |
|
|
allow_smaller: when computing box size with `margin`, whether to allow the image edges to be smaller than the |
|
|
final box edges. If `False`, part of a padded output box might be outside of the original image, if `True`, |
|
|
the image edges will be used as the box edges. Default to `True`. |
|
|
k_divisible: make each spatial dimension to be divisible by k, default to 1. |
|
|
if `k_divisible` is an int, the same `k` be applied to all the input spatial dimensions. |
|
|
mode: available modes for numpy array:{``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, |
|
|
``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``} |
|
|
available modes for PyTorch Tensor: {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}. |
|
|
One of the listed string values or a user supplied function. Defaults to ``"constant"``. |
|
|
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html |
|
|
https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html |
|
|
it also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
start_coord_key: key to record the start coordinate of spatial bounding box for foreground. |
|
|
end_coord_key: key to record the end coordinate of spatial bounding box for foreground. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
pad_kwargs: other arguments for the `np.pad` or `torch.pad` function. |
|
|
note that `np.pad` treats channel dimension as the first dimension. |
|
|
|
|
|
""" |
|
|
self.source_key = source_key |
|
|
self.start_coord_key = start_coord_key |
|
|
self.end_coord_key = end_coord_key |
|
|
cropper = CropForeground( |
|
|
select_fn=select_fn, |
|
|
channel_indices=channel_indices, |
|
|
margin=margin, |
|
|
allow_smaller=allow_smaller, |
|
|
k_divisible=k_divisible, |
|
|
lazy=lazy, |
|
|
**pad_kwargs, |
|
|
) |
|
|
super().__init__(keys, cropper=cropper, allow_missing_keys=allow_missing_keys, lazy=lazy) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, value: bool) -> None: |
|
|
self._lazy = value |
|
|
self.cropper.lazy = value |
|
|
|
|
|
@property |
|
|
def requires_current_data(self): |
|
|
return True |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
self.cropper: CropForeground |
|
|
box_start, box_end = self.cropper.compute_bounding_box(img=d[self.source_key]) |
|
|
if self.start_coord_key is not None: |
|
|
d[self.start_coord_key] = box_start |
|
|
if self.end_coord_key is not None: |
|
|
d[self.end_coord_key] = box_end |
|
|
|
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key, m in self.key_iterator(d, self.mode): |
|
|
d[key] = self.cropper.crop_pad(img=d[key], box_start=box_start, box_end=box_end, mode=m, lazy=lazy_) |
|
|
return d |
|
|
|
|
|
|
|
|
class RandWeightedCropd(Randomizable, MapTransform, LazyTransform, MultiSampleTrait): |
|
|
""" |
|
|
Samples a list of `num_samples` image patches according to the provided `weight_map`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: :py:class:`monai.transforms.compose.MapTransform` |
|
|
w_key: key for the weight map. The corresponding value will be used as the sampling weights, |
|
|
it should be a single-channel array in size, for example, `(1, spatial_dim_0, spatial_dim_1, ...)` |
|
|
spatial_size: the spatial size of the image patch e.g. [224, 224, 128]. |
|
|
If its components have non-positive values, the corresponding size of `img` will be used. |
|
|
num_samples: number of samples (image patches) to take in the returned list. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
|
|
|
See Also: |
|
|
:py:class:`monai.transforms.RandWeightedCrop` |
|
|
""" |
|
|
|
|
|
backend = SpatialCrop.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
w_key: str, |
|
|
spatial_size: Sequence[int] | int, |
|
|
num_samples: int = 1, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
): |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy) |
|
|
self.w_key = w_key |
|
|
self.cropper = RandWeightedCrop(spatial_size, num_samples, lazy=lazy) |
|
|
|
|
|
def set_random_state( |
|
|
self, seed: int | None = None, state: np.random.RandomState | None = None |
|
|
) -> RandWeightedCropd: |
|
|
super().set_random_state(seed, state) |
|
|
self.cropper.set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def randomize(self, weight_map: NdarrayOrTensor) -> None: |
|
|
self.cropper.randomize(weight_map) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, value: bool) -> None: |
|
|
self._lazy = value |
|
|
self.cropper.lazy = value |
|
|
|
|
|
def __call__( |
|
|
self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None |
|
|
) -> list[dict[Hashable, torch.Tensor]]: |
|
|
|
|
|
ret: list = [dict(data) for _ in range(self.cropper.num_samples)] |
|
|
|
|
|
for i in range(self.cropper.num_samples): |
|
|
for key in set(data.keys()).difference(set(self.keys)): |
|
|
ret[i][key] = deepcopy(data[key]) |
|
|
|
|
|
self.randomize(weight_map=data[self.w_key]) |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key in self.key_iterator(data): |
|
|
for i, im in enumerate(self.cropper(data[key], randomize=False, lazy=lazy_)): |
|
|
ret[i][key] = im |
|
|
return ret |
|
|
|
|
|
|
|
|
class RandCropByPosNegLabeld(Randomizable, MapTransform, LazyTransform, MultiSampleTrait): |
|
|
""" |
|
|
Dictionary-based version :py:class:`monai.transforms.RandCropByPosNegLabel`. |
|
|
Crop random fixed sized regions with the center being a foreground or background voxel |
|
|
based on the Pos Neg Ratio. |
|
|
Suppose all the expected fields specified by `keys` have same shape, |
|
|
and add `patch_index` to the corresponding metadata. |
|
|
And will return a list of dictionaries for all the cropped images. |
|
|
|
|
|
If a dimension of the expected spatial size is larger than the input image size, |
|
|
will not crop that dimension. So the cropped result may be smaller than the expected size, |
|
|
and the cropped results of several images may not have exactly the same shape. |
|
|
And if the crop ROI is partly out of the image, will automatically adjust the crop center |
|
|
to ensure the valid crop ROI. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: :py:class:`monai.transforms.compose.MapTransform` |
|
|
label_key: name of key for label image, this will be used for finding foreground/background. |
|
|
spatial_size: the spatial size of the crop region e.g. [224, 224, 128]. |
|
|
if a dimension of ROI size is larger than image size, will not crop that dimension of the image. |
|
|
if its components have non-positive values, the corresponding size of `data[label_key]` will be used. |
|
|
for example: if the spatial size of input data is [40, 40, 40] and `spatial_size=[32, 64, -1]`, |
|
|
the spatial size of output data will be [32, 40, 40]. |
|
|
pos: used with `neg` together to calculate the ratio ``pos / (pos + neg)`` for the probability |
|
|
to pick a foreground voxel as a center rather than a background voxel. |
|
|
neg: used with `pos` together to calculate the ratio ``pos / (pos + neg)`` for the probability |
|
|
to pick a foreground voxel as a center rather than a background voxel. |
|
|
num_samples: number of samples (crop regions) to take in each list. |
|
|
image_key: if image_key is not None, use ``label == 0 & image > image_threshold`` to select |
|
|
the negative sample(background) center. so the crop center will only exist on valid image area. |
|
|
image_threshold: if enabled image_key, use ``image > image_threshold`` to determine |
|
|
the valid image content area. |
|
|
fg_indices_key: if provided pre-computed foreground indices of `label`, will ignore above `image_key` and |
|
|
`image_threshold`, and randomly select crop centers based on them, need to provide `fg_indices_key` |
|
|
and `bg_indices_key` together, expect to be 1 dim array of spatial indices after flattening. |
|
|
a typical usage is to call `FgBgToIndicesd` transform first and cache the results. |
|
|
bg_indices_key: if provided pre-computed background indices of `label`, will ignore above `image_key` and |
|
|
`image_threshold`, and randomly select crop centers based on them, need to provide `fg_indices_key` |
|
|
and `bg_indices_key` together, expect to be 1 dim array of spatial indices after flattening. |
|
|
a typical usage is to call `FgBgToIndicesd` transform first and cache the results. |
|
|
allow_smaller: if `False`, an exception will be raised if the image is smaller than |
|
|
the requested ROI in any dimension. If `True`, any smaller dimensions will be set to |
|
|
match the cropped size (i.e., no cropping in that dimension). |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
|
|
|
Raises: |
|
|
ValueError: When ``pos`` or ``neg`` are negative. |
|
|
ValueError: When ``pos=0`` and ``neg=0``. Incompatible values. |
|
|
|
|
|
""" |
|
|
|
|
|
backend = RandCropByPosNegLabel.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
label_key: str, |
|
|
spatial_size: Sequence[int] | int, |
|
|
pos: float = 1.0, |
|
|
neg: float = 1.0, |
|
|
num_samples: int = 1, |
|
|
image_key: str | None = None, |
|
|
image_threshold: float = 0.0, |
|
|
fg_indices_key: str | None = None, |
|
|
bg_indices_key: str | None = None, |
|
|
allow_smaller: bool = False, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy) |
|
|
self.label_key = label_key |
|
|
self.image_key = image_key |
|
|
self.fg_indices_key = fg_indices_key |
|
|
self.bg_indices_key = bg_indices_key |
|
|
self.cropper = RandCropByPosNegLabel( |
|
|
spatial_size=spatial_size, |
|
|
pos=pos, |
|
|
neg=neg, |
|
|
num_samples=num_samples, |
|
|
image_threshold=image_threshold, |
|
|
allow_smaller=allow_smaller, |
|
|
lazy=lazy, |
|
|
) |
|
|
|
|
|
def set_random_state( |
|
|
self, seed: int | None = None, state: np.random.RandomState | None = None |
|
|
) -> RandCropByPosNegLabeld: |
|
|
super().set_random_state(seed, state) |
|
|
self.cropper.set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def randomize( |
|
|
self, |
|
|
label: torch.Tensor | None = None, |
|
|
fg_indices: NdarrayOrTensor | None = None, |
|
|
bg_indices: NdarrayOrTensor | None = None, |
|
|
image: torch.Tensor | None = None, |
|
|
) -> None: |
|
|
self.cropper.randomize(label=label, fg_indices=fg_indices, bg_indices=bg_indices, image=image) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, value: bool) -> None: |
|
|
self._lazy = value |
|
|
self.cropper.lazy = value |
|
|
|
|
|
@property |
|
|
def requires_current_data(self): |
|
|
return True |
|
|
|
|
|
def __call__( |
|
|
self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None |
|
|
) -> list[dict[Hashable, torch.Tensor]]: |
|
|
d = dict(data) |
|
|
fg_indices = d.pop(self.fg_indices_key, None) |
|
|
bg_indices = d.pop(self.bg_indices_key, None) |
|
|
|
|
|
self.randomize(d.get(self.label_key), fg_indices, bg_indices, d.get(self.image_key)) |
|
|
|
|
|
|
|
|
ret: list = [dict(d) for _ in range(self.cropper.num_samples)] |
|
|
|
|
|
for i in range(self.cropper.num_samples): |
|
|
for key in set(d.keys()).difference(set(self.keys)): |
|
|
ret[i][key] = deepcopy(d[key]) |
|
|
|
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key in self.key_iterator(d): |
|
|
for i, im in enumerate(self.cropper(d[key], randomize=False, lazy=lazy_)): |
|
|
ret[i][key] = im |
|
|
return ret |
|
|
|
|
|
|
|
|
class RandCropByLabelClassesd(Randomizable, MapTransform, LazyTransform, MultiSampleTrait): |
|
|
""" |
|
|
Dictionary-based version :py:class:`monai.transforms.RandCropByLabelClasses`. |
|
|
Crop random fixed sized regions with the center being a class based on the specified ratios of every class. |
|
|
The label data can be One-Hot format array or Argmax data. And will return a list of arrays for all the |
|
|
cropped images. For example, crop two (3 x 3) arrays from (5 x 5) array with `ratios=[1, 2, 3, 1]`:: |
|
|
|
|
|
cropper = RandCropByLabelClassesd( |
|
|
keys=["image", "label"], |
|
|
label_key="label", |
|
|
spatial_size=[3, 3], |
|
|
ratios=[1, 2, 3, 1], |
|
|
num_classes=4, |
|
|
num_samples=2, |
|
|
) |
|
|
data = { |
|
|
"image": np.array([ |
|
|
[[0.0, 0.3, 0.4, 0.2, 0.0], |
|
|
[0.0, 0.1, 0.2, 0.1, 0.4], |
|
|
[0.0, 0.3, 0.5, 0.2, 0.0], |
|
|
[0.1, 0.2, 0.1, 0.1, 0.0], |
|
|
[0.0, 0.1, 0.2, 0.1, 0.0]] |
|
|
]), |
|
|
"label": np.array([ |
|
|
[[0, 0, 0, 0, 0], |
|
|
[0, 1, 2, 1, 0], |
|
|
[0, 1, 3, 0, 0], |
|
|
[0, 0, 0, 0, 0], |
|
|
[0, 0, 0, 0, 0]] |
|
|
]), |
|
|
} |
|
|
result = cropper(data) |
|
|
|
|
|
The 2 randomly cropped samples of `label` can be: |
|
|
[[0, 1, 2], [[0, 0, 0], |
|
|
[0, 1, 3], [1, 2, 1], |
|
|
[0, 0, 0]] [1, 3, 0]] |
|
|
|
|
|
If a dimension of the expected spatial size is larger than the input image size, |
|
|
will not crop that dimension. So the cropped result may be smaller than expected size, and the cropped |
|
|
results of several images may not have exactly same shape. |
|
|
And if the crop ROI is partly out of the image, will automatically adjust the crop center to ensure the |
|
|
valid crop ROI. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: :py:class:`monai.transforms.compose.MapTransform` |
|
|
label_key: name of key for label image, this will be used for finding indices of every class. |
|
|
spatial_size: the spatial size of the crop region e.g. [224, 224, 128]. |
|
|
if a dimension of ROI size is larger than image size, will not crop that dimension of the image. |
|
|
if its components have non-positive values, the corresponding size of `label` will be used. |
|
|
for example: if the spatial size of input data is [40, 40, 40] and `spatial_size=[32, 64, -1]`, |
|
|
the spatial size of output data will be [32, 40, 40]. |
|
|
ratios: specified ratios of every class in the label to generate crop centers, including background class. |
|
|
if None, every class will have the same ratio to generate crop centers. |
|
|
num_classes: number of classes for argmax label, not necessary for One-Hot label. |
|
|
num_samples: number of samples (crop regions) to take in each list. |
|
|
image_key: if image_key is not None, only return the indices of every class that are within the valid |
|
|
region of the image (``image > image_threshold``). |
|
|
image_threshold: if enabled `image_key`, use ``image > image_threshold`` to |
|
|
determine the valid image content area and select class indices only in this area. |
|
|
indices_key: if provided pre-computed indices of every class, will ignore above `image` and |
|
|
`image_threshold`, and randomly select crop centers based on them, expect to be 1 dim array |
|
|
of spatial indices after flattening. a typical usage is to call `ClassesToIndices` transform first |
|
|
and cache the results for better performance. |
|
|
allow_smaller: if `False`, an exception will be raised if the image is smaller than |
|
|
the requested ROI in any dimension. If `True`, any smaller dimensions will remain |
|
|
unchanged. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
warn: if `True` prints a warning if a class is not present in the label. |
|
|
max_samples_per_class: maximum length of indices in each class to reduce memory consumption. |
|
|
Default is None, no subsampling. |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
|
|
""" |
|
|
|
|
|
backend = RandCropByLabelClasses.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
label_key: str, |
|
|
spatial_size: Sequence[int] | int, |
|
|
ratios: list[float | int] | None = None, |
|
|
num_classes: int | None = None, |
|
|
num_samples: int = 1, |
|
|
image_key: str | None = None, |
|
|
image_threshold: float = 0.0, |
|
|
indices_key: str | None = None, |
|
|
allow_smaller: bool = False, |
|
|
allow_missing_keys: bool = False, |
|
|
warn: bool = True, |
|
|
max_samples_per_class: int | None = None, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy) |
|
|
self.label_key = label_key |
|
|
self.image_key = image_key |
|
|
self.indices_key = indices_key |
|
|
self.cropper = RandCropByLabelClasses( |
|
|
spatial_size=spatial_size, |
|
|
ratios=ratios, |
|
|
num_classes=num_classes, |
|
|
num_samples=num_samples, |
|
|
image_threshold=image_threshold, |
|
|
allow_smaller=allow_smaller, |
|
|
warn=warn, |
|
|
max_samples_per_class=max_samples_per_class, |
|
|
lazy=lazy, |
|
|
) |
|
|
|
|
|
def set_random_state( |
|
|
self, seed: int | None = None, state: np.random.RandomState | None = None |
|
|
) -> RandCropByLabelClassesd: |
|
|
super().set_random_state(seed, state) |
|
|
self.cropper.set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def randomize( |
|
|
self, label: torch.Tensor, indices: list[NdarrayOrTensor] | None = None, image: torch.Tensor | None = None |
|
|
) -> None: |
|
|
self.cropper.randomize(label=label, indices=indices, image=image) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, value: bool) -> None: |
|
|
self._lazy = value |
|
|
self.cropper.lazy = value |
|
|
|
|
|
@property |
|
|
def requires_current_data(self): |
|
|
return True |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, Any], lazy: bool | None = None) -> list[dict[Hashable, torch.Tensor]]: |
|
|
d = dict(data) |
|
|
self.randomize(d.get(self.label_key), d.pop(self.indices_key, None), d.get(self.image_key)) |
|
|
|
|
|
|
|
|
ret: list = [dict(d) for _ in range(self.cropper.num_samples)] |
|
|
|
|
|
for i in range(self.cropper.num_samples): |
|
|
for key in set(d.keys()).difference(set(self.keys)): |
|
|
ret[i][key] = deepcopy(d[key]) |
|
|
|
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key in self.key_iterator(d): |
|
|
for i, im in enumerate(self.cropper(d[key], randomize=False, lazy=lazy_)): |
|
|
ret[i][key] = im |
|
|
return ret |
|
|
|
|
|
|
|
|
class ResizeWithPadOrCropd(Padd): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.ResizeWithPadOrCrop`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
See also: monai.transforms.MapTransform |
|
|
spatial_size: the spatial size of output data after padding or crop. |
|
|
If has non-positive values, the corresponding size of input image will be used (no padding). |
|
|
mode: available modes for numpy array:{``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, |
|
|
``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``} |
|
|
available modes for PyTorch Tensor: {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}. |
|
|
One of the listed string values or a user supplied function. Defaults to ``"constant"``. |
|
|
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html |
|
|
https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html |
|
|
It also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
method: {``"symmetric"``, ``"end"``} |
|
|
Pad image symmetrically on every side or only pad at the end sides. Defaults to ``"symmetric"``. |
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lazy: a flag to indicate whether this transform should execute lazily or not. Defaults to False. |
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|
pad_kwargs: other arguments for the `np.pad` or `torch.pad` function. |
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|
note that `np.pad` treats channel dimension as the first dimension. |
|
|
|
|
|
""" |
|
|
|
|
|
def __init__( |
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|
self, |
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|
keys: KeysCollection, |
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|
spatial_size: Sequence[int] | int, |
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|
mode: SequenceStr = PytorchPadMode.CONSTANT, |
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|
allow_missing_keys: bool = False, |
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|
method: str = Method.SYMMETRIC, |
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|
lazy: bool = False, |
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|
**pad_kwargs, |
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|
) -> None: |
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|
padcropper = ResizeWithPadOrCrop(spatial_size=spatial_size, method=method, **pad_kwargs, lazy=lazy) |
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|
super().__init__( |
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|
keys, padder=padcropper, mode=mode, allow_missing_keys=allow_missing_keys, lazy=lazy |
|
|
) |
|
|
|
|
|
|
|
|
class BoundingRectd(MapTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.BoundingRect`. |
|
|
|
|
|
Args: |
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|
keys: keys of the corresponding items to be transformed. |
|
|
See also: monai.transforms.MapTransform |
|
|
bbox_key_postfix: the output bounding box coordinates will be |
|
|
written to the value of `{key}_{bbox_key_postfix}`. |
|
|
select_fn: function to select expected foreground, default is to select values > 0. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
""" |
|
|
|
|
|
backend = BoundingRect.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
bbox_key_postfix: str = "bbox", |
|
|
select_fn: Callable = is_positive, |
|
|
allow_missing_keys: bool = False, |
|
|
): |
|
|
super().__init__(keys, allow_missing_keys) |
|
|
self.bbox = BoundingRect(select_fn=select_fn) |
|
|
self.bbox_key_postfix = bbox_key_postfix |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
|
|
""" |
|
|
See also: :py:class:`monai.transforms.utils.generate_spatial_bounding_box`. |
|
|
""" |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
bbox = self.bbox(d[key]) |
|
|
key_to_add = f"{key}_{self.bbox_key_postfix}" |
|
|
if key_to_add in d: |
|
|
raise KeyError(f"Bounding box data with key {key_to_add} already exists.") |
|
|
d[key_to_add] = bbox |
|
|
return d |
|
|
|
|
|
|
|
|
PadD = PadDict = Padd |
|
|
SpatialPadD = SpatialPadDict = SpatialPadd |
|
|
BorderPadD = BorderPadDict = BorderPadd |
|
|
DivisiblePadD = DivisiblePadDict = DivisiblePadd |
|
|
CropD = CropDict = Cropd |
|
|
RandCropD = RandCropDict = RandCropd |
|
|
SpatialCropD = SpatialCropDict = SpatialCropd |
|
|
CenterSpatialCropD = CenterSpatialCropDict = CenterSpatialCropd |
|
|
CenterScaleCropD = CenterScaleCropDict = CenterScaleCropd |
|
|
RandSpatialCropD = RandSpatialCropDict = RandSpatialCropd |
|
|
RandScaleCropD = RandScaleCropDict = RandScaleCropd |
|
|
RandSpatialCropSamplesD = RandSpatialCropSamplesDict = RandSpatialCropSamplesd |
|
|
CropForegroundD = CropForegroundDict = CropForegroundd |
|
|
RandWeightedCropD = RandWeightedCropDict = RandWeightedCropd |
|
|
RandCropByPosNegLabelD = RandCropByPosNegLabelDict = RandCropByPosNegLabeld |
|
|
RandCropByLabelClassesD = RandCropByLabelClassesDict = RandCropByLabelClassesd |
|
|
ResizeWithPadOrCropD = ResizeWithPadOrCropDict = ResizeWithPadOrCropd |
|
|
BoundingRectD = BoundingRectDict = BoundingRectd |
|
|
|