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""" |
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A collection of dictionary-based wrappers around the "vanilla" transforms for spatial operations |
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defined in :py:class:`monai.transforms.spatial.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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import warnings |
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from collections.abc import Hashable, Mapping, Sequence |
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from typing import Any, cast |
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import numpy as np |
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import torch |
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from monai.config import DtypeLike, KeysCollection, SequenceStr |
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from monai.config.type_definitions import NdarrayOrTensor |
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from monai.data.meta_obj import get_track_meta |
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from monai.data.meta_tensor import MetaTensor |
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from monai.networks.layers.simplelayers import GaussianFilter |
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from monai.transforms.croppad.array import CenterSpatialCrop |
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from monai.transforms.inverse import InvertibleTransform |
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from monai.transforms.spatial.array import ( |
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Affine, |
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Flip, |
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GridDistortion, |
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GridPatch, |
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GridSplit, |
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Orientation, |
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Rand2DElastic, |
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Rand3DElastic, |
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RandAffine, |
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RandAxisFlip, |
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RandGridDistortion, |
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RandGridPatch, |
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RandRotate, |
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RandSimulateLowResolution, |
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RandZoom, |
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ResampleToMatch, |
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Resize, |
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Rotate, |
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Rotate90, |
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Spacing, |
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SpatialResample, |
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Zoom, |
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) |
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from monai.transforms.traits import MultiSampleTrait |
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from monai.transforms.transform import LazyTransform, MapTransform, RandomizableTransform |
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from monai.transforms.utils import create_grid |
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from monai.utils import ( |
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GridSampleMode, |
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GridSamplePadMode, |
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InterpolateMode, |
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NumpyPadMode, |
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convert_to_tensor, |
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ensure_tuple, |
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ensure_tuple_rep, |
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fall_back_tuple, |
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) |
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from monai.utils.enums import TraceKeys |
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from monai.utils.module import optional_import |
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nib, _ = optional_import("nibabel") |
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__all__ = [ |
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"SpatialResampled", |
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"ResampleToMatchd", |
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"Spacingd", |
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"Orientationd", |
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"Rotate90d", |
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"RandRotate90d", |
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"Resized", |
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"Affined", |
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"RandAffined", |
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"Rand2DElasticd", |
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"Rand3DElasticd", |
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"Flipd", |
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"RandFlipd", |
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"GridDistortiond", |
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"RandGridDistortiond", |
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"RandAxisFlipd", |
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"Rotated", |
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"RandRotated", |
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"Zoomd", |
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"RandZoomd", |
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"SpatialResampleD", |
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"SpatialResampleDict", |
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"SpacingD", |
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"SpacingDict", |
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"OrientationD", |
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"OrientationDict", |
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"Rotate90D", |
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"Rotate90Dict", |
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"RandRotate90D", |
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"RandRotate90Dict", |
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"ResizeD", |
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"ResizeDict", |
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"AffineD", |
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"AffineDict", |
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"RandAffineD", |
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"RandAffineDict", |
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"Rand2DElasticD", |
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"Rand2DElasticDict", |
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"Rand3DElasticD", |
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|
"Rand3DElasticDict", |
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"FlipD", |
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|
"FlipDict", |
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|
"RandFlipD", |
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"RandFlipDict", |
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"GridDistortionD", |
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"GridDistortionDict", |
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"RandGridDistortionD", |
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"RandGridDistortionDict", |
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|
"RandAxisFlipD", |
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"RandAxisFlipDict", |
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"RotateD", |
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"RotateDict", |
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"RandRotateD", |
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"RandRotateDict", |
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"ZoomD", |
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"ZoomDict", |
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"RandZoomD", |
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"RandZoomDict", |
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"GridSplitd", |
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"GridSplitD", |
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"GridSplitDict", |
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"GridPatchd", |
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"GridPatchD", |
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|
"GridPatchDict", |
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|
"RandGridPatchd", |
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"RandGridPatchD", |
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|
"RandGridPatchDict", |
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"RandSimulateLowResolutiond", |
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"RandSimulateLowResolutionD", |
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"RandSimulateLowResolutionDict", |
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] |
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class SpatialResampled(MapTransform, InvertibleTransform, LazyTransform): |
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""" |
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|
Dictionary-based wrapper of :py:class:`monai.transforms.SpatialResample`. |
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|
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This transform assumes the ``data`` dictionary has a key for the input |
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|
data's metadata and contains ``src_affine`` and ``dst_affine`` required by |
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|
`SpatialResample`. The key is formed by ``key_{meta_key_postfix}``. The |
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transform will swap ``src_affine`` and ``dst_affine`` affine (with potential data type |
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|
changes) in the dictionary so that ``src_affine`` always refers to the current |
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status of affine. |
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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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|
See also: |
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|
:py:class:`monai.transforms.SpatialResample` |
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|
""" |
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backend = SpatialResample.backend |
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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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mode: SequenceStr = GridSampleMode.BILINEAR, |
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|
padding_mode: SequenceStr = GridSamplePadMode.BORDER, |
|
|
align_corners: Sequence[bool] | bool = False, |
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|
dtype: Sequence[DtypeLike] | DtypeLike = np.float64, |
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|
dst_keys: KeysCollection | None = "dst_affine", |
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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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|
""" |
|
|
Args: |
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|
keys: keys of the corresponding items to be transformed. |
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|
mode: {``"bilinear"``, ``"nearest"``} or spline interpolation order 0-5 (integers). |
|
|
Interpolation mode to calculate output values. Defaults to ``"bilinear"``. |
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|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
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|
When it's an integer, the numpy (cpu tensor)/cupy (cuda tensor) backends will be used |
|
|
and the value represents the order of the spline interpolation. |
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|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
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|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``} |
|
|
Padding mode for outside grid values. Defaults to ``"border"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When `mode` is an integer, using numpy/cupy backends, this argument accepts |
|
|
{'reflect', 'grid-mirror', 'constant', 'grid-constant', 'nearest', 'mirror', 'grid-wrap', 'wrap'}. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
align_corners: Geometrically, we consider the pixels of the input as squares rather than points. |
|
|
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample |
|
|
It also can be a sequence of bool, each element corresponds to a key in ``keys``. |
|
|
dtype: data type for resampling computation. Defaults to ``float64`` for best precision. |
|
|
If None, use the data type of input data. To be compatible with other modules, |
|
|
the output data type is always ``float32``. |
|
|
It also can be a sequence of dtypes, each element corresponds to a key in ``keys``. |
|
|
dst_keys: the key of the corresponding ``dst_affine`` in the metadata dictionary. |
|
|
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. |
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.sp_transform = SpatialResample(lazy=lazy) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
self.align_corners = ensure_tuple_rep(align_corners, len(self.keys)) |
|
|
self.dtype = ensure_tuple_rep(dtype, len(self.keys)) |
|
|
self.dst_keys = ensure_tuple_rep(dst_keys, len(self.keys)) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool) -> None: |
|
|
self._lazy = val |
|
|
self.sp_transform.lazy = val |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
d: dict = dict(data) |
|
|
for key, mode, padding_mode, align_corners, dtype, dst_key in self.key_iterator( |
|
|
d, self.mode, self.padding_mode, self.align_corners, self.dtype, self.dst_keys |
|
|
): |
|
|
d[key] = self.sp_transform( |
|
|
img=d[key], |
|
|
dst_affine=d[dst_key], |
|
|
spatial_size=None, |
|
|
mode=mode, |
|
|
padding_mode=padding_mode, |
|
|
align_corners=align_corners, |
|
|
dtype=dtype, |
|
|
lazy=lazy_, |
|
|
) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.sp_transform.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class ResampleToMatchd(MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.ResampleToMatch`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
""" |
|
|
|
|
|
backend = ResampleToMatch.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
key_dst: str, |
|
|
mode: SequenceStr = GridSampleMode.BILINEAR, |
|
|
padding_mode: SequenceStr = GridSamplePadMode.BORDER, |
|
|
align_corners: Sequence[bool] | bool = False, |
|
|
dtype: Sequence[DtypeLike] | DtypeLike = np.float64, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
): |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
key_dst: key of image to resample to match. |
|
|
mode: {``"bilinear"``, ``"nearest"``} or spline interpolation order 0-5 (integers). |
|
|
Interpolation mode to calculate output values. Defaults to ``"bilinear"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When it's an integer, the numpy (cpu tensor)/cupy (cuda tensor) backends will be used |
|
|
and the value represents the order of the spline interpolation. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``} |
|
|
Padding mode for outside grid values. Defaults to ``"border"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When `mode` is an integer, using numpy/cupy backends, this argument accepts |
|
|
{'reflect', 'grid-mirror', 'constant', 'grid-constant', 'nearest', 'mirror', 'grid-wrap', 'wrap'}. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
align_corners: Geometrically, we consider the pixels of the input as squares rather than points. |
|
|
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample |
|
|
It also can be a sequence of bool, each element corresponds to a key in ``keys``. |
|
|
dtype: data type for resampling computation. Defaults to ``float64`` for best precision. |
|
|
If None, use the data type of input data. To be compatible with other modules, |
|
|
the output data type is always ``float32``. |
|
|
It also can be a sequence of dtypes, 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 |
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.key_dst = key_dst |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
self.align_corners = ensure_tuple_rep(align_corners, len(self.keys)) |
|
|
self.dtype = ensure_tuple_rep(dtype, len(self.keys)) |
|
|
self.resampler = ResampleToMatch(lazy=lazy) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool) -> None: |
|
|
self._lazy = val |
|
|
self.resampler.lazy = val |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
d = dict(data) |
|
|
for key, mode, padding_mode, align_corners, dtype in self.key_iterator( |
|
|
d, self.mode, self.padding_mode, self.align_corners, self.dtype |
|
|
): |
|
|
d[key] = self.resampler( |
|
|
img=d[key], |
|
|
img_dst=d[self.key_dst], |
|
|
mode=mode, |
|
|
padding_mode=padding_mode, |
|
|
align_corners=align_corners, |
|
|
dtype=dtype, |
|
|
lazy=lazy_, |
|
|
) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.resampler.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class Spacingd(MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.Spacing`. |
|
|
|
|
|
This transform assumes the ``data`` dictionary has a key for the input |
|
|
data's metadata and contains `affine` field. The key is formed by ``key_{meta_key_postfix}``. |
|
|
|
|
|
After resampling the input array, this transform will write the new affine |
|
|
to the `affine` field of metadata which is formed by ``key_{meta_key_postfix}``. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
see also: |
|
|
:py:class:`monai.transforms.Spacing` |
|
|
""" |
|
|
|
|
|
backend = Spacing.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
pixdim: Sequence[float] | float, |
|
|
diagonal: bool = False, |
|
|
mode: SequenceStr = GridSampleMode.BILINEAR, |
|
|
padding_mode: SequenceStr = GridSamplePadMode.BORDER, |
|
|
align_corners: Sequence[bool] | bool = False, |
|
|
dtype: Sequence[DtypeLike] | DtypeLike = np.float64, |
|
|
scale_extent: bool = False, |
|
|
recompute_affine: bool = False, |
|
|
min_pixdim: Sequence[float] | float | None = None, |
|
|
max_pixdim: Sequence[float] | float | None = None, |
|
|
ensure_same_shape: bool = True, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
pixdim: output voxel spacing. if providing a single number, will use it for the first dimension. |
|
|
items of the pixdim sequence map to the spatial dimensions of input image, if length |
|
|
of pixdim sequence is longer than image spatial dimensions, will ignore the longer part, |
|
|
if shorter, will pad with `1.0`. |
|
|
if the components of the `pixdim` are non-positive values, the transform will use the |
|
|
corresponding components of the original pixdim, which is computed from the `affine` |
|
|
matrix of input image. |
|
|
diagonal: whether to resample the input to have a diagonal affine matrix. |
|
|
If True, the input data is resampled to the following affine:: |
|
|
|
|
|
np.diag((pixdim_0, pixdim_1, pixdim_2, 1)) |
|
|
|
|
|
This effectively resets the volume to the world coordinate system (RAS+ in nibabel). |
|
|
The original orientation, rotation, shearing are not preserved. |
|
|
|
|
|
If False, the axes orientation, orthogonal rotation and |
|
|
translations components from the original affine will be |
|
|
preserved in the target affine. This option will not flip/swap |
|
|
axes against the original ones. |
|
|
mode: {``"bilinear"``, ``"nearest"``} or spline interpolation order 0-5 (integers). |
|
|
Interpolation mode to calculate output values. Defaults to ``"bilinear"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When it's an integer, the numpy (cpu tensor)/cupy (cuda tensor) backends will be used |
|
|
and the value represents the order of the spline interpolation. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``} |
|
|
Padding mode for outside grid values. Defaults to ``"border"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When `mode` is an integer, using numpy/cupy backends, this argument accepts |
|
|
{'reflect', 'grid-mirror', 'constant', 'grid-constant', 'nearest', 'mirror', 'grid-wrap', 'wrap'}. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
align_corners: Geometrically, we consider the pixels of the input as squares rather than points. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
It also can be a sequence of bool, each element corresponds to a key in ``keys``. |
|
|
dtype: data type for resampling computation. Defaults to ``float64`` for best precision. |
|
|
If None, use the data type of input data. To be compatible with other modules, |
|
|
the output data type is always ``float32``. |
|
|
It also can be a sequence of dtypes, each element corresponds to a key in ``keys``. |
|
|
scale_extent: whether the scale is computed based on the spacing or the full extent of voxels, |
|
|
default False. The option is ignored if output spatial size is specified when calling this transform. |
|
|
See also: :py:func:`monai.data.utils.compute_shape_offset`. When this is True, `align_corners` |
|
|
should be `True` because `compute_shape_offset` already provides the corner alignment shift/scaling. |
|
|
recompute_affine: whether to recompute affine based on the output shape. The affine computed |
|
|
analytically does not reflect the potential quantization errors in terms of the output shape. |
|
|
Set this flag to True to recompute the output affine based on the actual pixdim. Default to ``False``. |
|
|
min_pixdim: minimal input spacing to be resampled. If provided, input image with a larger spacing than this |
|
|
value will be kept in its original spacing (not be resampled to `pixdim`). Set it to `None` to use the |
|
|
value of `pixdim`. Default to `None`. |
|
|
max_pixdim: maximal input spacing to be resampled. If provided, input image with a smaller spacing than this |
|
|
value will be kept in its original spacing (not be resampled to `pixdim`). Set it to `None` to use the |
|
|
value of `pixdim`. Default to `None`. |
|
|
ensure_same_shape: when the inputs have the same spatial shape, and almost the same pixdim, |
|
|
whether to ensure exactly the same output spatial shape. Default to True. |
|
|
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 |
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.spacing_transform = Spacing( |
|
|
pixdim, |
|
|
diagonal=diagonal, |
|
|
recompute_affine=recompute_affine, |
|
|
min_pixdim=min_pixdim, |
|
|
max_pixdim=max_pixdim, |
|
|
lazy=lazy, |
|
|
) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
self.align_corners = ensure_tuple_rep(align_corners, len(self.keys)) |
|
|
self.dtype = ensure_tuple_rep(dtype, len(self.keys)) |
|
|
self.scale_extent = ensure_tuple_rep(scale_extent, len(self.keys)) |
|
|
self.ensure_same_shape = ensure_same_shape |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool) -> None: |
|
|
self._lazy = val |
|
|
self.spacing_transform.lazy = val |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d: dict = dict(data) |
|
|
|
|
|
_init_shape, _pixdim, should_match = None, None, False |
|
|
output_shape_k = None |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
|
|
|
for key, mode, padding_mode, align_corners, dtype, scale_extent in self.key_iterator( |
|
|
d, self.mode, self.padding_mode, self.align_corners, self.dtype, self.scale_extent |
|
|
): |
|
|
if self.ensure_same_shape and isinstance(d[key], MetaTensor): |
|
|
if _init_shape is None and _pixdim is None: |
|
|
_init_shape, _pixdim = d[key].peek_pending_shape(), d[key].pixdim |
|
|
else: |
|
|
should_match = np.allclose(_init_shape, d[key].peek_pending_shape()) and np.allclose( |
|
|
_pixdim, d[key].pixdim, atol=1e-3 |
|
|
) |
|
|
d[key] = self.spacing_transform( |
|
|
data_array=d[key], |
|
|
mode=mode, |
|
|
padding_mode=padding_mode, |
|
|
align_corners=align_corners, |
|
|
dtype=dtype, |
|
|
scale_extent=scale_extent, |
|
|
output_spatial_shape=output_shape_k if should_match else None, |
|
|
lazy=lazy_, |
|
|
) |
|
|
if output_shape_k is None: |
|
|
output_shape_k = d[key].peek_pending_shape() if isinstance(d[key], MetaTensor) else d[key].shape[1:] |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.spacing_transform.inverse(cast(torch.Tensor, d[key])) |
|
|
return d |
|
|
|
|
|
|
|
|
class Orientationd(MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.Orientation`. |
|
|
|
|
|
This transform assumes the channel-first input format. |
|
|
In the case of using this transform for normalizing the orientations of images, |
|
|
it should be used before any anisotropic spatial transforms. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
""" |
|
|
|
|
|
backend = Orientation.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
axcodes: str | None = None, |
|
|
as_closest_canonical: bool = False, |
|
|
labels: Sequence[tuple[str, str]] | None = (("L", "R"), ("P", "A"), ("I", "S")), |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
axcodes: N elements sequence for spatial ND input's orientation. |
|
|
e.g. axcodes='RAS' represents 3D orientation: |
|
|
(Left, Right), (Posterior, Anterior), (Inferior, Superior). |
|
|
default orientation labels options are: 'L' and 'R' for the first dimension, |
|
|
'P' and 'A' for the second, 'I' and 'S' for the third. |
|
|
as_closest_canonical: if True, load the image as closest to canonical axis format. |
|
|
labels: optional, None or sequence of (2,) sequences |
|
|
(2,) sequences are labels for (beginning, end) of output axis. |
|
|
Defaults to ``(('L', 'R'), ('P', 'A'), ('I', 'S'))``. |
|
|
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: |
|
|
`nibabel.orientations.ornt2axcodes`. |
|
|
|
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.ornt_transform = Orientation( |
|
|
axcodes=axcodes, as_closest_canonical=as_closest_canonical, labels=labels, lazy=lazy |
|
|
) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool) -> None: |
|
|
self._lazy = val |
|
|
self.ornt_transform.lazy = val |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d: dict = dict(data) |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.ornt_transform(d[key], lazy=lazy_) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.ornt_transform.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class Rotate90d(MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.Rotate90`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
""" |
|
|
|
|
|
backend = Rotate90.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
k: int = 1, |
|
|
spatial_axes: tuple[int, int] = (0, 1), |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
k: number of times to rotate by 90 degrees. |
|
|
spatial_axes: 2 int numbers, defines the plane to rotate with 2 spatial axes. |
|
|
Default: (0, 1), this is the first two axis in 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 |
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.rotator = Rotate90(k, spatial_axes, lazy=lazy) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool) -> None: |
|
|
self._lazy = val |
|
|
self.rotator.lazy = val |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.rotator(d[key], lazy=lazy_) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.rotator.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class RandRotate90d(RandomizableTransform, MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based version :py:class:`monai.transforms.RandRotate90`. |
|
|
With probability `prob`, input arrays are rotated by 90 degrees |
|
|
in the plane specified by `spatial_axes`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
""" |
|
|
|
|
|
backend = Rotate90.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
prob: float = 0.1, |
|
|
max_k: int = 3, |
|
|
spatial_axes: tuple[int, int] = (0, 1), |
|
|
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` |
|
|
prob: probability of rotating. |
|
|
(Default 0.1, with 10% probability it returns a rotated array.) |
|
|
max_k: number of rotations will be sampled from `np.random.randint(max_k) + 1`. |
|
|
(Default 3) |
|
|
spatial_axes: 2 int numbers, defines the plane to rotate with 2 spatial axes. |
|
|
Default: (0, 1), this is the first two axis in 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 |
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
RandomizableTransform.__init__(self, prob) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
|
|
|
self.max_k = max_k |
|
|
self.spatial_axes = spatial_axes |
|
|
|
|
|
self._rand_k = 0 |
|
|
|
|
|
def randomize(self, data: Any | None = None) -> None: |
|
|
self._rand_k = self.R.randint(self.max_k) + 1 |
|
|
super().randomize(None) |
|
|
|
|
|
def __call__( |
|
|
self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None |
|
|
) -> Mapping[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
self.randomize() |
|
|
d = dict(data) |
|
|
|
|
|
|
|
|
|
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
rotator = Rotate90(self._rand_k, self.spatial_axes, lazy=lazy_) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = rotator(d[key]) if self._do_transform else convert_to_tensor(d[key], track_meta=get_track_meta()) |
|
|
self.push_transform(d[key], replace=True, lazy=lazy_) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
if not isinstance(d[key], MetaTensor): |
|
|
continue |
|
|
xform = self.pop_transform(d[key]) |
|
|
if xform[TraceKeys.DO_TRANSFORM]: |
|
|
d[key] = Rotate90().inverse_transform(d[key], xform[TraceKeys.EXTRA_INFO]) |
|
|
return d |
|
|
|
|
|
|
|
|
class Resized(MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.Resize`. |
|
|
|
|
|
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` |
|
|
spatial_size: expected shape of spatial dimensions after resize operation. |
|
|
if some components of the `spatial_size` are non-positive values, the transform will use the |
|
|
corresponding components of img size. For example, `spatial_size=(32, -1)` will be adapted |
|
|
to `(32, 64)` if the second spatial dimension size of img is `64`. |
|
|
size_mode: should be "all" or "longest", if "all", will use `spatial_size` for all the spatial dims, |
|
|
if "longest", rescale the image so that only the longest side is equal to specified `spatial_size`, |
|
|
which must be an int number in this case, keeping the aspect ratio of the initial image, refer to: |
|
|
https://albumentations.ai/docs/api_reference/augmentations/geometric/resize/ |
|
|
#albumentations.augmentations.geometric.resize.LongestMaxSize. |
|
|
mode: {``"nearest"``, ``"nearest-exact"``, ``"linear"``, ``"bilinear"``, ``"bicubic"``, ``"trilinear"``, ``"area"``} |
|
|
The interpolation mode. Defaults to ``"area"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.interpolate.html |
|
|
It also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
align_corners: This only has an effect when mode is |
|
|
'linear', 'bilinear', 'bicubic' or 'trilinear'. Default: None. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.interpolate.html |
|
|
It also can be a sequence of bool or None, each element corresponds to a key in ``keys``. |
|
|
anti_aliasing: bool |
|
|
Whether to apply a Gaussian filter to smooth the image prior |
|
|
to downsampling. It is crucial to filter when downsampling |
|
|
the image to avoid aliasing artifacts. See also ``skimage.transform.resize`` |
|
|
anti_aliasing_sigma: {float, tuple of floats}, optional |
|
|
Standard deviation for Gaussian filtering used when anti-aliasing. |
|
|
By default, this value is chosen as (s - 1) / 2 where s is the |
|
|
downsampling factor, where s > 1. For the up-size case, s < 1, no |
|
|
anti-aliasing is performed prior to rescaling. |
|
|
dtype: data type for resampling computation. Defaults to ``float32``. |
|
|
If None, use the data type of input data. |
|
|
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 = Resize.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
spatial_size: Sequence[int] | int, |
|
|
size_mode: str = "all", |
|
|
mode: SequenceStr = InterpolateMode.AREA, |
|
|
align_corners: Sequence[bool | None] | bool | None = None, |
|
|
anti_aliasing: Sequence[bool] | bool = False, |
|
|
anti_aliasing_sigma: Sequence[Sequence[float] | float | None] | Sequence[float] | float | None = None, |
|
|
dtype: Sequence[DtypeLike | torch.dtype] | DtypeLike | torch.dtype = np.float32, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.align_corners = ensure_tuple_rep(align_corners, len(self.keys)) |
|
|
self.dtype = ensure_tuple_rep(dtype, len(self.keys)) |
|
|
self.anti_aliasing = ensure_tuple_rep(anti_aliasing, len(self.keys)) |
|
|
self.anti_aliasing_sigma = ensure_tuple_rep(anti_aliasing_sigma, len(self.keys)) |
|
|
self.resizer = Resize(spatial_size=spatial_size, size_mode=size_mode, lazy=lazy) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool) -> None: |
|
|
self._lazy = val |
|
|
self.resizer.lazy = val |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key, mode, align_corners, anti_aliasing, anti_aliasing_sigma, dtype in self.key_iterator( |
|
|
d, self.mode, self.align_corners, self.anti_aliasing, self.anti_aliasing_sigma, self.dtype |
|
|
): |
|
|
d[key] = self.resizer( |
|
|
d[key], |
|
|
mode=mode, |
|
|
align_corners=align_corners, |
|
|
anti_aliasing=anti_aliasing, |
|
|
anti_aliasing_sigma=anti_aliasing_sigma, |
|
|
dtype=dtype, |
|
|
lazy=lazy_, |
|
|
) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.resizer.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class Affined(MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.Affine`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
""" |
|
|
|
|
|
backend = Affine.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
rotate_params: Sequence[float] | float | None = None, |
|
|
shear_params: Sequence[float] | float | None = None, |
|
|
translate_params: Sequence[float] | float | None = None, |
|
|
scale_params: Sequence[float] | float | None = None, |
|
|
affine: NdarrayOrTensor | None = None, |
|
|
spatial_size: Sequence[int] | int | None = None, |
|
|
mode: SequenceStr = GridSampleMode.BILINEAR, |
|
|
padding_mode: SequenceStr = GridSamplePadMode.REFLECTION, |
|
|
device: torch.device | None = None, |
|
|
dtype: DtypeLike | torch.dtype = np.float32, |
|
|
align_corners: bool = False, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
rotate_params: a rotation angle in radians, a scalar for 2D image, a tuple of 3 floats for 3D. |
|
|
Defaults to no rotation. |
|
|
shear_params: shearing factors for affine matrix, take a 3D affine as example:: |
|
|
|
|
|
[ |
|
|
[1.0, params[0], params[1], 0.0], |
|
|
[params[2], 1.0, params[3], 0.0], |
|
|
[params[4], params[5], 1.0, 0.0], |
|
|
[0.0, 0.0, 0.0, 1.0], |
|
|
] |
|
|
|
|
|
a tuple of 2 floats for 2D, a tuple of 6 floats for 3D. Defaults to no shearing. |
|
|
translate_params: a tuple of 2 floats for 2D, a tuple of 3 floats for 3D. Translation is in |
|
|
pixel/voxel relative to the center of the input image. Defaults to no translation. |
|
|
scale_params: scale factor for every spatial dims. a tuple of 2 floats for 2D, |
|
|
a tuple of 3 floats for 3D. Defaults to `1.0`. |
|
|
affine: if applied, ignore the params (`rotate_params`, etc.) and use the |
|
|
supplied matrix. Should be square with each side = num of image spatial |
|
|
dimensions + 1. |
|
|
spatial_size: output image spatial size. |
|
|
if `spatial_size` and `self.spatial_size` are not defined, or smaller than 1, |
|
|
the transform will use the spatial size of `img`. |
|
|
if some components of the `spatial_size` are non-positive values, the transform will use the |
|
|
corresponding components of img size. For example, `spatial_size=(32, -1)` will be adapted |
|
|
to `(32, 64)` if the second spatial dimension size of img is `64`. |
|
|
mode: {``"bilinear"``, ``"nearest"``} or spline interpolation order 0-5 (integers). |
|
|
Interpolation mode to calculate output values. Defaults to ``"bilinear"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When it's an integer, the numpy (cpu tensor)/cupy (cuda tensor) backends will be used |
|
|
and the value represents the order of the spline interpolation. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``} |
|
|
Padding mode for outside grid values. Defaults to ``"reflection"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When `mode` is an integer, using numpy/cupy backends, this argument accepts |
|
|
{'reflect', 'grid-mirror', 'constant', 'grid-constant', 'nearest', 'mirror', 'grid-wrap', 'wrap'}. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
device: device on which the tensor will be allocated. |
|
|
dtype: data type for resampling computation. Defaults to ``float32``. |
|
|
If ``None``, use the data type of input data. To be compatible with other modules, |
|
|
the output data type is always `float32`. |
|
|
align_corners: Defaults to False. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
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.compose.MapTransform` |
|
|
- :py:class:`RandAffineGrid` for the random affine parameters configurations. |
|
|
|
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.affine = Affine( |
|
|
rotate_params=rotate_params, |
|
|
shear_params=shear_params, |
|
|
translate_params=translate_params, |
|
|
scale_params=scale_params, |
|
|
affine=affine, |
|
|
spatial_size=spatial_size, |
|
|
device=device, |
|
|
dtype=dtype, |
|
|
align_corners=align_corners, |
|
|
lazy=lazy, |
|
|
) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool) -> None: |
|
|
self._lazy = val |
|
|
self.affine.lazy = val |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
d = dict(data) |
|
|
for key, mode, padding_mode in self.key_iterator(d, self.mode, self.padding_mode): |
|
|
d[key], _ = self.affine(d[key], mode=mode, padding_mode=padding_mode, lazy=lazy_) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.affine.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class RandAffined(RandomizableTransform, MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.RandAffine`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
""" |
|
|
|
|
|
backend = RandAffine.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
spatial_size: Sequence[int] | int | None = None, |
|
|
prob: float = 0.1, |
|
|
rotate_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
shear_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
translate_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
scale_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
mode: SequenceStr = GridSampleMode.BILINEAR, |
|
|
padding_mode: SequenceStr = GridSamplePadMode.REFLECTION, |
|
|
cache_grid: bool = False, |
|
|
device: torch.device | None = None, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
spatial_size: output image spatial size. |
|
|
if `spatial_size` and `self.spatial_size` are not defined, or smaller than 1, |
|
|
the transform will use the spatial size of `img`. |
|
|
if some components of the `spatial_size` are non-positive values, the transform will use the |
|
|
corresponding components of img size. For example, `spatial_size=(32, -1)` will be adapted |
|
|
to `(32, 64)` if the second spatial dimension size of img is `64`. |
|
|
prob: probability of returning a randomized affine grid. |
|
|
defaults to 0.1, with 10% chance returns a randomized grid. |
|
|
rotate_range: angle range in radians. If element `i` is a pair of (min, max) values, then |
|
|
`uniform[-rotate_range[i][0], rotate_range[i][1])` will be used to generate the rotation parameter |
|
|
for the `i`th spatial dimension. If not, `uniform[-rotate_range[i], rotate_range[i])` will be used. |
|
|
This can be altered on a per-dimension basis. E.g., `((0,3), 1, ...)`: for dim0, rotation will be |
|
|
in range `[0, 3]`, and for dim1 `[-1, 1]` will be used. Setting a single value will use `[-x, x]` |
|
|
for dim0 and nothing for the remaining dimensions. |
|
|
shear_range: shear range with format matching `rotate_range`, it defines the range to randomly select |
|
|
shearing factors(a tuple of 2 floats for 2D, a tuple of 6 floats for 3D) for affine matrix, |
|
|
take a 3D affine as example:: |
|
|
|
|
|
[ |
|
|
[1.0, params[0], params[1], 0.0], |
|
|
[params[2], 1.0, params[3], 0.0], |
|
|
[params[4], params[5], 1.0, 0.0], |
|
|
[0.0, 0.0, 0.0, 1.0], |
|
|
] |
|
|
|
|
|
translate_range: translate range with format matching `rotate_range`, it defines the range to randomly |
|
|
select pixel/voxel to translate for every spatial dims. |
|
|
scale_range: scaling range with format matching `rotate_range`. it defines the range to randomly select |
|
|
the scale factor to translate for every spatial dims. A value of 1.0 is added to the result. |
|
|
This allows 0 to correspond to no change (i.e., a scaling of 1.0). |
|
|
mode: {``"bilinear"``, ``"nearest"``} or spline interpolation order 0-5 (integers). |
|
|
Interpolation mode to calculate output values. Defaults to ``"bilinear"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When it's an integer, the numpy (cpu tensor)/cupy (cuda tensor) backends will be used |
|
|
and the value represents the order of the spline interpolation. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``} |
|
|
Padding mode for outside grid values. Defaults to ``"reflection"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When `mode` is an integer, using numpy/cupy backends, this argument accepts |
|
|
{'reflect', 'grid-mirror', 'constant', 'grid-constant', 'nearest', 'mirror', 'grid-wrap', 'wrap'}. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
cache_grid: whether to cache the identity sampling grid. |
|
|
If the spatial size is not dynamically defined by input image, enabling this option could |
|
|
accelerate the transform. |
|
|
device: device on which the tensor will be allocated. |
|
|
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.compose.MapTransform` |
|
|
- :py:class:`RandAffineGrid` for the random affine parameters configurations. |
|
|
|
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
RandomizableTransform.__init__(self, prob) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.rand_affine = RandAffine( |
|
|
prob=1.0, |
|
|
rotate_range=rotate_range, |
|
|
shear_range=shear_range, |
|
|
translate_range=translate_range, |
|
|
scale_range=scale_range, |
|
|
spatial_size=spatial_size, |
|
|
cache_grid=cache_grid, |
|
|
device=device, |
|
|
lazy=lazy, |
|
|
) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool) -> None: |
|
|
self._lazy = val |
|
|
self.rand_affine.lazy = val |
|
|
|
|
|
def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = None) -> RandAffined: |
|
|
self.rand_affine.set_random_state(seed, state) |
|
|
super().set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def __call__( |
|
|
self, data: Mapping[Hashable, NdarrayOrTensor], lazy: bool | None = None |
|
|
) -> dict[Hashable, NdarrayOrTensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
first_key: Hashable = self.first_key(d) |
|
|
if first_key == (): |
|
|
out: dict[Hashable, NdarrayOrTensor] = convert_to_tensor(d, track_meta=get_track_meta()) |
|
|
return out |
|
|
|
|
|
self.randomize(None) |
|
|
|
|
|
self.rand_affine.randomize() |
|
|
|
|
|
item = d[first_key] |
|
|
spatial_size = item.peek_pending_shape() if isinstance(item, MetaTensor) else item.shape[1:] |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
|
|
|
sp_size = fall_back_tuple(self.rand_affine.spatial_size, spatial_size) |
|
|
|
|
|
do_resampling = self._do_transform or (sp_size != ensure_tuple(spatial_size)) |
|
|
|
|
|
grid = None |
|
|
if do_resampling: |
|
|
grid = self.rand_affine.get_identity_grid(sp_size, lazy=lazy_) |
|
|
if self._do_transform: |
|
|
grid = self.rand_affine.rand_affine_grid(sp_size, grid=grid, lazy=lazy_) |
|
|
grid = 0 if grid is None else grid |
|
|
|
|
|
for key, mode, padding_mode in self.key_iterator(d, self.mode, self.padding_mode): |
|
|
|
|
|
if do_resampling: |
|
|
d[key] = self.rand_affine(d[key], None, mode, padding_mode, True, grid, lazy=lazy_) |
|
|
else: |
|
|
d[key] = convert_to_tensor(d[key], track_meta=get_track_meta(), dtype=torch.float32) |
|
|
self._do_transform = do_resampling |
|
|
self.push_transform(d[key], replace=True, lazy=lazy_) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
tr = self.pop_transform(d[key]) |
|
|
if TraceKeys.EXTRA_INFO not in tr[TraceKeys.EXTRA_INFO]: |
|
|
continue |
|
|
do_resampling = tr[TraceKeys.EXTRA_INFO][TraceKeys.EXTRA_INFO]["do_resampling"] |
|
|
if do_resampling: |
|
|
d[key].applied_operations.append(tr[TraceKeys.EXTRA_INFO]) |
|
|
d[key] = self.rand_affine.inverse(d[key]) |
|
|
|
|
|
return d |
|
|
|
|
|
|
|
|
class Rand2DElasticd(RandomizableTransform, MapTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.Rand2DElastic`. |
|
|
""" |
|
|
|
|
|
backend = Rand2DElastic.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
spacing: tuple[float, float] | float, |
|
|
magnitude_range: tuple[float, float], |
|
|
spatial_size: tuple[int, int] | int | None = None, |
|
|
prob: float = 0.1, |
|
|
rotate_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
shear_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
translate_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
scale_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
mode: SequenceStr = GridSampleMode.BILINEAR, |
|
|
padding_mode: SequenceStr = GridSamplePadMode.REFLECTION, |
|
|
device: torch.device | None = None, |
|
|
allow_missing_keys: bool = False, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
spacing: distance in between the control points. |
|
|
magnitude_range: 2 int numbers, the random offsets will be generated from |
|
|
``uniform[magnitude[0], magnitude[1])``. |
|
|
spatial_size: specifying output image spatial size [h, w]. |
|
|
if `spatial_size` and `self.spatial_size` are not defined, or smaller than 1, |
|
|
the transform will use the spatial size of `img`. |
|
|
if some components of the `spatial_size` are non-positive values, the transform will use the |
|
|
corresponding components of img size. For example, `spatial_size=(32, -1)` will be adapted |
|
|
to `(32, 64)` if the second spatial dimension size of img is `64`. |
|
|
prob: probability of returning a randomized affine grid. |
|
|
defaults to 0.1, with 10% chance returns a randomized grid, |
|
|
otherwise returns a ``spatial_size`` centered area extracted from the input image. |
|
|
rotate_range: angle range in radians. If element `i` is a pair of (min, max) values, then |
|
|
`uniform[-rotate_range[i][0], rotate_range[i][1])` will be used to generate the rotation parameter |
|
|
for the `i`th spatial dimension. If not, `uniform[-rotate_range[i], rotate_range[i])` will be used. |
|
|
This can be altered on a per-dimension basis. E.g., `((0,3), 1, ...)`: for dim0, rotation will be |
|
|
in range `[0, 3]`, and for dim1 `[-1, 1]` will be used. Setting a single value will use `[-x, x]` |
|
|
for dim0 and nothing for the remaining dimensions. |
|
|
shear_range: shear range with format matching `rotate_range`, it defines the range to randomly select |
|
|
shearing factors(a tuple of 2 floats for 2D) for affine matrix, take a 2D affine as example:: |
|
|
|
|
|
[ |
|
|
[1.0, params[0], 0.0], |
|
|
[params[1], 1.0, 0.0], |
|
|
[0.0, 0.0, 1.0], |
|
|
] |
|
|
|
|
|
translate_range: translate range with format matching `rotate_range`, it defines the range to randomly |
|
|
select pixel to translate for every spatial dims. |
|
|
scale_range: scaling range with format matching `rotate_range`. it defines the range to randomly select |
|
|
the scale factor to translate for every spatial dims. A value of 1.0 is added to the result. |
|
|
This allows 0 to correspond to no change (i.e., a scaling of 1.0). |
|
|
mode: {``"bilinear"``, ``"nearest"``} or spline interpolation order 0-5 (integers). |
|
|
Interpolation mode to calculate output values. Defaults to ``"bilinear"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When it's an integer, the numpy (cpu tensor)/cupy (cuda tensor) backends will be used |
|
|
and the value represents the order of the spline interpolation. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``} |
|
|
Padding mode for outside grid values. Defaults to ``"reflection"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When `mode` is an integer, using numpy/cupy backends, this argument accepts |
|
|
{'reflect', 'grid-mirror', 'constant', 'grid-constant', 'nearest', 'mirror', 'grid-wrap', 'wrap'}. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
device: device on which the tensor will be allocated. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
|
|
|
See also: |
|
|
- :py:class:`RandAffineGrid` for the random affine parameters configurations. |
|
|
- :py:class:`Affine` for the affine transformation parameters configurations. |
|
|
|
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
RandomizableTransform.__init__(self, prob) |
|
|
self.rand_2d_elastic = Rand2DElastic( |
|
|
spacing=spacing, |
|
|
magnitude_range=magnitude_range, |
|
|
prob=1.0, |
|
|
rotate_range=rotate_range, |
|
|
shear_range=shear_range, |
|
|
translate_range=translate_range, |
|
|
scale_range=scale_range, |
|
|
spatial_size=spatial_size, |
|
|
device=device, |
|
|
) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
|
|
|
def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = None) -> Rand2DElasticd: |
|
|
self.rand_2d_elastic.set_random_state(seed, state) |
|
|
super().set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
first_key: Hashable = self.first_key(d) |
|
|
|
|
|
if first_key == (): |
|
|
out: dict[Hashable, NdarrayOrTensor] = convert_to_tensor(d, track_meta=get_track_meta()) |
|
|
return out |
|
|
|
|
|
self.randomize(None) |
|
|
device = self.rand_2d_elastic.device |
|
|
if device is None and isinstance(d[first_key], torch.Tensor): |
|
|
device = d[first_key].device |
|
|
self.rand_2d_elastic.set_device(device) |
|
|
if isinstance(d[first_key], MetaTensor) and d[first_key].pending_operations: |
|
|
warnings.warn(f"data['{first_key}'] has pending operations, transform may return incorrect results.") |
|
|
sp_size = fall_back_tuple(self.rand_2d_elastic.spatial_size, d[first_key].shape[1:]) |
|
|
|
|
|
|
|
|
self.rand_2d_elastic.randomize(sp_size) |
|
|
|
|
|
if self._do_transform: |
|
|
grid = self.rand_2d_elastic.deform_grid(spatial_size=sp_size) |
|
|
grid = self.rand_2d_elastic.rand_affine_grid(grid=grid) |
|
|
grid = torch.nn.functional.interpolate( |
|
|
recompute_scale_factor=True, |
|
|
input=grid.unsqueeze(0), |
|
|
scale_factor=ensure_tuple_rep(self.rand_2d_elastic.deform_grid.spacing, 2), |
|
|
mode=InterpolateMode.BICUBIC.value, |
|
|
align_corners=False, |
|
|
) |
|
|
grid = CenterSpatialCrop(roi_size=sp_size)(grid[0]) |
|
|
else: |
|
|
grid = cast(torch.Tensor, create_grid(spatial_size=sp_size, device=device, backend="torch")) |
|
|
|
|
|
for key, mode, padding_mode in self.key_iterator(d, self.mode, self.padding_mode): |
|
|
d[key] = self.rand_2d_elastic.resampler(d[key], grid, mode=mode, padding_mode=padding_mode) |
|
|
return d |
|
|
|
|
|
|
|
|
class Rand3DElasticd(RandomizableTransform, MapTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.Rand3DElastic`. |
|
|
""" |
|
|
|
|
|
backend = Rand3DElastic.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
sigma_range: tuple[float, float], |
|
|
magnitude_range: tuple[float, float], |
|
|
spatial_size: tuple[int, int, int] | int | None = None, |
|
|
prob: float = 0.1, |
|
|
rotate_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
shear_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
translate_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
scale_range: Sequence[tuple[float, float] | float] | float | None = None, |
|
|
mode: SequenceStr = GridSampleMode.BILINEAR, |
|
|
padding_mode: SequenceStr = GridSamplePadMode.REFLECTION, |
|
|
device: torch.device | None = None, |
|
|
allow_missing_keys: bool = False, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
sigma_range: a Gaussian kernel with standard deviation sampled from |
|
|
``uniform[sigma_range[0], sigma_range[1])`` will be used to smooth the random offset grid. |
|
|
magnitude_range: the random offsets on the grid will be generated from |
|
|
``uniform[magnitude[0], magnitude[1])``. |
|
|
spatial_size: specifying output image spatial size [h, w, d]. |
|
|
if `spatial_size` and `self.spatial_size` are not defined, or smaller than 1, |
|
|
the transform will use the spatial size of `img`. |
|
|
if some components of the `spatial_size` are non-positive values, the transform will use the |
|
|
corresponding components of img size. For example, `spatial_size=(32, 32, -1)` will be adapted |
|
|
to `(32, 32, 64)` if the third spatial dimension size of img is `64`. |
|
|
prob: probability of returning a randomized affine grid. |
|
|
defaults to 0.1, with 10% chance returns a randomized grid, |
|
|
otherwise returns a ``spatial_size`` centered area extracted from the input image. |
|
|
rotate_range: angle range in radians. If element `i` is a pair of (min, max) values, then |
|
|
`uniform[-rotate_range[i][0], rotate_range[i][1])` will be used to generate the rotation parameter |
|
|
for the `i`th spatial dimension. If not, `uniform[-rotate_range[i], rotate_range[i])` will be used. |
|
|
This can be altered on a per-dimension basis. E.g., `((0,3), 1, ...)`: for dim0, rotation will be |
|
|
in range `[0, 3]`, and for dim1 `[-1, 1]` will be used. Setting a single value will use `[-x, x]` |
|
|
for dim0 and nothing for the remaining dimensions. |
|
|
shear_range: shear range with format matching `rotate_range`, it defines the range to randomly select |
|
|
shearing factors(a tuple of 6 floats for 3D) for affine matrix, take a 3D affine as example:: |
|
|
|
|
|
[ |
|
|
[1.0, params[0], params[1], 0.0], |
|
|
[params[2], 1.0, params[3], 0.0], |
|
|
[params[4], params[5], 1.0, 0.0], |
|
|
[0.0, 0.0, 0.0, 1.0], |
|
|
] |
|
|
|
|
|
translate_range: translate range with format matching `rotate_range`, it defines the range to randomly |
|
|
select voxel to translate for every spatial dims. |
|
|
scale_range: scaling range with format matching `rotate_range`. it defines the range to randomly select |
|
|
the scale factor to translate for every spatial dims. A value of 1.0 is added to the result. |
|
|
This allows 0 to correspond to no change (i.e., a scaling of 1.0). |
|
|
mode: {``"bilinear"``, ``"nearest"``} or spline interpolation order 0-5 (integers). |
|
|
Interpolation mode to calculate output values. Defaults to ``"bilinear"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When it's an integer, the numpy (cpu tensor)/cupy (cuda tensor) backends will be used |
|
|
and the value represents the order of the spline interpolation. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``} |
|
|
Padding mode for outside grid values. Defaults to ``"reflection"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When `mode` is an integer, using numpy/cupy backends, this argument accepts |
|
|
{'reflect', 'grid-mirror', 'constant', 'grid-constant', 'nearest', 'mirror', 'grid-wrap', 'wrap'}. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
device: device on which the tensor will be allocated. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
|
|
|
See also: |
|
|
- :py:class:`RandAffineGrid` for the random affine parameters configurations. |
|
|
- :py:class:`Affine` for the affine transformation parameters configurations. |
|
|
|
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
RandomizableTransform.__init__(self, prob) |
|
|
self.rand_3d_elastic = Rand3DElastic( |
|
|
sigma_range=sigma_range, |
|
|
magnitude_range=magnitude_range, |
|
|
prob=1.0, |
|
|
rotate_range=rotate_range, |
|
|
shear_range=shear_range, |
|
|
translate_range=translate_range, |
|
|
scale_range=scale_range, |
|
|
spatial_size=spatial_size, |
|
|
device=device, |
|
|
) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
|
|
|
def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = None) -> Rand3DElasticd: |
|
|
self.rand_3d_elastic.set_random_state(seed, state) |
|
|
super().set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
first_key: Hashable = self.first_key(d) |
|
|
|
|
|
if first_key == (): |
|
|
out: dict[Hashable, torch.Tensor] = convert_to_tensor(d, track_meta=get_track_meta()) |
|
|
return out |
|
|
|
|
|
self.randomize(None) |
|
|
if isinstance(d[first_key], MetaTensor) and d[first_key].pending_operations: |
|
|
warnings.warn(f"data['{first_key}'] has pending operations, transform may return incorrect results.") |
|
|
sp_size = fall_back_tuple(self.rand_3d_elastic.spatial_size, d[first_key].shape[1:]) |
|
|
|
|
|
|
|
|
self.rand_3d_elastic.randomize(sp_size) |
|
|
|
|
|
device = self.rand_3d_elastic.device |
|
|
if device is None and isinstance(d[first_key], torch.Tensor): |
|
|
device = d[first_key].device |
|
|
self.rand_3d_elastic.set_device(device) |
|
|
grid = create_grid(spatial_size=sp_size, device=device, backend="torch") |
|
|
if self._do_transform: |
|
|
gaussian = GaussianFilter(spatial_dims=3, sigma=self.rand_3d_elastic.sigma, truncated=3.0).to(device) |
|
|
offset = torch.as_tensor(self.rand_3d_elastic.rand_offset, device=device).unsqueeze(0) |
|
|
grid[:3] += gaussian(offset)[0] * self.rand_3d_elastic.magnitude |
|
|
grid = self.rand_3d_elastic.rand_affine_grid(grid=grid) |
|
|
|
|
|
for key, mode, padding_mode in self.key_iterator(d, self.mode, self.padding_mode): |
|
|
d[key] = self.rand_3d_elastic.resampler(d[key], grid, mode=mode, padding_mode=padding_mode) |
|
|
return d |
|
|
|
|
|
|
|
|
class Flipd(MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.Flip`. |
|
|
|
|
|
See `numpy.flip` for additional details. |
|
|
https://docs.scipy.org/doc/numpy/reference/generated/numpy.flip.html |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: Keys to pick data for transformation. |
|
|
spatial_axis: Spatial axes along which to flip over. Default is None. |
|
|
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 = Flip.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
spatial_axis: Sequence[int] | int | None = None, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.flipper = Flip(spatial_axis=spatial_axis) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool): |
|
|
self.flipper.lazy = val |
|
|
self._lazy = val |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.flipper(d[key], lazy=lazy_) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.flipper.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class RandFlipd(RandomizableTransform, MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based version :py:class:`monai.transforms.RandFlip`. |
|
|
|
|
|
See `numpy.flip` for additional details. |
|
|
https://docs.scipy.org/doc/numpy/reference/generated/numpy.flip.html |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: Keys to pick data for transformation. |
|
|
prob: Probability of flipping. |
|
|
spatial_axis: Spatial axes along which to flip over. Default is None. |
|
|
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 = Flip.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
prob: float = 0.1, |
|
|
spatial_axis: Sequence[int] | int | None = None, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
RandomizableTransform.__init__(self, prob) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.flipper = Flip(spatial_axis=spatial_axis, lazy=lazy) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool): |
|
|
self.flipper.lazy = val |
|
|
self._lazy = val |
|
|
|
|
|
def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = None) -> RandFlipd: |
|
|
super().set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
self.randomize(None) |
|
|
|
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key in self.key_iterator(d): |
|
|
if self._do_transform: |
|
|
d[key] = self.flipper(d[key], lazy=lazy_) |
|
|
else: |
|
|
d[key] = convert_to_tensor(d[key], track_meta=get_track_meta()) |
|
|
self.push_transform(d[key], replace=True, lazy=lazy_) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
xform = self.pop_transform(d[key]) |
|
|
if not xform[TraceKeys.DO_TRANSFORM]: |
|
|
continue |
|
|
with self.flipper.trace_transform(False): |
|
|
d[key] = self.flipper(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class RandAxisFlipd(RandomizableTransform, MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based version :py:class:`monai.transforms.RandAxisFlip`. |
|
|
|
|
|
See `numpy.flip` for additional details. |
|
|
https://docs.scipy.org/doc/numpy/reference/generated/numpy.flip.html |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: Keys to pick data for transformation. |
|
|
prob: Probability of flipping. |
|
|
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 = RandAxisFlip.backend |
|
|
|
|
|
def __init__( |
|
|
self, keys: KeysCollection, prob: float = 0.1, allow_missing_keys: bool = False, lazy: bool = False |
|
|
) -> None: |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
RandomizableTransform.__init__(self, prob) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.flipper = RandAxisFlip(prob=1.0, lazy=lazy) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool): |
|
|
self.flipper.lazy = val |
|
|
self._lazy = val |
|
|
|
|
|
def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = None) -> RandAxisFlipd: |
|
|
super().set_random_state(seed, state) |
|
|
self.flipper.set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
first_key: Hashable = self.first_key(d) |
|
|
if first_key == (): |
|
|
return d |
|
|
|
|
|
self.randomize(None) |
|
|
|
|
|
|
|
|
self.flipper.randomize(d[first_key]) |
|
|
|
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key in self.key_iterator(d): |
|
|
if self._do_transform: |
|
|
d[key] = self.flipper(d[key], randomize=False, lazy=lazy_) |
|
|
else: |
|
|
d[key] = convert_to_tensor(d[key], track_meta=get_track_meta()) |
|
|
self.push_transform(d[key], replace=True, lazy=lazy_) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
xform = self.pop_transform(d[key]) |
|
|
if xform[TraceKeys.DO_TRANSFORM]: |
|
|
d[key].applied_operations.append(xform[TraceKeys.EXTRA_INFO]) |
|
|
d[key] = self.flipper.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class Rotated(MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.Rotate`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: Keys to pick data for transformation. |
|
|
angle: Rotation angle(s) in radians. |
|
|
keep_size: If it is False, the output shape is adapted so that the |
|
|
input array is contained completely in the output. |
|
|
If it is True, the output shape is the same as the input. Default is True. |
|
|
mode: {``"bilinear"``, ``"nearest"``} |
|
|
Interpolation mode to calculate output values. Defaults to ``"bilinear"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
It also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``} |
|
|
Padding mode for outside grid values. Defaults to ``"border"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
It also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
align_corners: Defaults to False. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
It also can be a sequence of bool, each element corresponds to a key in ``keys``. |
|
|
dtype: data type for resampling computation. Defaults to ``float32``. |
|
|
If None, use the data type of input data. To be compatible with other modules, |
|
|
the output data type is always ``float32``. |
|
|
It also can be a sequence of dtype or None, 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 |
|
|
""" |
|
|
|
|
|
backend = Rotate.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
angle: Sequence[float] | float, |
|
|
keep_size: bool = True, |
|
|
mode: SequenceStr = GridSampleMode.BILINEAR, |
|
|
padding_mode: SequenceStr = GridSamplePadMode.BORDER, |
|
|
align_corners: Sequence[bool] | bool = False, |
|
|
dtype: Sequence[DtypeLike | torch.dtype] | DtypeLike | torch.dtype = np.float32, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.rotator = Rotate(angle=angle, keep_size=keep_size, lazy=lazy) |
|
|
|
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
self.align_corners = ensure_tuple_rep(align_corners, len(self.keys)) |
|
|
self.dtype = ensure_tuple_rep(dtype, len(self.keys)) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool): |
|
|
self.rotator.lazy = val |
|
|
self._lazy = val |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key, mode, padding_mode, align_corners, dtype in self.key_iterator( |
|
|
d, self.mode, self.padding_mode, self.align_corners, self.dtype |
|
|
): |
|
|
d[key] = self.rotator( |
|
|
d[key], mode=mode, padding_mode=padding_mode, align_corners=align_corners, dtype=dtype, lazy=lazy_ |
|
|
) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.rotator.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class RandRotated(RandomizableTransform, MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based version :py:class:`monai.transforms.RandRotate` |
|
|
Randomly rotates the input arrays. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: Keys to pick data for transformation. |
|
|
range_x: Range of rotation angle in radians in the plane defined by the first and second axes. |
|
|
If single number, angle is uniformly sampled from (-range_x, range_x). |
|
|
range_y: Range of rotation angle in radians in the plane defined by the first and third axes. |
|
|
If single number, angle is uniformly sampled from (-range_y, range_y). only work for 3D data. |
|
|
range_z: Range of rotation angle in radians in the plane defined by the second and third axes. |
|
|
If single number, angle is uniformly sampled from (-range_z, range_z). only work for 3D data. |
|
|
prob: Probability of rotation. |
|
|
keep_size: If it is False, the output shape is adapted so that the |
|
|
input array is contained completely in the output. |
|
|
If it is True, the output shape is the same as the input. Default is True. |
|
|
mode: {``"bilinear"``, ``"nearest"``} |
|
|
Interpolation mode to calculate output values. Defaults to ``"bilinear"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
It also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``} |
|
|
Padding mode for outside grid values. Defaults to ``"border"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
It also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
align_corners: Defaults to False. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.interpolate.html |
|
|
It also can be a sequence of bool, each element corresponds to a key in ``keys``. |
|
|
dtype: data type for resampling computation. Defaults to ``float64`` for best precision. |
|
|
If None, use the data type of input data. To be compatible with other modules, |
|
|
the output data type is always ``float32``. |
|
|
It also can be a sequence of dtype or None, 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 |
|
|
""" |
|
|
|
|
|
backend = RandRotate.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
range_x: tuple[float, float] | float = 0.0, |
|
|
range_y: tuple[float, float] | float = 0.0, |
|
|
range_z: tuple[float, float] | float = 0.0, |
|
|
prob: float = 0.1, |
|
|
keep_size: bool = True, |
|
|
mode: SequenceStr = GridSampleMode.BILINEAR, |
|
|
padding_mode: SequenceStr = GridSamplePadMode.BORDER, |
|
|
align_corners: Sequence[bool] | bool = False, |
|
|
dtype: Sequence[DtypeLike | torch.dtype] | DtypeLike | torch.dtype = np.float32, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
) -> None: |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
RandomizableTransform.__init__(self, prob) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.rand_rotate = RandRotate( |
|
|
range_x=range_x, range_y=range_y, range_z=range_z, prob=1.0, keep_size=keep_size, lazy=lazy |
|
|
) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
self.align_corners = ensure_tuple_rep(align_corners, len(self.keys)) |
|
|
self.dtype = ensure_tuple_rep(dtype, len(self.keys)) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool): |
|
|
self.rand_rotate.lazy = val |
|
|
self._lazy = val |
|
|
|
|
|
def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = None) -> RandRotated: |
|
|
super().set_random_state(seed, state) |
|
|
self.rand_rotate.set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
self.randomize(None) |
|
|
|
|
|
|
|
|
self.rand_rotate.randomize() |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
|
|
|
for key, mode, padding_mode, align_corners, dtype in self.key_iterator( |
|
|
d, self.mode, self.padding_mode, self.align_corners, self.dtype |
|
|
): |
|
|
if self._do_transform: |
|
|
d[key] = self.rand_rotate( |
|
|
d[key], |
|
|
mode=mode, |
|
|
padding_mode=padding_mode, |
|
|
align_corners=align_corners, |
|
|
dtype=dtype, |
|
|
randomize=False, |
|
|
lazy=lazy_, |
|
|
) |
|
|
else: |
|
|
d[key] = convert_to_tensor(d[key], track_meta=get_track_meta(), dtype=torch.float32) |
|
|
self.push_transform(d[key], replace=True, lazy=lazy_) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
xform = self.pop_transform(d[key]) |
|
|
if xform[TraceKeys.DO_TRANSFORM]: |
|
|
d[key].applied_operations.append(xform[TraceKeys.EXTRA_INFO]) |
|
|
d[key] = self.rand_rotate.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class Zoomd(MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.Zoom`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: Keys to pick data for transformation. |
|
|
zoom: The zoom factor along the spatial axes. |
|
|
If a float, zoom is the same for each spatial axis. |
|
|
If a sequence, zoom should contain one value for each spatial axis. |
|
|
mode: {``"nearest"``, ``"nearest-exact"``, ``"linear"``, ``"bilinear"``, ``"bicubic"``, ``"trilinear"``, ``"area"``} |
|
|
The interpolation mode. Defaults to ``"area"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.interpolate.html |
|
|
It also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
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 ``"edge"``. |
|
|
The mode to pad data after zooming. |
|
|
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html |
|
|
https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html |
|
|
align_corners: This only has an effect when mode is |
|
|
'linear', 'bilinear', 'bicubic' or 'trilinear'. Default: None. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.interpolate.html |
|
|
It also can be a sequence of bool or None, each element corresponds to a key in ``keys``. |
|
|
dtype: data type for resampling computation. Defaults to ``float32``. |
|
|
If None, use the data type of input data. |
|
|
keep_size: Should keep original size (pad if needed), default is True. |
|
|
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. |
|
|
|
|
|
""" |
|
|
|
|
|
backend = Zoom.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
zoom: Sequence[float] | float, |
|
|
mode: SequenceStr = InterpolateMode.AREA, |
|
|
padding_mode: SequenceStr = NumpyPadMode.EDGE, |
|
|
align_corners: Sequence[bool | None] | bool | None = None, |
|
|
dtype: Sequence[DtypeLike | torch.dtype] | DtypeLike | torch.dtype = np.float32, |
|
|
keep_size: bool = True, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
**kwargs, |
|
|
) -> None: |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
|
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
self.align_corners = ensure_tuple_rep(align_corners, len(self.keys)) |
|
|
self.dtype = ensure_tuple_rep(dtype, len(self.keys)) |
|
|
self.zoomer = Zoom(zoom=zoom, keep_size=keep_size, lazy=lazy, **kwargs) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool): |
|
|
self.zoomer.lazy = val |
|
|
self._lazy = val |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
for key, mode, padding_mode, align_corners, dtype in self.key_iterator( |
|
|
d, self.mode, self.padding_mode, self.align_corners, self.dtype |
|
|
): |
|
|
d[key] = self.zoomer( |
|
|
d[key], mode=mode, padding_mode=padding_mode, align_corners=align_corners, dtype=dtype, lazy=lazy_ |
|
|
) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.zoomer.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class RandZoomd(RandomizableTransform, MapTransform, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
Dict-based version :py:class:`monai.transforms.RandZoom`. |
|
|
|
|
|
This transform is capable of lazy execution. See the :ref:`Lazy Resampling topic<lazy_resampling>` |
|
|
for more information. |
|
|
|
|
|
Args: |
|
|
keys: Keys to pick data for transformation. |
|
|
prob: Probability of zooming. |
|
|
min_zoom: Min zoom factor. Can be float or sequence same size as image. |
|
|
If a float, select a random factor from `[min_zoom, max_zoom]` then apply to all spatial dims |
|
|
to keep the original spatial shape ratio. |
|
|
If a sequence, min_zoom should contain one value for each spatial axis. |
|
|
If 2 values provided for 3D data, use the first value for both H & W dims to keep the same zoom ratio. |
|
|
max_zoom: Max zoom factor. Can be float or sequence same size as image. |
|
|
If a float, select a random factor from `[min_zoom, max_zoom]` then apply to all spatial dims |
|
|
to keep the original spatial shape ratio. |
|
|
If a sequence, max_zoom should contain one value for each spatial axis. |
|
|
If 2 values provided for 3D data, use the first value for both H & W dims to keep the same zoom ratio. |
|
|
mode: {``"nearest"``, ``"nearest-exact"``, ``"linear"``, ``"bilinear"``, ``"bicubic"``, ``"trilinear"``, ``"area"``} |
|
|
The interpolation mode. Defaults to ``"area"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.interpolate.html |
|
|
It also can be a sequence of string, each element corresponds to a key in ``keys``. |
|
|
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 ``"edge"``. |
|
|
The mode to pad data after zooming. |
|
|
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html |
|
|
https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html |
|
|
align_corners: This only has an effect when mode is |
|
|
'linear', 'bilinear', 'bicubic' or 'trilinear'. Default: None. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.interpolate.html |
|
|
It also can be a sequence of bool or None, each element corresponds to a key in ``keys``. |
|
|
dtype: data type for resampling computation. Defaults to ``float32``. |
|
|
If None, use the data type of input data. |
|
|
keep_size: Should keep original size (pad if needed), default is True. |
|
|
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 args for `np.pad` API, note that `np.pad` treats channel dimension as the first dimension. |
|
|
more details: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html |
|
|
""" |
|
|
|
|
|
backend = RandZoom.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
prob: float = 0.1, |
|
|
min_zoom: Sequence[float] | float = 0.9, |
|
|
max_zoom: Sequence[float] | float = 1.1, |
|
|
mode: SequenceStr = InterpolateMode.AREA, |
|
|
padding_mode: SequenceStr = NumpyPadMode.EDGE, |
|
|
align_corners: Sequence[bool | None] | bool | None = None, |
|
|
dtype: Sequence[DtypeLike | torch.dtype] | DtypeLike | torch.dtype = np.float32, |
|
|
keep_size: bool = True, |
|
|
allow_missing_keys: bool = False, |
|
|
lazy: bool = False, |
|
|
**kwargs, |
|
|
) -> None: |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
RandomizableTransform.__init__(self, prob) |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
self.rand_zoom = RandZoom( |
|
|
prob=1.0, min_zoom=min_zoom, max_zoom=max_zoom, keep_size=keep_size, lazy=lazy, **kwargs |
|
|
) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
self.align_corners = ensure_tuple_rep(align_corners, len(self.keys)) |
|
|
self.dtype = ensure_tuple_rep(dtype, len(self.keys)) |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool): |
|
|
self.rand_zoom.lazy = val |
|
|
self._lazy = val |
|
|
|
|
|
def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = None) -> RandZoomd: |
|
|
super().set_random_state(seed, state) |
|
|
self.rand_zoom.set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = None) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
lazy: a flag to indicate whether this transform should execute lazily or not |
|
|
during this call. Setting this to False or True overrides the ``lazy`` flag set |
|
|
during initialization for this call. Defaults to None. |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
first_key: Hashable = self.first_key(d) |
|
|
if first_key == (): |
|
|
out: dict[Hashable, torch.Tensor] = convert_to_tensor(d, track_meta=get_track_meta()) |
|
|
return out |
|
|
|
|
|
self.randomize(None) |
|
|
|
|
|
|
|
|
self.rand_zoom.randomize(d[first_key]) |
|
|
lazy_ = self.lazy if lazy is None else lazy |
|
|
|
|
|
for key, mode, padding_mode, align_corners, dtype in self.key_iterator( |
|
|
d, self.mode, self.padding_mode, self.align_corners, self.dtype |
|
|
): |
|
|
if self._do_transform: |
|
|
d[key] = self.rand_zoom( |
|
|
d[key], |
|
|
mode=mode, |
|
|
padding_mode=padding_mode, |
|
|
align_corners=align_corners, |
|
|
dtype=dtype, |
|
|
randomize=False, |
|
|
lazy=lazy_, |
|
|
) |
|
|
else: |
|
|
d[key] = convert_to_tensor(d[key], track_meta=get_track_meta(), dtype=torch.float32) |
|
|
self.push_transform(d[key], replace=True, lazy=lazy_) |
|
|
return d |
|
|
|
|
|
def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
xform = self.pop_transform(d[key]) |
|
|
if xform[TraceKeys.DO_TRANSFORM]: |
|
|
d[key].applied_operations.append(xform[TraceKeys.EXTRA_INFO]) |
|
|
d[key] = self.rand_zoom.inverse(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class GridDistortiond(MapTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.GridDistortion`. |
|
|
""" |
|
|
|
|
|
backend = GridDistortion.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
num_cells: tuple[int] | int, |
|
|
distort_steps: list[tuple], |
|
|
mode: str = GridSampleMode.BILINEAR, |
|
|
padding_mode: str = GridSamplePadMode.BORDER, |
|
|
device: torch.device | None = None, |
|
|
allow_missing_keys: bool = False, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
num_cells: number of grid cells on each dimension. |
|
|
distort_steps: This argument is a list of tuples, where each tuple contains the distort steps of the |
|
|
corresponding dimensions (in the order of H, W[, D]). The length of each tuple equals to `num_cells + 1`. |
|
|
Each value in the tuple represents the distort step of the related cell. |
|
|
mode: {``"bilinear"``, ``"nearest"``} or spline interpolation order 0-5 (integers). |
|
|
Interpolation mode to calculate output values. Defaults to ``"bilinear"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When it's an integer, the numpy (cpu tensor)/cupy (cuda tensor) backends will be used |
|
|
and the value represents the order of the spline interpolation. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``} |
|
|
Padding mode for outside grid values. Defaults to ``"border"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When `mode` is an integer, using numpy/cupy backends, this argument accepts |
|
|
{'reflect', 'grid-mirror', 'constant', 'grid-constant', 'nearest', 'mirror', 'grid-wrap', 'wrap'}. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
device: device on which the tensor will be allocated. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
""" |
|
|
super().__init__(keys, allow_missing_keys) |
|
|
self.grid_distortion = GridDistortion(num_cells=num_cells, distort_steps=distort_steps, device=device) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
for key, mode, padding_mode in self.key_iterator(d, self.mode, self.padding_mode): |
|
|
d[key] = self.grid_distortion(d[key], mode=mode, padding_mode=padding_mode) |
|
|
return d |
|
|
|
|
|
|
|
|
class RandGridDistortiond(RandomizableTransform, MapTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.RandGridDistortion`. |
|
|
""" |
|
|
|
|
|
backend = RandGridDistortion.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
num_cells: tuple[int] | int = 5, |
|
|
prob: float = 0.1, |
|
|
distort_limit: tuple[float, float] | float = (-0.03, 0.03), |
|
|
mode: str = GridSampleMode.BILINEAR, |
|
|
padding_mode: str = GridSamplePadMode.BORDER, |
|
|
device: torch.device | None = None, |
|
|
allow_missing_keys: bool = False, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
num_cells: number of grid cells on each dimension. |
|
|
prob: probability of returning a randomized grid distortion transform. Defaults to 0.1. |
|
|
distort_limit: range to randomly distort. |
|
|
If single number, distort_limit is picked from (-distort_limit, distort_limit). |
|
|
Defaults to (-0.03, 0.03). |
|
|
mode: {``"bilinear"``, ``"nearest"``} or spline interpolation order 0-5 (integers). |
|
|
Interpolation mode to calculate output values. Defaults to ``"bilinear"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When it's an integer, the numpy (cpu tensor)/cupy (cuda tensor) backends will be used |
|
|
and the value represents the order of the spline interpolation. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``} |
|
|
Padding mode for outside grid values. Defaults to ``"border"``. |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.grid_sample.html |
|
|
When `mode` is an integer, using numpy/cupy backends, this argument accepts |
|
|
{'reflect', 'grid-mirror', 'constant', 'grid-constant', 'nearest', 'mirror', 'grid-wrap', 'wrap'}. |
|
|
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.map_coordinates.html |
|
|
It also can be a sequence, each element corresponds to a key in ``keys``. |
|
|
device: device on which the tensor will be allocated. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
|
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
RandomizableTransform.__init__(self, prob) |
|
|
self.rand_grid_distortion = RandGridDistortion( |
|
|
num_cells=num_cells, prob=1.0, distort_limit=distort_limit, device=device |
|
|
) |
|
|
self.mode = ensure_tuple_rep(mode, len(self.keys)) |
|
|
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys)) |
|
|
|
|
|
def set_random_state( |
|
|
self, seed: int | None = None, state: np.random.RandomState | None = None |
|
|
) -> RandGridDistortiond: |
|
|
super().set_random_state(seed, state) |
|
|
self.rand_grid_distortion.set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
self.randomize(None) |
|
|
if not self._do_transform: |
|
|
out: dict[Hashable, torch.Tensor] = convert_to_tensor(d, track_meta=get_track_meta()) |
|
|
return out |
|
|
|
|
|
first_key: Hashable = self.first_key(d) |
|
|
if first_key == (): |
|
|
out = convert_to_tensor(d, track_meta=get_track_meta()) |
|
|
return out |
|
|
if isinstance(d[first_key], MetaTensor) and d[first_key].pending_operations: |
|
|
warnings.warn(f"data['{first_key}'] has pending operations, transform may return incorrect results.") |
|
|
self.rand_grid_distortion.randomize(d[first_key].shape[1:]) |
|
|
|
|
|
for key, mode, padding_mode in self.key_iterator(d, self.mode, self.padding_mode): |
|
|
d[key] = self.rand_grid_distortion(d[key], mode=mode, padding_mode=padding_mode, randomize=False) |
|
|
return d |
|
|
|
|
|
|
|
|
class GridSplitd(MapTransform, MultiSampleTrait): |
|
|
""" |
|
|
Split the image into patches based on the provided grid in 2D. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
grid: a tuple define the shape of the grid upon which the image is split. Defaults to (2, 2) |
|
|
size: a tuple or an integer that defines the output patch sizes, |
|
|
or a dictionary that define it separately for each key, like {"image": 3, "mask", (2, 2)}. |
|
|
If it's an integer, the value will be repeated for each dimension. |
|
|
The default is None, where the patch size will be inferred from the grid shape. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
|
|
|
Note: This transform currently support only image with two spatial dimensions. |
|
|
""" |
|
|
|
|
|
backend = GridSplit.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
grid: tuple[int, int] = (2, 2), |
|
|
size: int | tuple[int, int] | dict[Hashable, int | tuple[int, int] | None] | None = None, |
|
|
allow_missing_keys: bool = False, |
|
|
): |
|
|
super().__init__(keys, allow_missing_keys) |
|
|
self.grid = grid |
|
|
self.size = size if isinstance(size, dict) else {key: size for key in self.keys} |
|
|
self.splitter = GridSplit(grid=grid) |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> list[dict[Hashable, NdarrayOrTensor]]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
n_outputs = np.prod(self.grid) |
|
|
output: list[dict[Hashable, NdarrayOrTensor]] = [dict(d) for _ in range(n_outputs)] |
|
|
for key in self.key_iterator(d): |
|
|
result = self.splitter(d[key], self.size[key]) |
|
|
for i in range(n_outputs): |
|
|
output[i][key] = result[i] |
|
|
return output |
|
|
|
|
|
|
|
|
class GridPatchd(MapTransform, MultiSampleTrait): |
|
|
""" |
|
|
Extract all the patches sweeping the entire image in a row-major sliding-window manner with possible overlaps. |
|
|
It can sort the patches and return all or a subset of them. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
patch_size: size of patches to generate slices for, 0 or None selects whole dimension |
|
|
offset: starting position in the array, default is 0 for each dimension. |
|
|
np.random.randint(0, patch_size, 2) creates random start between 0 and `patch_size` for a 2D image. |
|
|
num_patches: number of patches (or maximum number of patches) to return. |
|
|
If the requested number of patches is greater than the number of available patches, |
|
|
padding will be applied to provide exactly `num_patches` patches unless `threshold` is set. |
|
|
When `threshold` is set, this value is treated as the maximum number of patches. |
|
|
Defaults to None, which does not limit number of the patches. |
|
|
overlap: amount of overlap between patches in each dimension. Default to 0.0. |
|
|
sort_fn: when `num_patches` is provided, it determines if keep patches with highest values (`"max"`), |
|
|
lowest values (`"min"`), or in their default order (`None`). Default to None. |
|
|
threshold: a value to keep only the patches whose sum of intensities are less than the threshold. |
|
|
Defaults to no filtering. |
|
|
pad_mode: the mode for padding the input image by `patch_size` to include patches that cross boundaries. |
|
|
Available modes: (Numpy) {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, |
|
|
``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``} |
|
|
(PyTorch) {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}. |
|
|
One of the listed string values or a user supplied function. |
|
|
Defaults to `None`, which means no padding will be applied. |
|
|
See also: https://numpy.org/doc/stable/reference/generated/numpy.pad.html |
|
|
https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html |
|
|
requires pytorch >= 1.10 for best compatibility. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
pad_kwargs: other arguments for the `np.pad` or `torch.pad` function. |
|
|
note that `np.pad` treats channel dimension as the first dimension. |
|
|
|
|
|
Returns: |
|
|
dictionary, contains the all the original key/value with the values for `keys` |
|
|
replaced by the patches, a MetaTensor with following metadata: |
|
|
|
|
|
- `PatchKeys.LOCATION`: the starting location of the patch in the image, |
|
|
- `PatchKeys.COUNT`: total number of patches in the image, |
|
|
- "spatial_shape": spatial size of the extracted patch, and |
|
|
- "offset": the amount of offset for the patches in the image (starting position of the first patch) |
|
|
""" |
|
|
|
|
|
backend = GridPatch.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
patch_size: Sequence[int], |
|
|
offset: Sequence[int] | None = None, |
|
|
num_patches: int | None = None, |
|
|
overlap: float = 0.0, |
|
|
sort_fn: str | None = None, |
|
|
threshold: float | None = None, |
|
|
pad_mode: str | None = None, |
|
|
allow_missing_keys: bool = False, |
|
|
**pad_kwargs, |
|
|
): |
|
|
super().__init__(keys, allow_missing_keys) |
|
|
self.patcher = GridPatch( |
|
|
patch_size=patch_size, |
|
|
offset=offset, |
|
|
num_patches=num_patches, |
|
|
overlap=overlap, |
|
|
sort_fn=sort_fn, |
|
|
threshold=threshold, |
|
|
pad_mode=pad_mode, |
|
|
**pad_kwargs, |
|
|
) |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.patcher(d[key]) |
|
|
return d |
|
|
|
|
|
|
|
|
class RandGridPatchd(RandomizableTransform, MapTransform, MultiSampleTrait): |
|
|
""" |
|
|
Extract all the patches sweeping the entire image in a row-major sliding-window manner with possible overlaps, |
|
|
and with random offset for the minimal corner of the image, (0,0) for 2D and (0,0,0) for 3D. |
|
|
It can sort the patches and return all or a subset of them. |
|
|
|
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
patch_size: size of patches to generate slices for, 0 or None selects whole dimension |
|
|
min_offset: the minimum range of starting position to be selected randomly. Defaults to 0. |
|
|
max_offset: the maximum range of starting position to be selected randomly. |
|
|
Defaults to image size modulo patch size. |
|
|
num_patches: number of patches (or maximum number of patches) to return. |
|
|
If the requested number of patches is greater than the number of available patches, |
|
|
padding will be applied to provide exactly `num_patches` patches unless `threshold` is set. |
|
|
When `threshold` is set, this value is treated as the maximum number of patches. |
|
|
Defaults to None, which does not limit number of the patches. |
|
|
overlap: the amount of overlap of neighboring patches in each dimension (a value between 0.0 and 1.0). |
|
|
If only one float number is given, it will be applied to all dimensions. Defaults to 0.0. |
|
|
sort_fn: when `num_patches` is provided, it determines if keep patches with highest values (`"max"`), |
|
|
lowest values (`"min"`), in random ("random"), or in their default order (`None`). Default to None. |
|
|
threshold: a value to keep only the patches whose sum of intensities are less than the threshold. |
|
|
Defaults to no filtering. |
|
|
pad_mode: the mode for padding the input image by `patch_size` to include patches that cross boundaries. |
|
|
Available modes: (Numpy) {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, |
|
|
``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``} |
|
|
(PyTorch) {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}. |
|
|
One of the listed string values or a user supplied function. |
|
|
Defaults to `None`, which means no padding will be applied. |
|
|
See also: https://numpy.org/doc/stable/reference/generated/numpy.pad.html |
|
|
https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html |
|
|
requires pytorch >= 1.10 for best compatibility. |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
pad_kwargs: other arguments for the `np.pad` or `torch.pad` function. |
|
|
note that `np.pad` treats channel dimension as the first dimension. |
|
|
|
|
|
Returns: |
|
|
dictionary, contains the all the original key/value with the values for `keys` |
|
|
replaced by the patches, a MetaTensor with following metadata: |
|
|
|
|
|
- `PatchKeys.LOCATION`: the starting location of the patch in the image, |
|
|
- `PatchKeys.COUNT`: total number of patches in the image, |
|
|
- "spatial_shape": spatial size of the extracted patch, and |
|
|
- "offset": the amount of offset for the patches in the image (starting position of the first patch) |
|
|
|
|
|
""" |
|
|
|
|
|
backend = RandGridPatch.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
patch_size: Sequence[int], |
|
|
min_offset: Sequence[int] | int | None = None, |
|
|
max_offset: Sequence[int] | int | None = None, |
|
|
num_patches: int | None = None, |
|
|
overlap: float = 0.0, |
|
|
sort_fn: str | None = None, |
|
|
threshold: float | None = None, |
|
|
pad_mode: str | None = None, |
|
|
allow_missing_keys: bool = False, |
|
|
**pad_kwargs, |
|
|
): |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
self.patcher = RandGridPatch( |
|
|
patch_size=patch_size, |
|
|
min_offset=min_offset, |
|
|
max_offset=max_offset, |
|
|
num_patches=num_patches, |
|
|
overlap=overlap, |
|
|
sort_fn=sort_fn, |
|
|
threshold=threshold, |
|
|
pad_mode=pad_mode, |
|
|
**pad_kwargs, |
|
|
) |
|
|
|
|
|
def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = None) -> RandGridPatchd: |
|
|
super().set_random_state(seed, state) |
|
|
self.patcher.set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be processed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
|
|
|
Returns: |
|
|
a dictionary containing the transformed data, as well as any other data present in the dictionary |
|
|
""" |
|
|
d = dict(data) |
|
|
|
|
|
for key in self.key_iterator(d): |
|
|
self.patcher.randomize(d[key]) |
|
|
break |
|
|
for key in self.key_iterator(d): |
|
|
d[key] = self.patcher(d[key], randomize=False) |
|
|
return d |
|
|
|
|
|
|
|
|
class RandSimulateLowResolutiond(RandomizableTransform, MapTransform): |
|
|
""" |
|
|
Dictionary-based wrapper of :py:class:`monai.transforms.RandSimulateLowResolution`. |
|
|
Random simulation of low resolution corresponding to nnU-Net's SimulateLowResolutionTransform |
|
|
(https://github.com/MIC-DKFZ/batchgenerators/blob/7651ece69faf55263dd582a9f5cbd149ed9c3ad0/batchgenerators/transforms/resample_transforms.py#L23) |
|
|
First, the array/tensor is resampled at lower resolution as determined by the zoom_factor which is uniformly sampled |
|
|
from the `zoom_range`. Then, the array/tensor is resampled at the original resolution. |
|
|
""" |
|
|
|
|
|
backend = RandAffine.backend |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
keys: KeysCollection, |
|
|
prob: float = 0.1, |
|
|
downsample_mode: InterpolateMode | str = InterpolateMode.NEAREST, |
|
|
upsample_mode: InterpolateMode | str = InterpolateMode.TRILINEAR, |
|
|
zoom_range=(0.5, 1.0), |
|
|
align_corners=False, |
|
|
allow_missing_keys: bool = False, |
|
|
device: torch.device | None = None, |
|
|
) -> None: |
|
|
""" |
|
|
Args: |
|
|
keys: keys of the corresponding items to be transformed. |
|
|
prob: probability of performing this augmentation |
|
|
downsample_mode: interpolation mode for downsampling operation |
|
|
upsample_mode: interpolation mode for upsampling operation |
|
|
zoom_range: range from which the random zoom factor for the downsampling and upsampling operation is |
|
|
sampled. It determines the shape of the downsampled tensor. |
|
|
align_corners: This only has an effect when downsample_mode or upsample_mode is 'linear', 'bilinear', |
|
|
'bicubic' or 'trilinear'. Default: False |
|
|
See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.interpolate.html |
|
|
allow_missing_keys: don't raise exception if key is missing. |
|
|
device: device on which the tensor will be allocated. |
|
|
|
|
|
See also: |
|
|
- :py:class:`monai.transforms.compose.MapTransform` |
|
|
|
|
|
""" |
|
|
MapTransform.__init__(self, keys, allow_missing_keys) |
|
|
RandomizableTransform.__init__(self, prob) |
|
|
|
|
|
self.downsample_mode = downsample_mode |
|
|
self.upsample_mode = upsample_mode |
|
|
self.zoom_range = zoom_range |
|
|
self.align_corners = align_corners |
|
|
self.device = device |
|
|
|
|
|
self.sim_lowres_tfm = RandSimulateLowResolution( |
|
|
prob=1.0, |
|
|
downsample_mode=self.downsample_mode, |
|
|
upsample_mode=self.upsample_mode, |
|
|
zoom_range=self.zoom_range, |
|
|
align_corners=self.align_corners, |
|
|
device=self.device, |
|
|
) |
|
|
|
|
|
def set_random_state( |
|
|
self, seed: int | None = None, state: np.random.RandomState | None = None |
|
|
) -> RandSimulateLowResolutiond: |
|
|
super().set_random_state(seed, state) |
|
|
return self |
|
|
|
|
|
def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
|
|
""" |
|
|
Args: |
|
|
data: a dictionary containing the tensor-like data to be transformed. The ``keys`` specified |
|
|
in this dictionary must be tensor like arrays that are channel first and have at most |
|
|
three spatial dimensions |
|
|
""" |
|
|
d = dict(data) |
|
|
first_key: Hashable = self.first_key(d) |
|
|
if first_key == (): |
|
|
out: dict[Hashable, NdarrayOrTensor] = convert_to_tensor(d, track_meta=get_track_meta()) |
|
|
return out |
|
|
|
|
|
self.randomize(None) |
|
|
|
|
|
for key in self.key_iterator(d): |
|
|
|
|
|
if self._do_transform: |
|
|
d[key] = self.sim_lowres_tfm(d[key]) |
|
|
else: |
|
|
d[key] = convert_to_tensor(d[key], track_meta=get_track_meta(), dtype=torch.float32) |
|
|
return d |
|
|
|
|
|
|
|
|
SpatialResampleD = SpatialResampleDict = SpatialResampled |
|
|
ResampleToMatchD = ResampleToMatchDict = ResampleToMatchd |
|
|
SpacingD = SpacingDict = Spacingd |
|
|
OrientationD = OrientationDict = Orientationd |
|
|
Rotate90D = Rotate90Dict = Rotate90d |
|
|
RandRotate90D = RandRotate90Dict = RandRotate90d |
|
|
ResizeD = ResizeDict = Resized |
|
|
AffineD = AffineDict = Affined |
|
|
RandAffineD = RandAffineDict = RandAffined |
|
|
Rand2DElasticD = Rand2DElasticDict = Rand2DElasticd |
|
|
Rand3DElasticD = Rand3DElasticDict = Rand3DElasticd |
|
|
FlipD = FlipDict = Flipd |
|
|
RandFlipD = RandFlipDict = RandFlipd |
|
|
GridDistortionD = GridDistortionDict = GridDistortiond |
|
|
RandGridDistortionD = RandGridDistortionDict = RandGridDistortiond |
|
|
RandAxisFlipD = RandAxisFlipDict = RandAxisFlipd |
|
|
RotateD = RotateDict = Rotated |
|
|
RandRotateD = RandRotateDict = RandRotated |
|
|
ZoomD = ZoomDict = Zoomd |
|
|
RandZoomD = RandZoomDict = RandZoomd |
|
|
GridSplitD = GridSplitDict = GridSplitd |
|
|
GridPatchD = GridPatchDict = GridPatchd |
|
|
RandGridPatchD = RandGridPatchDict = RandGridPatchd |
|
|
RandSimulateLowResolutionD = RandSimulateLowResolutionDict = RandSimulateLowResolutiond |
|
|
|