# Copyright 2020 - 2021 MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
A collection of dictionary-based wrappers around the "vanilla" transforms for crop and pad operations
defined in :py:class:`monai.transforms.croppad.array`.
Class names are ended with 'd' to denote dictionary-based transforms.
"""
from copy import deepcopy
from enum import Enum
from itertools import chain
from math import floor
from typing import Any, Callable, Dict, Hashable, List, Mapping, Optional, Sequence, Tuple, Union
import numpy as np
from monai.config import IndexSelection, KeysCollection
from monai.data.utils import get_random_patch, get_valid_patch_size
from monai.transforms.croppad.array import (
BorderPad,
BoundingRect,
CenterSpatialCrop,
CropForeground,
DivisiblePad,
ResizeWithPadOrCrop,
SpatialCrop,
SpatialPad,
)
from monai.transforms.inverse import InvertibleTransform
from monai.transforms.transform import MapTransform, Randomizable
from monai.transforms.utils import generate_pos_neg_label_crop_centers, map_binary_to_indices, weighted_patch_samples
from monai.utils import ImageMetaKey as Key
from monai.utils import Method, NumpyPadMode, ensure_tuple, ensure_tuple_rep, fall_back_tuple
from monai.utils.enums import InverseKeys
__all__ = [
"NumpyPadModeSequence",
"SpatialPadd",
"BorderPadd",
"DivisiblePadd",
"SpatialCropd",
"CenterSpatialCropd",
"RandSpatialCropd",
"RandSpatialCropSamplesd",
"CropForegroundd",
"RandWeightedCropd",
"RandCropByPosNegLabeld",
"ResizeWithPadOrCropd",
"BoundingRectd",
"SpatialPadD",
"SpatialPadDict",
"BorderPadD",
"BorderPadDict",
"DivisiblePadD",
"DivisiblePadDict",
"SpatialCropD",
"SpatialCropDict",
"CenterSpatialCropD",
"CenterSpatialCropDict",
"RandSpatialCropD",
"RandSpatialCropDict",
"RandSpatialCropSamplesD",
"RandSpatialCropSamplesDict",
"CropForegroundD",
"CropForegroundDict",
"RandWeightedCropD",
"RandWeightedCropDict",
"RandCropByPosNegLabelD",
"RandCropByPosNegLabelDict",
"ResizeWithPadOrCropD",
"ResizeWithPadOrCropDict",
"BoundingRectD",
"BoundingRectDict",
]
NumpyPadModeSequence = Union[Sequence[Union[NumpyPadMode, str]], NumpyPadMode, str]
[docs]class SpatialPadd(MapTransform, InvertibleTransform):
"""
Dictionary-based wrapper of :py:class:`monai.transforms.SpatialPad`.
Performs padding to the data, symmetric for all sides or all on one side for each dimension.
"""
def __init__(
self,
keys: KeysCollection,
spatial_size: Union[Sequence[int], int],
method: Union[Method, str] = Method.SYMMETRIC,
mode: NumpyPadModeSequence = NumpyPadMode.CONSTANT,
allow_missing_keys: bool = False,
) -> None:
"""
Args:
keys: keys of the corresponding items to be transformed.
See also: :py:class:`monai.transforms.compose.MapTransform`
spatial_size: the spatial size of output data after padding.
If its components have non-positive values, the corresponding size of input image will be used.
method: {``"symmetric"``, ``"end"``}
Pad image symmetric on every side or only pad at the end sides. Defaults to ``"symmetric"``.
mode: {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, ``"mean"``,
``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
One of the listed string values or a user supplied function. Defaults to ``"constant"``.
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html
It also can be a sequence of string, each element corresponds to a key in ``keys``.
allow_missing_keys: don't raise exception if key is missing.
"""
super().__init__(keys, allow_missing_keys)
self.mode = ensure_tuple_rep(mode, len(self.keys))
self.padder = SpatialPad(spatial_size, method)
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = dict(data)
for key, m in self.key_iterator(d, self.mode):
self.push_transform(d, key, extra_info={"mode": m.value if isinstance(m, Enum) else m})
d[key] = self.padder(d[key], mode=m)
return d
[docs] def inverse(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = deepcopy(dict(data))
for key in self.key_iterator(d):
transform = self.get_most_recent_transform(d, key)
# Create inverse transform
orig_size = transform[InverseKeys.ORIG_SIZE]
if self.padder.method == Method.SYMMETRIC:
current_size = d[key].shape[1:]
roi_center = [floor(i / 2) if r % 2 == 0 else (i - 1) // 2 for r, i in zip(orig_size, current_size)]
else:
roi_center = [floor(r / 2) if r % 2 == 0 else (r - 1) // 2 for r in orig_size]
inverse_transform = SpatialCrop(roi_center, orig_size)
# Apply inverse transform
d[key] = inverse_transform(d[key])
# Remove the applied transform
self.pop_transform(d, key)
return d
[docs]class BorderPadd(MapTransform, InvertibleTransform):
"""
Pad the input data by adding specified borders to every dimension.
Dictionary-based wrapper of :py:class:`monai.transforms.BorderPad`.
"""
def __init__(
self,
keys: KeysCollection,
spatial_border: Union[Sequence[int], int],
mode: NumpyPadModeSequence = NumpyPadMode.CONSTANT,
allow_missing_keys: bool = False,
) -> None:
"""
Args:
keys: keys of the corresponding items to be transformed.
See also: :py:class:`monai.transforms.compose.MapTransform`
spatial_border: specified size for every spatial border. it can be 3 shapes:
- single int number, pad all the borders with the same size.
- length equals the length of image shape, pad every spatial dimension separately.
for example, image shape(CHW) is [1, 4, 4], spatial_border is [2, 1],
pad every border of H dim with 2, pad every border of W dim with 1, result shape is [1, 8, 6].
- length equals 2 x (length of image shape), pad every border of every dimension separately.
for example, image shape(CHW) is [1, 4, 4], spatial_border is [1, 2, 3, 4], pad top of H dim with 1,
pad bottom of H dim with 2, pad left of W dim with 3, pad right of W dim with 4.
the result shape is [1, 7, 11].
mode: {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, ``"mean"``,
``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
One of the listed string values or a user supplied function. Defaults to ``"constant"``.
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html
It also can be a sequence of string, each element corresponds to a key in ``keys``.
allow_missing_keys: don't raise exception if key is missing.
"""
super().__init__(keys, allow_missing_keys)
self.mode = ensure_tuple_rep(mode, len(self.keys))
self.padder = BorderPad(spatial_border=spatial_border)
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = dict(data)
for key, m in self.key_iterator(d, self.mode):
self.push_transform(d, key, extra_info={"mode": m.value if isinstance(m, Enum) else m})
d[key] = self.padder(d[key], mode=m)
return d
[docs] def inverse(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = deepcopy(dict(data))
for key in self.key_iterator(d):
transform = self.get_most_recent_transform(d, key)
# Create inverse transform
orig_size = np.array(transform[InverseKeys.ORIG_SIZE])
roi_start = np.array(self.padder.spatial_border)
# Need to convert single value to [min1,min2,...]
if roi_start.size == 1:
roi_start = np.full((len(orig_size)), roi_start)
# need to convert [min1,max1,min2,...] to [min1,min2,...]
elif roi_start.size == 2 * orig_size.size:
roi_start = roi_start[::2]
roi_end = np.array(transform[InverseKeys.ORIG_SIZE]) + roi_start
inverse_transform = SpatialCrop(roi_start=roi_start, roi_end=roi_end)
# Apply inverse transform
d[key] = inverse_transform(d[key])
# Remove the applied transform
self.pop_transform(d, key)
return d
[docs]class DivisiblePadd(MapTransform, InvertibleTransform):
"""
Pad the input data, so that the spatial sizes are divisible by `k`.
Dictionary-based wrapper of :py:class:`monai.transforms.DivisiblePad`.
"""
def __init__(
self,
keys: KeysCollection,
k: Union[Sequence[int], int],
mode: NumpyPadModeSequence = NumpyPadMode.CONSTANT,
allow_missing_keys: bool = False,
) -> None:
"""
Args:
keys: keys of the corresponding items to be transformed.
See also: :py:class:`monai.transforms.compose.MapTransform`
k: the target k for each spatial dimension.
if `k` is negative or 0, the original size is preserved.
if `k` is an int, the same `k` be applied to all the input spatial dimensions.
mode: {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, ``"mean"``,
``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
One of the listed string values or a user supplied function. Defaults to ``"constant"``.
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html
It also can be a sequence of string, each element corresponds to a key in ``keys``.
allow_missing_keys: don't raise exception if key is missing.
See also :py:class:`monai.transforms.SpatialPad`
"""
super().__init__(keys, allow_missing_keys)
self.mode = ensure_tuple_rep(mode, len(self.keys))
self.padder = DivisiblePad(k=k)
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = dict(data)
for key, m in self.key_iterator(d, self.mode):
self.push_transform(d, key, extra_info={"mode": m.value if isinstance(m, Enum) else m})
d[key] = self.padder(d[key], mode=m)
return d
[docs] def inverse(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = deepcopy(dict(data))
for key in self.key_iterator(d):
transform = self.get_most_recent_transform(d, key)
# Create inverse transform
orig_size = np.array(transform[InverseKeys.ORIG_SIZE])
current_size = np.array(d[key].shape[1:])
roi_start = np.floor((current_size - orig_size) / 2)
roi_end = orig_size + roi_start
inverse_transform = SpatialCrop(roi_start=roi_start, roi_end=roi_end)
# Apply inverse transform
d[key] = inverse_transform(d[key])
# Remove the applied transform
self.pop_transform(d, key)
return d
[docs]class SpatialCropd(MapTransform, InvertibleTransform):
"""
Dictionary-based wrapper of :py:class:`monai.transforms.SpatialCrop`.
General purpose cropper to produce sub-volume region of interest (ROI).
It can support to crop ND spatial (channel-first) data.
The cropped region can be parameterised in various ways:
- a list of slices for each spatial dimension (allows for use of -ve indexing and `None`)
- a spatial center and size
- the start and end coordinates of the ROI
"""
def __init__(
self,
keys: KeysCollection,
roi_center: Optional[Sequence[int]] = None,
roi_size: Optional[Sequence[int]] = None,
roi_start: Optional[Sequence[int]] = None,
roi_end: Optional[Sequence[int]] = None,
roi_slices: Optional[Sequence[slice]] = None,
allow_missing_keys: bool = False,
) -> None:
"""
Args:
keys: keys of the corresponding items to be transformed.
See also: :py:class:`monai.transforms.compose.MapTransform`
roi_center: voxel coordinates for center of the crop ROI.
roi_size: size of the crop ROI.
roi_start: voxel coordinates for start of the crop ROI.
roi_end: voxel coordinates for end of the crop ROI.
roi_slices: list of slices for each of the spatial dimensions.
allow_missing_keys: don't raise exception if key is missing.
"""
super().__init__(keys, allow_missing_keys)
self.cropper = SpatialCrop(roi_center, roi_size, roi_start, roi_end, roi_slices)
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = dict(data)
for key in self.key_iterator(d):
self.push_transform(d, key)
d[key] = self.cropper(d[key])
return d
[docs] def inverse(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = deepcopy(dict(data))
for key in self.key_iterator(d):
transform = self.get_most_recent_transform(d, key)
# Create inverse transform
orig_size = np.array(transform[InverseKeys.ORIG_SIZE])
current_size = np.array(d[key].shape[1:])
# get required pad to start and end
pad_to_start = np.array([s.indices(o)[0] for s, o in zip(self.cropper.slices, orig_size)])
pad_to_end = orig_size - current_size - pad_to_start
# interleave mins and maxes
pad = list(chain(*zip(pad_to_start.tolist(), pad_to_end.tolist())))
inverse_transform = BorderPad(pad)
# Apply inverse transform
d[key] = inverse_transform(d[key])
# Remove the applied transform
self.pop_transform(d, key)
return d
[docs]class CenterSpatialCropd(MapTransform, InvertibleTransform):
"""
Dictionary-based wrapper of :py:class:`monai.transforms.CenterSpatialCrop`.
Args:
keys: keys of the corresponding items to be transformed.
See also: monai.transforms.MapTransform
roi_size: the size of the crop region e.g. [224,224,128]
If its components have non-positive values, the corresponding size of input image will be used.
allow_missing_keys: don't raise exception if key is missing.
"""
def __init__(
self, keys: KeysCollection, roi_size: Union[Sequence[int], int], allow_missing_keys: bool = False
) -> None:
super().__init__(keys, allow_missing_keys)
self.cropper = CenterSpatialCrop(roi_size)
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = dict(data)
for key in self.key_iterator(d):
orig_size = d[key].shape[1:]
d[key] = self.cropper(d[key])
self.push_transform(d, key, orig_size=orig_size)
return d
[docs] def inverse(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = deepcopy(dict(data))
for key in self.key_iterator(d):
transform = self.get_most_recent_transform(d, key)
# Create inverse transform
orig_size = np.array(transform[InverseKeys.ORIG_SIZE])
current_size = np.array(d[key].shape[1:])
pad_to_start = np.floor((orig_size - current_size) / 2).astype(int)
# in each direction, if original size is even and current size is odd, += 1
pad_to_start[np.logical_and(orig_size % 2 == 0, current_size % 2 == 1)] += 1
pad_to_end = orig_size - current_size - pad_to_start
pad = list(chain(*zip(pad_to_start.tolist(), pad_to_end.tolist())))
inverse_transform = BorderPad(pad)
# Apply inverse transform
d[key] = inverse_transform(d[key])
# Remove the applied transform
self.pop_transform(d, key)
return d
[docs]class RandSpatialCropd(Randomizable, MapTransform, InvertibleTransform):
"""
Dictionary-based version :py:class:`monai.transforms.RandSpatialCrop`.
Crop image with random size or specific size ROI. It can crop at a random position as
center or at the image center. And allows to set the minimum size to limit the randomly
generated ROI. Suppose all the expected fields specified by `keys` have same shape.
Args:
keys: keys of the corresponding items to be transformed.
See also: monai.transforms.MapTransform
roi_size: if `random_size` is True, it specifies the minimum crop region.
if `random_size` is False, it specifies the expected ROI size to crop. e.g. [224, 224, 128]
If its components have non-positive values, the corresponding size of input image will be used.
random_center: crop at random position as center or the image center.
random_size: crop with random size or specific size ROI.
The actual size is sampled from `randint(roi_size, img_size)`.
allow_missing_keys: don't raise exception if key is missing.
"""
def __init__(
self,
keys: KeysCollection,
roi_size: Union[Sequence[int], int],
random_center: bool = True,
random_size: bool = True,
allow_missing_keys: bool = False,
) -> None:
MapTransform.__init__(self, keys, allow_missing_keys)
self.roi_size = roi_size
self.random_center = random_center
self.random_size = random_size
self._slices: Optional[Tuple[slice, ...]] = None
self._size: Optional[Sequence[int]] = None
[docs] def randomize(self, img_size: Sequence[int]) -> None:
self._size = fall_back_tuple(self.roi_size, img_size)
if self.random_size:
self._size = [self.R.randint(low=self._size[i], high=img_size[i] + 1) for i in range(len(img_size))]
if self.random_center:
valid_size = get_valid_patch_size(img_size, self._size)
self._slices = (slice(None),) + get_random_patch(img_size, valid_size, self.R)
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = dict(data)
self.randomize(d[self.keys[0]].shape[1:]) # image shape from the first data key
if self._size is None:
raise AssertionError
for key in self.key_iterator(d):
if self.random_center:
self.push_transform(d, key, {"slices": [(i.start, i.stop) for i in self._slices[1:]]}) # type: ignore
d[key] = d[key][self._slices]
else:
self.push_transform(d, key)
cropper = CenterSpatialCrop(self._size)
d[key] = cropper(d[key])
return d
[docs] def inverse(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = deepcopy(dict(data))
for key in self.key_iterator(d):
transform = self.get_most_recent_transform(d, key)
# Create inverse transform
orig_size = transform[InverseKeys.ORIG_SIZE]
random_center = self.random_center
pad_to_start = np.empty((len(orig_size)), dtype=np.int32)
pad_to_end = np.empty((len(orig_size)), dtype=np.int32)
if random_center:
for i, _slice in enumerate(transform[InverseKeys.EXTRA_INFO]["slices"]):
pad_to_start[i] = _slice[0]
pad_to_end[i] = orig_size[i] - _slice[1]
else:
current_size = d[key].shape[1:]
for i, (o_s, c_s) in enumerate(zip(orig_size, current_size)):
pad_to_start[i] = pad_to_end[i] = (o_s - c_s) / 2
if o_s % 2 == 0 and c_s % 2 == 1:
pad_to_start[i] += 1
elif o_s % 2 == 1 and c_s % 2 == 0:
pad_to_end[i] += 1
# interleave mins and maxes
pad = list(chain(*zip(pad_to_start.tolist(), pad_to_end.tolist())))
inverse_transform = BorderPad(pad)
# Apply inverse transform
d[key] = inverse_transform(d[key])
# Remove the applied transform
self.pop_transform(d, key)
return d
[docs]class RandSpatialCropSamplesd(Randomizable, MapTransform):
"""
Dictionary-based version :py:class:`monai.transforms.RandSpatialCropSamples`.
Crop image with random size or specific size ROI to generate a list of N samples.
It can crop at a random position as center or at the image center. And allows to set
the minimum size to limit the randomly generated ROI. Suppose all the expected fields
specified by `keys` have same shape, and add `patch_index` to the corresponding meta data.
It will return a list of dictionaries for all the cropped images.
Args:
keys: keys of the corresponding items to be transformed.
See also: monai.transforms.MapTransform
roi_size: if `random_size` is True, the spatial size of the minimum crop region.
if `random_size` is False, specify the expected ROI size to crop. e.g. [224, 224, 128]
num_samples: number of samples (crop regions) to take in the returned list.
random_center: crop at random position as center or the image center.
random_size: crop with random size or specific size ROI.
The actual size is sampled from `randint(roi_size, img_size)`.
meta_key_postfix: use `key_{postfix}` to to fetch the meta data according to the key data,
default is `meta_dict`, the meta data is a dictionary object.
used to add `patch_index` to the meta dict.
allow_missing_keys: don't raise exception if key is missing.
Raises:
ValueError: When ``num_samples`` is nonpositive.
"""
def __init__(
self,
keys: KeysCollection,
roi_size: Union[Sequence[int], int],
num_samples: int,
random_center: bool = True,
random_size: bool = True,
meta_key_postfix: str = "meta_dict",
allow_missing_keys: bool = False,
) -> None:
MapTransform.__init__(self, keys, allow_missing_keys)
if num_samples < 1:
raise ValueError(f"num_samples must be positive, got {num_samples}.")
self.num_samples = num_samples
self.cropper = RandSpatialCropd(keys, roi_size, random_center, random_size, allow_missing_keys)
self.meta_key_postfix = meta_key_postfix
[docs] def set_random_state(
self, seed: Optional[int] = None, state: Optional[np.random.RandomState] = None
) -> "Randomizable":
super().set_random_state(seed=seed, state=state)
self.cropper.set_random_state(state=self.R)
return self
[docs] def randomize(self, data: Optional[Any] = None) -> None:
pass
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> List[Dict[Hashable, np.ndarray]]:
ret = []
for i in range(self.num_samples):
d = dict(data)
# deep copy all the unmodified data
for key in set(data.keys()).difference(set(self.keys)):
d[key] = deepcopy(data[key])
cropped = self.cropper(d)
# add `patch_index` to the meta data
for key in self.key_iterator(d):
meta_data_key = f"{key}_{self.meta_key_postfix}"
if meta_data_key not in cropped:
cropped[meta_data_key] = {} # type: ignore
cropped[meta_data_key][Key.PATCH_INDEX] = i
ret.append(cropped)
return ret
[docs]class CropForegroundd(MapTransform, InvertibleTransform):
"""
Dictionary-based version :py:class:`monai.transforms.CropForeground`.
Crop only the foreground object of the expected images.
The typical usage is to help training and evaluation if the valid part is small in the whole medical image.
The valid part can be determined by any field in the data with `source_key`, for example:
- Select values > 0 in image field as the foreground and crop on all fields specified by `keys`.
- Select label = 3 in label field as the foreground to crop on all fields specified by `keys`.
- Select label > 0 in the third channel of a One-Hot label field as the foreground to crop all `keys` fields.
Users can define arbitrary function to select expected foreground from the whole source image or specified
channels. And it can also add margin to every dim of the bounding box of foreground object.
"""
def __init__(
self,
keys: KeysCollection,
source_key: str,
select_fn: Callable = lambda x: x > 0,
channel_indices: Optional[IndexSelection] = None,
margin: Union[Sequence[int], int] = 0,
k_divisible: Union[Sequence[int], int] = 1,
mode: Union[NumpyPadMode, str] = NumpyPadMode.CONSTANT,
start_coord_key: str = "foreground_start_coord",
end_coord_key: str = "foreground_end_coord",
allow_missing_keys: bool = False,
) -> None:
"""
Args:
keys: keys of the corresponding items to be transformed.
See also: :py:class:`monai.transforms.compose.MapTransform`
source_key: data source to generate the bounding box of foreground, can be image or label, etc.
select_fn: function to select expected foreground, default is to select values > 0.
channel_indices: if defined, select foreground only on the specified channels
of image. if None, select foreground on the whole image.
margin: add margin value to spatial dims of the bounding box, if only 1 value provided, use it for all dims.
k_divisible: make each spatial dimension to be divisible by k, default to 1.
if `k_divisible` is an int, the same `k` be applied to all the input spatial dimensions.
mode: padding mode {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, ``"mean"``,
``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
one of the listed string values or a user supplied function. Defaults to ``"constant"``.
see also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html
start_coord_key: key to record the start coordinate of spatial bounding box for foreground.
end_coord_key: key to record the end coordinate of spatial bounding box for foreground.
allow_missing_keys: don't raise exception if key is missing.
"""
super().__init__(keys, allow_missing_keys)
self.source_key = source_key
self.start_coord_key = start_coord_key
self.end_coord_key = end_coord_key
self.cropper = CropForeground(
select_fn=select_fn,
channel_indices=channel_indices,
margin=margin,
k_divisible=k_divisible,
mode=mode,
)
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = dict(data)
box_start, box_end = self.cropper.compute_bounding_box(img=d[self.source_key])
d[self.start_coord_key] = box_start
d[self.end_coord_key] = box_end
for key in self.key_iterator(d):
self.push_transform(d, key, extra_info={"box_start": box_start, "box_end": box_end})
d[key] = self.cropper.crop_pad(d[key], box_start, box_end)
return d
[docs] def inverse(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = deepcopy(dict(data))
for key in self.key_iterator(d):
transform = self.get_most_recent_transform(d, key)
# Create inverse transform
orig_size = np.asarray(transform[InverseKeys.ORIG_SIZE])
cur_size = np.asarray(d[key].shape[1:])
extra_info = transform[InverseKeys.EXTRA_INFO]
box_start = np.asarray(extra_info["box_start"])
box_end = np.asarray(extra_info["box_end"])
# first crop the padding part
roi_start = np.maximum(-box_start, 0)
roi_end = cur_size - np.maximum(box_end - orig_size, 0)
d[key] = SpatialCrop(roi_start=roi_start, roi_end=roi_end)(d[key])
# update bounding box to pad
pad_to_start = np.maximum(box_start, 0)
pad_to_end = orig_size - np.minimum(box_end, orig_size)
# interleave mins and maxes
pad = list(chain(*zip(pad_to_start.tolist(), pad_to_end.tolist())))
# second pad back the original size
d[key] = BorderPad(pad)(d[key])
# Remove the applied transform
self.pop_transform(d, key)
return d
[docs]class RandWeightedCropd(Randomizable, MapTransform):
"""
Samples a list of `num_samples` image patches according to the provided `weight_map`.
Args:
keys: keys of the corresponding items to be transformed.
See also: :py:class:`monai.transforms.compose.MapTransform`
w_key: key for the weight map. The corresponding value will be used as the sampling weights,
it should be a single-channel array in size, for example, `(1, spatial_dim_0, spatial_dim_1, ...)`
spatial_size: the spatial size of the image patch e.g. [224, 224, 128].
If its components have non-positive values, the corresponding size of `img` will be used.
num_samples: number of samples (image patches) to take in the returned list.
center_coord_key: if specified, the actual sampling location will be stored with the corresponding key.
meta_key_postfix: use `key_{postfix}` to to fetch the meta data according to the key data,
default is `meta_dict`, the meta data is a dictionary object.
used to add `patch_index` to the meta dict.
allow_missing_keys: don't raise exception if key is missing.
See Also:
:py:class:`monai.transforms.RandWeightedCrop`
"""
def __init__(
self,
keys: KeysCollection,
w_key: str,
spatial_size: Union[Sequence[int], int],
num_samples: int = 1,
center_coord_key: Optional[str] = None,
meta_key_postfix: str = "meta_dict",
allow_missing_keys: bool = False,
):
MapTransform.__init__(self, keys, allow_missing_keys)
self.spatial_size = ensure_tuple(spatial_size)
self.w_key = w_key
self.num_samples = int(num_samples)
self.center_coord_key = center_coord_key
self.meta_key_postfix = meta_key_postfix
self.centers: List[np.ndarray] = []
[docs] def randomize(self, weight_map: np.ndarray) -> None:
self.centers = weighted_patch_samples(
spatial_size=self.spatial_size, w=weight_map[0], n_samples=self.num_samples, r_state=self.R
)
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> List[Dict[Hashable, np.ndarray]]:
d = dict(data)
self.randomize(d[self.w_key])
_spatial_size = fall_back_tuple(self.spatial_size, d[self.w_key].shape[1:])
results: List[Dict[Hashable, np.ndarray]] = [{} for _ in range(self.num_samples)]
for key in self.key_iterator(d):
img = d[key]
if img.shape[1:] != d[self.w_key].shape[1:]:
raise ValueError(
f"data {key} and weight map {self.w_key} spatial shape mismatch: "
f"{img.shape[1:]} vs {d[self.w_key].shape[1:]}."
)
for i, center in enumerate(self.centers):
cropper = SpatialCrop(roi_center=center, roi_size=_spatial_size)
results[i][key] = cropper(img)
if self.center_coord_key:
results[i][self.center_coord_key] = center
# fill in the extra keys with unmodified data
for i in range(self.num_samples):
for key in set(data.keys()).difference(set(self.keys)):
results[i][key] = deepcopy(data[key])
# add `patch_index` to the meta data
for key in self.key_iterator(d):
meta_data_key = f"{key}_{self.meta_key_postfix}"
if meta_data_key not in results[i]:
results[i][meta_data_key] = {} # type: ignore
results[i][meta_data_key][Key.PATCH_INDEX] = i
return results
[docs]class RandCropByPosNegLabeld(Randomizable, MapTransform):
"""
Dictionary-based version :py:class:`monai.transforms.RandCropByPosNegLabel`.
Crop random fixed sized regions with the center being a foreground or background voxel
based on the Pos Neg Ratio.
Suppose all the expected fields specified by `keys` have same shape,
and add `patch_index` to the corresponding meta data.
And will return a list of dictionaries for all the cropped images.
Args:
keys: keys of the corresponding items to be transformed.
See also: :py:class:`monai.transforms.compose.MapTransform`
label_key: name of key for label image, this will be used for finding foreground/background.
spatial_size: the spatial size of the crop region e.g. [224, 224, 128].
If its components have non-positive values, the corresponding size of `data[label_key]` will be used.
pos: used with `neg` together to calculate the ratio ``pos / (pos + neg)`` for the probability
to pick a foreground voxel as a center rather than a background voxel.
neg: used with `pos` together to calculate the ratio ``pos / (pos + neg)`` for the probability
to pick a foreground voxel as a center rather than a background voxel.
num_samples: number of samples (crop regions) to take in each list.
image_key: if image_key is not None, use ``label == 0 & image > image_threshold`` to select
the negative sample(background) center. so the crop center will only exist on valid image area.
image_threshold: if enabled image_key, use ``image > image_threshold`` to determine
the valid image content area.
fg_indices_key: if provided pre-computed foreground indices of `label`, will ignore above `image_key` and
`image_threshold`, and randomly select crop centers based on them, need to provide `fg_indices_key`
and `bg_indices_key` together, expect to be 1 dim array of spatial indices after flattening.
a typical usage is to call `FgBgToIndicesd` transform first and cache the results.
bg_indices_key: if provided pre-computed background indices of `label`, will ignore above `image_key` and
`image_threshold`, and randomly select crop centers based on them, need to provide `fg_indices_key`
and `bg_indices_key` together, expect to be 1 dim array of spatial indices after flattening.
a typical usage is to call `FgBgToIndicesd` transform first and cache the results.
meta_key_postfix: use `key_{postfix}` to to fetch the meta data according to the key data,
default is `meta_dict`, the meta data is a dictionary object.
used to add `patch_index` to the meta dict.
allow_missing_keys: don't raise exception if key is missing.
Raises:
ValueError: When ``pos`` or ``neg`` are negative.
ValueError: When ``pos=0`` and ``neg=0``. Incompatible values.
"""
def __init__(
self,
keys: KeysCollection,
label_key: str,
spatial_size: Union[Sequence[int], int],
pos: float = 1.0,
neg: float = 1.0,
num_samples: int = 1,
image_key: Optional[str] = None,
image_threshold: float = 0.0,
fg_indices_key: Optional[str] = None,
bg_indices_key: Optional[str] = None,
meta_key_postfix: str = "meta_dict",
allow_missing_keys: bool = False,
) -> None:
MapTransform.__init__(self, keys, allow_missing_keys)
self.label_key = label_key
self.spatial_size: Union[Tuple[int, ...], Sequence[int], int] = spatial_size
if pos < 0 or neg < 0:
raise ValueError(f"pos and neg must be nonnegative, got pos={pos} neg={neg}.")
if pos + neg == 0:
raise ValueError("Incompatible values: pos=0 and neg=0.")
self.pos_ratio = pos / (pos + neg)
self.num_samples = num_samples
self.image_key = image_key
self.image_threshold = image_threshold
self.fg_indices_key = fg_indices_key
self.bg_indices_key = bg_indices_key
self.meta_key_postfix = meta_key_postfix
self.centers: Optional[List[List[np.ndarray]]] = None
[docs] def randomize(
self,
label: np.ndarray,
fg_indices: Optional[np.ndarray] = None,
bg_indices: Optional[np.ndarray] = None,
image: Optional[np.ndarray] = None,
) -> None:
self.spatial_size = fall_back_tuple(self.spatial_size, default=label.shape[1:])
if fg_indices is None or bg_indices is None:
fg_indices_, bg_indices_ = map_binary_to_indices(label, image, self.image_threshold)
else:
fg_indices_ = fg_indices
bg_indices_ = bg_indices
self.centers = generate_pos_neg_label_crop_centers(
self.spatial_size, self.num_samples, self.pos_ratio, label.shape[1:], fg_indices_, bg_indices_, self.R
)
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> List[Dict[Hashable, np.ndarray]]:
d = dict(data)
label = d[self.label_key]
image = d[self.image_key] if self.image_key else None
fg_indices = d.get(self.fg_indices_key) if self.fg_indices_key is not None else None
bg_indices = d.get(self.bg_indices_key) if self.bg_indices_key is not None else None
self.randomize(label, fg_indices, bg_indices, image)
if not isinstance(self.spatial_size, tuple):
raise AssertionError
if self.centers is None:
raise AssertionError
results: List[Dict[Hashable, np.ndarray]] = [{} for _ in range(self.num_samples)]
for i, center in enumerate(self.centers):
for key in self.key_iterator(d):
img = d[key]
cropper = SpatialCrop(roi_center=tuple(center), roi_size=self.spatial_size) # type: ignore
results[i][key] = cropper(img)
# fill in the extra keys with unmodified data
for key in set(data.keys()).difference(set(self.keys)):
results[i][key] = deepcopy(data[key])
# add `patch_index` to the meta data
for key in self.key_iterator(d):
meta_data_key = f"{key}_{self.meta_key_postfix}"
if meta_data_key not in results[i]:
results[i][meta_data_key] = {} # type: ignore
results[i][meta_data_key][Key.PATCH_INDEX] = i
return results
[docs]class ResizeWithPadOrCropd(MapTransform, InvertibleTransform):
"""
Dictionary-based wrapper of :py:class:`monai.transforms.ResizeWithPadOrCrop`.
Args:
keys: keys of the corresponding items to be transformed.
See also: monai.transforms.MapTransform
spatial_size: the spatial size of output data after padding or crop.
If has non-positive values, the corresponding size of input image will be used (no padding).
mode: {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, ``"mean"``,
``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
One of the listed string values or a user supplied function for padding. Defaults to ``"constant"``.
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html
It also can be a sequence of string, each element corresponds to a key in ``keys``.
allow_missing_keys: don't raise exception if key is missing.
"""
def __init__(
self,
keys: KeysCollection,
spatial_size: Union[Sequence[int], int],
mode: NumpyPadModeSequence = NumpyPadMode.CONSTANT,
allow_missing_keys: bool = False,
) -> None:
super().__init__(keys, allow_missing_keys)
self.mode = ensure_tuple_rep(mode, len(self.keys))
self.padcropper = ResizeWithPadOrCrop(spatial_size=spatial_size)
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = dict(data)
for key, m in self.key_iterator(d, self.mode):
orig_size = d[key].shape[1:]
d[key] = self.padcropper(d[key], mode=m)
self.push_transform(
d,
key,
orig_size=orig_size,
extra_info={
"mode": m.value if isinstance(m, Enum) else m,
},
)
return d
[docs] def inverse(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
d = deepcopy(dict(data))
for key in self.key_iterator(d):
transform = self.get_most_recent_transform(d, key)
# Create inverse transform
orig_size = np.array(transform[InverseKeys.ORIG_SIZE])
current_size = np.array(d[key].shape[1:])
# Unfortunately, we can't just use ResizeWithPadOrCrop with original size because of odd/even rounding.
# Instead, we first pad any smaller dimensions, and then we crop any larger dimensions.
# First, do pad
if np.any((orig_size - current_size) > 0):
pad_to_start = np.floor((orig_size - current_size) / 2).astype(int)
# in each direction, if original size is even and current size is odd, += 1
pad_to_start[np.logical_and(orig_size % 2 == 0, current_size % 2 == 1)] += 1
pad_to_start[pad_to_start < 0] = 0
pad_to_end = orig_size - current_size - pad_to_start
pad_to_end[pad_to_end < 0] = 0
pad = list(chain(*zip(pad_to_start.tolist(), pad_to_end.tolist())))
d[key] = BorderPad(pad)(d[key])
# Next crop
if np.any((orig_size - current_size) < 0):
if self.padcropper.padder.method == Method.SYMMETRIC:
roi_center = [floor(i / 2) if r % 2 == 0 else (i - 1) // 2 for r, i in zip(orig_size, current_size)]
else:
roi_center = [floor(r / 2) if r % 2 == 0 else (r - 1) // 2 for r in orig_size]
d[key] = SpatialCrop(roi_center, orig_size)(d[key])
# Remove the applied transform
self.pop_transform(d, key)
return d
[docs]class BoundingRectd(MapTransform):
"""
Dictionary-based wrapper of :py:class:`monai.transforms.BoundingRect`.
Args:
keys: keys of the corresponding items to be transformed.
See also: monai.transforms.MapTransform
bbox_key_postfix: the output bounding box coordinates will be
written to the value of `{key}_{bbox_key_postfix}`.
select_fn: function to select expected foreground, default is to select values > 0.
allow_missing_keys: don't raise exception if key is missing.
"""
def __init__(
self,
keys: KeysCollection,
bbox_key_postfix: str = "bbox",
select_fn: Callable = lambda x: x > 0,
allow_missing_keys: bool = False,
):
super().__init__(keys, allow_missing_keys)
self.bbox = BoundingRect(select_fn=select_fn)
self.bbox_key_postfix = bbox_key_postfix
[docs] def __call__(self, data: Mapping[Hashable, np.ndarray]) -> Dict[Hashable, np.ndarray]:
"""
See also: :py:class:`monai.transforms.utils.generate_spatial_bounding_box`.
"""
d = dict(data)
for key in self.key_iterator(d):
bbox = self.bbox(d[key])
key_to_add = f"{key}_{self.bbox_key_postfix}"
if key_to_add in d:
raise KeyError(f"Bounding box data with key {key_to_add} already exists.")
d[key_to_add] = bbox
return d
SpatialPadD = SpatialPadDict = SpatialPadd
BorderPadD = BorderPadDict = BorderPadd
DivisiblePadD = DivisiblePadDict = DivisiblePadd
SpatialCropD = SpatialCropDict = SpatialCropd
CenterSpatialCropD = CenterSpatialCropDict = CenterSpatialCropd
RandSpatialCropD = RandSpatialCropDict = RandSpatialCropd
RandSpatialCropSamplesD = RandSpatialCropSamplesDict = RandSpatialCropSamplesd
CropForegroundD = CropForegroundDict = CropForegroundd
RandWeightedCropD = RandWeightedCropDict = RandWeightedCropd
RandCropByPosNegLabelD = RandCropByPosNegLabelDict = RandCropByPosNegLabeld
ResizeWithPadOrCropD = ResizeWithPadOrCropDict = ResizeWithPadOrCropd
BoundingRectD = BoundingRectDict = BoundingRectd