Source code for monai.transforms.croppad.array

# 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
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"""
A collection of "vanilla" transforms for crop and pad operations
https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
"""

from itertools import chain
from math import ceil
from typing import Any, Callable, List, Optional, Sequence, Tuple, Union

import numpy as np
import torch

from monai.config import IndexSelection
from monai.data.utils import get_random_patch, get_valid_patch_size
from monai.transforms.transform import Randomizable, Transform
from monai.transforms.utils import (
    compute_divisible_spatial_size,
    generate_label_classes_crop_centers,
    generate_pos_neg_label_crop_centers,
    generate_spatial_bounding_box,
    is_positive,
    map_binary_to_indices,
    map_classes_to_indices,
    weighted_patch_samples,
)
from monai.utils import Method, NumpyPadMode, ensure_tuple, ensure_tuple_rep, fall_back_tuple, look_up_option

__all__ = [
    "SpatialPad",
    "BorderPad",
    "DivisiblePad",
    "SpatialCrop",
    "CenterSpatialCrop",
    "CenterScaleCrop",
    "RandSpatialCrop",
    "RandScaleCrop",
    "RandSpatialCropSamples",
    "CropForeground",
    "RandWeightedCrop",
    "RandCropByPosNegLabel",
    "RandCropByLabelClasses",
    "ResizeWithPadOrCrop",
    "BoundingRect",
]


[docs]class SpatialPad(Transform): """ Performs padding to the data, symmetric for all sides or all on one side for each dimension. Uses np.pad so in practice, a mode needs to be provided. See numpy.lib.arraypad.pad for additional details. Args: spatial_size: the spatial size of output data after padding, if a dimension of the input data size is bigger than the pad size, will not pad that dimension. If its components have non-positive values, the corresponding size of input image will be used (no padding). for example: if the spatial size of input data is [30, 30, 30] and `spatial_size=[32, 25, -1]`, the spatial size of output data will be [32, 30, 30]. method: {``"symmetric"``, ``"end"``} Pad image symmetrically on every side or only pad at the end sides. Defaults to ``"symmetric"``. mode: {``"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 np_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 """ def __init__( self, spatial_size: Union[Sequence[int], int], method: Union[Method, str] = Method.SYMMETRIC, mode: Union[NumpyPadMode, str] = NumpyPadMode.CONSTANT, **np_kwargs, ) -> None: self.spatial_size = spatial_size self.method: Method = look_up_option(method, Method) self.mode: NumpyPadMode = look_up_option(mode, NumpyPadMode) self.np_kwargs = np_kwargs def _determine_data_pad_width(self, data_shape: Sequence[int]) -> List[Tuple[int, int]]: spatial_size = fall_back_tuple(self.spatial_size, data_shape) if self.method == Method.SYMMETRIC: pad_width = [] for i, sp_i in enumerate(spatial_size): width = max(sp_i - data_shape[i], 0) pad_width.append((width // 2, width - (width // 2))) return pad_width return [(0, max(sp_i - data_shape[i], 0)) for i, sp_i in enumerate(spatial_size)]
[docs] def __call__(self, img: np.ndarray, mode: Optional[Union[NumpyPadMode, str]] = None) -> np.ndarray: """ Args: img: data to be transformed, assuming `img` is channel-first and padding doesn't apply to the channel dim. 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 ``self.mode``. See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html """ data_pad_width = self._determine_data_pad_width(img.shape[1:]) all_pad_width = [(0, 0)] + data_pad_width if not np.asarray(all_pad_width).any(): # all zeros, skip padding return img mode = look_up_option(self.mode if mode is None else mode, NumpyPadMode).value img = np.pad(img, all_pad_width, mode=mode, **self.np_kwargs) return img
[docs]class BorderPad(Transform): """ Pad the input data by adding specified borders to every dimension. Args: spatial_border: specified size for every spatial border. Any -ve values will be set to 0. 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 np_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 """ def __init__( self, spatial_border: Union[Sequence[int], int], mode: Union[NumpyPadMode, str] = NumpyPadMode.CONSTANT, **np_kwargs, ) -> None: self.spatial_border = spatial_border self.mode: NumpyPadMode = look_up_option(mode, NumpyPadMode) self.np_kwargs = np_kwargs
[docs] def __call__(self, img: np.ndarray, mode: Optional[Union[NumpyPadMode, str]] = None): """ Args: img: data to be transformed, assuming `img` is channel-first and padding doesn't apply to the channel dim. 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 ``self.mode``. See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html Raises: ValueError: When ``self.spatial_border`` does not contain ints. ValueError: When ``self.spatial_border`` length is not one of [1, len(spatial_shape), 2*len(spatial_shape)]. """ spatial_shape = img.shape[1:] spatial_border = ensure_tuple(self.spatial_border) if not all(isinstance(b, int) for b in spatial_border): raise ValueError(f"self.spatial_border must contain only ints, got {spatial_border}.") spatial_border = tuple(max(0, b) for b in spatial_border) if len(spatial_border) == 1: data_pad_width = [(spatial_border[0], spatial_border[0]) for _ in spatial_shape] elif len(spatial_border) == len(spatial_shape): data_pad_width = [(sp, sp) for sp in spatial_border[: len(spatial_shape)]] elif len(spatial_border) == len(spatial_shape) * 2: data_pad_width = [(spatial_border[2 * i], spatial_border[2 * i + 1]) for i in range(len(spatial_shape))] else: raise ValueError( f"Unsupported spatial_border length: {len(spatial_border)}, available options are " f"[1, len(spatial_shape)={len(spatial_shape)}, 2*len(spatial_shape)={2*len(spatial_shape)}]." ) mode = look_up_option(self.mode if mode is None else mode, NumpyPadMode).value return np.pad(img, [(0, 0)] + data_pad_width, mode=mode, **self.np_kwargs)
[docs]class DivisiblePad(Transform): """ Pad the input data, so that the spatial sizes are divisible by `k`. """ def __init__( self, k: Union[Sequence[int], int], mode: Union[NumpyPadMode, str] = NumpyPadMode.CONSTANT, method: Union[Method, str] = Method.SYMMETRIC, **np_kwargs, ) -> None: """ Args: 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 method: {``"symmetric"``, ``"end"``} Pad image symmetrically on every side or only pad at the end sides. Defaults to ``"symmetric"``. np_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 See also :py:class:`monai.transforms.SpatialPad` """ self.k = k self.mode: NumpyPadMode = NumpyPadMode(mode) self.method: Method = Method(method) self.np_kwargs = np_kwargs
[docs] def __call__(self, img: np.ndarray, mode: Optional[Union[NumpyPadMode, str]] = None) -> np.ndarray: """ Args: img: data to be transformed, assuming `img` is channel-first and padding doesn't apply to the channel dim. 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 ``self.mode``. See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html """ new_size = compute_divisible_spatial_size(spatial_shape=img.shape[1:], k=self.k) spatial_pad = SpatialPad( spatial_size=new_size, method=self.method, mode=mode or self.mode, **self.np_kwargs, ) return spatial_pad(img)
[docs]class SpatialCrop(Transform): """ General purpose cropper to produce sub-volume region of interest (ROI). If a dimension of the expected ROI size is bigger than the input image size, will not crop that dimension. So the cropped result may be smaller than the expected ROI, and the cropped results of several images may not have exactly the same shape. It can support to crop ND spatial (channel-first) data. The cropped region can be parameterised in various ways: - a list of slices for each spatial dimension (allows for use of -ve indexing and `None`) - a spatial center and size - the start and end coordinates of the ROI """ def __init__( self, roi_center: Union[Sequence[int], np.ndarray, None] = None, roi_size: Union[Sequence[int], np.ndarray, None] = None, roi_start: Union[Sequence[int], np.ndarray, None] = None, roi_end: Union[Sequence[int], np.ndarray, None] = None, roi_slices: Optional[Sequence[slice]] = None, ) -> None: """ Args: roi_center: voxel coordinates for center of the crop ROI. roi_size: size of the crop ROI, if a dimension of ROI size is bigger than image size, will not crop that dimension of the image. roi_start: voxel coordinates for start of the crop ROI. roi_end: voxel coordinates for end of the crop ROI, if a coordinate is out of image, use the end coordinate of image. roi_slices: list of slices for each of the spatial dimensions. """ if roi_slices: if not all(s.step is None or s.step == 1 for s in roi_slices): raise ValueError("Only slice steps of 1/None are currently supported") self.slices = list(roi_slices) else: if roi_center is not None and roi_size is not None: roi_center = np.asarray(roi_center, dtype=np.int16) roi_size = np.asarray(roi_size, dtype=np.int16) roi_start_np = np.maximum(roi_center - np.floor_divide(roi_size, 2), 0) roi_end_np = np.maximum(roi_start_np + roi_size, roi_start_np) else: if roi_start is None or roi_end is None: raise ValueError("Please specify either roi_center, roi_size or roi_start, roi_end.") roi_start_np = np.maximum(np.asarray(roi_start, dtype=np.int16), 0) roi_end_np = np.maximum(np.asarray(roi_end, dtype=np.int16), roi_start_np) # Allow for 1D by converting back to np.array (since np.maximum will convert to int) roi_start_np = roi_start_np if isinstance(roi_start_np, np.ndarray) else np.array([roi_start_np]) roi_end_np = roi_end_np if isinstance(roi_end_np, np.ndarray) else np.array([roi_end_np]) # convert to slices self.slices = [slice(s, e) for s, e in zip(roi_start_np, roi_end_np)]
[docs] def __call__(self, img: Union[np.ndarray, torch.Tensor]): """ Apply the transform to `img`, assuming `img` is channel-first and slicing doesn't apply to the channel dim. """ sd = min(len(self.slices), len(img.shape[1:])) # spatial dims slices = [slice(None)] + self.slices[:sd] return img[tuple(slices)]
[docs]class CenterSpatialCrop(Transform): """ Crop at the center of image with specified ROI size. If a dimension of the expected ROI size is bigger than the input image size, will not crop that dimension. So the cropped result may be smaller than the expected ROI, and the cropped results of several images may not have exactly the same shape. Args: roi_size: the spatial size of the crop region e.g. [224,224,128] if a dimension of ROI size is bigger than image size, will not crop that dimension of the image. If its components have non-positive values, the corresponding size of input image will be used. for example: if the spatial size of input data is [40, 40, 40] and `roi_size=[32, 64, -1]`, the spatial size of output data will be [32, 40, 40]. """ def __init__(self, roi_size: Union[Sequence[int], int]) -> None: self.roi_size = roi_size
[docs] def __call__(self, img: np.ndarray): """ Apply the transform to `img`, assuming `img` is channel-first and slicing doesn't apply to the channel dim. """ roi_size = fall_back_tuple(self.roi_size, img.shape[1:]) center = [i // 2 for i in img.shape[1:]] cropper = SpatialCrop(roi_center=center, roi_size=roi_size) return cropper(img)
[docs]class CenterScaleCrop(Transform): """ Crop at the center of image with specified scale of ROI size. Args: roi_scale: specifies the expected scale of image size to crop. e.g. [0.3, 0.4, 0.5] or a number for all dims. If its components have non-positive values, will use `1.0` instead, which means the input image size. """ def __init__(self, roi_scale: Union[Sequence[float], float]): self.roi_scale = roi_scale
[docs] def __call__(self, img: np.ndarray): img_size = img.shape[1:] ndim = len(img_size) roi_size = [ceil(r * s) for r, s in zip(ensure_tuple_rep(self.roi_scale, ndim), img_size)] sp_crop = CenterSpatialCrop(roi_size=roi_size) return sp_crop(img=img)
[docs]class RandSpatialCrop(Randomizable, Transform): """ Crop image with random size or specific size ROI. It can crop at a random position as center or at the image center. And allows to set the minimum and maximum size to limit the randomly generated ROI. Note: even `random_size=False`, if a dimension of the expected ROI size is bigger than the input image size, will not crop that dimension. So the cropped result may be smaller than the expected ROI, and the cropped results of several images may not have exactly the same shape. Args: roi_size: if `random_size` is True, it specifies the minimum crop region. if `random_size` is False, it specifies the expected ROI size to crop. e.g. [224, 224, 128] if a dimension of ROI size is bigger than image size, will not crop that dimension of the image. If its components have non-positive values, the corresponding size of input image will be used. for example: if the spatial size of input data is [40, 40, 40] and `roi_size=[32, 64, -1]`, the spatial size of output data will be [32, 40, 40]. max_roi_size: if `random_size` is True and `roi_size` specifies the min crop region size, `max_roi_size` can specify the max crop region size. if None, defaults to the input image size. if its components have non-positive values, the corresponding size of input image will be used. random_center: crop at random position as center or the image center. random_size: crop with random size or specific size ROI. if True, the actual size is sampled from `randint(roi_size, max_roi_size + 1)`. """ def __init__( self, roi_size: Union[Sequence[int], int], max_roi_size: Optional[Union[Sequence[int], int]] = None, random_center: bool = True, random_size: bool = True, ) -> None: self.roi_size = roi_size self.max_roi_size = max_roi_size self.random_center = random_center self.random_size = random_size self._size: Optional[Sequence[int]] = None self._slices: Optional[Tuple[slice, ...]] = None
[docs] def randomize(self, img_size: Sequence[int]) -> None: self._size = fall_back_tuple(self.roi_size, img_size) if self.random_size: max_size = img_size if self.max_roi_size is None else fall_back_tuple(self.max_roi_size, img_size) if any([i > j for i, j in zip(self._size, max_size)]): raise ValueError(f"min ROI size: {self._size} is bigger than max ROI size: {max_size}.") self._size = tuple((self.R.randint(low=self._size[i], high=max_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, img: np.ndarray): """ Apply the transform to `img`, assuming `img` is channel-first and slicing doesn't apply to the channel dim. """ self.randomize(img.shape[1:]) if self._size is None: raise AssertionError if self.random_center: return img[self._slices] cropper = CenterSpatialCrop(self._size) return cropper(img)
[docs]class RandScaleCrop(RandSpatialCrop): """ Subclass of :py:class:`monai.transforms.RandSpatialCrop`. Crop image with random size or specific size ROI. It can crop at a random position as center or at the image center. And allows to set the minimum and maximum scale of image size to limit the randomly generated ROI. Args: roi_scale: if `random_size` is True, it specifies the minimum crop size: `roi_scale * image spatial size`. if `random_size` is False, it specifies the expected scale of image size to crop. e.g. [0.3, 0.4, 0.5]. If its components have non-positive values, will use `1.0` instead, which means the input image size. max_roi_scale: if `random_size` is True and `roi_scale` specifies the min crop region size, `max_roi_scale` can specify the max crop region size: `max_roi_scale * image spatial size`. if None, defaults to the input image size. if its components have non-positive values, will use `1.0` instead, which means the input image size. random_center: crop at random position as center or the image center. random_size: crop with random size or specified size ROI by `roi_scale * image spatial size`. if True, the actual size is sampled from `randint(roi_scale * image spatial size, max_roi_scale * image spatial size + 1)`. """ def __init__( self, roi_scale: Union[Sequence[float], float], max_roi_scale: Optional[Union[Sequence[float], float]] = None, random_center: bool = True, random_size: bool = True, ) -> None: super().__init__(roi_size=-1, max_roi_size=None, random_center=random_center, random_size=random_size) self.roi_scale = roi_scale self.max_roi_scale = max_roi_scale
[docs] def __call__(self, img: np.ndarray): """ Apply the transform to `img`, assuming `img` is channel-first and slicing doesn't apply to the channel dim. """ img_size = img.shape[1:] ndim = len(img_size) self.roi_size = [ceil(r * s) for r, s in zip(ensure_tuple_rep(self.roi_scale, ndim), img_size)] if self.max_roi_scale is not None: self.max_roi_size = [ceil(r * s) for r, s in zip(ensure_tuple_rep(self.max_roi_scale, ndim), img_size)] else: self.max_roi_size = None return super().__call__(img=img)
[docs]class RandSpatialCropSamples(Randomizable, Transform): """ 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. It will return a list of cropped images. Note: even `random_size=False`, if a dimension of the expected ROI size is bigger than the input image size, will not crop that dimension. So the cropped result may be smaller than the expected ROI, and the cropped results of several images may not have exactly the same shape. Args: roi_size: if `random_size` is True, it specifies the minimum crop region. if `random_size` is False, it specifies the expected ROI size to crop. e.g. [224, 224, 128] if a dimension of ROI size is bigger than image size, will not crop that dimension of the image. If its components have non-positive values, the corresponding size of input image will be used. for example: if the spatial size of input data is [40, 40, 40] and `roi_size=[32, 64, -1]`, the spatial size of output data will be [32, 40, 40]. num_samples: number of samples (crop regions) to take in the returned list. max_roi_size: if `random_size` is True and `roi_size` specifies the min crop region size, `max_roi_size` can specify the max crop region size. if None, defaults to the input image size. if its components have non-positive values, the corresponding size of input image will be used. random_center: crop at random position as center or the image center. random_size: crop with random size or specific size ROI. The actual size is sampled from `randint(roi_size, img_size)`. Raises: ValueError: When ``num_samples`` is nonpositive. """ def __init__( self, roi_size: Union[Sequence[int], int], num_samples: int, max_roi_size: Optional[Union[Sequence[int], int]] = None, random_center: bool = True, random_size: bool = True, ) -> None: if num_samples < 1: raise ValueError(f"num_samples must be positive, got {num_samples}.") self.num_samples = num_samples self.cropper = RandSpatialCrop(roi_size, max_roi_size, random_center, random_size)
[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, img: np.ndarray) -> List[np.ndarray]: """ Apply the transform to `img`, assuming `img` is channel-first and cropping doesn't change the channel dim. """ return [self.cropper(img) for _ in range(self.num_samples)]
[docs]class CropForeground(Transform): """ Crop an image using a bounding box. The bounding box is generated by selecting foreground using select_fn at channels channel_indices. margin is added in each spatial dimension of the bounding box. The typical usage is to help training and evaluation if the valid part is small in the whole medical image. Users can define arbitrary function to select expected foreground from the whole image or specified channels. And it can also add margin to every dim of the bounding box of foreground object. For example: .. code-block:: python image = np.array( [[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 1, 3, 2, 0], [0, 1, 2, 1, 0], [0, 0, 0, 0, 0]]]) # 1x5x5, single channel 5x5 image def threshold_at_one(x): # threshold at 1 return x > 1 cropper = CropForeground(select_fn=threshold_at_one, margin=0) print(cropper(image)) [[[2, 1], [3, 2], [2, 1]]] """ def __init__( self, select_fn: Callable = is_positive, channel_indices: Optional[IndexSelection] = None, margin: Union[Sequence[int], int] = 0, return_coords: bool = False, k_divisible: Union[Sequence[int], int] = 1, mode: Union[NumpyPadMode, str] = NumpyPadMode.CONSTANT, ) -> None: """ Args: 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. return_coords: whether return the coordinates of spatial bounding box for foreground. 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 """ self.select_fn = select_fn self.channel_indices = ensure_tuple(channel_indices) if channel_indices is not None else None self.margin = margin self.return_coords = return_coords self.k_divisible = k_divisible self.mode: NumpyPadMode = look_up_option(mode, NumpyPadMode)
[docs] def compute_bounding_box(self, img: np.ndarray): """ Compute the start points and end points of bounding box to crop. And adjust bounding box coords to be divisible by `k`. """ box_start, box_end = generate_spatial_bounding_box(img, self.select_fn, self.channel_indices, self.margin) box_start_ = np.asarray(box_start, dtype=np.int16) box_end_ = np.asarray(box_end, dtype=np.int16) orig_spatial_size = box_end_ - box_start_ # make the spatial size divisible by `k` spatial_size = np.asarray(compute_divisible_spatial_size(spatial_shape=orig_spatial_size, k=self.k_divisible)) # update box_start and box_end box_start_ = box_start_ - np.floor_divide(np.asarray(spatial_size) - orig_spatial_size, 2) box_end_ = box_start_ + spatial_size return box_start_, box_end_
[docs] def crop_pad(self, img: np.ndarray, box_start: np.ndarray, box_end: np.ndarray): """ Crop and pad based on the bounding box. """ cropped = SpatialCrop(roi_start=box_start, roi_end=box_end)(img) pad_to_start = np.maximum(-box_start, 0) pad_to_end = np.maximum(box_end - np.asarray(img.shape[1:]), 0) pad = list(chain(*zip(pad_to_start.tolist(), pad_to_end.tolist()))) return BorderPad(spatial_border=pad, mode=self.mode)(cropped)
[docs] def __call__(self, img: np.ndarray): """ Apply the transform to `img`, assuming `img` is channel-first and slicing doesn't change the channel dim. """ box_start, box_end = self.compute_bounding_box(img) cropped = self.crop_pad(img, box_start, box_end) if self.return_coords: return cropped, box_start, box_end return cropped
[docs]class RandWeightedCrop(Randomizable, Transform): """ Samples a list of `num_samples` image patches according to the provided `weight_map`. Args: 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. weight_map: weight map used to generate patch samples. The weights must be non-negative. Each element denotes a sampling weight of the spatial location. 0 indicates no sampling. It should be a single-channel array in shape, for example, `(1, spatial_dim_0, spatial_dim_1, ...)`. """ def __init__( self, spatial_size: Union[Sequence[int], int], num_samples: int = 1, weight_map: Optional[np.ndarray] = None ): self.spatial_size = ensure_tuple(spatial_size) self.num_samples = int(num_samples) self.weight_map = weight_map 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 ) # using only the first channel as weight map
[docs] def __call__(self, img: np.ndarray, weight_map: Optional[np.ndarray] = None) -> List[np.ndarray]: """ Args: img: input image to sample patches from. assuming `img` is a channel-first array. weight_map: weight map used to generate patch samples. The weights must be non-negative. Each element denotes a sampling weight of the spatial location. 0 indicates no sampling. It should be a single-channel array in shape, for example, `(1, spatial_dim_0, spatial_dim_1, ...)` Returns: A list of image patches """ if weight_map is None: weight_map = self.weight_map if weight_map is None: raise ValueError("weight map must be provided for weighted patch sampling.") if img.shape[1:] != weight_map.shape[1:]: raise ValueError(f"image and weight map spatial shape mismatch: {img.shape[1:]} vs {weight_map.shape[1:]}.") self.randomize(weight_map) _spatial_size = fall_back_tuple(self.spatial_size, weight_map.shape[1:]) results = [] for center in self.centers: cropper = SpatialCrop(roi_center=center, roi_size=_spatial_size) results.append(cropper(img)) return results
[docs]class RandCropByPosNegLabel(Randomizable, Transform): """ Crop random fixed sized regions with the center being a foreground or background voxel based on the Pos Neg Ratio. And will return a list of arrays for all the cropped images. For example, crop two (3 x 3) arrays from (5 x 5) array with pos/neg=1:: [[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [[0, 1, 2], [[2, 1, 0], [0, 1, 3, 0, 0], --> [0, 1, 3], [3, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0]] [0, 0, 0]] [0, 0, 0, 0, 0]]] If a dimension of the expected spatial size is bigger than the input image size, will not crop that dimension. So the cropped result may be smaller than expected size, and the cropped results of several images may not have exactly same shape. Args: spatial_size: the spatial size of the crop region e.g. [224, 224, 128]. if a dimension of ROI size is bigger than image size, will not crop that dimension of the image. if its components have non-positive values, the corresponding size of `label` will be used. for example: if the spatial size of input data is [40, 40, 40] and `spatial_size=[32, 64, -1]`, the spatial size of output data will be [32, 40, 40]. label: the label image that is used for finding foreground/background, if None, must set at `self.__call__`. Non-zero indicates foreground, zero indicates background. 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: optional image data to help select valid area, can be same as `img` or another image array. if not None, use ``label == 0 & image > image_threshold`` to select the negative sample (background) center. So the crop center will only come from the valid image areas. image_threshold: if enabled `image`, use ``image > image_threshold`` to determine the valid image content areas. fg_indices: if provided pre-computed foreground indices of `label`, will ignore above `image` and `image_threshold`, and randomly select crop centers based on them, need to provide `fg_indices` and `bg_indices` together, expect to be 1 dim array of spatial indices after flattening. a typical usage is to call `FgBgToIndices` transform first and cache the results. bg_indices: if provided pre-computed background indices of `label`, will ignore above `image` and `image_threshold`, and randomly select crop centers based on them, need to provide `fg_indices` and `bg_indices` together, expect to be 1 dim array of spatial indices after flattening. a typical usage is to call `FgBgToIndices` transform first and cache the results. Raises: ValueError: When ``pos`` or ``neg`` are negative. ValueError: When ``pos=0`` and ``neg=0``. Incompatible values. """ def __init__( self, spatial_size: Union[Sequence[int], int], label: Optional[np.ndarray] = None, pos: float = 1.0, neg: float = 1.0, num_samples: int = 1, image: Optional[np.ndarray] = None, image_threshold: float = 0.0, fg_indices: Optional[np.ndarray] = None, bg_indices: Optional[np.ndarray] = None, ) -> None: self.spatial_size = ensure_tuple(spatial_size) self.label = label 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 = image self.image_threshold = image_threshold self.centers: Optional[List[List[np.ndarray]]] = None self.fg_indices = fg_indices self.bg_indices = bg_indices
[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: if self.fg_indices is not None and self.bg_indices is not None: fg_indices_ = self.fg_indices bg_indices_ = self.bg_indices else: 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, img: np.ndarray, label: Optional[np.ndarray] = None, image: Optional[np.ndarray] = None, fg_indices: Optional[np.ndarray] = None, bg_indices: Optional[np.ndarray] = None, ) -> List[np.ndarray]: """ Args: img: input data to crop samples from based on the pos/neg ratio of `label` and `image`. Assumes `img` is a channel-first array. label: the label image that is used for finding foreground/background, if None, use `self.label`. image: optional image data to help select valid area, can be same as `img` or another image array. use ``label == 0 & image > image_threshold`` to select the negative sample(background) center. so the crop center will only exist on valid image area. if None, use `self.image`. fg_indices: foreground indices to randomly select crop centers, need to provide `fg_indices` and `bg_indices` together. bg_indices: background indices to randomly select crop centers, need to provide `fg_indices` and `bg_indices` together. """ if label is None: label = self.label if label is None: raise ValueError("label should be provided.") if image is None: image = self.image self.randomize(label, fg_indices, bg_indices, image) results: List[np.ndarray] = [] if self.centers is not None: for center in self.centers: cropper = SpatialCrop(roi_center=tuple(center), roi_size=self.spatial_size) # type: ignore results.append(cropper(img)) return results
[docs]class RandCropByLabelClasses(Randomizable, Transform): """ Crop random fixed sized regions with the center being a class based on the specified ratios of every class. The label data can be One-Hot format array or Argmax data. And will return a list of arrays for all the cropped images. For example, crop two (3 x 3) arrays from (5 x 5) array with `ratios=[1, 2, 3, 1]`:: image = np.array([ [[0.0, 0.3, 0.4, 0.2, 0.0], [0.0, 0.1, 0.2, 0.1, 0.4], [0.0, 0.3, 0.5, 0.2, 0.0], [0.1, 0.2, 0.1, 0.1, 0.0], [0.0, 0.1, 0.2, 0.1, 0.0]] ]) label = np.array([ [[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 1, 3, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]] ]) cropper = RandCropByLabelClasses( spatial_size=[3, 3], ratios=[1, 2, 3, 1], num_classes=4, num_samples=2, ) label_samples = cropper(img=label, label=label, image=image) The 2 randomly cropped samples of `label` can be: [[0, 1, 2], [[0, 0, 0], [0, 1, 3], [1, 2, 1], [0, 0, 0]] [1, 3, 0]] If a dimension of the expected spatial size is bigger than the input image size, will not crop that dimension. So the cropped result may be smaller than expected size, and the cropped results of several images may not have exactly same shape. Args: spatial_size: the spatial size of the crop region e.g. [224, 224, 128]. if a dimension of ROI size is bigger than image size, will not crop that dimension of the image. if its components have non-positive values, the corresponding size of `label` will be used. for example: if the spatial size of input data is [40, 40, 40] and `spatial_size=[32, 64, -1]`, the spatial size of output data will be [32, 40, 40]. ratios: specified ratios of every class in the label to generate crop centers, including background class. if None, every class will have the same ratio to generate crop centers. label: the label image that is used for finding every classes, if None, must set at `self.__call__`. num_classes: number of classes for argmax label, not necessary for One-Hot label. num_samples: number of samples (crop regions) to take in each list. image: if image is not None, only return the indices of every class that are within the valid region of the image (``image > image_threshold``). image_threshold: if enabled `image`, use ``image > image_threshold`` to determine the valid image content area and select class indices only in this area. indices: if provided pre-computed indices of every class, will ignore above `image` and `image_threshold`, and randomly select crop centers based on them, expect to be 1 dim array of spatial indices after flattening. a typical usage is to call `ClassesToIndices` transform first and cache the results for better performance. """ def __init__( self, spatial_size: Union[Sequence[int], int], ratios: Optional[List[Union[float, int]]] = None, label: Optional[np.ndarray] = None, num_classes: Optional[int] = None, num_samples: int = 1, image: Optional[np.ndarray] = None, image_threshold: float = 0.0, indices: Optional[List[np.ndarray]] = None, ) -> None: self.spatial_size = ensure_tuple(spatial_size) self.ratios = ratios self.label = label self.num_classes = num_classes self.num_samples = num_samples self.image = image self.image_threshold = image_threshold self.centers: Optional[List[List[np.ndarray]]] = None self.indices = indices
[docs] def randomize( self, label: np.ndarray, indices: Optional[List[np.ndarray]] = None, image: Optional[np.ndarray] = None, ) -> None: self.spatial_size = fall_back_tuple(self.spatial_size, default=label.shape[1:]) indices_: List[np.ndarray] if indices is None: if self.indices is not None: indices_ = self.indices else: indices_ = map_classes_to_indices(label, self.num_classes, image, self.image_threshold) else: indices_ = indices self.centers = generate_label_classes_crop_centers( self.spatial_size, self.num_samples, label.shape[1:], indices_, self.ratios, self.R )
[docs] def __call__( self, img: np.ndarray, label: Optional[np.ndarray] = None, image: Optional[np.ndarray] = None, indices: Optional[List[np.ndarray]] = None, ) -> List[np.ndarray]: """ Args: img: input data to crop samples from based on the ratios of every class, assumes `img` is a channel-first array. label: the label image that is used for finding indices of every class, if None, use `self.label`. image: optional image data to help select valid area, can be same as `img` or another image array. use ``image > image_threshold`` to select the centers only in valid region. if None, use `self.image`. indices: list of indices for every class in the image, used to randomly select crop centers. """ if label is None: label = self.label if label is None: raise ValueError("label should be provided.") if image is None: image = self.image self.randomize(label, indices, image) results: List[np.ndarray] = [] if self.centers is not None: for center in self.centers: cropper = SpatialCrop(roi_center=tuple(center), roi_size=self.spatial_size) # type: ignore results.append(cropper(img)) return results
[docs]class ResizeWithPadOrCrop(Transform): """ Resize an image to a target spatial size by either centrally cropping the image or padding it evenly with a user-specified mode. When the dimension is smaller than the target size, do symmetric padding along that dim. When the dimension is larger than the target size, do central cropping along that dim. Args: 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 method: {``"symmetric"``, ``"end"``} Pad image symmetrically on every side or only pad at the end sides. Defaults to ``"symmetric"``. np_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 """ def __init__( self, spatial_size: Union[Sequence[int], int], mode: Union[NumpyPadMode, str] = NumpyPadMode.CONSTANT, method: Union[Method, str] = Method.SYMMETRIC, **np_kwargs, ): self.padder = SpatialPad(spatial_size=spatial_size, method=method, mode=mode, **np_kwargs) self.cropper = CenterSpatialCrop(roi_size=spatial_size)
[docs] def __call__(self, img: np.ndarray, mode: Optional[Union[NumpyPadMode, str]] = None) -> np.ndarray: """ Args: img: data to pad or crop, assuming `img` is channel-first and padding or cropping doesn't apply to the channel dim. 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. If None, defaults to the ``mode`` in construction. See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html """ return self.padder(self.cropper(img), mode=mode)
[docs]class BoundingRect(Transform): """ Compute coordinates of axis-aligned bounding rectangles from input image `img`. The output format of the coordinates is (shape is [channel, 2 * spatial dims]): [[1st_spatial_dim_start, 1st_spatial_dim_end, 2nd_spatial_dim_start, 2nd_spatial_dim_end, ..., Nth_spatial_dim_start, Nth_spatial_dim_end], ... [1st_spatial_dim_start, 1st_spatial_dim_end, 2nd_spatial_dim_start, 2nd_spatial_dim_end, ..., Nth_spatial_dim_start, Nth_spatial_dim_end]] The bounding boxes edges are aligned with the input image edges. This function returns [-1, -1, ...] if there's no positive intensity. Args: select_fn: function to select expected foreground, default is to select values > 0. """ def __init__(self, select_fn: Callable = is_positive) -> None: self.select_fn = select_fn
[docs] def __call__(self, img: np.ndarray) -> np.ndarray: """ See also: :py:class:`monai.transforms.utils.generate_spatial_bounding_box`. """ bbox = [] for channel in range(img.shape[0]): start_, end_ = generate_spatial_bounding_box(img, select_fn=self.select_fn, channel_indices=channel) bbox.append([i for k in zip(start_, end_) for i in k]) return np.stack(bbox, axis=0)