testbed/Project-MONAI__MONAI/monai/networks/utils.py

# Copyright 2020 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.
"""
Utilities and types for defining networks, these depend on PyTorch.
"""

import warnings
from typing import Any, Callable, Optional, Sequence, cast

import torch
import torch.nn as nn

from monai.utils import ensure_tuple_size


def one_hot(labels: torch.Tensor, num_classes: int, dtype: torch.dtype = torch.float, dim: int = 1) -> torch.Tensor:
    """
    For a tensor `labels` of dimensions B1[spatial_dims], return a tensor of dimensions `BN[spatial_dims]`
    for `num_classes` N number of classes.

    Example:

        For every value v = labels[b,1,h,w], the value in the result at [b,v,h,w] will be 1 and all others 0.
        Note that this will include the background label, thus a binary mask should be treated as having 2 classes.
    """
    assert labels.dim() > 0, "labels should have dim of 1 or more."

    # if `dim` is bigger, add singelton dim at the end
    if labels.ndimension() < dim + 1:
        shape = ensure_tuple_size(labels.shape, dim + 1, 1)
        labels = labels.reshape(*shape)

    sh = list(labels.shape)

    assert sh[dim] == 1, "labels should have a channel with length equals to one."
    sh[dim] = num_classes

    o = torch.zeros(size=sh, dtype=dtype, device=labels.device)
    labels = o.scatter_(dim=dim, index=labels.long(), value=1)

    return labels


def slice_channels(tensor: torch.Tensor, *slicevals: Optional[int]) -> torch.Tensor:
    slices = [slice(None)] * len(tensor.shape)
    slices[1] = slice(*slicevals)

    return tensor[slices]


def predict_segmentation(
    logits: torch.Tensor, mutually_exclusive: bool = False, threshold: float = 0.0
) -> torch.Tensor:
    """
    Given the logits from a network, computing the segmentation by thresholding all values above 0
    if multi-labels task, computing the `argmax` along the channel axis if multi-classes task,
    logits has shape `BCHW[D]`.

    Args:
        logits: raw data of model output.
        mutually_exclusive: if True, `logits` will be converted into a binary matrix using
            a combination of argmax, which is suitable for multi-classes task. Defaults to False.
        threshold: thresholding the prediction values if multi-labels task.
    """
    if not mutually_exclusive:
        return (cast(torch.Tensor, logits >= threshold)).int()
    else:
        if logits.shape[1] == 1:
            warnings.warn("single channel prediction, `mutually_exclusive=True` ignored, use threshold instead.")
            return (cast(torch.Tensor, logits >= threshold)).int()
        return logits.argmax(1, keepdim=True)


def normalize_transform(
    shape: Sequence[int],
    device: Optional[torch.device] = None,
    dtype: Optional[torch.dtype] = None,
    align_corners: bool = False,
) -> torch.Tensor:
    """
    Compute an affine matrix according to the input shape.
    The transform normalizes the homogeneous image coordinates to the
    range of `[-1, 1]`.

    Args:
        shape: input spatial shape
        device: device on which the returned affine will be allocated.
        dtype: data type of the returned affine
        align_corners: if True, consider -1 and 1 to refer to the centers of the
            corner pixels rather than the image corners.
            See also: https://pytorch.org/docs/stable/nn.functional.html#torch.nn.functional.grid_sample
    """
    norm = torch.tensor(shape, dtype=torch.float64, device=device)  # no in-place change
    if align_corners:
        norm[norm <= 1.0] = 2.0
        norm = 2.0 / (norm - 1.0)
        norm = torch.diag(torch.cat((norm, torch.ones((1,), dtype=torch.float64, device=device))))
        norm[:-1, -1] = -1.0
    else:
        norm[norm <= 0.0] = 2.0
        norm = 2.0 / norm
        norm = torch.diag(torch.cat((norm, torch.ones((1,), dtype=torch.float64, device=device))))
        norm[:-1, -1] = 1.0 / torch.tensor(shape, dtype=torch.float64, device=device) - 1.0
    norm = norm.unsqueeze(0).to(dtype=dtype)
    norm.requires_grad = False
    return norm


def to_norm_affine(
    affine: torch.Tensor, src_size: Sequence[int], dst_size: Sequence[int], align_corners: bool = False
) -> torch.Tensor:
    """
    Given ``affine`` defined for coordinates in the pixel space, compute the corresponding affine
    for the normalized coordinates.

    Args:
        affine: Nxdxd batched square matrix
        src_size: source image spatial shape
        dst_size: target image spatial shape
        align_corners: if True, consider -1 and 1 to refer to the centers of the
            corner pixels rather than the image corners.
            See also: https://pytorch.org/docs/stable/nn.functional.html#torch.nn.functional.grid_sample

    Raises:
        TypeError: When ``affine`` is not a ``torch.Tensor``.
        ValueError: When ``affine`` is not Nxdxd.
        ValueError: When ``src_size`` or ``dst_size`` dimensions differ from ``affine``.

    """
    if not torch.is_tensor(affine):
        raise TypeError(f"affine must be a torch.Tensor but is {type(affine).__name__}.")
    if affine.ndimension() != 3 or affine.shape[1] != affine.shape[2]:
        raise ValueError(f"affine must be Nxdxd, got {tuple(affine.shape)}.")
    sr = affine.shape[1] - 1
    if sr != len(src_size) or sr != len(dst_size):
        raise ValueError(f"affine suggests {sr}D, got src={len(src_size)}D, dst={len(dst_size)}D.")

    src_xform = normalize_transform(src_size, affine.device, affine.dtype, align_corners)
    dst_xform = normalize_transform(dst_size, affine.device, affine.dtype, align_corners)
    new_affine = src_xform @ affine @ torch.inverse(dst_xform)
    return new_affine


def normal_init(
    m, std: float = 0.02, normal_func: Callable[[torch.Tensor, float, float], Any] = torch.nn.init.normal_
) -> None:
    """
    Initialize the weight and bias tensors of `m' and its submodules to values from a normal distribution with a
    stddev of `std'. Weight tensors of convolution and linear modules are initialized with a mean of 0, batch
    norm modules with a mean of 1. The callable `normal_func', used to assign values, should have the same arguments
    as its default normal_(). This can be used with `nn.Module.apply` to visit submodules of a network.
    """
    cname = m.__class__.__name__

    if getattr(m, "weight", None) is not None and (cname.find("Conv") != -1 or cname.find("Linear") != -1):
        normal_func(m.weight.data, 0.0, std)
        if getattr(m, "bias", None) is not None:
            nn.init.constant_(m.bias.data, 0.0)

    elif cname.find("BatchNorm") != -1:
        normal_func(m.weight.data, 1.0, std)
        nn.init.constant_(m.bias.data, 0)


def icnr_init(conv, upsample_factor, init=nn.init.kaiming_normal_):
    """
    ICNR initialization for 2D/3D kernels adapted from Aitken et al.,2017 , "Checkerboard artifact free
    sub-pixel convolution".
    """
    out_channels, in_channels, *dims = conv.weight.shape
    scale_factor = upsample_factor ** len(dims)

    oc2 = int(out_channels / scale_factor)

    kernel = torch.zeros([oc2, in_channels] + dims)
    kernel = init(kernel)
    kernel = kernel.transpose(0, 1)
    kernel = kernel.reshape(oc2, in_channels, -1)
    kernel = kernel.repeat(1, 1, scale_factor)
    kernel = kernel.reshape([in_channels, out_channels] + dims)
    kernel = kernel.transpose(0, 1)
    conv.weight.data.copy_(kernel)


def pixelshuffle(x: torch.Tensor, dimensions: int, scale_factor: int) -> torch.Tensor:
    """
    Apply pixel shuffle to the tensor `x` with spatial dimensions `dimensions` and scaling factor `scale_factor`.

    See: Shi et al., 2016, "Real-Time Single Image and Video Super-Resolution
    Using a nEfficient Sub-Pixel Convolutional Neural Network."

    See: Aitken et al., 2017, "Checkerboard artifact free sub-pixel convolution".

    Args:
        x: Input tensor
        dimensions: number of spatial dimensions, typically 2 or 3 for 2D or 3D
        scale_factor: factor to rescale the spatial dimensions by, must be >=1

    Returns:
        Reshuffled version of `x`.

    Raises:
        ValueError: When input channels of `x` are not divisible by (scale_factor ** dimensions)
    """

    dim, factor = dimensions, scale_factor
    input_size = list(x.size())
    batch_size, channels = input_size[:2]
    scale_divisor = factor ** dim

    if channels % scale_divisor != 0:
        raise ValueError(
            f"Number of input channels ({channels}) must be evenly \
                        divisible by scale_factor ** dimensions ({scale_divisor})."
        )

    org_channels = channels // scale_divisor
    output_size = [batch_size, org_channels] + [d * factor for d in input_size[2:]]

    indices = tuple(range(2, 2 + 2 * dim))
    indices_factor, indices_dim = indices[:dim], indices[dim:]
    permute_indices = (0, 1) + sum(zip(indices_dim, indices_factor), ())

    x = x.reshape(batch_size, org_channels, *([factor] * dim + input_size[2:]))
    x = x.permute(permute_indices).reshape(output_size)
    return x