nomri / models /unet.py
samaonline
init
1b34a12
"""
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from typing import List, Tuple
import torch
from torch import nn
from torch.nn import functional as F
class Unet(nn.Module):
"""
PyTorch implementation of a U-Net model.
O. Ronneberger, P. Fischer, and Thomas Brox. U-net: Convolutional networks
for biomedical image segmentation. In International Conference on Medical
image computing and computer-assisted intervention, pages 234–241.
Springer, 2015.
"""
def __init__(
self,
in_chans: int,
out_chans: int,
chans: int = 32,
num_pool_layers: int = 4,
drop_prob: float = 0.0,
):
"""
Parameters
----------
in_chans : int
Number of channels in the input to the U-Net model.
out_chans : int
Number of channels in the output to the U-Net model.
chans : int, optional
Number of output channels of the first convolution layer. Default is 32.
num_pool_layers : int, optional
Number of down-sampling and up-sampling layers. Default is 4.
drop_prob : float, optional
Dropout probability. Default is 0.0.
"""
super().__init__()
self.in_chans = in_chans
self.out_chans = out_chans
self.chans = chans
self.num_pool_layers = num_pool_layers
self.drop_prob = drop_prob
self.down_sample_layers = nn.ModuleList([ConvBlock(in_chans, chans, drop_prob)])
ch = chans
for _ in range(num_pool_layers - 1):
self.down_sample_layers.append(ConvBlock(ch, ch * 2, drop_prob))
ch *= 2
self.conv = ConvBlock(ch, ch * 2, drop_prob)
self.up_conv = nn.ModuleList()
self.up_transpose_conv = nn.ModuleList()
for _ in range(num_pool_layers - 1):
self.up_transpose_conv.append(TransposeConvBlock(ch * 2, ch))
self.up_conv.append(ConvBlock(ch * 2, ch, drop_prob))
ch //= 2
self.up_transpose_conv.append(TransposeConvBlock(ch * 2, ch))
self.up_conv.append(
nn.Sequential(
ConvBlock(ch * 2, ch, drop_prob),
nn.Conv2d(ch, self.out_chans, kernel_size=1, stride=1),
)
)
def forward(self, image: torch.Tensor) -> torch.Tensor:
"""
Parameters
----------
image : torch.Tensor
Input 4D tensor of shape `(N, in_chans, H, W)`.
Returns
-------
torch.Tensor
Output tensor of shape `(N, out_chans, H, W)`.
"""
stack = []
output = image
# apply down-sampling layers
for layer in self.down_sample_layers:
output = layer(output)
stack.append(output)
output = F.avg_pool2d(output, kernel_size=2, stride=2, padding=0)
output = self.conv(output)
# apply up-sampling layers
for transpose_conv, conv in zip(self.up_transpose_conv, self.up_conv):
downsample_layer = stack.pop()
output = transpose_conv(output)
# reflect pad on the right/botton if needed to handle odd input dimensions
padding = [0, 0, 0, 0]
if output.shape[-1] != downsample_layer.shape[-1]:
padding[1] = 1 # padding right
if output.shape[-2] != downsample_layer.shape[-2]:
padding[3] = 1 # padding bottom
if torch.sum(torch.tensor(padding)) != 0:
output = F.pad(output, padding, "reflect")
output = torch.cat([output, downsample_layer], dim=1)
output = conv(output)
return output
class ConvBlock(nn.Module):
"""
A Convolutional Block that consists of two convolution layers each followed by
instance normalization, LeakyReLU activation and dropout.
"""
def __init__(self, in_chans: int, out_chans: int, drop_prob: float):
"""
Parameters
----------
in_chans : int
Number of channels in the input.
out_chans : int
Number of channels in the output.
drop_prob : float
Dropout probability.
"""
super().__init__()
self.in_chans = in_chans
self.out_chans = out_chans
self.drop_prob = drop_prob
self.layers = nn.Sequential(
nn.Conv2d(in_chans, out_chans, kernel_size=3, padding=1, bias=False),
nn.InstanceNorm2d(out_chans),
nn.LeakyReLU(negative_slope=0.2, inplace=True),
nn.Dropout2d(drop_prob),
nn.Conv2d(out_chans, out_chans, kernel_size=3, padding=1, bias=False),
nn.InstanceNorm2d(out_chans),
nn.LeakyReLU(negative_slope=0.2, inplace=True),
nn.Dropout2d(drop_prob),
)
def forward(self, image: torch.Tensor) -> torch.Tensor:
"""
Parameters
----------
image : ndarray
Input 4D tensor of shape `(N, in_chans, H, W)`.
Returns
-------
ndarray
Output tensor of shape `(N, out_chans, H, W)`.
"""
return self.layers(image)
class TransposeConvBlock(nn.Module):
"""
A Transpose Convolutional Block that consists of one convolution transpose
layers followed by instance normalization and LeakyReLU activation.
"""
def __init__(self, in_chans: int, out_chans: int):
"""
Parameters
----------
in_chans : int
Number of channels in the input.
out_chans : int
Number of channels in the output.
"""
super().__init__()
self.in_chans = in_chans
self.out_chans = out_chans
self.layers = nn.Sequential(
nn.ConvTranspose2d(
in_chans, out_chans, kernel_size=2, stride=2, bias=False
),
nn.InstanceNorm2d(out_chans),
nn.LeakyReLU(negative_slope=0.2, inplace=True),
)
def forward(self, image: torch.Tensor) -> torch.Tensor:
"""
Parameters
----------
image : torch.Tensor
Input 4D tensor of shape `(N, in_chans, H, W)`.
Returns
-------
torch.Tensor
Output tensor of shape `(N, out_chans, H*2, W*2)`.
"""
return self.layers(image)