attentionnet3D.py

import math
import torch
import torch.nn as nn
import torch.nn.functional as F
from collections import OrderedDict

__all__ = [
    'Attention3D', 'attention3d56', 'attention3d92'
]


''' Residual Bottleneck from Tencent/MedicalNet'''
class ResidualBlock(nn.Module):
    expansion = 4

    def __init__(self, inplanes, planes, stride=1, downsample=None):
        super(ResidualBlock, self).__init__()
        # Added for consistency
        planes = int(planes/4)
        self.conv1 = nn.Conv3d(inplanes, planes, kernel_size=1, bias=False)
        self.bn1 = nn.BatchNorm3d(planes)
        self.conv2 = nn.Conv3d(
            planes, planes, kernel_size=3, stride=stride, padding=1, bias=False)
        self.bn2 = nn.BatchNorm3d(planes)
        self.conv3 = nn.Conv3d(planes, planes * 4, kernel_size=1, bias=False)
        self.bn3 = nn.BatchNorm3d(planes * 4)
        self.relu = nn.ReLU(inplace=True)
        #self.downsample = downsample
        # Added: auto downsample
        self.downsample = nn.Sequential(nn.Conv3d(inplanes, planes *4 , kernel_size=1, stride=stride, bias = False), nn.BatchNorm3d(planes*4))
        self.stride = stride

    def forward(self, x):
        residual = x

        out = self.conv1(x)
        out = self.bn1(out)
        out = self.relu(out)

        out = self.conv2(out)
        out = self.bn2(out)
        out = self.relu(out)

        out = self.conv3(out)
        out = self.bn3(out)

        if self.downsample is not None:
            residual = self.downsample(x)

        out += residual
        out = self.relu(out)

        return out

class AttentionModule1(nn.Module):

    def __init__(self, in_channels, out_channels, p=1, t=2, r=1):
        super().__init__()
        #"""The hyperparameter p denotes the number of preprocessing Residual
        #Units before splitting into trunk branch and mask branch. t denotes
        #the number of Residual Units in trunk branch. r denotes the number of
        #Residual Units between adjacent pooling layer in the mask branch."""
        assert in_channels == out_channels

        self.pre = self._make_residual(in_channels, out_channels, p)
        self.trunk = self._make_residual(in_channels, out_channels, t)
        self.soft_resdown1 = self._make_residual(in_channels, out_channels, r)
        self.soft_resdown2 = self._make_residual(in_channels, out_channels, r)
        self.soft_resdown3 = self._make_residual(in_channels, out_channels, r)
        self.soft_resdown4 = self._make_residual(in_channels, out_channels, r)

        self.soft_resup1 = self._make_residual(in_channels, out_channels, r)
        self.soft_resup2 = self._make_residual(in_channels, out_channels, r)
        self.soft_resup3 = self._make_residual(in_channels, out_channels, r)
        self.soft_resup4 = self._make_residual(in_channels, out_channels, r)

        self.shortcut_short = ResidualBlock(in_channels, out_channels, 1)
        self.shortcut_long = ResidualBlock(in_channels, out_channels, 1)

        self.sigmoid = nn.Sequential(
            nn.BatchNorm3d(out_channels),
            nn.ReLU(inplace=True),
            nn.Conv3d(out_channels, out_channels, kernel_size=1),
            nn.BatchNorm3d(out_channels),
            nn.ReLU(inplace=True),
            nn.Conv3d(out_channels, out_channels, kernel_size=1),
            nn.Sigmoid()
        )

        self.last = self._make_residual(in_channels, out_channels, p)

    def forward(self, x):
        ###We make the size of the smallest output map in each mask branch 7*7 to be consistent
        #with the smallest trunk output map size.
        ###Thus 3,2,1 max-pooling layers are used in mask branch with input size 56 * 56, 28 * 28, 14 * 14 respectively.
        x = self.pre(x)
        input_size = (x.size(2), x.size(3), x.size(4))

        x_t = self.trunk(x)

        #first downsample out 28
        x_s = F.max_pool3d(x, kernel_size=3, stride=2, padding=1)
        x_s = self.soft_resdown1(x_s)

        #28 shortcut
        shape1 = (x_s.size(2), x_s.size(3), x_s.size(4))
        shortcut_long = self.shortcut_long(x_s)

        #seccond downsample out 14
        x_s = F.max_pool3d(x, kernel_size=3, stride=2, padding=1)
        x_s = self.soft_resdown2(x_s)

        #14 shortcut
        shape2 = (x_s.size(2), x_s.size(3), x_s.size(4))
        shortcut_short = self.soft_resdown3(x_s)

        #third downsample out 7
        x_s = F.max_pool3d(x, kernel_size=3, stride=2, padding=1)
        x_s = self.soft_resdown3(x_s)

        #mid ??? NOT IN THE PAPER
        x_s = self.soft_resdown4(x_s)
        x_s = self.soft_resup1(x_s)

        #first upsample out 14
        x_s = self.soft_resup2(x_s)
        x_s = F.interpolate(x_s, size=shape2)
        x_s += shortcut_short

        #second upsample out 28
        x_s = self.soft_resup3(x_s)
        x_s = F.interpolate(x_s, size=shape1)
        x_s += shortcut_long

        #thrid upsample out 54
        x_s = self.soft_resup4(x_s)
        x_s = F.interpolate(x_s, size=input_size)

        x_s = self.sigmoid(x_s)
        x = (1 + x_s) * x_t
        x = self.last(x)

        return x

    def _make_residual(self, in_channels, out_channels, p):

        layers = []
        for _ in range(p):
            layers.append(ResidualBlock(in_channels, out_channels, 1))

        return nn.Sequential(*layers)

class AttentionModule2(nn.Module):

    def __init__(self, in_channels, out_channels, p=1, t=2, r=1):
        super().__init__()
        #"""The hyperparameter p denotes the number of preprocessing Residual
        #Units before splitting into trunk branch and mask branch. t denotes
        #the number of Residual Units in trunk branch. r denotes the number of
        #Residual Units between adjacent pooling layer in the mask branch."""
        assert in_channels == out_channels

        self.pre = self._make_residual(in_channels, out_channels, p)
        self.trunk = self._make_residual(in_channels, out_channels, t)
        self.soft_resdown1 = self._make_residual(in_channels, out_channels, r)
        self.soft_resdown2 = self._make_residual(in_channels, out_channels, r)
        self.soft_resdown3 = self._make_residual(in_channels, out_channels, r)

        self.soft_resup1 = self._make_residual(in_channels, out_channels, r)
        self.soft_resup2 = self._make_residual(in_channels, out_channels, r)
        self.soft_resup3 = self._make_residual(in_channels, out_channels, r)

        self.shortcut = ResidualBlock(in_channels, out_channels, 1)

        self.sigmoid = nn.Sequential(
            nn.BatchNorm3d(out_channels),
            nn.ReLU(inplace=True),
            nn.Conv3d(out_channels, out_channels, kernel_size=1),
            nn.BatchNorm3d(out_channels),
            nn.ReLU(inplace=True),
            nn.Conv3d(out_channels, out_channels, kernel_size=1),
            nn.Sigmoid()
        )

        self.last = self._make_residual(in_channels, out_channels, p)

    def forward(self, x):
        x = self.pre(x)
        input_size = (x.size(2), x.size(3), x.size(4))

        x_t = self.trunk(x)

        #first downsample out 14
        x_s = F.max_pool3d(x, kernel_size=3, stride=2, padding=1)
        x_s = self.soft_resdown1(x_s)

        #14 shortcut
        shape1 = (x_s.size(2), x_s.size(3), x_s.size(4))
        shortcut = self.shortcut(x_s)

        #seccond downsample out 7
        x_s = F.max_pool3d(x, kernel_size=3, stride=2, padding=1)
        x_s = self.soft_resdown2(x_s)

        #mid
        x_s = self.soft_resdown3(x_s)
        x_s = self.soft_resup1(x_s)

        #first upsample out 14
        x_s = self.soft_resup2(x_s)
        x_s = F.interpolate(x_s, size=shape1)
        x_s += shortcut

        #second upsample out 28
        x_s = self.soft_resup3(x_s)
        x_s = F.interpolate(x_s, size=input_size)

        x_s = self.sigmoid(x_s)
        x = (1 + x_s) * x_t
        x = self.last(x)

        return x

    def _make_residual(self, in_channels, out_channels, p):

        layers = []
        for _ in range(p):
            layers.append(ResidualBlock(in_channels, out_channels, 1))

        return nn.Sequential(*layers)

class AttentionModule3(nn.Module):

    def __init__(self, in_channels, out_channels, p=1, t=2, r=1):
        super().__init__()

        assert in_channels == out_channels

        self.pre = self._make_residual(in_channels, out_channels, p)
        self.trunk = self._make_residual(in_channels, out_channels, t)
        self.soft_resdown1 = self._make_residual(in_channels, out_channels, r)
        self.soft_resdown2 = self._make_residual(in_channels, out_channels, r)

        self.soft_resup1 = self._make_residual(in_channels, out_channels, r)
        self.soft_resup2 = self._make_residual(in_channels, out_channels, r)

        self.shortcut = ResidualBlock(in_channels, out_channels, 1)

        self.sigmoid = nn.Sequential(
            nn.BatchNorm3d(out_channels),
            nn.ReLU(inplace=True),
            nn.Conv3d(out_channels, out_channels, kernel_size=1),
            nn.BatchNorm3d(out_channels),
            nn.ReLU(inplace=True),
            nn.Conv3d(out_channels, out_channels, kernel_size=1),
            nn.Sigmoid()
        )

        self.last = self._make_residual(in_channels, out_channels, p)

    def forward(self, x):
        x = self.pre(x)
        input_size = (x.size(2), x.size(3), x.size(4))

        x_t = self.trunk(x)

        #first downsample out 14
        x_s = F.max_pool3d(x, kernel_size=3, stride=2, padding=1)
        x_s = self.soft_resdown1(x_s)

        #mid
        x_s = self.soft_resdown2(x_s)
        x_s = self.soft_resup1(x_s)

        #first upsample out 14
        x_s = self.soft_resup2(x_s)
        x_s = F.interpolate(x_s, size=input_size)

        x_s = self.sigmoid(x_s)
        x = (1 + x_s) * x_t
        x = self.last(x)

        return x

    def _make_residual(self, in_channels, out_channels, p):

        layers = []
        for _ in range(p):
            layers.append(ResidualBlock(in_channels, out_channels, 1))

        return nn.Sequential(*layers)

class Attention3D(nn.Module):
    """residual attention netowrk
    Args:
        block_num: attention module number for each stage
    """

    def __init__(self, block_num, num_classes=100,pretrained=None):

        super().__init__()
        self.pre_conv = nn.Sequential(
            nn.Conv3d(3, 64, kernel_size=3, stride=1, padding=1),
            nn.BatchNorm3d(64),
            nn.ReLU(inplace=True)
        )

        self.stage1 = self._make_stage(64, 256, block_num[0], AttentionModule1)
        self.stage2 = self._make_stage(256, 512, block_num[1], AttentionModule2)
        self.stage3 = self._make_stage(512, 1024, block_num[2], AttentionModule3)
        self.stage4 = nn.Sequential(
            ResidualBlock(1024, 2048, stride=2),
            ResidualBlock(2048, 2048, stride=1),
            ResidualBlock(2048, 2048, stride=1)
        )
        self.avg = nn.AdaptiveAvgPool3d(1)
        self.classifier = nn.Linear(2048, num_classes)

        for m in self.modules():
            if isinstance(m, nn.Conv3d):
                m.weight = nn.init.kaiming_normal(m.weight, mode='fan_out')
            elif isinstance(m, nn.BatchNorm3d):
                m.weight.data.fill_(1)
                m.bias.data.zero_()

    def forward(self, x):
        x = self.pre_conv(x)
        x = self.stage1(x)
        x = self.stage2(x)
        x = self.stage3(x)
        x = self.stage4(x)
        x = self.avg(x)
        x = x.view(x.size(0), -1)
        x = self.classifier(x)

        return x

    def _make_stage(self, in_channels, out_channels, num, block):

        layers = []
        layers.append(ResidualBlock(in_channels, out_channels, stride=2))

        for _ in range(num):
            layers.append(block(out_channels, out_channels))

        return nn.Sequential(*layers)

def attention3d56(**kwargs):
    return Attention3D([1, 1, 1], **kwargs)

def attention3d92(**kwargs):
    return Attention3D([1, 2, 3], **kwargs)