[pytorch] 2D + 3D DenseNet代码实现，改写

liyihao76

已于 2022-10-28 21:23:58 修改

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分类专栏：医学图像文章标签： pytorch 深度学习 python

于 2022-10-25 21:25:56 首次发布

本文链接：https://blog.csdn.net/qq_38736504/article/details/127449180

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2D + 3D DenseNet代码

网络结构
DenseNet 2D
- 改写
DenseNet 3D

网络结构

本文只介绍DenseNet的代码实现，需要对其论文有一定基础的了解。代码参考
torchvision-densenet
monai-desenet
torchvision里densenet代码分析
 DenseNet代码研读
 3d-densenet
在这里插入图片描述

DenseNet 2D

import re
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.model_zoo as model_zoo
from collections import OrderedDict
from typing import Any, List, Optional, Tuple

class _DenseLayer(nn.Module):
    # 1.Dense layer的结构参照了ResNetV2的结构，BN->ReLU->Conv
    # 2.与ResNet的bottleneck稍有不同的是，此处仅做两次conv（1*1conv,3*3conv)，不需要第三次1*1conv将channel拉升回去
    # 由于Dense block中Tensor的channel数是随着Dense layer不断增加的
    # 所以Dense layer设计的就很”窄“（channel数很小，固定为growth_rate)，每层仅学习很少一部分的特征
    # 3.想象一下，如果设计的和bottleneck一样，输出的channel为[256, 512, 1024, 2048]，那么几次堆叠之后会非常的大
    def __init__(self, num_input_features: int, growth_rate: int, bn_size: int, drop_rate: float):
        # num_input_features : number of the input channel.
        # growth_rate: 代表每一层有多少个新的feature层添加进去 (paper里面是k). 增长速率，第二个卷积层输出特征图
        # bn_size: multiplicative factor for number of bottle neck layers.
        #        (i.e. bn_size * k features in the bottleneck layer 第一个卷积层输出特征图)
        super().__init__()
        self.layers = nn.Sequential()
        self.layers.add_module('norm1', nn.BatchNorm2d(num_input_features)) #这里要看到denselayer里其实主要包括两个卷积层，而且他们的channel数值得关注 #
        self.layers.add_module('relu1', nn.ReLU(inplace=True))
        self.layers.add_module('conv1', nn.Conv2d(num_input_features, bn_size *   
                        growth_rate, kernel_size=1, stride=1, bias=False))
        
        self.layers.add_module('norm2', nn.BatchNorm2d(bn_size * growth_rate))
        self.layers.add_module('relu2', nn.ReLU(inplace=True))
        self.layers.add_module('conv2', nn.Conv2d(bn_size * growth_rate, growth_rate,
                        kernel_size=3, stride=1, padding=1, bias=False)) #这里注意的是输出的channel数是growth_rate #
        # 每一Dense layer结束后dropout丢弃的feature maps的比例
        self.drop_rate = drop_rate
    
    def forward(self, x):#这里是前传，主要解决的就是要把输出整形，把layer的输出和输入要cat在一起 #
        new_features = self.layers(x)
        if self.drop_rate > 0:
            # 若设置了dropout丢弃比例，则按比例”丢弃一部分的features“（将该部分features置为0），channel数仍为growth_rate
            new_features = F.dropout(new_features, p=self.drop_rate, training=self.training) 
        # 最后将新生成的featrue map和输入的feature map在channel维度上concat起来
        # 1.不需要像ResNet一样将x进行变换使得channel数相等
        # 因为DenseNet 3*3conv stride=1 不会改变Tensor的h,w，并且最后是channel维度上的堆叠而不是相加
        # 2.原文中提到的内存消耗多也是因为这步，在一个block中需要把所有layer生成的feature都保存下来
        return torch.cat([x, new_features], 1) #在channel上cat在一起，以形成dense连接 #

在这里插入图片描述


class _DenseBlock(nn.Sequential):
    def __init__(self, num_layers, num_input_features, bn_size, growth_rate, drop_rate):
        # num_layers: number of layers in the block.
        super().__init__()
        # for循环就是根据num_layers逐层添加Dense Block注意每一层的输入num_input features不一样，
        # 是因为每一个DenseLayer之后feature的数目都会增加growth rate。
        # 直观一点理解，其实就是每一层的DenseLayer附带了自己学习到的feature还有自己本身一起传入下一个DenseLayer。
        for i in range(num_layers):
            # 由于一个DenseBlock中，每经过一个layer，宽度（channel）就会堆叠增加growth_rate，所以仅需要改变num_input_features即可
            layer = _DenseLayer(num_input_features + i * growth_rate, growth_rate, bn_size, drop_rate)
            self.add_module('denselayer%d' % (i + 1), layer)

在这里插入图片描述

# 在DenseBlock之间，还添加了Transition层，这个层的作用是为了进一步提高模型的紧凑性，可以减少过渡层的特征图的数量。
class _Transition(nn.Sequential):
    ''' 过渡层，两个作用 '''
    def __init__(self, num_input_features, num_output_features):
        super().__init__()
        self.add_module('norm', nn.BatchNorm2d(num_input_features))
        self.add_module('relu', nn.ReLU(inplace=True))
        # 作用一：即使每一层Dense layer都采取了很小的growth_rate，但是堆叠之后channel数难免会越来越大
        # 所以需要在每一个Dense block之后接transition层用1*1conv将channel再拉回到一个相对较低的值（一般为输入的一半）
        self.add_module('conv', nn.Conv2d(num_input_features, num_output_features,
                                          kernel_size=1, stride=1, bias=False))
        # 作用而：用average pooling改变图像分辨率，下采样
        self.add_module('pool', nn.AvgPool2d(kernel_size=2, stride=2))

class DenseNet(nn.Module):
    """
        Args:
        growth_rate (int) - how many filters to add each layer (`k` in paper)
        block_config (list of 4 ints) - how many layers in each pooling block
        num_init_features (int) - the number of filters to learn in the first convolution layer
        bn_size (int) - multiplicative factor for number of bottle neck layers
          (i.e. bn_size * k features in the bottleneck layer)
        drop_rate (float) - dropout rate after each dense layer
        num_classes (int) - number of classification classes
    """
    def __init__(
        self,
        growth_rate: int = 32,
        block_config: Tuple[int, int, int, int] = (6, 12, 24, 16),
        num_init_features: int = 64,
        bn_size: int = 4,
        drop_rate: float = 0,
        num_classes: int = 1000
    ):
        super().__init__()
        
        # First convolution 初始化层，图像进来后不是直接进入denseblock，先使用大的卷积核，大步长，进一步压缩图像尺寸
        # 注意的是nn.Sequential的用法，ordereddict使用的方法，给layer命名，
        # 还有就是各层的排列，conv->bn->relu->pool 经过这一个操作就是尺寸就成为了1/4，数据量压缩了
        self.features = nn.Sequential(OrderedDict([
            ('conv0', nn.Conv2d(3, num_init_features, kernel_size=7, stride=2, padding=3, bias=False)),
            ('norm0', nn.BatchNorm2d(num_init_features)),
            ('relu0', nn.ReLU(inplace=True)),
            ('pool0', nn.MaxPool2d(kernel_size=3, stride=2, padding=1)),
        ]))    #这里使用了batchnorm2d batchnorm 最近有group norm 是否可以换 
        
        # Each denseblock 创建denseblock
        num_features = num_init_features
        
        for i, num_layers in enumerate(block_config):
            block = _DenseBlock(num_layers=num_layers, num_input_features=num_features,
                                bn_size=bn_size, growth_rate=growth_rate, drop_rate=drop_rate)
            self.features.add_module('denseblock%d' % (i + 1), block)
            num_features = num_features + num_layers * growth_rate
            # 第四个Dense block后不再连接Transition层
            if i != len(block_config) - 1:
                # 此处可以看到，默认过渡层将channel变为原来输入的一半
                trans = _Transition(num_input_features=num_features, num_output_features=num_features // 2)
                self.features.add_module('transition%d' % (i + 1), trans)
                num_features = num_features // 2
        
        # Final batch norm
        self.features.add_module("norm5", nn.BatchNorm2d(num_features))
        
        # Linear layer
        self.classifier = nn.Linear(num_features, num_classes)
        
        
        # Official init from torch repo.
        for m in self.modules():
            if isinstance(m, nn.Conv2d):
                nn.init.kaiming_normal_(m.weight)
            elif isinstance(m, nn.BatchNorm2d):
                nn.init.constant_(m.weight, 1)
                nn.init.constant_(m.bias, 0)
            elif isinstance(m, nn.Linear):
                nn.init.constant_(m.bias, 0)
                
    def forward(self, x):
        features = self.features(x)
        out = F.relu(features, inplace=True)
        out = F.adaptive_avg_pool2d(out, (1, 1))
        out = torch.flatten(out, 1)
        out = self.classifier(out)
        return out

在这里插入图片描述

densenet121 = DenseNet(num_init_features=64, growth_rate=32, block_config=(6, 12, 24, 16))
densenet169 = DenseNet(num_init_features=64, growth_rate=32, block_config=(6, 12, 32, 32))
densenet201 = DenseNet(num_init_features=64, growth_rate=32, block_config=(6, 12, 48, 32))
densenet264 = DenseNet(num_init_features=64, growth_rate=32, block_config=(6, 12, 64, 48))

可视化

x=torch.randn(1,3,224,224)
X=densenet121(x)
print(X.shape) # torch.Size([1, 1000])

import netron
import torch.onnx
import onnx

modelData ='demo.onnx' # 定义模型数据保存的路径
torch.onnx.export(densenet121, x, modelData)  # 将 pytorch 模型以 onnx 格式导出并保存
onnx.save(onnx.shape_inference.infer_shapes(onnx.load(modelData)), modelData)
netron.start(modelData)

改写

class DenseNet_2d(nn.Module):
    """
        Args:
        growth_rate (int) - how many filters to add each layer (`k` in paper)
        block_config (list of 4 ints) - how many layers in each pooling block
        num_init_features (int) - the number of filters to learn in the first convolution layer
        bn_size (int) - multiplicative factor for number of bottle neck layers
          (i.e. bn_size * k features in the bottleneck layer)
        drop_rate (float) - dropout rate after each dense layer
        num_classes (int) - number of classification classes
    """
    def __init__(
        self,
        growth_rate: int = 32,
        block_config: Tuple[int, int, int, int] = (6, 12, 24, 16),
        num_init_features: int = 64,
        bn_size: int = 4,
        drop_rate: float = 0,
        num_classes: int = 1000
    ):
        super().__init__()
        
        # First convolution 初始化层，图像进来后不是直接进入denseblock，先使用大的卷积核，大步长，进一步压缩图像尺寸
        # 注意的是nn.Sequential的用法，ordereddict使用的方法，给layer命名，
        # 还有就是各层的排列，conv->bn->relu->pool 经过这一个操作就是尺寸就成为了1/4，数据量压缩了
        self.Conv1 = nn.Sequential(OrderedDict([
            ('conv0', nn.Conv2d(3, num_init_features, kernel_size=7, stride=2, padding=3, bias=False)),
            ('norm0', nn.BatchNorm2d(num_init_features)),
            ('relu0', nn.ReLU(inplace=True)),
            ('pool0', nn.MaxPool2d(kernel_size=3, stride=2, padding=1)),
        ]))    #这里使用了batchnorm2d batchnorm 最近有group norm 是否可以换 
        
        # Each denseblock 创建denseblock
        num_features = num_init_features
        
        ##############################
        self.Dense_Block_1 = _DenseBlock(num_layers=block_config[0], num_input_features=num_features,
                                bn_size=bn_size, growth_rate=growth_rate, drop_rate=drop_rate)
        
        num_features1_T = num_features + block_config[0] * growth_rate
        
        self.Transition_Layer_1 = _Transition(num_input_features=num_features1_T, num_output_features=num_features1_T // 2)
        
        num_features2 = num_features1_T // 2
        ################################
        
        self.Dense_Block_2 = _DenseBlock(num_layers=block_config[1], num_input_features=num_features2,
                                bn_size=bn_size, growth_rate=growth_rate, drop_rate=drop_rate)
        
        num_features2_T = num_features2 + block_config[1] * growth_rate
        
        self.Transition_Layer_2 = _Transition(num_input_features=num_features2_T, num_output_features=num_features2_T // 2)
        
        num_features3 = num_features2_T // 2
        ################################
        
        self.Dense_Block_3 = _DenseBlock(num_layers=block_config[2], num_input_features=num_features3,
                                bn_size=bn_size, growth_rate=growth_rate, drop_rate=drop_rate)
        
        num_features3_T = num_features3 + block_config[2] * growth_rate
        
        self.Transition_Layer_3 = _Transition(num_input_features=num_features3_T, num_output_features=num_features3_T // 2)
        
        num_features4 = num_features3_T // 2
        ################################
        
        self.Dense_Block_4 = _DenseBlock(num_layers=block_config[3], num_input_features=num_features4,
                                bn_size=bn_size, growth_rate=growth_rate, drop_rate=drop_rate)
        
        num_features5 = num_features4 + block_config[3] * growth_rate
        
        self.finale_bn = nn.BatchNorm2d(num_features5)

        
#         for i, num_layers in enumerate(block_config):
#             block = _DenseBlock(num_layers=num_layers, num_input_features=num_features,
#                                 bn_size=bn_size, growth_rate=growth_rate, drop_rate=drop_rate)
#             self.features.add_module('denseblock%d' % (i + 1), block)
#             num_features = num_features + num_layers * growth_rate
#             # 第四个Dense block后不再连接Transition层
#             if i != len(block_config) - 1:
#                 # 此处可以看到，默认过渡层将channel变为原来输入的一半
#                 trans = _Transition(num_input_features=num_features, num_output_features=num_features // 2)
#                 self.features.add_module('transition%d' % (i + 1), trans)
#                 num_features = num_features // 2
        
        # Final batch norm
        #self.features.add_module("norm5", nn.BatchNorm2d(num_features))
        
        
        # Linear layer
        self.classifier = nn.Linear(num_features5, num_classes)
        
        
        # Official init from torch repo.
        for m in self.modules():
            if isinstance(m, nn.Conv2d):
                nn.init.kaiming_normal_(m.weight)
            elif isinstance(m, nn.BatchNorm2d):
                nn.init.constant_(m.weight, 1)
                nn.init.constant_(m.bias, 0)
            elif isinstance(m, nn.Linear):
                nn.init.constant_(m.bias, 0)
                
    def forward(self, x):
        #features = self.features(x)
        out = self.Conv1(x)
        
        out = self.Dense_Block_1(out)
        out = self.Transition_Layer_1(out)
        
        out = self.Dense_Block_2(out)
        out = self.Transition_Layer_2(out)
        
        out = self.Dense_Block_3(out)
        out = self.Transition_Layer_3(out)
        
        out = self.Dense_Block_4(out)
        out = self.finale_bn(out)
        
        out = F.relu(out, inplace=True)
        out = F.adaptive_avg_pool2d(out, (1, 1))
        out = torch.flatten(out, 1)
        out = self.classifier(out)
        return out

DenseNet 3D

class _DenseLayer_3d(nn.Sequential):

    def __init__(self, num_input_features, growth_rate, bn_size, drop_rate):
        super().__init__()
        self.add_module('norm1', nn.BatchNorm3d(num_input_features))
        self.add_module('relu1', nn.ReLU(inplace=True))
        self.add_module(
            'conv1',
            nn.Conv3d(num_input_features,
                      bn_size * growth_rate,
                      kernel_size=1,
                      stride=1,
                      bias=False))
        self.add_module('norm2', nn.BatchNorm3d(bn_size * growth_rate))
        self.add_module('relu2', nn.ReLU(inplace=True))
        self.add_module(
            'conv2',
            nn.Conv3d(bn_size * growth_rate,
                      growth_rate,
                      kernel_size=3,
                      stride=1,
                      padding=1,
                      bias=False))
        self.drop_rate = drop_rate

    def forward(self, x):
        new_features = super().forward(x)
        if self.drop_rate > 0:
            new_features = F.dropout(new_features,
                                     p=self.drop_rate,
                                     training=self.training)
        return torch.cat([x, new_features], 1)

class _DenseBlock_3d(nn.Sequential):

    def __init__(self, num_layers, num_input_features, bn_size, growth_rate, drop_rate):
        super().__init__()
        for i in range(num_layers):
            layer = _DenseLayer_3d(num_input_features + i * growth_rate,
                                growth_rate, bn_size, drop_rate)
            self.add_module('denselayer{}'.format(i + 1), layer)

class _Transition_3d(nn.Sequential):

    def __init__(self, num_input_features, num_output_features):
        super().__init__()
        self.add_module('norm', nn.BatchNorm3d(num_input_features))
        self.add_module('relu', nn.ReLU(inplace=True))
        self.add_module(
            'conv',
            nn.Conv3d(num_input_features,
                      num_output_features,
                      kernel_size=1,
                      stride=1,
                      bias=False))
        self.add_module('pool', nn.AvgPool3d(kernel_size=2, stride=2))

class DenseNet_3d(nn.Module):
    """Densenet-BC model class
    Args:
        growth_rate (int) - how many filters to add each layer (k in paper)
        block_config (list of 4 ints) - how many layers in each pooling block
        num_init_features (int) - the number of filters to learn in the first convolution layer
        bn_size (int) - multiplicative factor for number of bottle neck layers
          (i.e. bn_size * k features in the bottleneck layer)
        drop_rate (float) - dropout rate after each dense layer
        num_classes (int) - number of classification classes
    """

    def __init__(self,
                 growth_rate=32,
                 block_config=(6, 12, 24, 16),
                 num_init_features=64,
                 bn_size=4,
                 drop_rate=0,
                 num_classes=1000):

        super().__init__()

        # First convolution
        self.features = nn.Sequential(OrderedDict([
                         ('conv1',nn.Conv3d(1,num_init_features,
                                  kernel_size=(7, 7, 7),
                                  stride=(2, 2, 2),
                                  padding=(3, 3, 3),
                                  bias=False)),
                         ('norm1', nn.BatchNorm3d(num_init_features)),
                         ('relu1', nn.ReLU(inplace=True)),
                         ('pool1', nn.MaxPool3d(kernel_size=3, stride=2, padding=1))]))

        # Each denseblock
        num_features = num_init_features
        
        for i, num_layers in enumerate(block_config):
            block = _DenseBlock_3d(num_layers=num_layers,
                                   num_input_features=num_features,
                                   bn_size=bn_size,
                                   growth_rate=growth_rate,
                                   drop_rate=drop_rate)
            
            self.features.add_module('denseblock{}'.format(i + 1), block)
            num_features = num_features + num_layers * growth_rate
            
            if i != len(block_config) - 1:
                trans = _Transition_3d(num_input_features=num_features,num_output_features=num_features // 2)
                self.features.add_module('transition{}'.format(i + 1), trans)
                num_features = num_features // 2

        # Final batch norm
        self.features.add_module('norm5', nn.BatchNorm3d(num_features))

        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) or isinstance(m, nn.BatchNorm2d):
                m.weight.data.fill_(1)
                m.bias.data.zero_()

        # Linear layer
        self.classifier = nn.Linear(num_features, num_classes)

        for m in self.modules():
            if isinstance(m, nn.Conv3d):
                nn.init.kaiming_normal_(m.weight,
                                        mode='fan_out',
                                        nonlinearity='relu')
            elif isinstance(m, nn.BatchNorm3d):
                nn.init.constant_(m.weight, 1)
                nn.init.constant_(m.bias, 0)
            elif isinstance(m, nn.Linear):
                nn.init.constant_(m.bias, 0)

    def forward(self, x):
        features = self.features(x)
        out = F.relu(features, inplace=True)
        out = F.adaptive_avg_pool3d(out, output_size=(1, 1, 1))
        out = torch.flatten(out,1)
        out = self.classifier(out)
        return out

densenet121_3d = DenseNet_3d(num_init_features=64, growth_rate=32, block_config=(6, 12, 24, 16))
densenet169_3d = DenseNet_3d(num_init_features=64, growth_rate=32, block_config=(6, 12, 32, 32))
densenet201_3d = DenseNet_3d(num_init_features=64, growth_rate=32, block_config=(6, 12, 48, 32))
densenet264_3d = DenseNet_3d(num_init_features=64, growth_rate=32, block_config=(6, 12, 64, 48))

x=torch.randn(1,1,224,224,224)
X=densenet121_3d(x)
print(X.shape) # torch.Size([1, 1000])

import netron
import torch.onnx
import onnx

modelData ='demo.onnx' # 定义模型数据保存的路径
torch.onnx.export(densenet121_3d, x, modelData)  # 将 pytorch 模型以 onnx 格式导出并保存
onnx.save(onnx.shape_inference.infer_shapes(onnx.load(modelData)), modelData)
netron.start(modelData)