2D UNet3+ Pytorch实现 脑肿瘤分割
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2022-07-05 11:05:33
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一、网络介绍
论文下载地址及论文翻译与解读:
玖零猴：UNet3+(UNet+++)论文翻译与详细解读原代码链接: 链接
二、BraTs数据预处理
本文用的训练集和验证集均来自BraTs2018的训练集(其中HGG:210个病人,LGG:75个病人)
但由于BraTs只公开训练集数据,没有测试集数据,如果在训练集中再拆一部分用来作测试集的话,那训练集便少了许多,训练数据如果过少,容易出现过拟合现象,即在训练集中表现好,而在测试集中表现差,此时的网络泛化能力变差了.为了解决数据少的问题,灵机一动的我想出了一个办法.
因为BraTs2019的训练集在BraTs2018的基础上增多了,其中HGG增加了49例,LGG增加了1例,那么我就把这些新增的作为我的测试集
下面我提供百度云盘给大家下载,这是原始数据
BraTs18数据集下载地址(不包含测试集,提供的验证集无GT)
链接：https://pan.baidu.com/s/1Ry41OVl9VLOMzhQQR9qXuA 提取码：qvmo
BraTs19数据集下载地址如下(不包含测试集,提供的验证集无GT)
链接: https://pan.baidu.com/s/1S5XGTdHkwFnagKS-5vWYBg 提取码: 2333
数据的预处理以及实现代码
把上面两年的数据下下来,然后我对数据的预处理方法是链接
完整的实现代码(jupyter notebook打开)
https://github.com/Merofine/BraTS2Dpreprocessing- GetTrainingSets.ipynb——>训练集和验证集
- GetTestingSetsFrom2019.ipynb-—>测试集
代码执行完后,获得npy数据
<如果大家嫌麻烦,我这里提供预处理好的npy数据>
链接:https://pan.baidu.com/s/1W3rcl9I-Y8DwWu5p4o--cw 密码:hfe7
三、运行环境的安装
1、系统环境 WIN10 + CUDA 92 + CUDNN7 + ANACONDA
2、ANACONDA指令快速配置环境,先下载下面文件
https://download.csdn.net/downl
四、核心代码
# -*- coding: utf-8 -*-
import torch
import torch.nn as nn
import torch.nn.functional as F
from layers import unetConv2
from init_weights import init_weights
'''
UNet 3+
'''
class UNet_3Plus(nn.Module):
def __init__(self, args):
super(UNet_3Plus, self).__init__()
self.args = args
in_channels = 4
n_classes = 3
feature_scale = 4
is_deconv = True
is_batchnorm = True
self.is_deconv = is_deconv
self.in_channels = in_channels
self.is_batchnorm = is_batchnorm
self.feature_scale = feature_scale
filters = [64, 128, 256, 512, 1024]
## -------------Encoder--------------
self.conv1 = unetConv2(self.in_channels, filters[0], self.is_batchnorm)
self.maxpool1 = nn.MaxPool2d(kernel_size=2)
self.conv2 = unetConv2(filters[0], filters[1], self.is_batchnorm)
self.maxpool2 = nn.MaxPool2d(kernel_size=2)
self.conv3 = unetConv2(filters[1], filters[2], self.is_batchnorm)
self.maxpool3 = nn.MaxPool2d(kernel_size=2)
self.conv4 = unetConv2(filters[2], filters[3], self.is_batchnorm)
self.maxpool4 = nn.MaxPool2d(kernel_size=2)
self.conv5 = unetConv2(filters[3], filters[4], self.is_batchnorm)
## -------------Decoder--------------
self.CatChannels = filters[0]
self.CatBlocks = 5
self.UpChannels = self.CatChannels * self.CatBlocks
'''stage 4d'''
# h1->320*320, hd4->40*40, Pooling 8 times
self.h1_PT_hd4 = nn.MaxPool2d(8, 8, ceil_mode=True)
self.h1_PT_hd4_conv = nn.Conv2d(filters[0], self.CatChannels, 3, padding=1)
self.h1_PT_hd4_bn = nn.BatchNorm2d(self.CatChannels)
self.h1_PT_hd4_relu = nn.ReLU(inplace=True)
# h2->160*160, hd4->40*40, Pooling 4 times
self.h2_PT_hd4 = nn.MaxPool2d(4, 4, ceil_mode=True)
self.h2_PT_hd4_conv = nn.Conv2d(filters[1], self.CatChannels, 3, padding=1)
self.h2_PT_hd4_bn = nn.BatchNorm2d(self.CatChannels)
self.h2_PT_hd4_relu = nn.ReLU(inplace=True)
# h3->80*80, hd4->40*40, Pooling 2 times
self.h3_PT_hd4 = nn.MaxPool2d(2, 2, ceil_mode=True)
self.h3_PT_hd4_conv = nn.Conv2d(filters[2], self.CatChannels, 3, padding=1)
self.h3_PT_hd4_bn = nn.BatchNorm2d(self.CatChannels)
self.h3_PT_hd4_relu = nn.ReLU(inplace=True)
# h4->40*40, hd4->40*40, Concatenation
self.h4_Cat_hd4_conv = nn.Conv2d(filters[3], self.CatChannels, 3, padding=1)
self.h4_Cat_hd4_bn = nn.BatchNorm2d(self.CatChannels)
self.h4_Cat_hd4_relu = nn.ReLU(inplace=True)
# hd5->20*20, hd4->40*40, Upsample 2 times
self.hd5_UT_hd4 = nn.Upsample(scale_factor=2, mode='bilinear') # 14*14
self.hd5_UT_hd4_conv = nn.Conv2d(filters[4], self.CatChannels, 3, padding=1)
self.hd5_UT_hd4_bn = nn.BatchNorm2d(self.CatChannels)
self.hd5_UT_hd4_relu = nn.ReLU(inplace=True)
# fusion(h1_PT_hd4, h2_PT_hd4, h3_PT_hd4, h4_Cat_hd4, hd5_UT_hd4)
self.conv4d_1 = nn.Conv2d(self.UpChannels, self.UpChannels, 3, padding=1) # 16
self.bn4d_1 = nn.BatchNorm2d(self.UpChannels)
self.relu4d_1 = nn.ReLU(inplace=True)
'''stage 3d'''
# h1->320*320, hd3->80*80, Pooling 4 times
self.h1_PT_hd3 = nn.MaxPool2d(4, 4, ceil_mode=True)
self.h1_PT_hd3_conv = nn.Conv2d(filters[0], self.CatChannels, 3, padding=1)
self.h1_PT_hd3_bn = nn.BatchNorm2d(self.CatChannels)
self.h1_PT_hd3_relu = nn.ReLU(inplace=True)
# h2->160*160, hd3->80*80, Pooling 2 times
self.h2_PT_hd3 = nn.MaxPool2d(2, 2, ceil_mode=True)
self.h2_PT_hd3_conv = nn.Conv2d(filters[1], self.CatChannels, 3, padding=1)
self.h2_PT_hd3_bn = nn.BatchNorm2d(self.CatChannels)
self.h2_PT_hd3_relu = nn.ReLU(inplace=True)
# h3->80*80, hd3->80*80, Concatenation
self.h3_Cat_hd3_conv = nn.Conv2d(filters[2], self.CatChannels, 3, padding=1)
self.h3_Cat_hd3_bn = nn.BatchNorm2d(self.CatChannels)
self.h3_Cat_hd3_relu = nn.ReLU(inplace=True)
# hd4->40*40, hd4->80*80, Upsample 2 times
self.hd4_UT_hd3 = nn.Upsample(scale_factor=2, mode='bilinear') # 14*14
self.hd4_UT_hd3_conv = nn.Conv2d(self.UpChannels, self.CatChannels, 3, padding=1)
self.hd4_UT_hd3_bn = nn.BatchNorm2d(self.CatChannels)
self.hd4_UT_hd3_relu = nn.ReLU(inplace=True)
# hd5->20*20, hd4->80*80, Upsample 4 times
self.hd5_UT_hd3 = nn.Upsample(scale_factor=4, mode='bilinear') # 14*14
self.hd5_UT_hd3_conv = nn.Conv2d(filters[4], self.CatChannels, 3, padding=1)
self.hd5_UT_hd3_bn = nn.BatchNorm2d(self.CatChannels)
self.hd5_UT_hd3_relu = nn.ReLU(inplace=True)
# fusion(h1_PT_hd3, h2_PT_hd3, h3_Cat_hd3, hd4_UT_hd3, hd5_UT_hd3)
self.conv3d_1 = nn.Conv2d(self.UpChannels, self.UpChannels, 3, padding=1) # 16
self.bn3d_1 = nn.BatchNorm2d(self.UpChannels)
self.relu3d_1 = nn.ReLU(inplace=True)
'''stage 2d '''
# h1->320*320, hd2->160*160, Pooling 2 times
self.h1_PT_hd2 = nn.MaxPool2d(2, 2, ceil_mode=True)
self.h1_PT_hd2_conv = nn.Conv2d(filters[0], self.CatChannels, 3, padding=1)
self.h1_PT_hd2_bn = nn.BatchNorm2d(self.CatChannels)
self.h1_PT_hd2_relu = nn.ReLU(inplace=True)
# h2->160*160, hd2->160*160, Concatenation
self.h2_Cat_hd2_conv = nn.Conv2d(filters[1], self.CatChannels, 3, padding=1)
self.h2_Cat_hd2_bn = nn.BatchNorm2d(self.CatChannels)
self.h2_Cat_hd2_relu = nn.ReLU(inplace=True)
# hd3->80*80, hd2->160*160, Upsample 2 times
self.hd3_UT_hd2 = nn.Upsample(scale_factor=2, mode='bilinear') # 14*14
self.hd3_UT_hd2_conv = nn.Conv2d(self.UpChannels, self.CatChannels, 3, padding=1)
self.hd3_UT_hd2_bn = nn.BatchNorm2d(self.CatChannels)
self.hd3_UT_hd2_relu = nn.ReLU(inplace=True)
# hd4->40*40, hd2->160*160, Upsample 4 times
self.hd4_UT_hd2 = nn.Upsample(scale_factor=4, mode='bilinear') # 14*14
self.hd4_UT_hd2_conv = nn.Conv2d(self.UpChannels, self.CatChannels, 3, padding=1)
self.hd4_UT_hd2_bn = nn.BatchNorm2d(self.CatChannels)
self.hd4_UT_hd2_relu = nn.ReLU(inplace=True)
# hd5->20*20, hd2->160*160, Upsample 8 times
self.hd5_UT_hd2 = nn.Upsample(scale_factor=8, mode='bilinear') # 14*14
self.hd5_UT_hd2_conv = nn.Conv2d(filters[4], self.CatChannels, 3, padding=1)
self.hd5_UT_hd2_bn = nn.BatchNorm2d(self.CatChannels)
self.hd5_UT_hd2_relu = nn.ReLU(inplace=True)
# fusion(h1_PT_hd2, h2_Cat_hd2, hd3_UT_hd2, hd4_UT_hd2, hd5_UT_hd2)
self.conv2d_1 = nn.Conv2d(self.UpChannels, self.UpChannels, 3, padding=1) # 16
self.bn2d_1 = nn.BatchNorm2d(self.UpChannels)
self.relu2d_1 = nn.ReLU(inplace=True)
'''stage 1d'''
# h1->320*320, hd1->320*320, Concatenation
self.h1_Cat_hd1_conv = nn.Conv2d(filters[0], self.CatChannels, 3, padding=1)
self.h1_Cat_hd1_bn = nn.BatchNorm2d(self.CatChannels)
self.h1_Cat_hd1_relu = nn.ReLU(inplace=True)
# hd2->160*160, hd1->320*320, Upsample 2 times
self.hd2_UT_hd1 = nn.Upsample(scale_factor=2, mode='bilinear') # 14*14
self.hd2_UT_hd1_conv = nn.Conv2d(self.UpChannels, self.CatChannels, 3, padding=1)
self.hd2_UT_hd1_bn = nn.BatchNorm2d(self.CatChannels)
self.hd2_UT_hd1_relu = nn.ReLU(inplace=True)
# hd3->80*80, hd1->320*320, Upsample 4 times
self.hd3_UT_hd1 = nn.Upsample(scale_factor=4, mode='bilinear') # 14*14
self.hd3_UT_hd1_conv = nn.Conv2d(self.UpChannels, self.CatChannels, 3, padding=1)
self.hd3_UT_hd1_bn = nn.BatchNorm2d(self.CatChannels)
self.hd3_UT_hd1_relu = nn.ReLU(inplace=True)
# hd4->40*40, hd1->320*320, Upsample 8 times
self.hd4_UT_hd1 = nn.Upsample(scale_factor=8, mode='bilinear') # 14*14
self.hd4_UT_hd1_conv = nn.Conv2d(self.UpChannels, self.CatChannels, 3, padding=1)
self.hd4_UT_hd1_bn = nn.BatchNorm2d(self.CatChannels)
self.hd4_UT_hd1_relu = nn.ReLU(inplace=True)
# hd5->20*20, hd1->320*320, Upsample 16 times
self.hd5_UT_hd1 = nn.Upsample(scale_factor=16, mode='bilinear') # 14*14
self.hd5_UT_hd1_conv = nn.Conv2d(filters[4], self.CatChannels, 3, padding=1)
self.hd5_UT_hd1_bn = nn.BatchNorm2d(self.CatChannels)
self.hd5_UT_hd1_relu = nn.ReLU(inplace=True)
# fusion(h1_Cat_hd1, hd2_UT_hd1, hd3_UT_hd1, hd4_UT_hd1, hd5_UT_hd1)
self.conv1d_1 = nn.Conv2d(self.UpChannels, self.UpChannels, 3, padding=1) # 16
self.bn1d_1 = nn.BatchNorm2d(self.UpChannels)
self.relu1d_1 = nn.ReLU(inplace=True)
# output
self.outconv1 = nn.Conv2d(self.UpChannels, n_classes, 3, padding=1)
# initialise weights
for m in self.modules():
if isinstance(m, nn.Conv2d):
init_weights(m, init_type='kaiming')
elif isinstance(m, nn.BatchNorm2d):
init_weights(m, init_type='kaiming')
def forward(self, inputs):
## -------------Encoder-------------
h1 = self.conv1(inputs) # h1->320*320*64
h2 = self.maxpool1(h1)
h2 = self.conv2(h2) # h2->160*160*128
h3 = self.maxpool2(h2)
h3 = self.conv3(h3) # h3->80*80*256
h4 = self.maxpool3(h3)
h4 = self.conv4(h4) # h4->40*40*512
h5 = self.maxpool4(h4)
hd5 = self.conv5(h5) # h5->20*20*1024
## -------------Decoder-------------
h1_PT_hd4 = self.h1_PT_hd4_relu(self.h1_PT_hd4_bn(self.h1_PT_hd4_conv(self.h1_PT_hd4(h1))))
h2_PT_hd4 = self.h2_PT_hd4_relu(self.h2_PT_hd4_bn(self.h2_PT_hd4_conv(self.h2_PT_hd4(h2))))
h3_PT_hd4 = self.h3_PT_hd4_relu(self.h3_PT_hd4_bn(self.h3_PT_hd4_conv(self.h3_PT_hd4(h3))))
h4_Cat_hd4 = self.h4_Cat_hd4_relu(self.h4_Cat_hd4_bn(self.h4_Cat_hd4_conv(h4)))
hd5_UT_hd4 = self.hd5_UT_hd4_relu(self.hd5_UT_hd4_bn(self.hd5_UT_hd4_conv(self.hd5_UT_hd4(hd5))))
hd4 = self.relu4d_1(self.bn4d_1(self.conv4d_1(
torch.cat((h1_PT_hd4, h2_PT_hd4, h3_PT_hd4, h4_Cat_hd4, hd5_UT_hd4), 1)))) # hd4->40*40*UpChannels
h1_PT_hd3 = self.h1_PT_hd3_relu(self.h1_PT_hd3_bn(self.h1_PT_hd3_conv(self.h1_PT_hd3(h1))))
h2_PT_hd3 = self.h2_PT_hd3_relu(self.h2_PT_hd3_bn(self.h2_PT_hd3_conv(self.h2_PT_hd3(h2))))
h3_Cat_hd3 = self.h3_Cat_hd3_relu(self.h3_Cat_hd3_bn(self.h3_Cat_hd3_conv(h3)))
hd4_UT_hd3 = self.hd4_UT_hd3_relu(self.hd4_UT_hd3_bn(self.hd4_UT_hd3_conv(self.hd4_UT_hd3(hd4))))
hd5_UT_hd3 = self.hd5_UT_hd3_relu(self.hd5_UT_hd3_bn(self.hd5_UT_hd3_conv(self.hd5_UT_hd3(hd5))))
hd3 = self.relu3d_1(self.bn3d_1(self.conv3d_1(
torch.cat((h1_PT_hd3, h2_PT_hd3, h3_Cat_hd3, hd4_UT_hd3, hd5_UT_hd3), 1)))) # hd3->80*80*UpChannels
h1_PT_hd2 = self.h1_PT_hd2_relu(self.h1_PT_hd2_bn(self.h1_PT_hd2_conv(self.h1_PT_hd2(h1))))
h2_Cat_hd2 = self.h2_Cat_hd2_relu(self.h2_Cat_hd2_bn(self.h2_Cat_hd2_conv(h2)))
hd3_UT_hd2 = self.hd3_UT_hd2_relu(self.hd3_UT_hd2_bn(self.hd3_UT_hd2_conv(self.hd3_UT_hd2(hd3))))
hd4_UT_hd2 = self.hd4_UT_hd2_relu(self.hd4_UT_hd2_bn(self.hd4_UT_hd2_conv(self.hd4_UT_hd2(hd4))))
hd5_UT_hd2 = self.hd5_UT_hd2_relu(self.hd5_UT_hd2_bn(self.hd5_UT_hd2_conv(self.hd5_UT_hd2(hd5))))
hd2 = self.relu2d_1(self.bn2d_1(self.conv2d_1(
torch.cat((h1_PT_hd2, h2_Cat_hd2, hd3_UT_hd2, hd4_UT_hd2, hd5_UT_hd2), 1)))) # hd2->160*160*UpChannels
h1_Cat_hd1 = self.h1_Cat_hd1_relu(self.h1_Cat_hd1_bn(self.h1_Cat_hd1_conv(h1)))
hd2_UT_hd1 = self.hd2_UT_hd1_relu(self.hd2_UT_hd1_bn(self.hd2_UT_hd1_conv(self.hd2_UT_hd1(hd2))))
hd3_UT_hd1 = self.hd3_UT_hd1_relu(self.hd3_UT_hd1_bn(self.hd3_UT_hd1_conv(self.hd3_UT_hd1(hd3))))
hd4_UT_hd1 = self.hd4_UT_hd1_relu(self.hd4_UT_hd1_bn(self.hd4_UT_hd1_conv(self.hd4_UT_hd1(hd4))))
hd5_UT_hd1 = self.hd5_UT_hd1_relu(self.hd5_UT_hd1_bn(self.hd5_UT_hd1_conv(self.hd5_UT_hd1(hd5))))
hd1 = self.relu1d_1(self.bn1d_1(self.conv1d_1(
torch.cat((h1_Cat_hd1, hd2_UT_hd1, hd3_UT_hd1, hd4_UT_hd1, hd5_UT_hd1), 1)))) # hd1->320*320*UpChannels
d1 = self.outconv1(hd1) # d1->320*320*n_classes
return d1
完整代码请私聊博主~(QQ:704783475)
五、训练
python train.py --arch=“unet3d” --dataset=“Jiu0Monkey”
六、测试
python test.py --name="jiu0Monkey_unet3d_woDS"
七、与其它模型对比