基于 U-Net 的视网膜血管分割是一种应用深度学习的方法，特别是 U-Net 结构，用于从眼底图像中分割出视网膜血管。U-Net 是一种全卷积神经网络（FCN），通常用于图像分割任务。以下是基于 U-Net 的视网膜血管分割的内容：
框架结构：
代码结构：
U-Net分割代码：
unet_model.py
bash
import torch.nn.functional as F
from .unet_parts import *
class UNet(nn.Module):
def __init__(self, n_channels, n_classes, bilinear=True):
super(UNet, self).__init__()
self.n_channels = n_channels
self.n_classes = n_classes
self.bilinear = bilinear
self.inc = DoubleConv(n_channels, 64)
self.down1 = Down(64, 128)
self.down2 = Down(128, 256)
self.down3 = Down(256, 512)
self.down4 = Down(512, 512)
self.up1 = Up(1024, 256, bilinear)
self.up2 = Up(512, 128, bilinear)
self.up3 = Up(256, 64, bilinear)
self.up4 = Up(128, 64, bilinear)
self.outc = OutConv(64, n_classes)
def forward(self, x):
x1 = self.inc(x)
# 在编码器下采样过程加空间注意力
# x2 = self.down1(self.sp1(x1))
# x3 = self.down2(self.sp2(x2))
# x4 = self.down3(self.sp3(x3))
# x5 = self.down4(self.sp4(x4))
x2 = self.down1(x1)
x3 = self.down2(x2)
x4 = self.down3(x3)
x5 = self.down4(x4)
x = self.up1(x5, x4)
x = self.up2(x, x3)
x = self.up3(x, x2)
x = self.up4(x, x1)
logits = self.outc(x)
return logits
if __name__ == '__main__':
net = UNet(n_channels=3, n_classes=1)
print(net)unet_parts.py
python
import torch
import torch.nn as nn
import torch.nn.functional as F
class DoubleConv(nn.Module):
"""(convolution => [BN] => ReLU) * 2"""
def __init__(self, in_channels, out_channels):
super().__init__()
self.double_conv = nn.Sequential(
nn.Conv2d(in_channels, out_channels, kernel_size=3, padding=1),
nn.BatchNorm2d(out_channels),
nn.ReLU(inplace=True),
nn.Conv2d(out_channels, out_channels, kernel_size=3, padding=1),
nn.BatchNorm2d(out_channels),
nn.ReLU(inplace=True)
)
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):
return self.double_conv(x)
class Down(nn.Module):
"""Downscaling with maxpool then double conv"""
def __init__(self, in_channels, out_channels):
super().__init__()
self.maxpool_conv = nn.Sequential(
nn.MaxPool2d(2),
DoubleConv(in_channels, out_channels)
)
def forward(self, x):
return self.maxpool_conv(x)
class Up(nn.Module):
"""Upscaling then double conv"""
def __init__(self, in_channels, out_channels, bilinear=True):
super().__init__()
# if bilinear, use the normal convolutions to reduce the number of channels
if bilinear:
self.up = nn.Upsample(scale_factor=2, mode='bilinear', align_corners=True)
else:
self.up = nn.ConvTranspose2d(in_channels // 2, in_channels // 2, kernel_size=2, stride=2)
self.conv = DoubleConv(in_channels, out_channels)
def forward(self, x1, x2):
x1 = self.up(x1)
# input is CHW
diffY = torch.tensor([x2.size()[2] - x1.size()[2]])
diffX = torch.tensor([x2.size()[3] - x1.size()[3]])
x1 = F.pad(x1, [diffX // 2, diffX - diffX // 2,
diffY // 2, diffY - diffY // 2])
x = torch.cat([x2, x1], dim=1)
return self.conv(x)
class OutConv(nn.Module):
def __init__(self, in_channels, out_channels):
super(OutConv, self).__init__()
self.conv = nn.Conv2d(in_channels, out_channels, kernel_size=1)
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):
return self.conv(x)trainval.py
bash
from model.unet_model import UNet
from utils.dataset import FundusSeg_Loader
from torch import optim
import torch.nn as nn
import torch
import sys
import matplotlib.pyplot as plt
from tqdm import tqdm
import time
train_data_path = "DRIVE/drive_train/"
valid_data_path = "DRIVE/drive_test/"
# hyperparameter-settings
N_epochs = 500
Init_lr = 0.00001
def train_net(net, device, epochs=N_epochs, batch_size=1, lr=Init_lr):
# 加载训练集
train_dataset = FundusSeg_Loader(train_data_path, 1)
valid_dataset = FundusSeg_Loader(valid_data_path, 0)
train_loader = torch.utils.data.DataLoader(dataset=train_dataset, batch_size=batch_size, shuffle=True)
valid_loader = torch.utils.data.DataLoader(dataset=valid_dataset, batch_size=batch_size, shuffle=False)
print('Traing images: %s' % len(train_loader))
print('Valid images: %s' % len(valid_loader))
# 定义RMSprop算法
optimizer = optim.RMSprop(net.parameters(), lr=lr, weight_decay=1e-8, momentum=0.9)
# 定义Loss算法
# BCEWithLogitsLoss会对predict进行sigmoid处理
# criterion 常被用来定义损失函数，方便调换损失函数
criterion = nn.BCEWithLogitsLoss()
# 训练epochs次
# 求最小值，所以初始化为正无穷
best_loss = float('inf')
train_loss_list = []
val_loss_list = []
for epoch in range(epochs):
# 训练模式
net.train()
train_loss = 0
print(f'Epoch {epoch + 1}/{epochs}')
# SGD
# train_loss_list = []
# val_loss_list = []
with tqdm(total=train_loader.__len__()) as pbar:
for i, (image, label, filename) in enumerate(train_loader):
optimizer.zero_grad()
# 将数据拷贝到device中
image = image.to(device=device, dtype=torch.float32)
label = label.to(device=device, dtype=torch.float32)
# 使用网络参数，输出预测结果
pred = net(image)
# print(pred)
# 计算loss
loss = criterion(pred, label)
# print(loss)
train_loss = train_loss + loss.item()
loss.backward()
optimizer.step()
pbar.set_postfix(loss=float(loss.cpu()), epoch=epoch)
pbar.update(1)
train_loss_list.append(train_loss / i)
print('Loss/train', train_loss / i)
# Validation
net.eval()
val_loss = 0
for i, (image, label, filename) in tqdm(enumerate(valid_loader), total=len(valid_loader)):
image = image.to(device=device, dtype=torch.float32)
label = label.to(device=device, dtype=torch.float32)
pred = net(image)
loss = criterion(pred, label)
val_loss = val_loss + loss.item()
# net.state_dict()就是用来保存模型参数的
if val_loss < best_loss:
best_loss = val_loss
torch.save(net.state_dict(), 'best_model.pth')
print('saving model............................................')
val_loss_list.append(val_loss / i)
print('Loss/valid', val_loss / i)
sys.stdout.flush()
return val_loss_list, train_loss_list
if __name__ == "__main__":
# 选择设备cuda
device = torch.device('cuda')
# 加载网络，图片单通道1，分类为1。
net = UNet(n_channels=3, n_classes=1)
# 将网络拷贝到deivce中
net.to(device=device)
# 开始训练
val_loss_list, train_loss_list = train_net(net, device)
# 保存loss值到txt文件
fileObject1 = open('train_loss.txt', 'w')
for train_loss in train_loss_list:
fileObject1.write(str(train_loss))
fileObject1.write('\n')
fileObject1.close()
fileObject2 = open('val_loss.txt', 'w')
for val_loss in val_loss_list:
fileObject2.write(str(val_loss))
fileObject2.write('\n')
fileObject2.close()
# 我这里迭代了5次，所以x的取值范围为(0，5)，然后再将每次相对应的5损失率附在x上
x = range(0, N_epochs)
y1 = val_loss_list
y2 = train_loss_list
# 两行一列第一个
plt.subplot(1, 1, 1)
plt.plot(x, y1, 'r.-', label=u'val_loss')
plt.plot(x, y2, 'g.-', label =u'train_loss')
plt.title('loss')
plt.xlabel('epochs')
plt.ylabel('loss')
plt.savefig("accuracy_loss.jpg")
plt.show()predict.py
c
import numpy as np
import torch
import cv2
from model.unet_model import UNet
from utils.dataset import FundusSeg_Loader
import copy
from sklearn.metrics import roc_auc_score
model_path='./best_model.pth'
test_data_path = "DRIVE/drive_test/"
save_path='./results/'
if __name__ == "__main__":
test_dataset = FundusSeg_Loader(test_data_path,0)
test_loader = torch.utils.data.DataLoader(dataset=test_dataset, batch_size=1, shuffle=False)
print('Testing images: %s' %len(test_loader))
# 选择设备CUDA
device = torch.device('cuda')
# 加载网络，图片单通道，分类为1。
net = UNet(n_channels=3, n_classes=1)
# 将网络拷贝到deivce中
net.to(device=device)
# 加载模型参数
print(f'Loading model {model_path}')
net.load_state_dict(torch.load(model_path, map_location=device))
# 测试模式
net.eval()
tp = 0
tn = 0
fp = 0
fn = 0
pred_list = []
label_list = []
for image, label, filename in test_loader:
image = image.to(device=device, dtype=torch.float32)
pred = net(image)
# Normalize to [0, 1]
pred = torch.sigmoid(pred)
pred = np.array(pred.data.cpu()[0])[0]
pred_list.append(pred)
# ConfusionMAtrix
pred_bin = copy.deepcopy(pred)
label = np.array(label.data.cpu()[0])[0]
label_list.append(label)
pred_bin[pred_bin >= 0.5] = 1
pred_bin[pred_bin < 0.5] = 0
tp += ((pred_bin == 1) & (label == 1)).sum()
tn += ((pred_bin == 0) & (label == 0)).sum()
fn += ((pred_bin == 0) & (label == 1)).sum()
fp += ((pred_bin == 1) & (label == 0)).sum()
# 保存图片
pred = pred * 255
save_filename = save_path + filename[0] + '.png'
cv2.imwrite(save_filename, pred)
print(f'{save_filename} done!')
# Evaluaiton Indicators
precision = tp / (tp + fp) # 预测为真并且正确/预测正确样本总和
sen = tp / (tp + fn) # 预测为真并且正确/正样本总和
spe = tn / (tn + fp)
acc = (tp + tn) / (tp + tn + fp + fn)
f1score = 2 * precision * sen / (precision + sen)
# auc computing
pred_auc = np.stack(pred_list, axis=0)
label_auc = np.stack(label_list, axis=0)
auc = roc_auc_score(label_auc.reshape(-1), pred_auc.reshape(-1))
print(f'Precision: {precision} Sen: {sen} Spe:{spe} F1-score: {f1score} Acc: {acc} AUC: {auc}')dataset.py
python
import torch
import cv2
import os
import glob
from torch.utils.data import Dataset
# import random
# from PIL import Image
# import numpy as np
class FundusSeg_Loader(Dataset):
def __init__(self, data_path, is_train):
# 初始化函数，读取所有data_path下的图片
self.data_path = data_path
self.imgs_path = glob.glob(os.path.join(data_path, 'image/*.tif'))
self.labels_path = glob.glob(os.path.join(data_path, 'label/*.tif'))
self.is_train = is_train
print(self.imgs_path)
print(self.labels_path)
def __getitem__(self, index):
# 根据index读取图片
image_path = self.imgs_path[index]
if self.is_train == 1:
label_path = image_path.replace('image', 'label')
label_path = label_path.replace('training', 'manual1')
else:
label_path = image_path.replace('image', 'label')
label_path = label_path.replace('test.tif', 'manual1.tif')
# 读取训练图片和标签图片
image = cv2.imread(image_path)
label = cv2.imread(label_path)
# image = np.array(image)
# label = np.array(label)
# label = cv2.imread(label_path)
# image = cv2.resize(image, (600,400))
# label = cv2.resize(label, (600,400))
# 转为单通道的图片
# image = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
label = cv2.cvtColor(label, cv2.COLOR_BGR2GRAY)
# label = Image.fromarray(label)
# label = label.convert("1")
# reshape()函数可以改变数组的形状，并且原始数据不发生变化。
image = image.transpose(2, 0, 1)
# image = image.reshape(1, label.shape[0], label.shape[1])
label = label.reshape(1, label.shape[0], label.shape[1])
# 处理标签，将像素值为255的改为1
if label.max() > 1:
label[label > 1] = 1
return image, label, image_path[len(image_path)-12:len(image_path)-4]
def __len__(self):
# 返回训练集大小
return len(self.imgs_path)visual.py
python
import numpy as np
import matplotlib.pyplot as plt
import pylab as pl
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
data1_loss =np.loadtxt("E:\\code\\UNet_lr00001\\train_loss.txt",dtype=str )
data2_loss = np.loadtxt("E:\\code\\UNet_lr00001\\val_loss.txt",dtype=str)
x = range(0,10)
y = data1_loss[:, 0]
x1 = range(0,10)
y1 = data2_loss[:, 0]
fig = plt.figure(figsize = (7,5)) #figsize是图片的大小`
ax1 = fig.add_subplot(1, 1, 1) # ax1是子图的名字`
pl.plot(x,y,'g-',label=u'Dense_Unet(block layer=5)')
# ''g''代表"green",表示画出的曲线是绿色，"-"代表画的曲线是实线，可自行选择，label代表的是图例的名称，一般要在名称前面加一个u，如果名称是中文，会显示不出来，目前还不知道怎么解决。
p2 = pl.plot(x, y,'r-', label = u'train_loss')
pl.legend()
#显示图例
p3 = pl.plot(x1,y1, 'b-', label = u'val_loss')
pl.legend()
pl.xlabel(u'epoch')
pl.ylabel(u'loss')
plt.title('Compare loss for different models in training')
这种基于 U-Net 的方法已在医学图像分割领域取得了一些成功，特别是在视网膜图像处理中。通过深度学习的方法，这种技术能够更准确地提取视网膜血管，为眼科医生提供辅助诊断和治疗的信息。
如有疑问，请评论。