pytorch版Unet实现医学图像分割

目录

1 model

2 dataset

3 main

4 下载资源

---

1 model

import torch.nn as nn
import torch
from torch import autograd

class DoubleConv(nn.Module):
    def __init__(self, in_ch, out_ch):
        super(DoubleConv, self).__init__()
        self.conv = nn.Sequential(
            nn.Conv2d(in_ch, out_ch, 3, padding=1),
            nn.BatchNorm2d(out_ch),
            nn.ReLU(inplace=True),
            nn.Conv2d(out_ch, out_ch, 3, padding=1),
            nn.BatchNorm2d(out_ch),
            nn.ReLU(inplace=True)
        )

    def forward(self, input):
        return self.conv(input)


class Unet(nn.Module):
    def __init__(self,in_ch,out_ch):
        super(Unet, self).__init__()

        self.conv1 = DoubleConv(in_ch, 64)
        self.pool1 = nn.MaxPool2d(2)
        self.conv2 = DoubleConv(64, 128)
        self.pool2 = nn.MaxPool2d(2)
        self.conv3 = DoubleConv(128, 256)
        self.pool3 = nn.MaxPool2d(2)
        self.conv4 = DoubleConv(256, 512)
        self.pool4 = nn.MaxPool2d(2)
        self.conv5 = DoubleConv(512, 1024)
        self.up6 = nn.ConvTranspose2d(1024, 512, 2, stride=2)
        self.conv6 = DoubleConv(1024, 512)
        self.up7 = nn.ConvTranspose2d(512, 256, 2, stride=2)
        self.conv7 = DoubleConv(512, 256)
        self.up8 = nn.ConvTranspose2d(256, 128, 2, stride=2)
        self.conv8 = DoubleConv(256, 128)
        self.up9 = nn.ConvTranspose2d(128, 64, 2, stride=2)
        self.conv9 = DoubleConv(128, 64)
        self.conv10 = nn.Conv2d(64,out_ch, 1)

    def forward(self,x):
        c1=self.conv1(x)
        p1=self.pool1(c1)
        c2=self.conv2(p1)
        p2=self.pool2(c2)
        c3=self.conv3(p2)
        p3=self.pool3(c3)
        c4=self.conv4(p3)
        p4=self.pool4(c4)
        c5=self.conv5(p4)
        up_6= self.up6(c5)
        merge6 = torch.cat([up_6, c4], dim=1)
        c6=self.conv6(merge6)
        up_7=self.up7(c6)
        merge7 = torch.cat([up_7, c3], dim=1)
        c7=self.conv7(merge7)
        up_8=self.up8(c7)
        merge8 = torch.cat([up_8, c2], dim=1)
        c8=self.conv8(merge8)
        up_9=self.up9(c8)
        merge9=torch.cat([up_9,c1],dim=1)
        c9=self.conv9(merge9)
        c10=self.conv10(c9)
        out = nn.Sigmoid()(c10)
        return out

2 dataset

import torch.utils.data as data
import PIL.Image as Image
import os


def make_dataset(root):
    imgs=[]
    n=len(os.listdir(root))//2
    for i in range(n):
        img=os.path.join(root,"%03d.png"%i)
        mask=os.path.join(root,"%03d_mask.png"%i)
        imgs.append((img,mask))
    return imgs


class LiverDataset(data.Dataset):
    def __init__(self, root, transform=None, target_transform=None):
        imgs = make_dataset(root)
        self.imgs = imgs
        self.transform = transform
        self.target_transform = target_transform

    def __getitem__(self, index):
        x_path, y_path = self.imgs[index]
        img_x = Image.open(x_path)
        img_y = Image.open(y_path)
        if self.transform is not None:
            img_x = self.transform(img_x)
        if self.target_transform is not None:
            img_y = self.target_transform(img_y)
        return img_x, img_y

    def __len__(self):
        return len(self.imgs)

3 main

import numpy as np
import torch
import argparse
from torch.utils.data import DataLoader
from torch import autograd, optim
from torchvision.transforms import transforms
from unet import Unet
from dataset import LiverDataset


# 是否使用cuda

device = torch.device("cuda" if torch.cuda.is_available() else "cpu")

# 把多个步骤整合到一起, channel=（channel-mean）/std, 因为是分别对三个通道处理
x_transforms = transforms.Compose([
    transforms.ToTensor(),  # -> [0,1]
    transforms.Normalize([0.5, 0.5, 0.5], [0.5, 0.5, 0.5])  # ->[-1,1]
])

# mask只需要转换为tensor
y_transforms = transforms.ToTensor()

# 参数解析器,用来解析从终端读取的命令
parse = argparse.ArgumentParser()


def train_model(model, criterion, optimizer, dataload, num_epochs=20):
    for epoch in range(num_epochs):
        print('Epoch {}/{}'.format(epoch, num_epochs - 1))
        print('-' * 10)
        dt_size = len(dataload.dataset)
        epoch_loss = 0
        step = 0
        for x, y in dataload:
            step += 1
            inputs = x.to(device)
            labels = y.to(device)
            # zero the parameter gradients
            optimizer.zero_grad()
            # forward
            outputs = model(inputs)
            loss = criterion(outputs, labels)
            loss.backward()
            optimizer.step()
            epoch_loss += loss.item()
            print("%d/%d,train_loss:%0.3f" % (step, (dt_size - 1) // dataload.batch_size + 1, loss.item()))
        print("epoch %d loss:%0.3f" % (epoch, epoch_loss))
        torch.save(model.state_dict(), 'weights_%d.pth' % epoch)
    return model


# 训练模型
def train():
    model = Unet(3, 1).to(device)
    batch_size = args.batch_size
    criterion = torch.nn.BCELoss()
    optimizer = optim.Adam(model.parameters())
    liver_dataset = LiverDataset("data/train",transform=x_transforms,target_transform=y_transforms)
    dataloaders = DataLoader(liver_dataset, batch_size=batch_size, shuffle=True, num_workers=4)
    train_model(model, criterion, optimizer, dataloaders)


# 显示模型的输出结果
def test():
    model = Unet(3, 1)
    model.load_state_dict(torch.load(args.ckp,map_location='cpu'))
    liver_dataset = LiverDataset("data/val", transform=x_transforms,target_transform=y_transforms)
    dataloaders = DataLoader(liver_dataset, batch_size=1)
    model.eval()
    import matplotlib.pyplot as plt
    plt.ion()
    with torch.no_grad():
        for x, _ in dataloaders:
            y=model(x)
            img_y=torch.squeeze(y).numpy()
            plt.imshow(img_y)
            plt.pause(0.01)
        plt.show()


parse = argparse.ArgumentParser()
# parse.add_argument("action", type=str, help="train or test")
parse.add_argument("--batch_size", type=int, default=1)
parse.add_argument("--ckp", type=str, help="the path of model weight file")
args = parse.parse_args()

# train
#train()

# test()
args.ckp = "weights_19.pth"
test()

测试结果：

4 下载资源

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