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基于Pytorch肺部感染识别案例(采用ResNet网络结构)

开发技术 开发技术 2022-05-28 次浏览

一、整体流程

1. 数据集下载地址:https:/​/​www.​kaggle.​com/​paultimothymooney/​chest-​xray-​pneumonia/​download

2. 数据集展示

基于Pytorch肺部感染识别案例(采用ResNet网络结构)

 基于Pytorch肺部感染识别案例(采用ResNet网络结构)

案例主要流程:

第一步:加载预训练模型ResNet,该模型已在ImageNet上训练过。

第二步:冻结预训练模型中低层卷积层的参数(权重)

第三步:用可训练参数的多层替换分类层。

第四步:在训练集上训练分类层。

第五步:微调超参数,根据需要解冻更多层。

 基于Pytorch肺部感染识别案例(采用ResNet网络结构)

ResNet 网络结构图

基于Pytorch肺部感染识别案例(采用ResNet网络结构)

 基于Pytorch肺部感染识别案例(采用ResNet网络结构)

 二、显示图片功能

#1加载库
import torch
import torch.nn as nn
import numpy as np
import matplotlib.pyplot as plt
from torchvision import datasets, transforms
import os
from torchvision.utils import make_grid

from torch.utils.data import DataLoader
#2、定义一个方法:显示图片
def img_show(inp, title=None):
    plt.figure(figsize=(14,3))
    inp = inp.numpy().transpose((1,2,0)) #转成numpy,然后转置
    mean = np.array([0.485, 0.456, 0.406])
    std = np.array([0.229, 0.224,0.225])
    inp = std * inp + mean
    inp = np.clip(inp, 0, 1)
    plt.imshow(inp)
    if title is not None:
        plt.title(title)
    plt.pause(0.001)
    plt.show()
def main():
    pass
    #3、定义超参数
    BATCH_SIZE = 8
    DEVICE = torch.device("gpu" if torch.cuda.is_available() else "cpu")

    #4、图片转换    使用字典进行转换
    data_transforms = {
        'train': transforms.Compose([
            transforms.Resize(300),
            transforms.RandomResizedCrop(300) ,#随机裁剪
            transforms.RandomHorizontalFlip(),
            transforms.CenterCrop(256),
            transforms.ToTensor(), #转为张量
            transforms.Normalize([0.485, 0.456, 0.406],
                                 [0.229, 0.224, 0.225]) #正则化

        ]),
        'val': transforms.Compose([
            transforms.Resize(300),
            transforms.CenterCrop(256),
            transforms.ToTensor(), #转为张量
            transforms.Normalize([0.485, 0.456, 0.406],
                                 [0.229, 0.224, 0.225]) #正则化
        ])
    }

    #5、操作数据集
    # 5.1、数据集路径
    data_path = "D:/chest_xray/"
    #5.2、加载数据集的train val
    img_datasets = { x : datasets.ImageFolder(os.path.join(data_path,x),
                        data_transforms[x]) for x in ["train","val"]}
    #5.3、为数据集创建一个迭代器,读取数据
    dataloaders = {x : DataLoader(img_datasets[x], shuffle=True,
                        batch_size= BATCH_SIZE) for x in ["train","val"]
                                  }
    # 5.4、训练集和验证集的大小(图片的数量)
    data_sizes = {x : len(img_datasets[x]) for x in ["train","val"]}
    # 5.5、获取标签类别名称 NORMAL 正常 -- PNEUMONIA 感染
    target_names = img_datasets['train'].classes
    #6 显示一个batch_size 的图片(8张图片)
    #6.1 读取8张图片
    datas ,targets = next(iter(dataloaders['train'])) #iter把对象变为可迭代对象,next去迭代
    #6.2、将若干正图片平成一副图像
    out = make_grid(datas, norm = 4, padding = 10)
    #6.3显示图片
    img_show(out, title=[target_names[x] for x in targets]) #title拿到类别,也就是标签呢

if __name__ == '__main__':
    main()

上面代码实现的功能就是展示图片样例 (未完待续)

显示数据集中的图片样例:

基于Pytorch肺部感染识别案例(采用ResNet网络结构)

 三、迁移学习,进行模型的微调

迁移学习(Transfer learning) 就是把已经训练好的模型参数迁移到新的模型来帮助新模型训练。

 基于Pytorch肺部感染识别案例(采用ResNet网络结构)

 后面这个代码使用Jupter NoteBook

案例:肺部检测
# 1 加入必要的库
import torch
import torch.nn as nn
import numpy as np
import torch.optim as optim
from torch.optim import lr_scheduler
from torchvision import datasets, transforms, utils, models
import time
import matplotlib.pyplot as plt
from torch.utils.data import DataLoader
from torch.utils.tensorboard.writer import SummaryWriter
import os
import torchvision
import copy
# 2 加载数据集
​
# 2.1 图像变化设置
data_transforms = {
    "train":
        transforms.Compose([
            transforms.RandomResizedCrop(300), 
            transforms.RandomHorizontalFlip(), 
            transforms.CenterCrop(256),
            transforms.ToTensor(),
            transforms.Normalize([0.485, 0.456, 0.406],
                                 [0.229, 0.224, 0.225])
        ]),
    
    "val":
        transforms.Compose([
            transforms.Resize(300),
            transforms.CenterCrop(256),
            transforms.ToTensor(),
            transforms.Normalize([0.485, 0.456, 0.406],
                                 [0.229, 0.224, 0.225])
        ]),
    
    'test':
        transforms.Compose([
        transforms.Resize(size=300),
        transforms.CenterCrop(size=256),
        transforms.ToTensor(),
        transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224,
        0.225])
        ]),
    
}
# 3 可视化图片
def imshow(inp, title=None):
    inp = inp.numpy().transpose((1,2,0))
    mean = np.array([0.485, 0.456, 0.406])
    std = np.array([0.229, 0.224, 0.225])
    inp = std * inp + mean
    inp = np.clip(inp, 0, 1)
    plt.imshow(inp)
    if title is not None:
        plt.title(title)
    plt.pause(0.001)
# 6 可视化模型预测
​
def visualize_model(model, num_images=6):
    """显示预测的图片结果
        Args:
            model: 训练后的模型
            num_images: 需要显示的图片数量
        
        Returns:
            无
    """
    was_training = model.training
    model.eval()
    images_so_far = 0
    fig = plt.figure()
    with torch.no_grad():
        for i, (datas, targets) in enumerate(dataloaders['val']):
            datas, targets = datas.to(device), targets.to(device)
            outputs = model(datas) # 预测数据
            _, preds = torch.max(outputs, 1) # 获取每行数据的最大值
            for j in range(datas.size()[0]):
                images_so_far += 1 # 累计图片数量
                ax = plt.subplot(num_images // 2, 2, images_so_far) # 显示图片
                ax.axis('off') # 关闭坐标轴
                ax.set_title('predicted:{}'.format(class_names[preds[j]]))
                imshow(datas.cpu().data[j])
                if images_so_far == num_images:
                    model.train(mode=was_training)
                    return
        model.train(mode=was_training)
# 7 定义训练函数
def train(model, device, train_loader, criterion, optimizer, epoch, writer):
    # 作用:声明在模型训练时,采用Batch Normalization 和 Dropout
    # Batch Normalization : 对网络中间的每层进行归一化处理,保证每层所提取的特征分布不会被破坏
    # Dropout : 减少过拟合
    model.train()
    total_loss = 0.0 # 总损失初始化为0.0
    # 循环读取训练数据,更新模型参数
    for batch_id, (data, target) in enumerate(train_loader):
        data, target = data.to(device), target.to(device)
        optimizer.zero_grad() # 梯度初始化为零
        output = model(data) # 训练后的输出
        loss = criterion(output, target) # 计算损失
        loss.backward() # 反向传播
        optimizer.step() # 参数更新
        total_loss += loss.item() # 累计损失
    # 写入日志
    writer.add_scalar('Train Loss', total_loss / len(train_loader), epoch)
    writer.flush() # 刷新
    return total_loss / len(train_loader) # 返回平均损失值
# 8 定义测试函数
def test(model, device, test_loader, criterion, epoch, writer):
    # 作用:声明在模型训练时,不采用Batch Normalization 和 Dropout
    model.eval()
    # 损失和正确
    total_loss = 0.0
    correct = 0.0
    # 循环读取数据
    with torch.no_grad():
        for data, target in test_loader:
            data, target = data.to(device), target.to(device)
            # 预测输出
            output = model(data)
            # 计算损失
            total_loss += criterion(output, target).item()
            # 获取预测结果中每行数据概率最大的下标
            _,preds = torch.max(output, dim=1) 
            # pred = output.data.max(1)[1]
            # 累计预测正确的个数
            correct += torch.sum(preds == target.data)
            # correct += pred.eq(target.data).cpu().sum()
            
            ######## 增加 #######
            misclassified_images(preds, writer, target, data, output, epoch) # 记录错误分类的图片
            
        # 总损失
        total_loss /= len(test_loader)
        # 正确率
        accuracy = correct / len(test_loader)
        # 写入日志
        writer.add_scalar('Test Loss', total_loss, epoch)
        writer.add_scalar('Accuracy', accuracy, epoch)
        writer.flush()
        # 输出信息
        print("Test Loss : {:.4f}, Accuracy : {:.4f}".format(total_loss, accuracy))
        return total_loss, accuracy
# 定义函数,获取Tensorboard的writer
def tb_writer():
    timestr = time.strftime("%Y%m%d_%H%M%S")
    writer = SummaryWriter('logdir/' + timestr)
    return writer
​
# 8 模型微调
​
# 定义一个池化层处理函数
class AdaptiveConcatPool2d(nn.Module):
    def __init__(self, size=None):
        super().__init__()
        size = size or (1,1) # 池化层的卷积核大小,默认值为(1,1)
        self.pool_one = nn.AdaptiveAvgPool2d(size) # 池化层1
        self.pool_two = nn.AdaptiveMaxPool2d(size) # 池化层2
    def forward(self, x):
        return torch.cat([self.pool_one(x), self.pool_two(x)], 1) # 连接两个池化层
 
def get_model():
    model_pre = models.resnet50(pretrained=True) # 获取预训练模型
​
    # 冻结预训练模型中所有参数
    for param in model_pre.parameters():
        param.requires_grad = False
​
    # 替换ResNet最后的两层网络,返回一个新的模型(迁移学习)
    model_pre.avgpool = AdaptiveConcatPool2d() # 池化层替换
    model_pre.fc = nn.Sequential(
            nn.Flatten(), # 所有维度拉平
            nn.BatchNorm1d(4096), # 正则化处理
            nn.Dropout(0.5), # 丢掉神经元
            nn.Linear(4096, 512), # 线性层处理
            nn.ReLU(), # 激活函数
            nn.BatchNorm1d(512), # 正则化处理
            nn.Dropout(p=0.5), # 丢掉神经元
            nn.Linear(512, 2), # 线性层
            nn.LogSoftmax(dim=1) # 损失函数
    )
    return model_pre
​
def train_epochs(model, device, dataloaders, criterion, optimizer, num_epochs, writer):
    """
    Returns:
        返回一个训练过后最好的模型
    """
    print("{0:>20} | {1:>20} | {2:>20} | {3:>20} |".format('Epoch', 'Training Loss', 'Test Loss', 'Accuracy'))
    best_score = np.inf # 假设最好的预测值
    start = time.time() # 开始时间
    
    # 开始循环读取数据进行训练和验证
    for epoch in num_epochs:
        
        train_loss = train(model, device, dataloaders['train'], criterion, optimizer, epoch, writer)
        
        test_loss, accuracy = test(model, device, dataloaders['val'], criterion, epoch, writer)
        
        if test_loss < best_score:
            best_score = test_loss
            torch.save(model.state_dict(), model_path) # 保存模型 # state_dict变量存放训练过程中需要学习的权重和偏置系数
        
        print("{0:>20} | {1:>20} | {2:>20} | {3:>20.2f} |".format(epoch, train_loss, test_loss, accuracy))
        
        writer.flush()
        
    # 训练完所耗费的总时间
    time_all = time.time() - start
    # 输出时间信息
    print("Training complete in {:.2f}m {:.2f}s".format(time_all // 60, time_all % 60))
def train_epochs(model, device, dataloaders, criterion, optimizer, num_epochs, writer):
    """
    Returns:
        返回一个训练过后最好的模型
    """
    print("{0:>20} | {1:>20} | {2:>20} | {3:>20} |".format('Epoch', 'Training Loss', 'Test Loss', 'Accuracy'))
    best_score = np.inf # 假设最好的预测值
    start = time.time() # 开始时间
    
    # 开始循环读取数据进行训练和验证
    for epoch in num_epochs:
        
        train_loss = train(model, device, dataloaders['train'], criterion, optimizer, epoch, writer)
        
        test_loss, accuracy = test(model, device, dataloaders['val'], criterion, epoch, writer)
        
        if test_loss < best_score:
            best_score = test_loss
            torch.save(model.state_dict(), model_path) # 保存模型 # state_dict变量存放训练过程中需要学习的权重和偏置系数
        
        print("{0:>20} | {1:>20} | {2:>20} | {3:>20.2f} |".format(epoch, train_loss, test_loss, accuracy))
        
        writer.flush()
        
    # 训练完所耗费的总时间
    time_all = time.time() - start
    # 输出时间信息
    print("Training complete in {:.2f}m {:.2f}s".format(time_all // 60, time_all % 60))
def misclassified_images(pred, writer, target, data, output, epoch, count=10):
    misclassified = (pred != target.data) # 记录预测值与真实值不同的True和False
    for index, image_tensor in enumerate(data[misclassified][:count]):
        # 显示预测不同的前10张图片
        img_name = '{}->Predict-{}x{}-Actual'.format(
                epoch,
                LABEL[pred[misclassified].tolist()[index]],
                LABEL[target.data[misclassified].tolist()[index]],
        )
        writer.add_image(img_name, inv_normalize(image_tensor), epoch)
# 9 训练和验证

# 定义超参数
model_path = 'model.pth'
batch_size = 16
device = torch.device('gpu' if torch.cuda.is_available() else 'cpu') # gpu和cpu选择

# 2.2 加载数据
data_path = "D:/chest_xray/" # 数据集所在的文件夹路径

# 2.2.1 加载数据集
image_datasets = {x : datasets.ImageFolder(os.path.join(data_path, x), data_transforms[x]) for x in ['train', 'val', 'test']}

# 2.2.2 为数据集创建iterator
dataloaders = {x : DataLoader(image_datasets[x], batch_size=batch_size, shuffle=True) for x in ['train', 'val', 'test']}

# 2.2.3 训练集和验证集的大小
data_sizes = {x : len(image_datasets[x]) for x in ['train', 'val', 'test']}

# 2.2.4 训练集所对应的标签
class_names = image_datasets['train'].classes # 一共有2个:NORMAL正常 vs PNEUMONIA肺炎
LABEL = dict((v, k ) for k, v in image_datasets['train'].class_to_idx.items())

print("-" * 50)

# 4 获取trian中的一批数据
datas, targets = next(iter(dataloaders['train']))

# 5 显示这批数据
out = torchvision.utils.make_grid(datas)

imshow(out, title=[class_names[x] for x in targets])

# 将tensor转换为image
inv_normalize = transforms.Normalize(
mean=[-0.485/0.229, -0.456/0.224, -0.406/0.225],
std=[1/0.229, 1/0.224, 1/0.255]
)

writer = tb_writer()
images, labels = next(iter(dataloaders['train'])) # 获取一批数据
grid = torchvision.utils.make_grid([inv_normalize(image) for image in images[:32]]) # 读取32张图片
writer.add_image('X-Ray grid', grid, 0) # 添加到TensorBoard
writer.flush() # 将数据读取到存储器中

model = get_model().to(device) # 获取模型
criterion = nn.NLLLoss() # 损失函数
optimizer = optim.Adam(model.parameters())
train_epochs(model, device, dataloaders, criterion, optimizer, range(0,10), writer)
writer.close() 
# 9 训练和验证
​
# 定义超参数
model_path = 'model.pth'
batch_size = 16
device = torch.device('gpu' if torch.cuda.is_available() else 'cpu') # gpu和cpu选择
​
# 2.2 加载数据
data_path = "D:/chest_xray/" # 数据集所在的文件夹路径
​
# 2.2.1 加载数据集
image_datasets = {x : datasets.ImageFolder(os.path.join(data_path, x), data_transforms[x]) for x in ['train', 'val', 'test']}
​
# 2.2.2 为数据集创建iterator
dataloaders = {x : DataLoader(image_datasets[x], batch_size=batch_size, shuffle=True) for x in ['train', 'val', 'test']}
​
# 2.2.3 训练集和验证集的大小
data_sizes = {x : len(image_datasets[x]) for x in ['train', 'val', 'test']}
​
# 2.2.4 训练集所对应的标签
class_names = image_datasets['train'].classes # 一共有2个:NORMAL正常 vs PNEUMONIA肺炎
LABEL = dict((v, k ) for k, v in image_datasets['train'].class_to_idx.items())
​
print("-" * 50)
​
# 4 获取trian中的一批数据
datas, targets = next(iter(dataloaders['train']))
​
# 5 显示这批数据
out = torchvision.utils.make_grid(datas)
​
imshow(out, title=[class_names[x] for x in targets])
​
# 将tensor转换为image
inv_normalize = transforms.Normalize(
mean=[-0.485/0.229, -0.456/0.224, -0.406/0.225],
std=[1/0.229, 1/0.224, 1/0.255]
)
​
writer = tb_writer()
images, labels = next(iter(dataloaders['train'])) # 获取一批数据
grid = torchvision.utils.make_grid([inv_normalize(image) for image in images[:32]]) # 读取32张图片
writer.add_image('X-Ray grid', grid, 0) # 添加到TensorBoard
writer.flush() # 将数据读取到存储器中
​
model = get_model().to(device) # 获取模型
criterion = nn.NLLLoss() # 损失函数
optimizer = optim.Adam(model.parameters())
train_epochs(model, device, dat

 基于Pytorch肺部感染识别案例(采用ResNet网络结构)

 

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