utils.py

import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.backends.cudnn as cudnn
import torchvision.transforms.functional as TF
import numpy as np
import os
import math
import random
import logging
import logging.handlers
from matplotlib import pyplot as plt
from scipy.ndimage import zoom
import SimpleITK as sitk
from medpy import metric


def set_seed(seed):
    # for hash
    os.environ['PYTHONHASHSEED'] = str(seed)
    # for python and numpy
    random.seed(seed)
    np.random.seed(seed)
    # for cpu gpu
    torch.manual_seed(seed)
    torch.cuda.manual_seed(seed)
    torch.cuda.manual_seed_all(seed)
    # for cudnn
    cudnn.benchmark = False
    cudnn.deterministic = True


def get_logger(name, log_dir):
    '''
    Args:
        name(str): name of logger
        log_dir(str): path of log
    '''

    if not os.path.exists(log_dir):
        os.makedirs(log_dir)

    logger = logging.getLogger(name)
    logger.setLevel(logging.INFO)

    info_name = os.path.join(log_dir, '{}.info.log'.format(name))
    info_handler = logging.handlers.TimedRotatingFileHandler(info_name,
                                                             when='D',
                                                             encoding='utf-8')
    info_handler.setLevel(logging.INFO)

    formatter = logging.Formatter('%(asctime)s - %(message)s',
                                  datefmt='%Y-%m-%d %H:%M:%S')

    info_handler.setFormatter(formatter)

    logger.addHandler(info_handler)

    return logger


def log_config_info(config, logger):
    config_dict = config.__dict__
    log_info = f'#----------Config info----------#'
    logger.info(log_info)
    for k, v in config_dict.items():
        if k[0] == '_':
            continue
        else:
            log_info = f'{k}: {v},'
            logger.info(log_info)



def get_optimizer(config, model):
    assert config.opt in ['Adadelta', 'Adagrad', 'Adam', 'AdamW', 'Adamax', 'ASGD', 'RMSprop', 'Rprop', 'SGD'], 'Unsupported optimizer!'

    if config.opt == 'Adadelta':
        return torch.optim.Adadelta(
            model.parameters(),
            lr = config.lr,
            rho = config.rho,
            eps = config.eps,
            weight_decay = config.weight_decay
        )
    elif config.opt == 'Adagrad':
        return torch.optim.Adagrad(
            model.parameters(),
            lr = config.lr,
            lr_decay = config.lr_decay,
            eps = config.eps,
            weight_decay = config.weight_decay
        )
    elif config.opt == 'Adam':
        return torch.optim.Adam(
            model.parameters(),
            lr = config.lr,
            betas = config.betas,
            eps = config.eps,
            weight_decay = config.weight_decay,
            amsgrad = config.amsgrad
        )
    elif config.opt == 'AdamW':
        return torch.optim.AdamW(
            model.parameters(),
            lr = config.lr,
            betas = config.betas,
            eps = config.eps,
            weight_decay = config.weight_decay,
            amsgrad = config.amsgrad
        )
    elif config.opt == 'Adamax':
        return torch.optim.Adamax(
            model.parameters(),
            lr = config.lr,
            betas = config.betas,
            eps = config.eps,
            weight_decay = config.weight_decay
        )
    elif config.opt == 'ASGD':
        return torch.optim.ASGD(
            model.parameters(),
            lr = config.lr,
            lambd = config.lambd,
            alpha  = config.alpha,
            t0 = config.t0,
            weight_decay = config.weight_decay
        )
    elif config.opt == 'RMSprop':
        return torch.optim.RMSprop(
            model.parameters(),
            lr = config.lr,
            momentum = config.momentum,
            alpha = config.alpha,
            eps = config.eps,
            centered = config.centered,
            weight_decay = config.weight_decay
        )
    elif config.opt == 'Rprop':
        return torch.optim.Rprop(
            model.parameters(),
            lr = config.lr,
            etas = config.etas,
            step_sizes = config.step_sizes,
        )
    elif config.opt == 'SGD':
        return torch.optim.SGD(
            model.parameters(),
            lr = config.lr,
            momentum = config.momentum,
            weight_decay = config.weight_decay,
            dampening = config.dampening,
            nesterov = config.nesterov
        )
    else: # default opt is SGD
        return torch.optim.SGD(
            model.parameters(),
            lr = 0.01,
            momentum = 0.9,
            weight_decay = 0.05,
        )


def get_scheduler(config, optimizer):
    assert config.sch in ['StepLR', 'MultiStepLR', 'ExponentialLR', 'CosineAnnealingLR', 'ReduceLROnPlateau',
                        'CosineAnnealingWarmRestarts', 'WP_MultiStepLR', 'WP_CosineLR'], 'Unsupported scheduler!'
    if config.sch == 'StepLR':
        scheduler = torch.optim.lr_scheduler.StepLR(
            optimizer,
            step_size = config.step_size,
            gamma = config.gamma,
            last_epoch = config.last_epoch
        )
    elif config.sch == 'MultiStepLR':
        scheduler = torch.optim.lr_scheduler.MultiStepLR(
            optimizer,
            milestones = config.milestones,
            gamma = config.gamma,
            last_epoch = config.last_epoch
        )
    elif config.sch == 'ExponentialLR':
        scheduler = torch.optim.lr_scheduler.ExponentialLR(
            optimizer,
            gamma = config.gamma,
            last_epoch = config.last_epoch
        )
    elif config.sch == 'CosineAnnealingLR':
        scheduler = torch.optim.lr_scheduler.CosineAnnealingLR(
            optimizer,
            T_max = config.T_max,
            eta_min = config.eta_min,
            last_epoch = config.last_epoch
        )
    elif config.sch == 'ReduceLROnPlateau':
        scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(
            optimizer, 
            mode = config.mode, 
            factor = config.factor, 
            patience = config.patience, 
            threshold = config.threshold, 
            threshold_mode = config.threshold_mode, 
            cooldown = config.cooldown, 
            min_lr = config.min_lr, 
            eps = config.eps
        )
    elif config.sch == 'CosineAnnealingWarmRestarts':
        scheduler = torch.optim.lr_scheduler.CosineAnnealingWarmRestarts(
            optimizer,
            T_0 = config.T_0,
            T_mult = config.T_mult,
            eta_min = config.eta_min,
            last_epoch = config.last_epoch
        )
    elif config.sch == 'WP_MultiStepLR':
        lr_func = lambda epoch: epoch / config.warm_up_epochs if epoch <= config.warm_up_epochs else config.gamma**len(
                [m for m in config.milestones if m <= epoch])
        scheduler = torch.optim.lr_scheduler.LambdaLR(optimizer, lr_lambda=lr_func)
    elif config.sch == 'WP_CosineLR':
        lr_func = lambda epoch: epoch / config.warm_up_epochs if epoch <= config.warm_up_epochs else 0.5 * (
                math.cos((epoch - config.warm_up_epochs) / (config.epochs - config.warm_up_epochs) * math.pi) + 1)
        scheduler = torch.optim.lr_scheduler.LambdaLR(optimizer, lr_lambda=lr_func)

    return scheduler



def save_imgs(img, msk, msk_pred, i, save_path, datasets, threshold=0.5, test_data_name=None):
    img = img.squeeze(0).permute(1,2,0).detach().cpu().numpy()
    img = img / 255. if img.max() > 1.1 else img
    if datasets == 'retinal':
        msk = np.squeeze(msk, axis=0)
        msk_pred = np.squeeze(msk_pred, axis=0)
    else:
        msk = np.where(np.squeeze(msk, axis=0) > 0.5, 1, 0)
        msk_pred = np.where(np.squeeze(msk_pred, axis=0) > threshold, 1, 0) 

    plt.figure(figsize=(7,15))

    plt.subplot(3,1,1)
    plt.imshow(img)
    plt.axis('off')

    plt.subplot(3,1,2)
    plt.imshow(msk, cmap= 'gray')
    plt.axis('off')

    plt.subplot(3,1,3)
    plt.imshow(msk_pred, cmap = 'gray')
    plt.axis('off')

    if test_data_name is not None:
        save_path = save_path + test_data_name + '_'
    plt.savefig(save_path + str(i) +'.png')
    plt.close()
    


class BCELoss(nn.Module):
    def __init__(self):
        super(BCELoss, self).__init__()
        self.bceloss = nn.BCELoss()

    def forward(self, pred, target):
        size = pred.size(0)
        pred_ = pred.view(size, -1)
        target_ = target.view(size, -1)

        return self.bceloss(pred_, target_)


class DiceLoss(nn.Module):
    def __init__(self):
        super(DiceLoss, self).__init__()

    def forward(self, pred, target):
        smooth = 1
        size = pred.size(0)

        pred_ = pred.view(size, -1)
        target_ = target.view(size, -1)
        intersection = pred_ * target_
        dice_score = (2 * intersection.sum(1) + smooth)/(pred_.sum(1) + target_.sum(1) + smooth)
        dice_loss = 1 - dice_score.sum()/size

        return dice_loss
    

class nDiceLoss(nn.Module):
    def __init__(self, n_classes):
        super(nDiceLoss, self).__init__()
        self.n_classes = n_classes

    def _one_hot_encoder(self, input_tensor):
        tensor_list = []
        for i in range(self.n_classes):
            temp_prob = input_tensor == i  # * torch.ones_like(input_tensor)
            tensor_list.append(temp_prob.unsqueeze(1))
        output_tensor = torch.cat(tensor_list, dim=1)
        return output_tensor.float()

    def _dice_loss(self, score, target):
        target = target.float()
        smooth = 1e-5
        intersect = torch.sum(score * target)
        y_sum = torch.sum(target * target)
        z_sum = torch.sum(score * score)
        loss = (2 * intersect + smooth) / (z_sum + y_sum + smooth)
        loss = 1 - loss
        return loss

    def forward(self, inputs, target, weight=None, softmax=False):
        if softmax:
            inputs = torch.softmax(inputs, dim=1)
        target = self._one_hot_encoder(target)
        if weight is None:
            weight = [1] * self.n_classes
        assert inputs.size() == target.size(), 'predict {} & target {} shape do not match'.format(inputs.size(), target.size())
        class_wise_dice = []
        loss = 0.0
        for i in range(0, self.n_classes):
            dice = self._dice_loss(inputs[:, i], target[:, i])
            class_wise_dice.append(1.0 - dice.item())
            loss += dice * weight[i]
        return loss / self.n_classes


class CeDiceLoss(nn.Module):
    def __init__(self, num_classes, loss_weight=[0.4, 0.6]):
        super(CeDiceLoss, self).__init__()
        self.celoss = nn.CrossEntropyLoss()
        self.diceloss = nDiceLoss(num_classes)
        self.loss_weight = loss_weight
    
    def forward(self, pred, target):
        loss_ce = self.celoss(pred, target[:].long())
        loss_dice = self.diceloss(pred, target, softmax=True)
        loss = self.loss_weight[0] * loss_ce + self.loss_weight[1] * loss_dice
        return loss


class BceDiceLoss(nn.Module):
    def __init__(self, wb=1, wd=1):
        super(BceDiceLoss, self).__init__()
        self.bce = BCELoss()
        self.dice = DiceLoss()
        self.wb = wb
        self.wd = wd

    def forward(self, pred, target):
        bceloss = self.bce(pred, target)
        diceloss = self.dice(pred, target)

        loss = self.wd * diceloss + self.wb * bceloss
        return loss
    

class GT_BceDiceLoss(nn.Module):
    def __init__(self, wb=1, wd=1):
        super(GT_BceDiceLoss, self).__init__()
        self.bcedice = BceDiceLoss(wb, wd)

    def forward(self, gt_pre, out, target):
        bcediceloss = self.bcedice(out, target)
        gt_pre5, gt_pre4, gt_pre3, gt_pre2, gt_pre1 = gt_pre
        gt_loss = self.bcedice(gt_pre5, target) * 0.1 + self.bcedice(gt_pre4, target) * 0.2 + self.bcedice(gt_pre3, target) * 0.3 + self.bcedice(gt_pre2, target) * 0.4 + self.bcedice(gt_pre1, target) * 0.5
        return bcediceloss + gt_loss



class myToTensor:
    def __init__(self):
        pass
    def __call__(self, data):
        image, mask = data
        return torch.tensor(image).permute(2,0,1), torch.tensor(mask).permute(2,0,1)
       

class myResize:
    def __init__(self, size_h=256, size_w=256):
        self.size_h = size_h
        self.size_w = size_w
    def __call__(self, data):
        image, mask = data
        return TF.resize(image, [self.size_h, self.size_w]), TF.resize(mask, [self.size_h, self.size_w])
       

class myRandomHorizontalFlip:
    def __init__(self, p=0.5):
        self.p = p
    def __call__(self, data):
        image, mask = data
        if random.random() < self.p: return TF.hflip(image), TF.hflip(mask)
        else: return image, mask
            

class myRandomVerticalFlip:
    def __init__(self, p=0.5):
        self.p = p
    def __call__(self, data):
        image, mask = data
        if random.random() < self.p: return TF.vflip(image), TF.vflip(mask)
        else: return image, mask


class myRandomRotation:
    def __init__(self, p=0.5, degree=[0,360]):
        self.angle = random.uniform(degree[0], degree[1])
        self.p = p
    def __call__(self, data):
        image, mask = data
        if random.random() < self.p: return TF.rotate(image,self.angle), TF.rotate(mask,self.angle)
        else: return image, mask 


class myNormalize:
    def __init__(self, data_name, train=True):
        if data_name == 'isic18':
            if train:
                self.mean = 157.561
                self.std = 26.706
            else:
                self.mean = 149.034
                self.std = 32.022
        elif data_name == 'isic17':
            if train:
                self.mean = 159.922
                self.std = 28.871
            else:
                self.mean = 148.429
                self.std = 25.748
        elif data_name == 'isic18_82':
            if train:
                self.mean = 156.2899
                self.std = 26.5457
            else:
                self.mean = 149.8485
                self.std = 35.3346
            
    def __call__(self, data):
        img, msk = data
        img_normalized = (img-self.mean)/self.std
        img_normalized = ((img_normalized - np.min(img_normalized)) 
                            / (np.max(img_normalized)-np.min(img_normalized))) * 255.
        return img_normalized, msk
    


from thop import profile		 ## 导入thop模块
def cal_params_flops(model, size, logger):
    input = torch.randn(1, 3, size, size).cuda()
    flops, params = profile(model, inputs=(input,))
    print('flops',flops/1e9)			## 打印计算量
    print('params',params/1e6)			## 打印参数量

    total = sum(p.numel() for p in model.parameters())
    print("Total params: %.2fM" % (total/1e6))
    logger.info(f'flops: {flops/1e9}, params: {params/1e6}, Total params: : {total/1e6:.4f}')






def calculate_metric_percase(pred, gt):
    pred[pred > 0] = 1
    gt[gt > 0] = 1
    if pred.sum() > 0 and gt.sum()>0:
        dice = metric.binary.dc(pred, gt)
        hd95 = metric.binary.hd95(pred, gt)
        return dice, hd95
    elif pred.sum() > 0 and gt.sum()==0:
        return 1, 0
    else:
        return 0, 0



def test_single_volume(image, label, net, classes, patch_size=[256, 256], 
                    test_save_path=None, case=None, z_spacing=1, val_or_test=False):
    image, label = image.squeeze(0).cpu().detach().numpy(), label.squeeze(0).cpu().detach().numpy()
    if len(image.shape) == 3:
        prediction = np.zeros_like(label)
        for ind in range(image.shape[0]):
            slice = image[ind, :, :]
            x, y = slice.shape[0], slice.shape[1]
            if x != patch_size[0] or y != patch_size[1]:
                slice = zoom(slice, (patch_size[0] / x, patch_size[1] / y), order=3)  # previous using 0
            input = torch.from_numpy(slice).unsqueeze(0).unsqueeze(0).float().cuda()
            net.eval()
            with torch.no_grad():
                outputs = net(input)
                out = torch.argmax(torch.softmax(outputs, dim=1), dim=1).squeeze(0)
                out = out.cpu().detach().numpy()
                if x != patch_size[0] or y != patch_size[1]:
                    pred = zoom(out, (x / patch_size[0], y / patch_size[1]), order=0)
                else:
                    pred = out
                prediction[ind] = pred
    else:
        input = torch.from_numpy(image).unsqueeze(
            0).unsqueeze(0).float().cuda()
        net.eval()
        with torch.no_grad():
            out = torch.argmax(torch.softmax(net(input), dim=1), dim=1).squeeze(0)
            prediction = out.cpu().detach().numpy()
    metric_list = []
    for i in range(1, classes):
        metric_list.append(calculate_metric_percase(prediction == i, label == i))

    if test_save_path is not None and val_or_test is True:
        img_itk = sitk.GetImageFromArray(image.astype(np.float32))
        prd_itk = sitk.GetImageFromArray(prediction.astype(np.float32))
        lab_itk = sitk.GetImageFromArray(label.astype(np.float32))
        img_itk.SetSpacing((1, 1, z_spacing))
        prd_itk.SetSpacing((1, 1, z_spacing))
        lab_itk.SetSpacing((1, 1, z_spacing))
        sitk.WriteImage(prd_itk, test_save_path + '/'+case + "_pred.nii.gz")
        sitk.WriteImage(img_itk, test_save_path + '/'+ case + "_img.nii.gz")
        sitk.WriteImage(lab_itk, test_save_path + '/'+ case + "_gt.nii.gz")
        # cv2.imwrite(test_save_path + '/'+case + '.png', prediction*255)
    return metric_list