今天实现了一个基于NestedUNet++的医学图像分割系统

import os
from glob import glob

import cv2
import numpy as np
from tqdm import tqdm


def main():
    img_size = 96

    paths = glob('D:\\pythonProject\\unet++\\unet++\\inputs\\*')
    paths = [p for p in paths if os.path.isdir(p) and not p.endswith(('.csv', 'dsb2018_96'))]
    paths = [os.path.join(p, sub) for p in paths if os.path.basename(p) == 'stage1_train' for sub in os.listdir(p) if
            os.path.isdir(os.path.join(p, sub))]

    output_base = 'D:\\pythonProject\\unet++\\unet++\\inputs\\dsb2018_96'
    os.makedirs(f"{output_base}\\images", exist_ok=True)
    os.makedirs(f"{output_base}\\masks\\0", exist_ok=True)

    if not paths:
        return

    for i in tqdm(range(len(paths))):
        path = paths[i]
        img_name = f"{os.path.basename(path)}.png"
        img_path = os.path.join(path, 'images', img_name)
        img = cv2.imread(img_path)

        if img is None:
            continue

        mask = np.zeros((img.shape[0], img.shape[1]))
        for mask_path in glob(os.path.join(path, 'masks', '*')):
            mask_gray = cv2.imread(mask_path, cv2.IMREAD_GRAYSCALE)
            if mask_gray is not None:
                mask[mask_gray > 127] = 1
        if len(img.shape) == 2:
            img = np.tile(img[..., None], (1, 1, 3))
        if img.shape[2] == 4:
            img = img[..., :3]
        img = cv2.resize(img, (img_size, img_size))
        mask = cv2.resize(mask, (img_size, img_size))
        cv2.imwrite(os.path.join(f"{output_base}/images", img_name), img)
        cv2.imwrite(os.path.join(f"{output_base}/masks/0", img_name), (mask * 255).astype('uint8'))


if __name__ == '__main__':
    main()

import albumentations as albu
import argparse
import os
from glob import glob
import matplotlib.pyplot as plt
import numpy as np
import cv2
import torch
import torch.backends.cudnn as cudnn
import yaml
from albumentations.augmentations import transforms
from albumentations.core.composition import Compose
from sklearn.model_selection import train_test_split
from tqdm import tqdm

import archs
from dataset import Dataset
from metrics import iou_score
from utils import AverageMeter
"""
需要指定参数：--name dsb2018_96_NestedUNet_woDS
"""

def parse_args():
    parser = argparse.ArgumentParser()

    parser.add_argument('--name', default="dsb2018_96_NestedUNet_woDS",
                        help='model name')

    args = parser.parse_args()

    return args


def main():
    args = parse_args()

    with open('models/%s/config.yml' %args.name, 'r') as f:
    # with open('models/dsb2018_96_NestedUNet_woDS/config.yml', 'r') as f:
        config = yaml.load(f, Loader=yaml.FullLoader)

    print('-'*20)
    for key in config.keys():
        print('%s: %s' % (key, str(config[key])))
    print('-'*20)

    cudnn.benchmark = True

    # create model
    print("=> creating model %s" % config['arch'])
    model = archs.__dict__[config['arch']](config['num_classes'],
                                           config['input_channels'],
                                           config['deep_supervision'])

    model = model.cuda()

    # Data loading code
    img_ids = glob(os.path.join('inputs', config['dataset'], 'images', '*' + config['img_ext']))
    img_ids = [os.path.splitext(os.path.basename(p))[0] for p in img_ids]

    _, val_img_ids = train_test_split(img_ids, test_size=0.2, random_state=41)

    model.load_state_dict(torch.load('models/%s/model.pth' %
                                     config['name']))
    model.eval()

    val_transform = Compose([
        albu.Resize(config['input_h'], config['input_w']),
        transforms.Normalize(),
    ])

    val_dataset = Dataset(
        img_ids=val_img_ids,
        img_dir=os.path.join('inputs', config['dataset'], 'images'),
        mask_dir=os.path.join('inputs', config['dataset'], 'masks'),
        img_ext=config['img_ext'],
        mask_ext=config['mask_ext'],
        num_classes=config['num_classes'],
        transform=val_transform)
    val_loader = torch.utils.data.DataLoader(
        val_dataset,
        batch_size=config['batch_size'],
        shuffle=False,
        num_workers=config['num_workers'],
        drop_last=False)

    avg_meter = AverageMeter()

    for c in range(config['num_classes']):
        os.makedirs(os.path.join('outputs', config['name'], str(c)), exist_ok=True)
    with torch.no_grad():
        for input, target, meta in tqdm(val_loader, total=len(val_loader)):
            input = input.cuda()
            target = target.cuda()

            # compute output
            if config['deep_supervision']:
                output = model(input)[-1]
            else:
                output = model(input)

            iou = iou_score(output, target)
            avg_meter.update(iou, input.size(0))

            output = torch.sigmoid(output).cpu().numpy()

            for i in range(len(output)):
                for c in range(config['num_classes']):
                    cv2.imwrite(os.path.join('outputs', config['name'], str(c), meta['img_id'][i] + '.jpg'),
                                (output[i, c] * 255).astype('uint8'))

    print('IoU: %.4f' % avg_meter.avg)
    
    plot_examples(input, target, model,num_examples=3)
    
    torch.cuda.empty_cache()

def plot_examples(datax, datay, model,num_examples=6):
    fig, ax = plt.subplots(nrows=num_examples, ncols=3, figsize=(18,4*num_examples))
    m = datax.shape[0]
    for row_num in range(num_examples):
        image_indx = np.random.randint(m)
        image_arr = model(datax[image_indx:image_indx+1]).squeeze(0).detach().cpu().numpy()
        ax[row_num][0].imshow(np.transpose(datax[image_indx].cpu().numpy(), (1,2,0))[:,:,0])
        ax[row_num][0].set_title("Orignal Image")
        ax[row_num][1].imshow(np.squeeze((image_arr > 0.40)[0,:,:].astype(int)))
        ax[row_num][1].set_title("Segmented Image localization")
        ax[row_num][2].imshow(np.transpose(datay[image_indx].cpu().numpy(), (1,2,0))[:,:,0])
        ax[row_num][2].set_title("Target image")
    plt.show()


if __name__ == '__main__':
    main()

import albumentations as albu

import argparse
import os
from collections import OrderedDict
from glob import glob

import pandas as pd
import torch
import torch.backends.cudnn as cudnn
import torch.nn as nn
import torch.optim as optim
import yaml
from albumentations.core.composition import Compose, OneOf
from sklearn.model_selection import train_test_split
from torch.optim import lr_scheduler
from tqdm import tqdm

import archs
import losses
from dataset import Dataset
from metrics import iou_score
from utils import AverageMeter, str2bool

ARCH_NAMES = archs.__all__
LOSS_NAMES = losses.__all__
LOSS_NAMES.append('BCEWithLogitsLoss')

"""
指定参数：
--dataset dsb2018_96 
--arch NestedUNet
"""


def parse_args():
    parser = argparse.ArgumentParser()

    parser.add_argument('--name', default="dsb2018_96_NestedUNet_woDS",
                        help='model name: (default: arch+timestamp)')
    parser.add_argument('--epochs', default=100, type=int, metavar='N',
                        help='number of total epochs to run')
    parser.add_argument('-b', '--batch_size', default=8, type=int,
                        metavar='N', help='mini-batch size (default: 16)')

    # model
    parser.add_argument('--arch', '-a', metavar='ARCH', default='NestedUNet',
                        choices=ARCH_NAMES,
                        help='model architecture: ' +
                             ' | '.join(ARCH_NAMES) +
                             ' (default: NestedUNet)')
    parser.add_argument('--deep_supervision', default=False, type=str2bool)
    parser.add_argument('--input_channels', default=3, type=int,
                        help='input channels')
    parser.add_argument('--num_classes', default=1, type=int,
                        help='number of classes')
    parser.add_argument('--input_w', default=96, type=int,
                        help='image width')
    parser.add_argument('--input_h', default=96, type=int,
                        help='image height')

    # loss
    parser.add_argument('--loss', default='BCEDiceLoss',
                        choices=LOSS_NAMES,
                        help='loss: ' +
                             ' | '.join(LOSS_NAMES) +
                             ' (default: BCEDiceLoss)')

    # dataset
    parser.add_argument('--dataset', default='dsb2018_96',
                        help='dataset name')
    parser.add_argument('--img_ext', default='.png',
                        help='image file extension')
    parser.add_argument('--mask_ext', default='.png',
                        help='mask file extension')

    # optimizer
    parser.add_argument('--optimizer', default='SGD',
                        choices=['Adam', 'SGD'],
                        help='loss: ' +
                             ' | '.join(['Adam', 'SGD']) +
                             ' (default: Adam)')
    parser.add_argument('--lr', '--learning_rate', default=1e-3, type=float,
                        metavar='LR', help='initial learning rate')
    parser.add_argument('--momentum', default=0.9, type=float,
                        help='momentum')
    parser.add_argument('--weight_decay', default=1e-4, type=float,
                        help='weight decay')
    parser.add_argument('--nesterov', default=False, type=str2bool,
                        help='nesterov')

    # scheduler
    parser.add_argument('--scheduler', default='CosineAnnealingLR',
                        choices=['CosineAnnealingLR', 'ReduceLROnPlateau', 'MultiStepLR', 'ConstantLR'])
    parser.add_argument('--min_lr', default=1e-5, type=float,
                        help='minimum learning rate')
    parser.add_argument('--factor', default=0.1, type=float)
    parser.add_argument('--patience', default=2, type=int)
    parser.add_argument('--milestones', default='1,2', type=str)
    parser.add_argument('--gamma', default=2 / 3, type=float)
    parser.add_argument('--early_stopping', default=-1, type=int,
                        metavar='N', help='early stopping (default: -1)')

    parser.add_argument('--num_workers', default=0, type=int)

    config = parser.parse_args()

    return config


def train(config, train_loader, model, criterion, optimizer):
    avg_meters = {'loss': AverageMeter(),
                  'iou': AverageMeter()}

    model.train()

    pbar = tqdm(total=len(train_loader))
    for input, target, _ in train_loader:
        input = input.to(device)
        target = target.to(device)

        # compute output
        if config['deep_supervision']:
            outputs = model(input)
            loss = 0
            for output in outputs:
                loss += criterion(output, target)
            loss /= len(outputs)
            iou = iou_score(outputs[-1], target)
        else:
            output = model(input)
            loss = criterion(output, target)
            iou = iou_score(output, target)

        # compute gradient and do optimizing step
        optimizer.zero_grad()
        loss.backward()
        optimizer.step()

        avg_meters['loss'].update(loss.item(), input.size(0))
        avg_meters['iou'].update(iou, input.size(0))

        postfix = OrderedDict([
            ('loss', avg_meters['loss'].avg),
            ('iou', avg_meters['iou'].avg),
        ])
        pbar.set_postfix(postfix)
        pbar.update(1)
    pbar.close()

    return OrderedDict([('loss', avg_meters['loss'].avg),
                        ('iou', avg_meters['iou'].avg)])


def validate(config, val_loader, model, criterion):
    avg_meters = {'loss': AverageMeter(),
                  'iou': AverageMeter()}

    model.eval()

    with torch.no_grad():
        pbar = tqdm(total=len(val_loader))
        for input, target, _ in val_loader:
            input = input.to(device)
            target = target.to(device)

            # compute output
            if config['deep_supervision']:
                outputs = model(input)
                loss = 0
                for output in outputs:
                    loss += criterion(output, target)
                loss /= len(outputs)
                iou = iou_score(outputs[-1], target)
            else:
                output = model(input)
                loss = criterion(output, target)
                iou = iou_score(output, target)

            avg_meters['loss'].update(loss.item(), input.size(0))
            avg_meters['iou'].update(iou, input.size(0))

            postfix = OrderedDict([
                ('loss', avg_meters['loss'].avg),
                ('iou', avg_meters['iou'].avg),
            ])
            pbar.set_postfix(postfix)
            pbar.update(1)
        pbar.close()

    return OrderedDict([('loss', avg_meters['loss'].avg),
                        ('iou', avg_meters['iou'].avg)])


def main():
    global device
    device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
    print(f'Using device: {device}')

    config = vars(parse_args())

    if config['name'] is None:
        if config['deep_supervision']:
            config['name'] = '%s_%s_wDS' % (config['dataset'], config['arch'])
        else:
            config['name'] = '%s_%s_woDS' % (config['dataset'], config['arch'])
    os.makedirs('models/%s' % config['name'], exist_ok=True)

    print('-' * 20)
    for key in config:
        print('%s: %s' % (key, config[key]))
    print('-' * 20)

    with open('models/%s/config.yml' % config['name'], 'w') as f:
        yaml.dump(config, f)

    # define loss function (criterion)
    if config['loss'] == 'BCEWithLogitsLoss':
        criterion = nn.BCEWithLogitsLoss().to(device)
    else:
        criterion = losses.__dict__[config['loss']]().to(device)

    cudnn.benchmark = True

    # create model
    print("=> creating model %s" % config['arch'])
    model = archs.__dict__[config['arch']](config['num_classes'],
                                           config['input_channels'],
                                           config['deep_supervision'])

    model = model.to(device)

    params = filter(lambda p: p.requires_grad, model.parameters())
    if config['optimizer'] == 'Adam':
        optimizer = optim.Adam(
            params, lr=config['lr'], weight_decay=config['weight_decay'])
    elif config['optimizer'] == 'SGD':
        optimizer = optim.SGD(params, lr=config['lr'], momentum=config['momentum'],
                              nesterov=config['nesterov'], weight_decay=config['weight_decay'])
    else:
        raise NotImplementedError

    if config['scheduler'] == 'CosineAnnealingLR':
        scheduler = lr_scheduler.CosineAnnealingLR(
            optimizer, T_max=config['epochs'], eta_min=config['min_lr'])
    elif config['scheduler'] == 'ReduceLROnPlateau':
        scheduler = lr_scheduler.ReduceLROnPlateau(optimizer, factor=config['factor'], patience=config['patience'],
                                                   verbose=1, min_lr=config['min_lr'])
    elif config['scheduler'] == 'MultiStepLR':
        scheduler = lr_scheduler.MultiStepLR(optimizer, milestones=[int(e) for e in config['milestones'].split(',')],
                                             gamma=config['gamma'])
    elif config['scheduler'] == 'ConstantLR':
        scheduler = None
    else:
        raise NotImplementedError

    # Data loading code
    img_ids = glob(os.path.join('inputs', config['dataset'], 'images', '*' + config['img_ext']))
    img_ids = [os.path.splitext(os.path.basename(p))[0] for p in img_ids]

    train_img_ids, val_img_ids = train_test_split(img_ids, test_size=0.2, random_state=41)
    # 数据增强：替换 RandomBrightness 为 RandomBrightnessContrast
    train_transform = Compose([
        albu.RandomRotate90(),
        albu.HorizontalFlip(p=0.5),
        OneOf([
            albu.HueSaturationValue(),  # 色调、饱和度、明度调整
            albu.RandomBrightnessContrast(),  # 亮度和对比度调整（替代原RandomBrightness）
            albu.RandomGamma(),  # 伽马校正（补充一个亮度相关的增强）
        ], p=1),
        albu.Resize(config['input_h'], config['input_w']),
        albu.Normalize(),
    ])

    val_transform = Compose([
        albu.Resize(config['input_h'], config['input_w']),
        albu.Normalize(),
    ])

    train_dataset = Dataset(
        img_ids=train_img_ids,
        img_dir=os.path.join('inputs', config['dataset'], 'images'),
        mask_dir=os.path.join('inputs', config['dataset'], 'masks'),
        img_ext=config['img_ext'],
        mask_ext=config['mask_ext'],
        num_classes=config['num_classes'],
        transform=train_transform)
    val_dataset = Dataset(
        img_ids=val_img_ids,
        img_dir=os.path.join('inputs', config['dataset'], 'images'),
        mask_dir=os.path.join('inputs', config['dataset'], 'masks'),
        img_ext=config['img_ext'],
        mask_ext=config['mask_ext'],
        num_classes=config['num_classes'],
        transform=val_transform)

    train_loader = torch.utils.data.DataLoader(
        train_dataset,
        batch_size=config['batch_size'],
        shuffle=True,
        num_workers=config['num_workers'],
        drop_last=True)
    val_loader = torch.utils.data.DataLoader(
        val_dataset,
        batch_size=config['batch_size'],
        shuffle=False,
        num_workers=config['num_workers'],
        drop_last=False)

    log = OrderedDict([
        ('epoch', []),
        ('lr', []),
        ('loss', []),
        ('iou', []),
        ('val_loss', []),
        ('val_iou', []),
    ])

    best_iou = 0
    trigger = 0
    for epoch in range(config['epochs']):
        print('Epoch [%d/%d]' % (epoch, config['epochs']))

        # train for one epoch
        train_log = train(config, train_loader, model, criterion, optimizer)
        # evaluate on validation set
        val_log = validate(config, val_loader, model, criterion)

        if config['scheduler'] == 'CosineAnnealingLR':
            scheduler.step()
        elif config['scheduler'] == 'ReduceLROnPlateau':
            scheduler.step(val_log['loss'])

        # 修复：num_epochs→config['epochs']，val_log['val_iou']→val_log['iou']
        print('epoch [{}/{}], train loss: {:.4f}, train iou: {:.4f}, val loss: {:.4f}, val iou: {:.4f}'.format(
            epoch + 1, config['epochs'], train_log['loss'], train_log['iou'], val_log['loss'], val_log['iou']))

        log['epoch'].append(epoch)
        log['lr'].append(config['lr'])
        log['loss'].append(train_log['loss'])
        log['iou'].append(train_log['iou'])
        log['val_loss'].append(val_log['loss'])
        # 修复：val_log['val_iou']→val_log['iou']
        log['val_iou'].append(val_log['iou'])

        pd.DataFrame(log).to_csv('models/%s/log.csv' %
                                 config['name'], index=False)

        trigger += 1

        if val_log['iou'] > best_iou:
            torch.save(model.state_dict(), 'models/%s/model.pth' %
                       config['name'])
            best_iou = val_log['iou']
            print("=> saved best model")
            trigger = 0

        # early stopping
        if config['early_stopping'] >= 0 and trigger >= config['early_stopping']:
            print("=> early stopping")
            break

        torch.cuda.empty_cache()


if __name__ == '__main__':
    main()

import os

import cv2
import numpy as np
import torch
import torch.utils.data


class Dataset(torch.utils.data.Dataset):
    def __init__(self, img_ids, img_dir, mask_dir, img_ext, mask_ext, num_classes, transform=None):
        """
        Args:
            img_ids (list): Image ids.
            img_dir: Image file directory.
            mask_dir: Mask file directory.
            img_ext (str): Image file extension.
            mask_ext (str): Mask file extension.
            num_classes (int): Number of classes.
            transform (Compose, optional): Compose transforms of albumentations. Defaults to None.
        
        Note:
            Make sure to put the files as the following structure:
            <dataset name>
            ├── images
            |   ├── 0a7e06.jpg
            │   ├── 0aab0a.jpg
            │   ├── 0b1761.jpg
            │   ├── ...
            |
            └── masks
                ├── 0
                |   ├── 0a7e06.png
                |   ├── 0aab0a.png
                |   ├── 0b1761.png
                |   ├── ...
                |
                ├── 1
                |   ├── 0a7e06.png
                |   ├── 0aab0a.png
                |   ├── 0b1761.png
                |   ├── ...
                ...
        """
        self.img_ids = img_ids
        self.img_dir = img_dir
        self.mask_dir = mask_dir
        self.img_ext = img_ext
        self.mask_ext = mask_ext
        self.num_classes = num_classes
        self.transform = transform

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

    def __getitem__(self, idx):
        img_id = self.img_ids[idx]
        
        img = cv2.imread(os.path.join(self.img_dir, img_id + self.img_ext))

        mask = []
        for i in range(self.num_classes):
            mask.append(cv2.imread(os.path.join(self.mask_dir, str(i),
                        img_id + self.mask_ext), cv2.IMREAD_GRAYSCALE)[..., None])
        mask = np.dstack(mask)

        if self.transform is not None:
            augmented = self.transform(image=img, mask=mask)#这个包比较方便，能把mask也一并做掉
            img = augmented['image']#参考https://github.com/albumentations-team/albumentations
            mask = augmented['mask']
        
        img = img.astype('float32') / 255
        img = img.transpose(2, 0, 1)
        mask = mask.astype('float32') / 255
        mask = mask.transpose(2, 0, 1)
        
        return img, mask, {'img_id': img_id}

import torch
from torch import nn

__all__ = ['UNet', 'NestedUNet']


class VGGBlock(nn.Module):
    def __init__(self, in_channels, middle_channels, out_channels):
        super().__init__()
        self.relu = nn.ReLU(inplace=True)
        self.conv1 = nn.Conv2d(in_channels, middle_channels, 3, padding=1)
        self.bn1 = nn.BatchNorm2d(middle_channels)
        self.conv2 = nn.Conv2d(middle_channels, out_channels, 3, padding=1)
        self.bn2 = nn.BatchNorm2d(out_channels)

    def forward(self, x):
        out = self.conv1(x)
        out = self.bn1(out)
        out = self.relu(out)

        out = self.conv2(out)
        out = self.bn2(out)
        out = self.relu(out)

        return out


class UNet(nn.Module):
    def __init__(self, num_classes, input_channels=3, **kwargs):
        super().__init__()

        nb_filter = [32, 64, 128, 256, 512]

        self.pool = nn.MaxPool2d(2, 2)
        self.up = nn.Upsample(scale_factor=2, mode='bilinear', align_corners=True)#scale_factor:放大的倍数  插值

        self.conv0_0 = VGGBlock(input_channels, nb_filter[0], nb_filter[0])
        self.conv1_0 = VGGBlock(nb_filter[0], nb_filter[1], nb_filter[1])
        self.conv2_0 = VGGBlock(nb_filter[1], nb_filter[2], nb_filter[2])
        self.conv3_0 = VGGBlock(nb_filter[2], nb_filter[3], nb_filter[3])
        self.conv4_0 = VGGBlock(nb_filter[3], nb_filter[4], nb_filter[4])

        self.conv3_1 = VGGBlock(nb_filter[3]+nb_filter[4], nb_filter[3], nb_filter[3])
        self.conv2_2 = VGGBlock(nb_filter[2]+nb_filter[3], nb_filter[2], nb_filter[2])
        self.conv1_3 = VGGBlock(nb_filter[1]+nb_filter[2], nb_filter[1], nb_filter[1])
        self.conv0_4 = VGGBlock(nb_filter[0]+nb_filter[1], nb_filter[0], nb_filter[0])

        self.final = nn.Conv2d(nb_filter[0], num_classes, kernel_size=1)


    def forward(self, input):
        x0_0 = self.conv0_0(input)
        x1_0 = self.conv1_0(self.pool(x0_0))
        x2_0 = self.conv2_0(self.pool(x1_0))
        x3_0 = self.conv3_0(self.pool(x2_0))
        x4_0 = self.conv4_0(self.pool(x3_0))

        x3_1 = self.conv3_1(torch.cat([x3_0, self.up(x4_0)], 1))
        x2_2 = self.conv2_2(torch.cat([x2_0, self.up(x3_1)], 1))
        x1_3 = self.conv1_3(torch.cat([x1_0, self.up(x2_2)], 1))
        x0_4 = self.conv0_4(torch.cat([x0_0, self.up(x1_3)], 1))

        output = self.final(x0_4)
        return output


class NestedUNet(nn.Module):
    def __init__(self, num_classes, input_channels=3, deep_supervision=False, **kwargs):
        super().__init__()

        nb_filter = [32, 64, 128, 256, 512]

        self.deep_supervision = deep_supervision

        self.pool = nn.MaxPool2d(2, 2)
        self.up = nn.Upsample(scale_factor=2, mode='bilinear', align_corners=True)

        self.conv0_0 = VGGBlock(input_channels, nb_filter[0], nb_filter[0])
        self.conv1_0 = VGGBlock(nb_filter[0], nb_filter[1], nb_filter[1])
        self.conv2_0 = VGGBlock(nb_filter[1], nb_filter[2], nb_filter[2])
        self.conv3_0 = VGGBlock(nb_filter[2], nb_filter[3], nb_filter[3])
        self.conv4_0 = VGGBlock(nb_filter[3], nb_filter[4], nb_filter[4])

        self.conv0_1 = VGGBlock(nb_filter[0]+nb_filter[1], nb_filter[0], nb_filter[0])
        self.conv1_1 = VGGBlock(nb_filter[1]+nb_filter[2], nb_filter[1], nb_filter[1])
        self.conv2_1 = VGGBlock(nb_filter[2]+nb_filter[3], nb_filter[2], nb_filter[2])
        self.conv3_1 = VGGBlock(nb_filter[3]+nb_filter[4], nb_filter[3], nb_filter[3])

        self.conv0_2 = VGGBlock(nb_filter[0]*2+nb_filter[1], nb_filter[0], nb_filter[0])
        self.conv1_2 = VGGBlock(nb_filter[1]*2+nb_filter[2], nb_filter[1], nb_filter[1])
        self.conv2_2 = VGGBlock(nb_filter[2]*2+nb_filter[3], nb_filter[2], nb_filter[2])

        self.conv0_3 = VGGBlock(nb_filter[0]*3+nb_filter[1], nb_filter[0], nb_filter[0])
        self.conv1_3 = VGGBlock(nb_filter[1]*3+nb_filter[2], nb_filter[1], nb_filter[1])

        self.conv0_4 = VGGBlock(nb_filter[0]*4+nb_filter[1], nb_filter[0], nb_filter[0])

        if self.deep_supervision:
            self.final1 = nn.Conv2d(nb_filter[0], num_classes, kernel_size=1)
            self.final2 = nn.Conv2d(nb_filter[0], num_classes, kernel_size=1)
            self.final3 = nn.Conv2d(nb_filter[0], num_classes, kernel_size=1)
            self.final4 = nn.Conv2d(nb_filter[0], num_classes, kernel_size=1)
        else:
            self.final = nn.Conv2d(nb_filter[0], num_classes, kernel_size=1)


    def forward(self, input):
        print('input:',input.shape)
        x0_0 = self.conv0_0(input)
        print('x0_0:',x0_0.shape)
        x1_0 = self.conv1_0(self.pool(x0_0))
        print('x1_0:',x1_0.shape)
        x0_1 = self.conv0_1(torch.cat([x0_0, self.up(x1_0)], 1))
        print('x0_1:',x0_1.shape)

        x2_0 = self.conv2_0(self.pool(x1_0))
        print('x2_0:',x2_0.shape)
        x1_1 = self.conv1_1(torch.cat([x1_0, self.up(x2_0)], 1))
        print('x1_1:',x1_1.shape)
        x0_2 = self.conv0_2(torch.cat([x0_0, x0_1, self.up(x1_1)], 1))
        print('x0_2:',x0_2.shape)

        x3_0 = self.conv3_0(self.pool(x2_0))
        print('x3_0:',x3_0.shape)
        x2_1 = self.conv2_1(torch.cat([x2_0, self.up(x3_0)], 1))
        print('x2_1:',x2_1.shape)
        x1_2 = self.conv1_2(torch.cat([x1_0, x1_1, self.up(x2_1)], 1))
        print('x1_2:',x1_2.shape)
        x0_3 = self.conv0_3(torch.cat([x0_0, x0_1, x0_2, self.up(x1_2)], 1))
        print('x0_3:',x0_3.shape)
        x4_0 = self.conv4_0(self.pool(x3_0))
        print('x4_0:',x4_0.shape)
        x3_1 = self.conv3_1(torch.cat([x3_0, self.up(x4_0)], 1))
        print('x3_1:',x3_1.shape)
        x2_2 = self.conv2_2(torch.cat([x2_0, x2_1, self.up(x3_1)], 1))
        print('x2_2:',x2_2.shape)
        x1_3 = self.conv1_3(torch.cat([x1_0, x1_1, x1_2, self.up(x2_2)], 1))
        print('x1_3:',x1_3.shape)
        x0_4 = self.conv0_4(torch.cat([x0_0, x0_1, x0_2, x0_3, self.up(x1_3)], 1))
        print('x0_4:',x0_4.shape)

        if self.deep_supervision:
            output1 = self.final1(x0_1)
            output2 = self.final2(x0_2)
            output3 = self.final3(x0_3)
            output4 = self.final4(x0_4)
            return [output1, output2, output3, output4]

        else:
            output = self.final(x0_4)
            return output