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train_backbone.py
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train_backbone.py
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import os,tqdm,sys,time,argparse
sys.path.insert(0, os.path.join(os.path.dirname(__file__), 'lib'))
import numpy as np
import torch.cuda.amp as amp
scaler = amp.GradScaler()
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.data
import torch.distributed as dist
from utils.losses import BCELoss,OhemCELoss2D,DiceLoss
from utils.EndoMetric import general_dice, general_jaccard
from utils.summary import create_summary, create_logger, create_saver, DisablePrint
from utils.LoadModel import load_model_full,load_model
##------------------------------ Training settings ------------------------------##
parser = argparse.ArgumentParser(description='real-time segmentation')
parser.add_argument('--local_rank', type=int, default=0)
parser.add_argument('--dist', action='store_true')
parser.add_argument('--root_dir', type=str, default='./results/endo18')
parser.add_argument('--dataset', type=str, choices=['endovis2018','colon_oct'],default='endovis2018')
parser.add_argument('--data_tag', type=str, default='type')
parser.add_argument('--log_name', type=str, default='DLV3PLUS_clean')
parser.add_argument('--data_type', type=str, choices=['clean','noisy'], default='noisy')
parser.add_argument('--data_ver', type=int, default=0)
parser.add_argument('--arch', type=str, choices=['puredeeplab18','swinPlus','RAUNet'], default='swinPlus')
parser.add_argument('--pre_log_name', type=str, default=None)
parser.add_argument('--pre_checkpoint', type=str, default=None)
parser.add_argument('--lr', type=float, default=1e-4)
parser.add_argument('--weight_decay', type=float, default=1e-4)
parser.add_argument('--batch_size', type=int, default=4)
parser.add_argument('--num_epochs', type=int, default=100)
parser.add_argument('--loss', type=str, default='ohem')
parser.add_argument('--gpus', type=str, default='3')
parser.add_argument('--downsample', type=int, default=1)
parser.add_argument('--h', type=int, default=512)
parser.add_argument('--w', type=int, default=640)
parser.add_argument('--log_interval', type=int, default=50)
parser.add_argument('--val_interval', type=int, default=1)
parser.add_argument('--num_workers', type=int, default=4)
parser.add_argument('--t', type=int, default=1)
parser.add_argument('--step', type=int, default=1)
parser.add_argument('--ver', type=int, default=1)
parser.add_argument('--tag', type=int, default=1)
# parser.add_argument('--freeze_name', type=str, )
# parser.add_argument('--spatial_layer', type=int, )
parser.add_argument('--global_n', type=int, default=0)
parser.add_argument('--pretrain_ep', type=int, default=20)
parser.add_argument('--decay', type=int, default=2)
parser.add_argument('--reset', type=str, default=None)
parser.add_argument('--reset_ep', type=int)
cfg = parser.parse_args()
##------------------------------ Training settings ------------------------------##
def main():
################################################ def part ################################################
##------------------------------ train model ------------------------------##
def train(epoch):
print('\n Epoch: %d' % epoch)
model.train()
tic = time.perf_counter()
tr_loss = []
for batch_idx, batch in enumerate(train_loader):
for k in batch:
if not k=='path':
batch[k] = batch[k].to(device=cfg.device).float()
# print('shape of input image:', batch['image'].shape) #4, 3, 272, 480
with amp.autocast():
#print(batch['image'].shape)
outputs , _ = model(batch['image'])
if cfg.loss == 'ohem':
loss = compute_loss(outputs, batch['label'].long())
else:
loss = compute_loss(outputs, batch['label'])
tr_loss.append(loss.detach().cpu().numpy())
optimizer.zero_grad()
scaler.scale(loss).backward()
scaler.step(optimizer)
scaler.update()
if batch_idx % cfg.log_interval == 0:
duration = time.perf_counter() - tic
tic = time.perf_counter()
print('[%d/%d-%d/%d]' % (epoch, cfg.num_epochs, batch_idx, len(train_loader))+
'loss:{:.4f} Time:{:.4f}'.format(loss.item(),duration))
summary_writer.add_scalar('Tr_loss', np.mean(tr_loss), epoch)
return
##------------------------------ validation model ------------------------------##
def val_map_endo(epoch):
print('\n Val@Epoch: %d' % epoch)
model.eval()
torch.cuda.empty_cache()
metrics = np.zeros((2,))
metrics_seq = np.zeros((2, 4))
count_seq = np.zeros((4,))
dice_each = np.zeros((12,))
iou_each = np.zeros((12,))
tool_each = np.zeros((12,))
count = 0
with torch.no_grad():
for inputs in tqdm.tqdm(val_loader):
inputs['image'] = inputs['image'].to(cfg.device).float()
# print('shape:', inputs['image'].shape) #1,3,256,480
tic = time.perf_counter()
output,_ = model(inputs['image'])
output = F.interpolate(output, (ori_h,ori_w), mode='bilinear', align_corners=True)
output = F.softmax(output,dim=1)
output = torch.argmax(output,dim=1)
output = output.cpu().numpy()
duration = time.perf_counter() - tic
dice = general_dice(inputs['label'].numpy(),
output) # dice containing each tool class
iou = general_jaccard(inputs['label'].numpy(), output)
for i in range(len(dice)):
tool_id = dice[i][0]
dice_each[tool_id] += dice[i][1]
iou_each[tool_id] += iou[i][1]
tool_each[tool_id] += 1
frame_dice = np.mean([dice[i][1] for i in range(len(dice))])
frame_iou = np.mean([iou[i][1] for i in range(len(dice))])
#overall
metrics[0] += frame_dice # dice of each frame
metrics[1] += frame_iou
count += 1
#----for seq
seq_ind = int(inputs['path'][0]) - 1 #seq: 0-3
metrics_seq[0][seq_ind] += frame_dice
metrics_seq[1][seq_ind] += frame_iou
count_seq[seq_ind] += 1
for j in range(12):
dice_each[j] /= tool_each[j]
iou_each[j] /= tool_each[j]
dice_each_f = [float('{:.4f}'.format(i)) for i in dice_each]
iou_each_f = [float('{:.4f}'.format(i)) for i in iou_each]
print(count)
metrics[0] /= count
metrics[1] /= count
print(metrics)
dc, jc = metrics[0], metrics[1]
metrics_seq[0] /= count_seq
dice_seq = [float('{:.4f}'.format(i)) for i in metrics_seq[0]]
metrics_seq[1] /= count_seq
iou_seq = [float('{:.4f}'.format(i)) for i in metrics_seq[1]]
print('Dice:{:.4f} IoU:{:.4f} Time:{:.4f}'.format(dc, jc, duration))
print('Dice_seq1:{:.4f}, seq2:{:.4f}, seq3:{:.4f}, seq4:{:.4f}'.format(dice_seq[0], dice_seq[1], dice_seq[2],dice_seq[3]))
print('IOU_seq1:{:.4f}, seq2:{:.4f}, seq3:{:.4f}, seq4:{:.4f}'.format(iou_seq[0], iou_seq[1], iou_seq[2],iou_seq[3]))
summary_writer.add_scalar('Dice', dc, epoch)
summary_writer.add_scalar('IoU', jc, epoch)
return jc
def val_map_oct(epoch):
print('\n Val@Epoch: %d' % epoch)
model.eval()
torch.cuda.empty_cache()
metrics = np.zeros((2,))
count = 0
with torch.no_grad():
for inputs in tqdm.tqdm(val_loader):
inputs['image'] = inputs['image'].to(cfg.device).float()
# print('shape:', inputs['image'].shape) #1,3,256,480
tic = time.perf_counter()
output,_ = model(inputs['image'])
output = F.interpolate(output, (ori_h,ori_w), mode='bilinear', align_corners=True)
output = F.softmax(output,dim=1)
output = torch.argmax(output,dim=1)
output = output.cpu().numpy()
duration = time.perf_counter() - tic
dice = general_dice(inputs['label'].numpy(),
output) # dice containing each tool class
iou = general_jaccard(inputs['label'].numpy(), output)
frame_dice = np.mean([dice[i][1] for i in range(len(dice))])
frame_iou = np.mean([iou[i][1] for i in range(len(dice))])
#overall
metrics[0] += frame_dice # dice of each frame
metrics[1] += frame_iou
count += 1
print(count)
metrics[0] /= count
metrics[1] /= count
print(metrics)
dc, jc = metrics[0], metrics[1]
print('Dice:{:.4f} IoU:{:.4f} Time:{:.4f}'.format(dc, jc, duration))
summary_writer.add_scalar('Dice', dc, epoch)
summary_writer.add_scalar('IoU', jc, epoch)
return jc
################################################ def part ################################################
################################################ main part ################################################
##------------------------------ Enviroment ------------------------------##
os.environ['CUDA_VISIBLE_DEVICES']=cfg.gpus
torch.backends.cudnn.benchmark = True # disable this if OOM at beginning of training
num_gpus = torch.cuda.device_count()
if cfg.dist:
cfg.device = torch.device('cuda:%d' % cfg.local_rank)
torch.cuda.set_device(cfg.local_rank)
dist.init_process_group(backend='nccl', init_method='env://',
world_size=num_gpus, rank=cfg.local_rank)
else:
cfg.device = torch.device('cuda')
cfg.log_name += '_ver_' + str(cfg.ver)
cfg.log_dir = os.path.join(cfg.root_dir, cfg.log_name, 'logs')
cfg.ckpt_dir = os.path.join(cfg.root_dir, cfg.log_name, 'ckpt')
os.makedirs(cfg.log_dir, exist_ok=True)
os.makedirs(cfg.ckpt_dir, exist_ok=True)
saver = create_saver(cfg.local_rank, save_dir=cfg.ckpt_dir)
logger = create_logger(cfg.local_rank, save_dir=cfg.log_dir)
summary_writer = create_summary(cfg.local_rank, log_dir=cfg.log_dir)
print = logger.info
print(cfg)
##------------------------------ dataset ------------------------------##
print('Setting up data...')
if cfg.dataset=='endovis2018':
h,w = [cfg.h,cfg.w]
ori_h, ori_w = [1024, 1280]
print('size of endovis2018 data %d, %d.' %(h,w))
if cfg.data_type=='clean':
from dataset.Endovis2018_backbone import endovis2018
train_dataset = endovis2018('train_clean', t=cfg.t, arch='swinPlus',rate=1, global_n=cfg.global_n,h = h, w = w)
val_dataset = endovis2018('test_part', t=cfg.t,arch='swinPlus', rate=1, global_n=cfg.global_n,h = h, w = w)
classes = train_dataset.class_num
elif cfg.data_type=='noisy':
from dataset.Endovis2018_backbone import endovis2018
train_dataset = endovis2018('train', t=cfg.t, arch='swinPlus',rate=1, global_n=cfg.global_n, data_ver=cfg.data_ver,h = h, w = w)
val_dataset = endovis2018('test_part', t=cfg.t,arch='swinPlus', rate=1, global_n=cfg.global_n, data_ver=cfg.data_ver,h = h, w = w)
classes = train_dataset.class_num
elif cfg.dataset=='colon_oct':
h,w = [cfg.h,cfg.w]
ori_h, ori_w = [1024, 1024]
print('size of colon_oct data %d, %d.' %(h,w))
from dataset.Colon_OCT import Colon_OCT
train_dataset = Colon_OCT('train', t=cfg.t, arch='swinPlus',rate=1, global_n=cfg.global_n,h = h, w = w)
val_dataset = Colon_OCT('test_part', t=cfg.t,arch='swinPlus', rate=1, global_n=cfg.global_n,h = h, w = w)
classes = train_dataset.class_num
##------------------------------ build model ------------------------------##
if 'puredeeplab' in cfg.arch:
from net.Ours.base18 import DeepLabV3Plus
model = DeepLabV3Plus(classes, 18)
elif 'swin' in cfg.arch:
from net.Ours.base18 import TswinPlus
model = TswinPlus(classes,h,w)
elif 'RAUNet' in cfg.arch:
from net.Ours.RAUNet import RAUNet
model = RAUNet(classes)
else:
raise NotImplementedError
# load pretrain model
if cfg.pre_log_name is not None:
cfg.pre_ckpt_path = os.path.join(cfg.root_dir, cfg.pre_log_name, 'ckpt', 'checkpoint.t7')
print('initialize the model from:', cfg.pre_ckpt_path)
model = load_model(model, cfg.pre_ckpt_path)
##------------------------------ combile model ------------------------------##
optimizer = torch.optim.Adam(model.parameters(), cfg.lr,weight_decay=cfg.weight_decay)
loss_functions = {'bce': BCELoss(), 'ohem':OhemCELoss2D(w*h//16//(cfg.downsample**2)), 'dice':DiceLoss}
compute_loss = loss_functions[cfg.loss]
torch.cuda.empty_cache()
print('Starting training...')
best = 0
best_ep = 0
gpus = cfg.gpus.split(',')
if len(cfg.gpus)>1:
model = nn.DataParallel(model, device_ids=list(map(int,gpus))).cuda()
else:
model = model.to(cfg.device)
##------------------------------ dataloader ------------------------------##
train_loader = torch.utils.data.DataLoader(train_dataset,
batch_size=cfg.batch_size,
shuffle= True,
num_workers=cfg.num_workers,
pin_memory=True,
drop_last=True)
val_loader = torch.utils.data.DataLoader(val_dataset, batch_size=1,
shuffle=False, num_workers=cfg.num_workers, pin_memory=True, drop_last=False)
##------------------------------ resume training ------------------------------##
if cfg.reset:
pre_ckpt_path = os.path.join(cfg.root_dir, cfg.log_name, 'ckpt', 'latestcheckpoint.t7')
print('initialize the model from: %s' % pre_ckpt_path)
model = load_model_full(model, pre_ckpt_path)
best_ep = cfg.reset_ep
if cfg.dataset=='endovis2018':
best = val_map_endo(best_ep)
else:
best = val_map_oct(best_ep)
##------------------------------ training section ------------------------------##
for epoch in range(best_ep + 1, cfg.num_epochs + 1):
train(epoch)
if cfg.val_interval > 0 and epoch % cfg.val_interval == 0:
if cfg.dataset=='endovis2018':
save_map = val_map_endo(epoch)
else:
save_map = val_map_oct(epoch)
if save_map > best:
best = save_map
best_ep = epoch
print(saver.save(model.state_dict(), 'epoch_{}_checkpoint'.format(epoch)))
else:
if epoch - best_ep > 100:
break
print(saver.save(model.state_dict(), 'latestcheckpoint'))
summary_writer.close()
################################################ main part ################################################
if __name__ == '__main__':
with DisablePrint(local_rank=cfg.local_rank):
# tensorboard --logdir './MS-TFAL/results/endo18/DLV3PLUS_clean_ver_0/logs'
main()