def val_seg(args, model):
info = json.load(open(osp.join(args.list_dir, 'info.json'), 'r'))
normalize = dt.Normalize(mean=info['mean'], std=info['std'])
t = []
if args.resize:
t.append(dt.Resize(args.resize))
if args.crop_size:
t.append(dt.RandomCrop(args.crop_size))
t.extend([dt.Label_Transform(), dt.ToTensor(), normalize])
dataset = SegList(args.data_dir,
'val',
dt.Compose(t),
list_dir=args.list_dir)
val_loader = torch.utils.data.DataLoader(dataset,
batch_size=1,
shuffle=False,
num_workers=args.workers,
pin_memory=False)
cudnn.benchmark = True
dice_avg, dice_1, dice_2, dice_3, dice_list, auc, auc_1, auc_2, auc_3 = val(
args, val_loader, model)
return dice_avg, dice_1, dice_2, dice_3, dice_list, auc, auc_1, auc_2, auc_3
def test_seg(args, result_path):
print('Loading test model ...')
if args.fusion:
# 1
net_1 = net_builder('unet_nested')
net_1 = nn.DataParallel(net_1).cuda()
checkpoint_1 = torch.load(
'result/ori_3D/train/unet_nested_nopre_mix_33_NEW_multi_2_another/checkpoint/model_best.pth.tar'
)
net_1.load_state_dict(checkpoint_1['state_dict'])
# 2
net_2 = net_builder('unet')
net_2 = nn.DataParallel(net_2).cuda()
checkpoint_2 = torch.load(
'result/ori_3D/train/unet_nopre_mix_3_NEW_multi_2/checkpoint/model_best.pth.tar'
)
net_2.load_state_dict(checkpoint_2['state_dict'])
net = [net_1, net_2]
else:
net = net_builder(args.seg_name)
net = nn.DataParallel(net).cuda()
checkpoint = torch.load(args.seg_path)
net.load_state_dict(checkpoint['state_dict'])
#print('model loaded!')
info = json.load(open(osp.join(args.list_dir, 'info_test.json'), 'r'))
normalize = st.Normalize(mean=info['mean'], std=info['std'])
t = []
if args.resize:
t.append(st.Resize(args.resize))
t.extend([st.ToTensor(), normalize])
dataset = SegList(args.data_dir,
'test',
st.Compose(t),
list_dir=args.list_dir)
test_loader = torch.utils.data.DataLoader(dataset,
batch_size=1,
shuffle=False,
num_workers=args.workers,
pin_memory=False)
cudnn.benchmark = True
if args.fusion:
test_fusion(args, test_loader, net, result_path)
else:
test(args, test_loader, net, result_path)
def train_seg(args,result_path,logger):
for k, v in args.__dict__.items():
print(k, ':', v)
# load the net
net = net_builder(args.name,args.model_path,args.pretrained)
model = torch.nn.DataParallel(net).cuda()
param = count_param(model)
print('###################################')
print('Model #%s# parameters: %.2f M' % (args.name,param/1e6))
# set the loss criterion
criterion = loss_builder(args.loss)
# Data loading code
info = json.load(open(osp.join(args.list_dir, 'info.json'), 'r'))
normalize = dt.Normalize(mean=info['mean'],std=info['std'])
# data transforms
t = []
if args.resize:
t.append(dt.Resize(args.resize))
if args.random_rotate > 0:
t.append(dt.RandomRotate(args.random_rotate))
if args.random_scale > 0:
t.append(dt.RandomScale(args.random_scale))
if args.crop_size:
t.append(dt.RandomCrop(args.crop_size))
t.extend([dt.Label_Transform(),
dt.RandomHorizontalFlip(),
dt.ToTensor(),
normalize])
train_loader = torch.utils.data.DataLoader(
SegList(args.data_dir, 'train', dt.Compose(t),list_dir=args.list_dir),batch_size=args.batch_size,
shuffle=True, num_workers=args.workers,pin_memory=True, drop_last=True)
# define loss function (criterion) and pptimizer
if args.optimizer == 'SGD': #SGD optimizer
optimizer = torch.optim.SGD(net.parameters(),
args.lr,
momentum=args.momentum,
weight_decay=args.weight_decay)
elif args.optimizer == 'Adam': #Adam optimizer
optimizer = torch.optim.Adam(net.parameters(),
args.lr,
betas=(0.9, 0.99),
weight_decay=args.weight_decay)
cudnn.benchmark = True
best_dice = 0
start_epoch = 0
# load the pretrained model
if args.model_path:
print("=> loading pretrained model '{}'".format(args.model_path))
checkpoint = torch.load(args.model_path)
model.load_state_dict(checkpoint['state_dict'])
# optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
start_epoch = checkpoint['epoch']
best_dice = checkpoint['best_dice']
dice_epoch = checkpoint['dice_epoch']
model.load_state_dict(checkpoint['state_dict'])
print("=> loaded checkpoint '{}' (epoch {})"
.format(args.resume, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
# main training
for epoch in range(start_epoch, args.epochs):
lr = adjust_learning_rate(args,optimizer, epoch)
logger_vis.info('Epoch: [{0}]\tlr {1:.06f}'.format(epoch, lr))
# train for one epoch
loss,dice_train,dice_1,dice_2,dice_3,dice_4,dice_5,dice_6,dice_7,dice_8,dice_9 = train(args,train_loader, model, criterion, optimizer, epoch)
# evaluate on validation set
dice_val,dice_11,dice_22,dice_33,dice_44,dice_55,dice_66,dice_77,dice_88,dice_99,dice_list = val_seg(args,model)
# save best checkpoints
is_best = dice_val > best_dice
best_dice = max(dice_val, best_dice)
checkpoint_dir = osp.join(result_path,'checkpoint')
if not exists(checkpoint_dir):
os.makedirs(checkpoint_dir)
checkpoint_latest = checkpoint_dir+'/checkpoint_latest.pth.tar'
save_checkpoint({
'epoch': epoch + 1,
'state_dict': model.state_dict(),
'dice_epoch':dice_val,
'best_dice': best_dice,
}, is_best, checkpoint_dir,filename=checkpoint_latest)
if args.save_every_checkpoint:
if (epoch + 1) % 1 == 0:
history_path = checkpoint_dir+'/checkpoint_{:03d}.pth.tar'.format(epoch + 1)
shutil.copyfile(checkpoint_latest, history_path)
logger.append([epoch,dice_train,dice_val,dice_1,dice_11,dice_2,dice_22,dice_3,dice_33,dice_4,dice_44,dice_5,dice_55,dice_6,dice_66,dice_7,dice_77,dice_8,dice_88,dice_9,dice_99])