def test_calculate_metric(epoch_num):
net = VNetRec(n_channels=1,
n_classes=num_classes,
normalization='batchnorm',
has_dropout=False).cuda()
save_mode_path = os.path.join(snapshot_path,
'iter_' + str(epoch_num) + '.pth')
net.load_state_dict(torch.load(save_mode_path))
print("init weight from {}".format(save_mode_path))
net.eval()
avg_metric = dist_test_all_case(net,
image_list,
num_classes=num_classes,
patch_size=(96, 128, 160),
stride_xy=18,
stride_z=4,
save_result=True,
test_save_path=test_save_path)
return avg_metric
if not os.path.exists(snapshot_path):
os.makedirs(snapshot_path)
if os.path.exists(snapshot_path + '/code'):
shutil.rmtree(snapshot_path + '/code')
shutil.copytree('.', snapshot_path + '/code',
shutil.ignore_patterns(['.git', '__pycache__']))
logging.basicConfig(filename=snapshot_path + "/log.txt",
level=logging.INFO,
format='[%(asctime)s.%(msecs)03d] %(message)s',
datefmt='%H:%M:%S')
logging.getLogger().addHandler(logging.StreamHandler(sys.stdout))
logging.info(str(args))
net = VNetRec(n_channels=1,
n_classes=num_classes,
normalization='batchnorm',
has_dropout=True)
net = net.cuda()
db_train = LAHeart(base_dir=train_data_path,
split='train',
num=16,
transform=transforms.Compose([
RandomRotFlip(),
RandomCrop(patch_size),
ToTensor(),
]))
def worker_init_fn(worker_id):
random.seed(args.seed + worker_id)
if __name__ == "__main__":
## make logger file
if not os.path.exists(snapshot_path):
os.makedirs(snapshot_path)
if os.path.exists(snapshot_path + '/code'):
shutil.rmtree(snapshot_path + '/code')
shutil.copytree('.', snapshot_path + '/code', shutil.ignore_patterns(['.git','__pycache__']))
logging.basicConfig(filename=snapshot_path+"/log.txt", level=logging.INFO,
format='[%(asctime)s.%(msecs)03d] %(message)s', datefmt='%H:%M:%S')
logging.getLogger().addHandler(logging.StreamHandler(sys.stdout))
logging.info(str(args))
net = VNetRec(n_channels=1, n_classes=num_classes, normalization='batchnorm', has_dropout=True)
net = net.cuda()
db_train = LAHeart(base_dir=train_data_path,
split='train',
num=16,
transform = transforms.Compose([
RandomRotFlip(),
RandomCrop(patch_size),
ToTensor(),
]))
def worker_init_fn(worker_id):
random.seed(args.seed+worker_id)
trainloader = DataLoader(db_train, batch_size=batch_size, shuffle=True, num_workers=4, pin_memory=True, worker_init_fn=worker_init_fn)