test.py

import argparse
import logging
import os
import random
import sys
import numpy as np
import torch
import torch.backends.cudnn as cudnn
import torch.nn as nn
from torch.utils.data import DataLoader
from tqdm import tqdm
from datasets.dataset_synapse import Synapse_dataset
try:
    from datasets.dataset_acdc import BaseDataSets as ACDC_dataset
except:
    pass
from utils import test_single_volume
from rwkv_unet import RWKV_UNet
import ttach as tta

parser = argparse.ArgumentParser()
parser.add_argument('--volume_path', type=str,
                    default='./data/Synapse/test_vol_h5', help='root dir for validation volume data')  # for acdc volume_path=root_dir
parser.add_argument('--dataset', type=str,
                    default='Synapse', help='experiment_name')
parser.add_argument('--num_classes', type=int,
                    default=4, help='output channel of network')
parser.add_argument('--list_dir', type=str,
                    default='./lists/lists_Synapse', help='list dir')

parser.add_argument('--max_iterations', type=int,default=20000, help='maximum epoch number to train')
parser.add_argument('--max_epochs', type=int, default=60, help='maximum epoch number to train')
parser.add_argument('--batch_size', type=int, default=24,
                    help='batch_size per gpu')
parser.add_argument('--img_size', type=int, default=224, help='input patch size of network input')
parser.add_argument('--is_savenii', action="store_true", help='whether to save results during inference')
parser.add_argument('--test_save_dir', type=str, default='../predictions', help='saving prediction as nii!')
parser.add_argument('--deterministic', type=int,  default=1, help='whether use deterministic training')
parser.add_argument('--base_lr', type=float,  default=0.001, help='segmentation network learning rate')
parser.add_argument('--seed', type=int, default=1234, help='random seed')
parser.add_argument('--path_specific', type=str, default=None)
args = parser.parse_args()


def inference(args, model, test_save_path=None):
    db_test = args.Dataset(base_dir=args.volume_path, split="test_vol", list_dir=args.list_dir)
    testloader = DataLoader(db_test, batch_size=1, shuffle=False, num_workers=1)
    logging.info("{} test iterations per epoch".format(len(testloader)))
    model.eval()
    metric_list = 0.0
    for i_batch, sampled_batch in tqdm(enumerate(testloader)):
        h, w = sampled_batch["image"].size()[2:]
        image, label, case_name = sampled_batch["image"], sampled_batch["label"], sampled_batch['case_name'][0]
        metric_i = test_single_volume(image, label, model, classes=args.num_classes, patch_size=[args.img_size, args.img_size],
                                      test_save_path=test_save_path, case=case_name, z_spacing=args.z_spacing)
        metric_list += np.array(metric_i)
        logging.info('idx %d case %s mean_dice %f mean_hd95 %f' % (i_batch, case_name, np.mean(metric_i, axis=0)[0], np.mean(metric_i, axis=0)[1]))
    metric_list = metric_list / len(db_test)
    for i in range(1, args.num_classes):
        logging.info('Mean class %d mean_dice %f mean_hd95 %f' % (i, metric_list[i-1][0], metric_list[i-1][1]))
    performance = np.mean(metric_list, axis=0)[0]
    mean_hd95 = np.mean(metric_list, axis=0)[1]
    logging.info('Testing performance in best val model: mean_dice : %f mean_hd95 : %f' % (performance, mean_hd95))
    return "Testing Finished!"



if __name__ == "__main__":

    if not args.deterministic:
        cudnn.benchmark = True
        cudnn.deterministic = False
    else:
        cudnn.benchmark = False
        cudnn.deterministic = True
    random.seed(args.seed)
    np.random.seed(args.seed)
    torch.manual_seed(args.seed)
    torch.cuda.manual_seed(args.seed)

    dataset_config = {
        'ACDC': {
            'Dataset': ACDC_dataset,  # datasets.dataset_acdc.BaseDataSets,
            'volume_path': './data/ACDC',
            'list_dir': None,
            'num_classes': 4,
            'z_spacing': 5,
            'info': '3D'
        },
        'Synapse': {
            'Dataset': Synapse_dataset,
            'volume_path': './data/Synapse/test_vol_h5',
            'list_dir': './lists/lists_Synapse',
            'num_classes': 9,
            'z_spacing': 1,
        },
    }
    dataset_name = args.dataset
    args.num_classes = dataset_config[dataset_name]['num_classes']
    args.volume_path = dataset_config[dataset_name]['volume_path']
    args.Dataset = dataset_config[dataset_name]['Dataset']
    args.list_dir = dataset_config[dataset_name]['list_dir']
    args.z_spacing = dataset_config[dataset_name]['z_spacing']
    args.is_pretrain = True

    # name the same snapshot defined in train script!
    args.exp = 'rwkv' + dataset_name + str(args.img_size)
    snapshot_path = "./models/{}/{}".format(args.exp, 'exp1')
    snapshot_path = snapshot_path + '_pretrain' if args.is_pretrain else snapshot_path
    snapshot_path = snapshot_path + '_epo' + str(args.max_epochs) if args.max_epochs != 30 else snapshot_path
    snapshot_path = snapshot_path+'_bs'+str(args.batch_size)
    snapshot_path = snapshot_path + '_lr' + str(args.base_lr) if args.base_lr != 0.01 else snapshot_path
    snapshot_path = snapshot_path + '_'+str(args.img_size)
    snapshot_path = snapshot_path + '_s'+str(args.seed) if args.seed!=1234 else snapshot_path
    snapshot = os.path.join(snapshot_path, 'best_model.pth')
    if not os.path.exists(snapshot): snapshot = snapshot.replace('best_model', 'epoch_'+str(args.max_epochs-1))
    if path_specific != None:
            snapshot=path_specific
    net = RWKV_UNet(in_channels=1, img_size=args.img_size, num_classes=args.num_classes,pretrained_path=None).cuda()
    transforms = tta.Compose(
    [
        tta.HorizontalFlip(), 
        #tta.Rotate90(angles=[0, 90]), #for ACDC
    ]
)
    net.load_state_dict(torch.load(snapshot), strict=False)
    net = tta.SegmentationTTAWrapper(net, transforms)
    snapshot_name = snapshot_path.split('/')[-1]

    log_folder = './test_log/test_log_' + args.exp
    os.makedirs(log_folder, exist_ok=True)
    logging.basicConfig(filename=log_folder + '/'+snapshot_name+".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))
    logging.info(snapshot_name)

    if args.is_savenii:
        args.test_save_dir = './predictions'
        test_save_path = os.path.join(args.test_save_dir, args.exp, snapshot_name)
        os.makedirs(test_save_path, exist_ok=True)
    else:
        test_save_path = None
    inference(args, net, test_save_path)