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.datasets_synapse import Synapse_dataset
from networks.msa2net import  Msa2Net
from trainer import trainer_synapse

from utils import test_single_volume, AddNoise # Noise Class is Added from utils.py

parser = argparse.ArgumentParser()
parser.add_argument(
    "--volume_path",
    type=str,
    default="/images/PublicDataset/Transunet_synaps/project_TransUNet/data/Synapse/",
    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=9, help="output channel of network")
parser.add_argument("--list_dir", type=str, default="./lists/lists_Synapse", help="list dir")
parser.add_argument("--output_dir", type=str, default="./model_out", help="output dir")
parser.add_argument("--max_iterations", type=int, default=30000, help="maximum epoch number to train")
parser.add_argument("--max_epochs", type=int, default=400, 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=0.05, help="segmentation network learning rate")
parser.add_argument("--seed", type=int, default=1234, help="random seed")
parser.add_argument("--add_noise", type=str, default = 1, help = 'noise is added')
parser.add_argument("--noise_type", type=str, default = 'none', help = 'each noises hyperparams must be checked') # Argument parser of Noise Type
parser.add_argument('--weights_fpath', type=str, help='weights file path') # path for best model's weights
parser.add_argument("--model_name", type=str, default="MSA2Net", help="model_name")
# parser.add_argument('--cfg', type=str, required=True, metavar="FILE", help='path to config file', )
parser.add_argument(
    "--opts",
    help="Modify config options by adding 'KEY VALUE' pairs. ",
    default=None,
    nargs="+",
)
parser.add_argument("--zip", action="store_true", help="use zipped dataset instead of folder dataset")
parser.add_argument(
    "--cache-mode",
    type=str,
    default="part",
    choices=["no", "full", "part"],
    help="no: no cache, "
    "full: cache all data, "
    "part: sharding the dataset into nonoverlapping pieces and only cache one piece",
)
parser.add_argument("--resume", help="resume from checkpoint")
parser.add_argument("--accumulation-steps", type=int, help="gradient accumulation steps")
parser.add_argument(
    "--use-checkpoint", action="store_true", help="whether to use gradient checkpointing to save memory"
)
parser.add_argument(
    "--amp-opt-level",
    type=str,
    default="O1",
    choices=["O0", "O1", "O2"],
    help="mixed precision opt level, if O0, no amp is used",
)
parser.add_argument("--tag", help="tag of experiment")
parser.add_argument("--eval", action="store_true", help="Perform evaluation only")
parser.add_argument("--throughput", action="store_true", help="Test throughput only")

args = parser.parse_args()
if args.dataset == "Synapse":
    args.volume_path = os.path.join(args.volume_path, "test_vol_h5")
# config = get_config(args)


def inference(args, model, test_save_path=None):
    db_test = args.Dataset(base_dir=args.volume_path, split="test_vol", img_size=args.img_size, 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()
    
#     if args.add_noise: 
        
#         if args.noise_type == 'gaussian':
#             noise = AddNoise(noise_type = 'gaussian', mean = 0.0, std = 50.0)
        
#         if args.noise_type == 'saltpepper':
#             noise = AddNoise(noise_type = 'salt_pepper', salt_prob = 0.1, pepper_prob = 0.1) 
            
#         if args.noise_type == 'speckle':
#             noise = AddNoise(noise_type = 'speckle', std = 100.0)
            
            
    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]
#         print(image.shape)
        
#         if args.add_noise:
#             image = noise(image)
        
        metric_i = test_single_volume(
            image,
            label,
            model,
            classes=args.num_classes,
            noise =args.noise_type,
            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__":
    os.environ["CUDA_VISIBLE_DEVICES"] = "0"
    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 = {
        "Synapse": {
            "Dataset": Synapse_dataset,
            "z_spacing": 1,
        },
    }
    dataset_name = args.dataset
    args.Dataset = dataset_config[dataset_name]["Dataset"]
    args.z_spacing = dataset_config[dataset_name]["z_spacing"]
    args.is_pretrain = True
    
    net = Msa2Net().cuda()
    
    snapshot = args.weights_fpath

    snapshot = os.path.join(args.output_dir, snapshot)

    if not os.path.exists(snapshot):
        snapshot = snapshot.replace("best_model", "transfilm_epoch_" + str(args.max_epochs - 1))
        
    net.load_state_dict(torch.load(snapshot))
#     net = torch.load(snapshot)
    #print("self trained Sina unet", msg)
    print("self trained Sina unet")
    snapshot_name = snapshot.split("/")[-1]

    log_folder = "./test_log/test_log_"
    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 = os.path.join(args.output_dir, "predictions")
        test_save_path = args.test_save_dir
        os.makedirs(test_save_path, exist_ok=True)
    else:
        test_save_path = None
    inference(args, net, test_save_path)