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test_ACDC.py
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test_ACDC.py
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import os
import sys
import logging
import argparse
import random
import numpy as np
import torch
from torch.utils.data import DataLoader
import torch.backends.cudnn as cudnn
from tqdm import tqdm
from utils.utils import test_single_volume
from utils.dataset_ACDC import ACDCdataset, RandomGenerator
from lib.networks import TransCASCADE, PVT_CASCADE
from lib.cnn_vit_backbone import CONFIGS as CONFIGS_ViT_seg
def inference(args, model, testloader, test_save_path=None):
logging.info("{} test iterations per epoch".format(len(testloader)))
model.eval()
metric_list = 0.0
with torch.no_grad():
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, mean_jacard %f mean_asd %f' % (i_batch, case_name, np.mean(metric_i, axis=0)[0], np.mean(metric_i, axis=0)[1], np.mean(metric_i, axis=0)[2], np.mean(metric_i, axis=0)[3]))
metric_list = metric_list / len(testloader)
for i in range(1, args.num_classes):
logging.info('Mean class (%d) mean_dice %f mean_hd95 %f, mean_jacard %f mean_asd %f' % (i, metric_list[i-1][0], metric_list[i-1][1], metric_list[i-1][2], metric_list[i-1][3]))
performance = np.mean(metric_list, axis=0)[0]
mean_hd95 = np.mean(metric_list, axis=0)[1]
mean_jacard = np.mean(metric_list, axis=0)[2]
mean_asd = np.mean(metric_list, axis=0)[3]
logging.info('Testing performance in best val model: mean_dice : %f mean_hd95 : %f, mean_jacard : %f mean_asd : %f' % (performance, mean_hd95, mean_jacard, mean_asd))
logging.info("Testing Finished!")
return performance, mean_hd95, mean_jacard, mean_asd
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--batch_size", default=12, help="batch size")
parser.add_argument("--lr", default=0.0001, help="learning rate")
parser.add_argument("--max_epochs", default=150)
parser.add_argument("--img_size", default=224)
parser.add_argument("--save_path", default="./model_pth/ACDC")
parser.add_argument("--n_gpu", default=1)
parser.add_argument("--checkpoint", default=None)
parser.add_argument("--list_dir", default="./data/ACDC/lists_ACDC")
parser.add_argument("--root_dir", default="./data/ACDC/")
parser.add_argument("--volume_path", default="./data/ACDC/test")
parser.add_argument("--z_spacing", default=10)
parser.add_argument("--num_classes", default=4)
parser.add_argument('--test_save_dir', default='./predictions', help='saving prediction as nii!')
parser.add_argument('--deterministic', type=int, default=1,
help='whether use deterministic training')
parser.add_argument('--seed', type=int,
default=2222, help='random seed')
parser.add_argument('--n_skip', type=int,
default=3, help='using number of skip-connect, default is num')
parser.add_argument('--vit_name', type=str,
default='R50-ViT-B_16', help='select one vit model')
parser.add_argument('--vit_patches_size', type=int,
default=16, help='vit_patches_size, default is 16')
args = parser.parse_args()
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)
config_vit = CONFIGS_ViT_seg[args.vit_name]
config_vit.n_classes = args.num_classes
config_vit.n_skip = args.n_skip
args.is_pretrain = True
args.exp = 'TransCASCADE_' + str(args.img_size)
snapshot_path = "{}/{}/{}".format(args.save_path, args.exp, 'TransCASCADE')
snapshot_path = snapshot_path + '_pretrain' if args.is_pretrain else snapshot_path
snapshot_path += '_' + args.vit_name
snapshot_path = snapshot_path + '_skip' + str(args.n_skip)
snapshot_path = snapshot_path + '_vitpatch' + str(args.vit_patches_size) if args.vit_patches_size!=16 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.lr) if args.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
config_vit.patches.size = (args.vit_patches_size, args.vit_patches_size)
if args.vit_name.find('R50') !=-1:
config_vit.patches.grid = (int(args.img_size/args.vit_patches_size), int(args.img_size/args.vit_patches_size))
net = TransCASCADE(config_vit, img_size=args.img_size, num_classes=config_vit.n_classes).cuda()
#net = PVT_CASCADE(n_class=config_vit.n_classes).cuda()
snapshot = os.path.join(snapshot_path, 'best.pth')
if not os.path.exists(snapshot): snapshot = snapshot.replace('best', 'epoch_'+str(args.max_epochs-1))
net.load_state_dict(torch.load(snapshot))
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)
args.test_save_dir = os.path.join(snapshot_path, args.test_save_dir)
test_save_path = os.path.join(args.test_save_dir, args.exp, snapshot_name)
os.makedirs(test_save_path, exist_ok=True)
db_test =ACDCdataset(base_dir=args.volume_path,list_dir=args.list_dir, split="test")
testloader = DataLoader(db_test, batch_size=1, shuffle=False)
results = inference(args, net, testloader, test_save_path)