import argparse
import os
import os.path as osp
import json
import time
from tqdm import tqdm
from PIL import Image
import numpy as np
import torch
import torchvision.datasets as datasets
from torchvision import transforms
import torch.utils.data as data
import mmcv
from mmaction.datasets.pipelines import Compose
from mmaction.models import build_model
# Multi GPU
from mmcv.parallel import MMDataParallel, MMDistributedDataParallel
from mmcv.parallel import collate
def parse_args():
parser = argparse.ArgumentParser(description='workflow recognition')
parser.add_argument("--local_rank", type=int, help="Local rank. Necessary for using the torch.distributed.launch utility.")
parser.add_argument('--data_path', default='.', help='dataset prefix')
parser.add_argument('--output_prefix', default='', help='output prefix')
parser.add_argument('--task_type', default='active_bleeding', help='active_bleeding')
parser.add_argument('--data_list', default=None, help='video list of the dataset, the format should be')
parser.add_argument(
'--frame_interval',
type=int,
default=30,
help='the sampling frequency of frame in the untrimed video')
parser.add_argument(
'--temporal_stride',
type=int,
default=30,
help='clip in frame interval')
parser.add_argument('--ckpt', default='.pth', help='checkpoint for feature extraction')
parser.add_argument(
'--batch_size', type=int, default=256, help='input batch size')
parser.add_argument(
'--numModel', type=int, default=1, help='number of the model')
parser.add_argument(
'--config_file', type=str, default='ckpt/phase.py', help='config_file')
parser.add_argument(
'--num_class', type=int, default=2, help='active bleeding : 2')
parser.add_argument(
'--kfold', type=int, default=1, help='cross validation')
parser.add_argument(
'--multigpu', type=int, default=1, help='cross validation')
args = parser.parse_args()
return args
class mmaction_inference():
def __init__(self, args):
self.args = args
self.config = mmcv.Config.fromfile(args.config_file)
self.ckpt = args.ckpt
self.num_class = args.num_class
self.kfold = args.kfold
self.data_path = args.data_path
self.datalist = open(args.data_list).readlines()
self.datalist = [x.strip() for x in self.datalist]
# multi gpu
self.device = torch.device("cuda:{}".format(args.local_rank) if torch.cuda.is_available() else "cpu")
self.data_set()
self.model_set()
def data_set(self):
# Data Setting
self.img_norm_cfg = self.config['img_norm_cfg']
self.img_norm_cfg['mean'] = [i / 255.0 for i in self.img_norm_cfg['mean']]
self.img_norm_cfg['std'] = [i / 255.0 for i in self.img_norm_cfg['std']]
self.clip_len = self.config['data']['test']['pipeline'][0]['clip_len'] # clip len
self.transform = transforms.Compose([
transforms.Scale(224),
transforms.CenterCrop(224),
# transforms.PILToTensor(),
transforms.ToTensor(),
transforms.Normalize(mean=self.img_norm_cfg['mean'], std=self.img_norm_cfg['std']),
# transforms.ToPILImage(),
])
kfold = self.kfold
if kfold == 1:
test_patient = [3, 4, 6, 13, 17, 18, 22, 116, 208, 303]
elif kfold == 2:
test_patient = [1, 7, 10, 19, 56, 74, 100, 117, 203, 304]
elif kfold == 3:
test_patient = [5, 48, 76, 94, 202, 204, 206, 209, 301, 305]
def model_set(self):
# Model Setting
model = build_model(self.config['model'])
state_dict = torch.load(self.ckpt)['state_dict']
model.load_state_dict(state_dict)
# self.model = model.cuda()
if self.args.multigpu > 1:
self.model = MMDataParallel(
model.cuda(0), device_ids=[self.args.local_rank], output_device=self.args.local_rank)
self.model = self.model.to(self.device)
else:
self.model = model.cuda()
def forward(self):
prog_bar = mmcv.ProgressBar(len(self.datalist))
probability = dict()
for videoID in self.datalist:
videoID = videoID.strip()
frame_dir = os.path.join(self.data_path, videoID)
output_dir = os.path.join(self.args.output_prefix, videoID)
if not osp.exists(output_dir):
os.system(f'mkdir -p {output_dir}')
start = time.time()
print('\nstart', videoID)
inference_time_output_file = self.args.task_type + '_time.txt'
inference_time_output_file = osp.join(output_dir, inference_time_output_file)
output_file = self.args.task_type + '.json'
output_file = osp.join(output_dir, output_file)
# first frame
framelist = sorted(os.listdir(frame_dir))[::self.args.frame_interval]
probability[videoID] = np.zeros((len(framelist), self.num_class))
first_dataset = GastricDataset(data_path=frame_dir, datalist=framelist, temporal_stride=self.args.temporal_stride, windows=self.clip_len, transform=self.transform)
# first_loader = torch.utils.data.DataLoader(first_dataset, batch_size=self.args.batch_size, shuffle=False, num_workers=8, pin_memory=True)
# middle frame
framelist = sorted(os.listdir(frame_dir))[::self.args.frame_interval]
framelist = [framelist[0]] * ((self.clip_len - 1) // 2) + framelist[:-1* ((self.clip_len - 1) // 2)]
middle_dataset = GastricDataset(data_path=frame_dir, datalist=framelist, temporal_stride=self.args.temporal_stride, windows=self.clip_len, transform=self.transform)
# middle_loader = torch.utils.data.DataLoader(middle_dataset, batch_size=self.args.batch_size, shuffle=False, num_workers=8, pin_memory=True)
# last frame
framelist = sorted(os.listdir(frame_dir))[::self.args.frame_interval]
framelist = [framelist[0]] * (self.clip_len - 1) + framelist[:-1* (self.clip_len - 1)]
last_dataset = GastricDataset(data_path=frame_dir, datalist=framelist, temporal_stride=self.args.temporal_stride, windows=self.clip_len, transform=self.transform)
# last_loader = torch.utils.data.DataLoader(last_dataset, batch_size=self.args.batch_size, shuffle=False, num_workers=8, pin_memory=True)
dataset = ConcatDataset(first_dataset, middle_dataset, last_dataset)
if self.args.multigpu > 1:
rank, world_size = get_dist_info()
sampler = DistributedSampler(
dataset, world_size, rank, shuffle=False, seed=None)
else:
sampler=None
data_loader = torch.utils.data.DataLoader(dataset,sampler=sampler,
batch_size=self.args.batch_size, shuffle=False, num_workers=6, pin_memory=True)
with torch.no_grad():
self.model.eval()
idx = 0
for batch_idx, (images1,images2,images3) in enumerate(tqdm(data_loader)):#zip(first_loader, middle_loader, last_loader), total=len(first_loader))):
# images1, images2, images3 = images1.cuda(), images2.cuda(), images3.cuda()
images = torch.cat((images1.unsqueeze(1), images2.unsqueeze(1), images3.unsqueeze(1)), dim=1).cuda()
prob = self.model(images, return_loss=False, infer_3d=True) #+ self.model(images2, return_loss=False, infer_3d=True) + self.model(images3, return_loss=False, infer_3d=True)
probability[videoID][idx:idx+images1.size(0)] = prob.squeeze().cpu().numpy()
idx += images1.size(0)
results = self.save2json(probability[videoID])
with open(output_file, "w") as json_file:
json.dump(results, json_file)
end = time.time()
with open(inference_time_output_file, 'w') as f:
f.write(str(end - start))
prog_bar.update()
def save2json(self, prob):
result = dict()
result['labels'] = {0 : 'Normal', 1: 'Actvie Bleeding'}
result['prediction'] = dict()
predictions = []
for idx in range(len(prob)):
predictions.append(str(np.argmax(prob[idx])))
result['result'] = predictions
probabilitys = []
for idx in range(len(prob)):
probabilitys.append(list(prob[idx]))
result['prob'] = probabilitys
result['frameInterval'] = str(self.args.frame_interval)
return result
def main():
args = parse_args()
inference = mmaction_inference(args)
inference.forward()
# enumerate Untrimmed videos, extract feature from each of them
class ConcatDataset(data.Dataset):
def __init__(self, *datasets):
self.datasets = datasets
def __getitem__(self, i):
return tuple(d[i] for d in self.datasets)
def __len__(self):
return min(len(d) for d in self.datasets)
class GastricDataset(data.Dataset):
"Characterizes a dataset for PyTorch"
def __init__(self, data_path, datalist, temporal_stride, windows, transform=None):
"Initialization"
self.data_path = data_path
self.transform = transform
self.temporal_stride = temporal_stride
self.windows = windows
self.datalist = datalist
def __len__(self):
"Denotes the total number of samples"
return len(self.datalist)
def read_images(self, data):
X = []
ts = self.temporal_stride
frameNum = int(data[-10:-4])
iamge = None
for i in range(0, self.windows):
image_path = os.path.join(self.data_path, 'frame' + str((i*ts) \
+ frameNum).zfill(10) + '.jpg')
if os.path.exists(image_path):
image =Image.open(image_path)
if self.transform is not None:
image = self.transform(image)
X.append(image)
X = torch.stack(X, dim=0)
return X
def __getitem__(self, index):
"Generates one sample of data"
# Select sample
data = self.datalist[index]
# Load data
X = self.read_images(data) # (input) spatial images
# BatchSize, Channel, Temporal, Width, Height
X = X.permute(1, 0, 2, 3)
return X
if __name__ == '__main__':
main()