python-argparse,read/write,os.path

argparse

import argparse
parser=argparse.ArgumentParser(description='test param')
parser.add_argument('--test_video_path',type=str)
parser.add_argument('--epoch',type=int)
parser.add_argument('--loss',type=float)
args=parser.parse_args()
test_video_path=args.test_video_path
epoch=args.epoch 
loss=args.loss

read/write

read

read code 1

for line in open(predict_file):
            line=line.split(' ')[2]
            data_list.append(line)

read code 2

with open(predict_file) as f:
            lines=f.readlines()
            for line in lines:
                line=line.rstrip()
                line=line.split(' ')[2]
                data_list.append(line)

read code 3

import yaml
with open('config.yml','r') as yamlfile:
    cfg=yaml.load(yamlfile)
img_W=cfg['img_W']
img_H=cfg['img_H']
time_length=cfg['time_length']
img_size=(img_W,img_H)

write

write code 1

import os
with open(os.path.join(test_result_path,'{}_predict.txt'.format(video_name)),'a') as f:
                f.write('{:04d} loss {:.6f}\n'.format(frame_num,frame_loss))

write code 2

import h5py
dataset_file=h5py.File('{}.h5'.format(style),'w')
create_dataset=dataset_file.create_dataset('data',(total_rows,time_length,img_W,img_H,1),maxshape=(None,time_length,img_W,img_H,1))
create_dataset[:,:]=h5_data
dataset_file.close()

os.path

create file folder

import os
if not os.path.exists(test_result_path):
        os.makedirs(test_result_path)

file list

file list 1

import os
import tqdm
for video_path in tqdm(os.listdir(test_video_path)):
        video=os.path.join(test_video_path,video_path)
        video_name=video.split('/')[-1].split('.')[0]
        print("######process {}".format(video))

file list 2

import os
import h5py
import tqdm
h5s_filelist=sorted([os.path.join(h5_store_path,item) for item in os.listdir(h5_store_path)])
dataset_path=os.path.join('/'.join(h5_store_path.split('/')[:-1]))
for h5_file_num,h5_file in enumerate(tqdm(h5s_filelist)):
        h5_data_file=h5py.File(h5_file,'r')
        h5_data=h5_data_file['data']
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这段代码在运行时import SimpleITK as sitkimport numpy as npimport os# 设置文件路径data_path = 'C:/Users/Administrator/Desktop/LiTS2017/'save_path = 'C:/Users/Administrator/Desktop/2D-LiTS2017/'if not os.path.exists(save_path): os.makedirs(save_path)# 定义函数将3D图像保存为2D的.png格式def save_image_as_png(image, save_folder, name_prefix): for i in range(image.shape[2]): slice = np.squeeze(image[:, :, i]) slice = slice.astype(np.float32) slice *= 255.0/slice.max() slice = slice.astype(np.uint8) save_name = os.path.join(save_folder, name_prefix + '_' + str(i) + '.png') sitk.WriteImage(sitk.GetImageFromArray(slice), save_name)# 读取Training Batch 1中的图像image_path = os.path.join(data_path, 'Training Batch 1/volume-0.nii')image = sitk.ReadImage(image_path)image_array = sitk.GetArrayFromImage(image)save_folder = os.path.join(save_path, 'image')if not os.path.exists(save_folder): os.makedirs(save_folder)save_image_as_png(image_array, save_folder, 'img')# 读取Training Batch 2中的标签label_path = os.path.join(data_path, 'Training Batch 2/segmentation-0.nii')label = sitk.ReadImage(label_path)label_array = sitk.GetArrayFromImage(label)# 将标签转换为灰度图并保存label_array[label_array == 1] = 128label_array[label_array == 2] = 255save_folder = os.path.join(save_path, 'mask')if not os.path.exists(save_folder): os.makedirs(save_folder)save_image_as_png(label_array, save_folder, 'mask')会出现RuntimeWarning: divide by zero encountered in true_divide slice *= 255.0/slice.max()这种情况,修复它,并给出完整代码
05-24

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