1、读写nii.gz文件

 1 ## using simpleITK to load and save data.
 2 import SimpleITK as sitk
 3 itk_img = sitk.ReadImage('./nifti.nii.gz')
 4 img = sitk.GetArrayFromImage(itk_img)
 5 print("img shape:",img.shape)
 6  
 7 ## save 
 8 out = sitk.GetImageFromArray(img)
 9 # # out.SetSpacing(itk_img.GetSpacing())
10 # # out.SetOrigin(itk_img.GetOrigin())
11 sitk.WriteImage(out,'simpleitk_save.nii.gz')

2、对于神经网络输出概率生成二值图保存

 1 import os
 2 import SimpleITK as sitk
 3 from glob import glob
 4 
 5 
 6 def save_prob2label(prob_dir, save_labeldir):
 7     all_prob_seg = glob(os.path.join(prob_dir, "*.nrrd"))
 8     for index, file in enumerate(all_prob_seg):
 9         print("processing", index, '/', len(all_prob_seg), file)
10         label_file = file.replace(prob_dir, save_labeldir).replace(".nrrd", ".nii.gz")
11         prob_img = sitk.ReadImage(file)
12         prob_arr = sitk.GetArrayFromImage(prob_img)
13         label_arr = (prob_arr > Dice_value) * 1
14         label_img = sitk.GetImageFromArray(label_arr)
15         sitk.WriteImage(label_img, label_file)
16 
17 
18 if __name__ == '__main__':
19 
20     prob_nrrd_dir = r'C:\Users\wmz\Desktop\input'
21     save_label_dir = r'C:\Users\wmz\Desktop\test'
22     Dice_value = 0.5
23     save_prob2label(prob_nrrd_dir, save_label_dir)