SimpleITK 读写nii.gz文件

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.GetArrayFrImage(itk_img) 5 print("img shape:",img.shape) 6 7 ## save 8 out = sitk.GetImageFrArray(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 fr 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.GetArrayFrImage(prob_img) 13 label_arr = (prob_arr > Dice_value) * 1 14 label_img = sitk.GetImageFrArray(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)

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