SimpleITK写入数据

1. 问题
如果直接用sitk.GetImageFromArray(),然后sitk.WriteImage(),会使得生成的数据spacing,Origin等属性都变成默认的，比如spacing会变成[1,1,1]

# lost header, including spacing
img_npy = sitk.GetArrayFromImage(img_sitk)
new_img_npy = img_npy[z_begin: z_end, :, :]
new_mask_npy = mask_npy[z_begin: z_end, :, :]
new_img_sitk = sitk.GetImageFromArray(new_img_npy)
new_mask_sitk = sitk.GetImageFromArray(new_mask_npy)
sitk.WriteImage(new_img_sitk, out_path_img)
sitk.WriteImage(new_mask_sitk, out_path_label)

2. 解决办法
如果只是像上面那种简单的裁剪，直接在sitk操作可以解决（但是要注意sitk.GetArrayFromImage()前后数据存储顺序的变化），比如上面的代码可以改成：

sitk.WriteImage(img_sitk[:, :, z_begin:z_end], images_path)
sitk.WriteImage(mask_sitk[:, :, z_begin: z_end], label_path)

这样更简洁，而且不会损失头文件
如果要取出Array操作，那存之前最好设置一下头文件的重要属性:

def copy_geometry(image: sitk.Image, ref: sitk.Image):
    image.SetOrigin(ref.GetOrigin())
    image.SetDirection(ref.GetDirection())
    image.SetSpacing(ref.GetSpacing())
    return image

img_out_itk = sitk.GetImageFromArray(image)
img_out_itk = copy_geometry(img_out_itk, img_in)
sitk.WriteImage(img_out_itk, output_file)