[Python] Python 旋转、flip Nifti三维数据 (Python Rotate and Flip Nifti volume)

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1. __author__ = 'xin yang'  
2.   
3.   
4. import os  
5. import nibabel as nib  
6. import numpy as np  
7. import math  
8.   
9.   
10. src_us_folder = 'G:/Temp/Data/src/us'  
11. src_seg_folder = 'G:/Temp/Data/src/seg'  
12.   
13. aug_us_folder = 'G:/Temp/Data/aug/us'  
14. aug_seg_folder = 'G:/Temp/Data/aug/seg'  
15.   
16. img_n= 10  
17. rotate_theta = np.array([0, math.pi/2])  
18.   
19. # augmentation  
20. aug_cnt = 0  
21. for k in range(img_n):  
22.     src_us_file = os.path.join(src_us_folder, (str(k) + '.nii'))  
23.     src_seg_file = os.path.join(src_seg_folder, (str(k) + '_seg.nii'))  
24.     # load .nii files  
25.     src_us_vol = nib.load(src_us_file)  
26.     src_seg_vol = nib.load(src_seg_file)  
27.     # volume data  
28.     us_vol_data = src_us_vol.get_data()  
29.     us_vol_data = (np.array(us_vol_data)).astype('uint8')  
30.     seg_vol_data = src_seg_vol.get_data()  
31.     seg_vol_data = (np.array(seg_vol_data)).astype('uint8')  
32.     # get refer affine matrix  
33.     ref_affine = src_us_vol.affine  
34.   
35.     ############### flip volume ###############  
36.     flip_us_vol = np.fliplr(us_vol_data)  
37.     flip_seg_vol = np.fliplr(seg_vol_data)  
38.     # construct new volumes  
39.     new_us_vol = nib.Nifti1Image(flip_us_vol, ref_affine)  
40.     new_seg_vol = nib.Nifti1Image(flip_seg_vol, ref_affine)  
41.     # save  
42.     aug_us_file = os.path.join(aug_us_folder, (str(aug_cnt) + '.nii'))  
43.     aug_seg_file = os.path.join(aug_seg_folder, (str(aug_cnt) + '_seg.nii'))  
44.     nib.save(new_us_vol, aug_us_file)  
45.     nib.save(new_seg_vol, aug_seg_file)  
46.   
47.     aug_cnt = aug_cnt + 1  
48.   
49.     ############### rotate volume ###############  
50.     for t in range(len(rotate_theta)):  
51.         print 'rotating %d theta of %d volume...' % (t, k)  
52.         cos_gamma = np.cos(t)  
53.         sin_gamma = np.sin(t)  
54.         rot_affine = np.array([[1, 0, 0, 0],  
55.                                [0, cos_gamma, -sin_gamma, 0],  
56.                                [0, sin_gamma, cos_gamma, 0],  
57.                                [0, 0, 0, 1]])  
58.         new_affine = rot_affine.dot(ref_affine)  
59.         # construct new volumes  
60.         new_us_vol = nib.Nifti1Image(us_vol_data, new_affine)  
61.         new_seg_vol = nib.Nifti1Image(seg_vol_data, new_affine)  
62.         # save  
63.         aug_us_file = os.path.join(aug_us_folder, (str(aug_cnt) + '.nii'))  
64.         aug_seg_file = os.path.join(aug_seg_folder, (str(aug_cnt) + '_seg.nii'))  
65.         nib.save(new_us_vol, aug_us_file)  
66.         nib.save(new_seg_vol, aug_seg_file)  
67.   
68.         aug_cnt = aug_cnt + 1  

[Note]

This NiBabel toolbox based rotation only changes the affine matrix information in the header, that is, the volume data is not affected. When you use ITK-Snap to load the .nii file, the data will be transformed according to the affine matrix. That means, the transformation is done by the ITK-Snap software.

This kind of transformation can't be recognised by Nifti toolbox in Matlab, when you use 'load_nii' function to load the file generated above. You will encounter the problem like:

'Non-orthogonal rotation or shearing found inside the affine matrix in this NIfTI file.'

You need to really 'reslice' the volume data under the affine matrix, as the following code shows:

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1. rot_nii_path = 'G:\Temp\Data\aug\0.nii';  
2. res_rot_nii_path = 'G:\Temp\Data\aug\0_res.nii';  
3. reslice_nii(rot_nii_path, res_rot_nii_path, [], [], [], 2);  

You can refer to the source file of  Nifti toolbox in Matlab  for the parameter setting of 'reslice_nii' function. You should pay attention to the last parameter for interpolation. 'Nearest' and 'Linear' will generate different data types.