- __author__ = 'xin yang'
- import os
- import nibabel as nib
- import numpy as np
- import math
- src_us_folder = 'G:/Temp/Data/src/us'
- src_seg_folder = 'G:/Temp/Data/src/seg'
- aug_us_folder = 'G:/Temp/Data/aug/us'
- aug_seg_folder = 'G:/Temp/Data/aug/seg'
- img_n= 10
- rotate_theta = np.array([0, math.pi/2])
- # augmentation
- aug_cnt = 0
- for k in range(img_n):
- src_us_file = os.path.join(src_us_folder, (str(k) + '.nii'))
- src_seg_file = os.path.join(src_seg_folder, (str(k) + '_seg.nii'))
- # load .nii files
- src_us_vol = nib.load(src_us_file)
- src_seg_vol = nib.load(src_seg_file)
- # volume data
- us_vol_data = src_us_vol.get_data()
- us_vol_data = (np.array(us_vol_data)).astype('uint8')
- seg_vol_data = src_seg_vol.get_data()
- seg_vol_data = (np.array(seg_vol_data)).astype('uint8')
- # get refer affine matrix
- ref_affine = src_us_vol.affine
- ############### flip volume ###############
- flip_us_vol = np.fliplr(us_vol_data)
- flip_seg_vol = np.fliplr(seg_vol_data)
- # construct new volumes
- new_us_vol = nib.Nifti1Image(flip_us_vol, ref_affine)
- new_seg_vol = nib.Nifti1Image(flip_seg_vol, ref_affine)
- # save
- aug_us_file = os.path.join(aug_us_folder, (str(aug_cnt) + '.nii'))
- aug_seg_file = os.path.join(aug_seg_folder, (str(aug_cnt) + '_seg.nii'))
- nib.save(new_us_vol, aug_us_file)
- nib.save(new_seg_vol, aug_seg_file)
- aug_cnt = aug_cnt + 1
- ############### rotate volume ###############
- for t in range(len(rotate_theta)):
- print 'rotating %d theta of %d volume...' % (t, k)
- cos_gamma = np.cos(t)
- sin_gamma = np.sin(t)
- rot_affine = np.array([[1, 0, 0, 0],
- [0, cos_gamma, -sin_gamma, 0],
- [0, sin_gamma, cos_gamma, 0],
- [0, 0, 0, 1]])
- new_affine = rot_affine.dot(ref_affine)
- # construct new volumes
- new_us_vol = nib.Nifti1Image(us_vol_data, new_affine)
- new_seg_vol = nib.Nifti1Image(seg_vol_data, new_affine)
- # save
- aug_us_file = os.path.join(aug_us_folder, (str(aug_cnt) + '.nii'))
- aug_seg_file = os.path.join(aug_seg_folder, (str(aug_cnt) + '_seg.nii'))
- nib.save(new_us_vol, aug_us_file)
- nib.save(new_seg_vol, aug_seg_file)
- 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:
- rot_nii_path = 'G:\Temp\Data\aug\0.nii';
- res_rot_nii_path = 'G:\Temp\Data\aug\0_res.nii';
- reslice_nii(rot_nii_path, res_rot_nii_path, [], [], [], 2);