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python nii图像扩充

51自学网 2020-11-01 11:37:41
  医学CAD

python nii图像扩充

 

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import os
import nibabel as nib
import numpy as np
import math
  
src_us_folder = 'F:/src/ori'
src_seg_folder = 'G:/src/seg'
  
aug_us_folder = 'G:/aug/ori'
aug_seg_folder = 'G:/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

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Ubuntu+python将nii图像保存成png格式
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