python 读取.nii格式图像实例

 # encoding=utf8 ''' 查看和显示nii文件 ''' import matplotlib matplotlib.use('TkAgg') from matplotlib import pylab as plt import nibabel as nib from nibabel import nifti1 from nibabel.viewers import OrthoSlicer3D example_filename = '../ADNI_nii/ADNI_002_S_0413_MR_MPR____N3__Scaled_2_Br_20081001114937668_S14782_I118675.nii' img = nib.load(example_filename) print (img) print (img.header['db_name'])  #输出头信息 width,height,queue=img.dataobj.shape OrthoSlicer3D(img.dataobj).show() num = 1 for i in range(0,queue,10): img_arr = img.dataobj[:,:,i] plt.subplot(5,4,num) plt.imshow(img_arr,cmap='gray') num +=1 plt.show() 

 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