python读取nii文件_python 读取.nii格式图像实例

我就废话不多说了，大家还是直接看代码吧~

# 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()

3D显示结果：

ADNI数据维度(256，256，170)分段显示：

补充知识：python nii图像扩充

我就废话不多说了，大家还是直接看代码吧~

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

以上这篇python 读取.nii格式图像实例就是小编分享给大家的全部内容了，希望能给大家一个参考，也希望大家多多支持python博客。