在python中读取*.mhd/*.raw格式

Question

任何人都可以告诉我如何在python中读取包含.mhd / .raw文件的数据集？

Answer 1

最简单的方法是使用SimpleITK(MedPy也使用ITK作为.mhd/.raw文件).命令

pip install SimpleITK

适用于许多python版本.对于阅读.mhd/.raw,您可以使用来自kaggle的代码

import SimpleITK as sitk
import numpy as np
'''
This funciton reads a '.mhd' file using SimpleITK and return the image array, origin and spacing of the image.
'''

def load_itk(filename):
    # Reads the image using SimpleITK
    itkimage = sitk.ReadImage(filename)

    # Convert the image to a  numpy array first and then shuffle the dimensions to get axis in the order z,y,x
    ct_scan = sitk.GetArrayFromImage(itkimage)

    # Read the origin of the ct_scan, will be used to convert the coordinates from world to voxel and vice versa.
    origin = np.array(list(reversed(itkimage.GetOrigin())))

    # Read the spacing along each dimension
    spacing = np.array(list(reversed(itkimage.GetSpacing())))

    return ct_scan, origin, spacing

Answer 2

安装SimpleITK后,使用skimage可能会更容易

import skimage.io as io
img = io.imread('file.mhd', plugin='simpleitk')

这将为您提供z,y,x排序的numpy数组.

Answer 3

添加上述帖子，您可以从从此处下载的 CT-Scan .mhd 文件开始，并使用以下代码显示/保存 29 个图像（假设您在当前目录中下载了标头和原始文件）：

import SimpleITK as sitk
import matplotlib.pylab as plt
ct_scans = sitk.GetArrayFromImage(sitk.ReadImage("training_001_ct.mhd", sitk.sitkFloat32))
plt.figure(figsize=(20,16))
plt.gray()
plt.subplots_adjust(0,0,1,1,0.01,0.01)
for i in range(ct_scans.shape[0]):
    plt.subplot(5,6,i+1), plt.imshow(ct_scans[i]), plt.axis('off')
    # use plt.savefig(...) here if you want to save the images as .jpg, e.g.,
plt.show()

以下是读取并动画显示的相同 CT 扫描 .mhd 文件SimpleITK：