python读取并转换原始的3d图像文件

Question

我正在使用原始格式的ct扫描医学图像。它基本上是体素的3d矩阵（512 * 512 * nb的切片）。我想将文件的每个片段提取到单独的文件中。

import numpy as np
import matplotlib.pyplot as plt

# reading the raw image into a string. The image files can be found at:
# https://grand-challenge.org/site/anode09/details/
f = open('test01.raw', 'rb')
img_str = f.read()

# converting to a uint16 numpy array
img_arr = np.fromstring(img_str, np.uint16)

# get the first image and plot it
im1 = img_arr[0:512*512]
im1 = np.reshape(im1, (512, 512))
plt.imshow(im1, cmap=plt.cm.gray_r)
plt.show()

结果肯定看起来像胸部ct扫描，但图像的纹理很奇怪，好像像素放错了位置。

某些相关信息可能位于相关的.mhd信息文件中，但我不确定在哪里查看：

ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 1 0 0 0 1 0 0 0 1
Offset = 0 0 0
CenterOfRotation = 0 0 0
AnatomicalOrientation = RPI
ElementSpacing = 0.697266 0.697266 0.7
DimSize = 512 512 459
ElementType = MET_SHORT
ElementDataFile = test01.raw

Answer 1

以这种方式尝试：

Dim_size=np.array((512,512,459),dtype=np.int) #Or read that from your mhd info File

f = open(FileName,'rb') #only opens the file for reading
img_arr=np.fromfile(f,dtype=np.uint16)
img_arr=img_arr.reshape(Dim_size[0],Dim_size[1],Dim_size[2])

如果你是内存有限，请以块的形式阅读文件

f = open(FileName,'rb') #only opens the file for reading
for i in range(0,Dim_size[2]):
    img_arr=np.fromfile(f,dtype=np.uint16,count=Dim_size[0]*Dim_size[1])
    img=img.reshape(Dim_size[0],Dim_size[1])
    #Do something with the Slice

显示raw-File中实际内容的一个好方法也是在ImageJ中读取它。对于读取此类ITK兼容文件，甚至可以使用PlugIn，但直接原始导入也应该有效。 https://imagej.net/Welcome http://ij-plugins.sourceforge.net/plugins/3d-io/