Python 2.7 VTK:3D矩阵&x27；s的体积有错误的尺寸

我想将三维矩阵（X*Y分辨率的Z切片）可视化为经典的三维体素。 我在MATLAB中生成矩阵，并在Python中导入它。 然后，根据代码和，我提出了这个解决方案。 在这个演示中，我使用了一个矩阵，它应该生成一个包含4个2*3体素切片的3D图像

在MATLAB中

C(:,:,1) =

   5   5   5
   5   5   5


C(:,:,2) =

   15   15   15
   15   15   15


C(:,:,3) =

   25   25   25
   25   25   25


C(:,:,4) =

   35   35   35
   35   35   35

在python中：

Cmat = spio.loadmat('CMAT.mat')['C']
>>>print Cmat.shape
(2, 3, 4)

Cmat = np.ascontiguousarray(Cmat.T)
>>>print Cmat
[[[ 5  5]
  [ 5  5]
  [ 5  5]]

 [[15 15]
  [15 15]
  [15 15]]


 [[25 25]
  [25 25]
  [25 25]]

 [[35 35]
  [35 35]
  [35 35]]]

下面的代码将生成此图像（为了方便起见，我旋转了此图像）：

结果的形状不是2*3*4，切片的大小也不一样，我做错了什么？我试着调整一下

dataImporter.SetDataExtent
dataImporter.SetWholeExtent
dataImporter.SetDataSpacing

如果我改变的话，可以通过多种方式重塑矩阵 dataImporter.SetDataExtent（0,1,0,1,0,1） dataImporter.SetWholeExtent（0,1,0,1,0,1）

我得到了一个2x2x2的立方体 但如果我打电话

dataImporter.SetDataExtent(0, 1, 0, 2, 0, 1)
dataImporter.SetWholeExtent(0, 1, 0, 2, 0, 1)

我获得2x4x2实体（而不是2x3x2）

如果我打电话

dataImporter.SetDataExtent(0, 1, 0, 10, 0, 2)
dataImporter.SetWholeExtent(0, 1, 0, 10, 0, 2)

我得到一个2x20x4的实体

这似乎与setDataExtent和SetWholeExtent的文档相矛盾：

*数据的维度必须等于（范围[0]+1）*（范围+1）*（范围数据范围+1）*（范围数据范围+1）。例如，对于二维图像，请使用（0，宽度-1，0，高度-1，0,0）*

有什么想法吗

完整代码如下 MATLAB：

Python:

import vtk
from numpy import *
import numpy as np
import scipy.io as spio

data_matrix = zeros([2, 3, 4], dtype=uint8)

Cmat = spio.loadmat('CMAT.mat')['C']
Cmat = np.ascontiguousarray(Cmat.T)
print Cmat
data_matrix = Cmat
# For VTK to be able to use the data, it must be stored as a VTK-image. This can be done by the vtkImageImport-class which
# imports raw data and stores it.
dataImporter = vtk.vtkImageImport()
# The previously created array is converted to a string of chars and imported.
data_string = data_matrix.tostring()
dataImporter.CopyImportVoidPointer(data_string, len(data_string))
# The type of the newly imported data is set to unsigned char (uint8)
dataImporter.SetDataScalarTypeToUnsignedChar()
# Because the data that is imported only contains an intensity value (it isn't RGB-coded or something similar), the importer
# must be told this is the case.
dataImporter.SetNumberOfScalarComponents(1)
# The following two functions describe how the data is stored and the dimensions of the array it is stored in.
dataImporter.SetDataExtent(0, 1, 0, 2, 0, 3)
dataImporter.SetWholeExtent(0, 1, 0, 2, 0, 3)

# This class stores color data and can create color tables from a few color points. For this demo, we want the three cubes
# to be of the colors red green and blue.
colorFunc = vtk.vtkColorTransferFunction()
colorFunc.AddRGBPoint(5, 1, 0.0, 0.0)  # Red
colorFunc.AddRGBPoint(15, 0.0, 1, 0.0) # Green
colorFunc.AddRGBPoint(25, 0.0, 0.0, 1) # Blue
colorFunc.AddRGBPoint(35, 0.0, 0, 0.0) # Black

# The previous two classes stored properties. Because we want to apply these properties to the volume we want to render,
# we have to store them in a class that stores volume properties.
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorFunc)

volumeMapper = vtk.vtkOpenGLGPUVolumeRayCastMapper()
volumeMapper.SetInputConnection(dataImporter.GetOutputPort())

# The class vtkVolume is used to pair the previously declared volume as well as the properties to be used when rendering that volume.
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)

# With almost everything else ready, its time to initialize the renderer and window, as well as creating a method for exiting the application
renderer = vtk.vtkRenderer()
renderWin = vtk.vtkRenderWindow()
renderWin.AddRenderer(renderer)
renderInteractor = vtk.vtkRenderWindowInteractor()
renderInteractor.SetRenderWindow(renderWin)

# We add the volume to the renderer ...
renderer.AddVolume(volume)
# ... set background color to white ...
renderer.SetBackground(1, 1, 1)
# ... and set window size.
renderWin.SetSize(400, 400)


# A simple function to be called when the user decides to quit the application.
def exitCheck(obj, event):
    if obj.GetEventPending() != 0:
        obj.SetAbortRender(1)


# Tell the application to use the function as an exit check.
renderWin.AddObserver("AbortCheckEvent", exitCheck)

renderInteractor.Initialize()
# Because nothing will be rendered without any input, we order the first render manually before control is handed over to the main-loop.
renderWin.Render()
renderInteractor.Start()

我唯一的缺点是这些体素不是立方体，但它们的一个维度是其他维度的两倍。但仍然无法解释为什么4个切片中只有2个受到影响

[更新]： 似乎只有第一个和最后一个切片的大小是其他切片的一半。使用20x30x40矩阵，可以看到第一个和最后一个切片比其他切片薄。

---

这是一个老问题，也许你已经找到了答案

我的第一个猜测是，数据的存储方式与预期的读取方式之间存在某种不一致。可能，MATLAB将3D矩阵存储为列主数据结构，而VTK则将这些数据恢复为行主数据结构。

---

另一种可能性是，当读取文件并获得2x20x4实体时，会交换尺寸

这是一个老问题，也许你已经找到了答案

我的第一个猜测是，数据的存储方式与预期的读取方式之间存在某种不一致。可能，MATLAB将3D矩阵存储为列主数据结构，而VTK则将这些数据恢复为行主数据结构。

---

另一种可能性是，当读取文件并获得2x20x4实体时，会交换尺寸

谢谢，很遗憾，我没有找到这个问题的解决方案。另一方面，我最终根本不需要VTK，就是这样。谢谢，不幸的是，我没有找到解决这个问题的方法。另一方面，我最终根本不需要VTK，就这样。

import vtk
from numpy import *
import numpy as np
import scipy.io as spio

data_matrix = zeros([2, 3, 4], dtype=uint8)

Cmat = spio.loadmat('CMAT.mat')['C']
Cmat = np.ascontiguousarray(Cmat.T)
print Cmat
data_matrix = Cmat
# For VTK to be able to use the data, it must be stored as a VTK-image. This can be done by the vtkImageImport-class which
# imports raw data and stores it.
dataImporter = vtk.vtkImageImport()
# The previously created array is converted to a string of chars and imported.
data_string = data_matrix.tostring()
dataImporter.CopyImportVoidPointer(data_string, len(data_string))
# The type of the newly imported data is set to unsigned char (uint8)
dataImporter.SetDataScalarTypeToUnsignedChar()
# Because the data that is imported only contains an intensity value (it isn't RGB-coded or something similar), the importer
# must be told this is the case.
dataImporter.SetNumberOfScalarComponents(1)
# The following two functions describe how the data is stored and the dimensions of the array it is stored in.
dataImporter.SetDataExtent(0, 1, 0, 2, 0, 3)
dataImporter.SetWholeExtent(0, 1, 0, 2, 0, 3)

# This class stores color data and can create color tables from a few color points. For this demo, we want the three cubes
# to be of the colors red green and blue.
colorFunc = vtk.vtkColorTransferFunction()
colorFunc.AddRGBPoint(5, 1, 0.0, 0.0)  # Red
colorFunc.AddRGBPoint(15, 0.0, 1, 0.0) # Green
colorFunc.AddRGBPoint(25, 0.0, 0.0, 1) # Blue
colorFunc.AddRGBPoint(35, 0.0, 0, 0.0) # Black

# The previous two classes stored properties. Because we want to apply these properties to the volume we want to render,
# we have to store them in a class that stores volume properties.
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorFunc)

volumeMapper = vtk.vtkOpenGLGPUVolumeRayCastMapper()
volumeMapper.SetInputConnection(dataImporter.GetOutputPort())

# The class vtkVolume is used to pair the previously declared volume as well as the properties to be used when rendering that volume.
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)

# With almost everything else ready, its time to initialize the renderer and window, as well as creating a method for exiting the application
renderer = vtk.vtkRenderer()
renderWin = vtk.vtkRenderWindow()
renderWin.AddRenderer(renderer)
renderInteractor = vtk.vtkRenderWindowInteractor()
renderInteractor.SetRenderWindow(renderWin)

# We add the volume to the renderer ...
renderer.AddVolume(volume)
# ... set background color to white ...
renderer.SetBackground(1, 1, 1)
# ... and set window size.
renderWin.SetSize(400, 400)


# A simple function to be called when the user decides to quit the application.
def exitCheck(obj, event):
    if obj.GetEventPending() != 0:
        obj.SetAbortRender(1)


# Tell the application to use the function as an exit check.
renderWin.AddObserver("AbortCheckEvent", exitCheck)

renderInteractor.Initialize()
# Because nothing will be rendered without any input, we order the first render manually before control is handed over to the main-loop.
renderWin.Render()
renderInteractor.Start()