VTK：3D矩阵的音量尺寸错误

Question

我想将3-D矩阵（X * Y分辨率的Z切片）可视化为经典的3-d体素。 我在MATLAB中生成矩阵并将其导入Python。 然后，按照代码here和here，我想出了这个解决方案。 通过这个演示，我使用的矩阵应该生成一个包含4片2 * 3体素的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]]]

接下来的代码会产生这个图像（我为了方便而旋转）：

产生的形状不是2 * 3 * 4而切片的大小不一样，我做错了什么？我试图调整

dataImporter.SetDataExtent
dataImporter.SetWholeExtent
dataImporter.SetDataSpacing

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

我按预期获得了一个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)

我获得了2x4x2固体（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)

我获得了2x20x4实体

这似乎与setDataExtent和SetWholeExtent：

的文档相矛盾

*您的数据维度必须等于（范围1 - 范围[0] +1）*（范围4 - 范围3 + 1）*（范围{ {3}} - {DataExtent {3}} + 1）。例如，对于2D图像使用（0，宽度-1,0，高度-1,0,0）。*

任何想法？

以下完整代码 MATLAB：

C = zeros(2,3,4)
C(:,:,1) = 5;
C(:,:,2) = 15;
C(:,:,3) = 25;
C(:,:,4) = 35;

save Cmat C

的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()

我唯一的假设是这些体素不是立方体，但其中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个受此影响。

[UPDATE]： 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，可以看出第一个和最后一个切片比其余切片更薄。 5

Answer 1

这是一个古老的问题，可能您已经找到答案了。

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。 MATLAB可能会将3D矩阵存储为以列为主的数据结构，而VTK将以行为主的数据恢复。 另一种可能是读取文件并获得2x20x4实体时会交换尺寸。