Vtk volume rendering¶
As I had some problems in figuring out how to use VTK to render data contained in a three dimensional numpy array, I have decided to share my code. This code is based on the otherwise excellent documentation for VTK and the now outdated vtkImageImportFromArray-class created by David Gobbi found at http://public.kitware.com/cgi-bin/cvsweb.cgi/vtk/python/?cvsroot=vtk
The example is very simple, for more advanced functionality: read the documentation.
import vtk from numpy import * # We begin by creating the data we want to render. # For this tutorial, we create a 3D-image containing three overlaping cubes. # This data can of course easily be replaced by data from a medical CT-scan or anything else three dimensional. # The only limit is that the data must be reduced to unsigned 8 bit or 16 bit integers. data_matrix = zeros([75, 75, 75], dtype=uint8) data_matrix[0:35, 0:35, 0:35] = 50 data_matrix[25:55, 25:55, 25:55] = 100 data_matrix[45:74, 45:74, 45:74] = 150 # 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 preaviusly 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 isnt RGB-coded or someting 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. For this # simple case, all axes are of length 75 and begins with the first element. For other data, this is probably not the case. # I have to admit however, that I honestly dont know the difference between SetDataExtent() and SetWholeExtent() although # VTK complains if not both are used. dataImporter.SetDataExtent(0, 74, 0, 74, 0, 74) dataImporter.SetWholeExtent(0, 74, 0, 74, 0, 74) # The following class is used to store transparencyv-values for later retrival. In our case, we want the value 0 to be # completly opaque whereas the three different cubes are given different transperancy-values to show how it works. alphaChannelFunc = vtk.vtkPiecewiseFunction() alphaChannelFunc.AddPoint(0, 0.0) alphaChannelFunc.AddPoint(50, 0.05) alphaChannelFunc.AddPoint(100, 0.1) alphaChannelFunc.AddPoint(150, 0.2) # 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(50, 1.0, 0.0, 0.0) colorFunc.AddRGBPoint(100, 0.0, 1.0, 0.0) colorFunc.AddRGBPoint(150, 0.0, 0.0, 1.0) # The preavius 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 prpoperties. volumeProperty = vtk.vtkVolumeProperty() volumeProperty.SetColor(colorFunc) volumeProperty.SetScalarOpacity(alphaChannelFunc) # This class describes how the volume is rendered (through ray tracing). compositeFunction = vtk.vtkVolumeRayCastCompositeFunction() # We can finally create our volume. We also have to specify the data for it, as well as how the data will be rendered. volumeMapper = vtk.vtkVolumeRayCastMapper() volumeMapper.SetVolumeRayCastFunction(compositeFunction) volumeMapper.SetInputConnection(dataImporter.GetOutputPort()) # The class vtkVolume is used to pair the preaviusly 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()
To exit the application, simply press q.
In my opinion, the volume renderer creates extremely ugly images if not the following option is used:
Section author: Unknown, PauliVirtanen