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 This code is based on the otherwise excellent documentation for VTK and the now outdated vtkImageImportFromArray-class created by David Gobbi found at http://public.kitware.com/cgi-bin/cvsweb.cgi/vtk/python/?cvsroot=vtk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.
1 import vtk 2 from numpy import * 3 4 # We begin by creating the data we want to render. 5 # For this tutorial, we create a 3D-image containing three overlaping cubes. 6 # This data can of course easily be replaced by data from a medical CT-scan or anything else three dimensional. 7 # The only limit is that the data must be reduced to unsigned 8 bit or 16 bit integers. 8 data_matrix = zeros([75, 75, 75], dtype=uint8) 9 data_matrix[0:35, 0:35, 0:35] = 50 10 data_matrix[25:55, 25:55, 25:55] = 100 11 data_matrix[45:74, 45:74, 45:74] = 150 12 13 # 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 14 # imports raw data and stores it. 15 dataImporter = vtk.vtkImageImport() 16 # The preaviusly created array is converted to a string of chars and imported. 17 data_string = data_matrix.tostring() 18 dataImporter.CopyImportVoidPointer(data_string, len(data_string)) 19 # The type of the newly imported data is set to unsigned char (uint8) 20 dataImporter.SetDataScalarTypeToUnsignedChar() 21 # Because the data that is imported only contains an intensity value (it isnt RGB-coded or someting similar), the importer 22 # must be told this is the case. 23 dataImporter.SetNumberOfScalarComponents(1) 24 # The following two functions describe how the data is stored and the dimensions of the array it is stored in. For this 25 # simple case, all axes are of length 75 and begins with the first element. For other data, this is probably not the case. 26 # I have to admit however, that I honestly dont know the difference between SetDataExtent() and SetWholeExtent() although 27 # VTK complains if not both are used. 28 dataImporter.SetDataExtent(0, 74, 0, 74, 0, 74) 29 dataImporter.SetWholeExtent(0, 74, 0, 74, 0, 74) 30 31 # The following class is used to store transparencyv-values for later retrival. In our case, we want the value 0 to be 32 # completly opaque whereas the three different cubes are given different transperancy-values to show how it works. 33 alphaChannelFunc = vtk.vtkPiecewiseFunction() 34 alphaChannelFunc.AddPoint(0, 0.0) 35 alphaChannelFunc.AddPoint(50, 0.05) 36 alphaChannelFunc.AddPoint(100, 0.1) 37 alphaChannelFunc.AddPoint(150, 0.2) 38 39 # This class stores color data and can create color tables from a few color points. For this demo, we want the three cubes 40 # to be of the colors red green and blue. 41 colorFunc = vtk.vtkColorTransferFunction() 42 colorFunc.AddRGBPoint(50, 1.0, 0.0, 0.0) 43 colorFunc.AddRGBPoint(100, 0.0, 1.0, 0.0) 44 colorFunc.AddRGBPoint(150, 0.0, 0.0, 1.0) 45 46 # The preavius two classes stored properties. Because we want to apply these properties to the volume we want to render, 47 # we have to store them in a class that stores volume prpoperties. 48 volumeProperty = vtk.vtkVolumeProperty() 49 volumeProperty.SetColor(colorFunc) 50 volumeProperty.SetScalarOpacity(alphaChannelFunc) 51 52 # This class describes how the volume is rendered (through ray tracing). 53 compositeFunction = vtk.vtkVolumeRayCastCompositeFunction() 54 # We can finally create our volume. We also have to specify the data for it, as well as how the data will be rendered. 55 volumeMapper = vtk.vtkVolumeRayCastMapper() 56 volumeMapper.SetVolumeRayCastFunction(compositeFunction) 57 volumeMapper.SetInputConnection(dataImporter.GetOutputPort()) 58 59 # The class vtkVolume is used to pair the preaviusly declared volume as well as the properties to be used when rendering that volume. 60 volume = vtk.vtkVolume() 61 volume.SetMapper(volumeMapper) 62 volume.SetProperty(volumeProperty) 63 64 # With almost everything else ready, its time to initialize the renderer and window, as well as creating a method for exiting the application 65 renderer = vtk.vtkRenderer() 66 renderWin = vtk.vtkRenderWindow() 67 renderWin.AddRenderer(renderer) 68 renderInteractor = vtk.vtkRenderWindowInteractor() 69 renderInteractor.SetRenderWindow(renderWin) 70 71 # We add the volume to the renderer ... 72 renderer.AddVolume(volume) 73 # ... set background color to white ... 74 renderer.SetBackground(1, 1, 1) 75 # ... and set window size. 76 renderWin.SetSize(400, 400) 77 78 # A simple function to be called when the user decides to quit the application. 79 def exitCheck(obj, event): 80 if obj.GetEventPending() != 0: 81 obj.SetAbortRender(1) 82 83 # Tell the application to use the function as an exit check. 84 renderWin.AddObserver("AbortCheckEvent", exitCheck) 85 86 renderInteractor.Initialize() 87 # Because nothing will be rendered without any input, we order the first render manually before control is handed over to the main-loop. 88 renderWin.Render() 89 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: