def BuildBackdrop (minX, maxX, minY, maxY, minZ, maxZ, thickness):
    global basePlane
    global baseMapper
    global base
    global backPlane
    global backMapper
    global back
    global left
    global leftPlane
    global leftMapper
    
    if not basePlane:
        basePlane = vtk.vtkCubeSource()
    basePlane.SetCenter( (maxX + minX)/2.0, minY, (maxZ + minZ)/2.0)
    basePlane.SetXLength(maxX-minX)
    basePlane.SetYLength(thickness)
    basePlane.SetZLength(maxZ - minZ)

    if not baseMapper:
        baseMapper = vtk.vtkPolyDataMapper()
    baseMapper.SetInput(basePlane.GetOutput())

    if not base:
        base = vtk.vtkActor()
    base.SetMapper(baseMapper)

    if not backPlane:
        backPlane = vtk.vtkCubeSource()
    backPlane.SetCenter( (maxX + minX)/2.0, (maxY + minY)/2.0, minZ)
    backPlane.SetXLength(maxX-minX)
    backPlane.SetYLength(maxY - minY)
    backPlane.SetZLength(thickness)

    if not backMapper:
        backMapper = vtk.vtkPolyDataMapper()
    backMapper.SetInput(backPlane.GetOutput())

    if not back:
        back = vtk.vtkActor()
    back.SetMapper(backMapper)

    if not leftPlane:
        leftPlane = vtk.vtkCubeSource()
    leftPlane.SetCenter( minX, (maxY+minY)/2.0, (maxZ+minZ)/2.0)
    leftPlane.SetXLength(thickness)
    leftPlane.SetYLength(maxY-minY)
    leftPlane.SetZLength(maxZ-minZ)

    if not leftMapper:
        leftMapper = vtk.vtkPolyDataMapper()
    leftMapper.SetInput(leftPlane.GetOutput())

    if not left:
        left = vtk.vtkActor()
    left.SetMapper(leftMapper)

    return [base, back, left] 

    def addCube(self,pos,tam,img=False):
        jpegfile = "struct.jpg"
        
        # Read the image data from a file
        reader = vtk.vtkJPEGReader()
        reader.SetFileName(jpegfile)
         
        (x,y,z) = pos
        (i,j,k) = tam

        cubito = vtk.vtkCubeSource()
        cubito.SetXLength(0.2*i)
        cubito.SetYLength(0.2*j)
        cubito.SetZLength(0.2*k)
        cubito.SetCenter((x,y,z)) 
        if img == True:
            
            # Create texture object
            texture = vtk.vtkTexture()
            if vtk.VTK_MAJOR_VERSION <= 5:
                texture.SetInput(reader.GetOutput())
            else:
                texture.SetInputConnection(reader.GetOutputPort())
            # Map texture coordinates
            map_to_sphere = vtk.vtkTextureMapToPlane()
            if vtk.VTK_MAJOR_VERSION <= 5:
                map_to_sphere.SetInput(cubito.GetOutput())
            else:
                map_to_sphere.SetInputConnection(cubito.GetOutputPort())
            #map_to_sphere.PreventSeamOn()
             
            # Create mapper and set the mapped texture as input
            mapper = vtk.vtkPolyDataMapper()
            if vtk.VTK_MAJOR_VERSION <= 5:
                mapper.SetInput(map_to_sphere.GetOutput())
            else:
                mapper.SetInputConnection(map_to_sphere.GetOutputPort())
            
        

        planeMapper = vtk.vtkPolyDataMapper()
        planeMapper.SetInputConnection(cubito.GetOutputPort())
        planeActor = (vtk.vtkActor())
        if (img == True):
            planeActor.SetMapper(mapper)
        else:
            planeActor.SetMapper(planeMapper)# mapper planeMapper
        planeActor.DragableOn()
        planeActor.SetDragable(1)
        if (img== True):
            planeActor.SetTexture(texture)
        else:
            planeActor.GetProperty().SetColor(.0,.3,.6)
            planeActor.GetProperty().SetOpacity(0.95)
        #planeActor.GetProperty().SetAmbient(0)
        #planeActor.GetProperty().SetDiffuse(0.9)
        #planeActor.GetProperty().SetSpecular(0.1)
        self.render.AddActor(planeActor)
        
        return planeActor

    def __init__(self):

        # Creates a cube image of height 0, thus creating a plane.
        cube = vtk.vtkCubeSource()
        cube.SetXLength(120)
        cube.SetYLength(120)
        cube.SetZLength(0)

        #cubeTransform = vtk.vtkTransform()
        #cubeTransform.Translate(0, 0, 0)
        
        cubeMapper = vtk.vtkPolyDataMapper()
        cubeMapper.SetInputConnection(cube.GetOutputPort())
        
        cubeTransformFilter = vtk.vtkTransformPolyDataFilter()
        cubeTransformFilter.SetInputConnection(cube.GetOutputPort())
        #cubeTransformFilter.SetTransform(cubeTransform)
        
        appendFilter = vtk.vtkAppendPolyData()
        #appendFilter.AddInputConnection(line.GetOutputPort())
        appendFilter.AddInputConnection(cubeTransformFilter.GetOutputPort())
       
        # gets the location of the tablet
        self.x = GlobalVariables.imageXDist/2.0 # @UndefinedVariable
        self.y = GlobalVariables.imageYDist/2.0 # @UndefinedVariable
        self.z = GlobalVariables.imageZDist/2.0 # @UndefinedVariable
        
        # moves the cube actor which is what moves the cursor
        self.cubeActor = vtk.vtkActor()
        self.cubeActor.SetMapper(cubeMapper)
        self.cubeActor.GetProperty().SetColor(0.2, 0.6, 0.8)
        self.cubeActor.SetPosition(self.x,self.y,self.z)#(self.sampleSpacing[0]/2,self.sampleSpacing[1]/2,self.sampleSpacing[2]/2)#(-30, -30, -150) #(70,90,50)

    def __init__(self):

        pypes.pypeScript.__init__(self)

        self.CubeSource = vtk.vtkCubeSource()
        self.CubeActor = vtk.vtkActor()
        
        self.BoxActive = 0
        self.BoxBounds = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]

        self.CroppedImage = vtk.vtkImageData()

        self.vmtkRenderer = None
        self.OwnRenderer = 0

        self.PlaneWidgetX = None
        self.PlaneWidgetY = None
        self.PlaneWidgetZ = None
        self.BoxWidget = None

        self.Image = None

        self.Interactive = 1

        self.SetScriptName('vmtkimagevoiselector')
        self.SetScriptDoc('select a cubical volume of interest and get rid of the rest of the image')
        self.SetInputMembers([
            ['Image','i','vtkImageData',1,'','the input image','vmtkimagereader'],
            ['Interactive','interactive','bool',1,'','toggle interactivity'],
            ['BoxBounds','boxbounds','float',6,'','bounds of the cubical region of interest'],
            ['vmtkRenderer','renderer','vmtkRenderer',1,'','external renderer']
            ])
        self.SetOutputMembers([
            ['Image','o','vtkImageData',1,'','the output image','vmtkimagewriter']
            ])

    def __init__(self, parent = None):
        QtGui.QMainWindow.__init__(self, parent)

        self.frame = QtGui.QFrame()

        self.vl = QtGui.QVBoxLayout()
        self.vtkWidget = QVTKRenderWindowInteractor(self.frame)
        self.vl.addWidget(self.vtkWidget)

        self.ren = vtk.vtkRenderer()
        self.vtkWidget.GetRenderWindow().AddRenderer(self.ren)
        self.interactor = self.vtkWidget.GetRenderWindow().GetInteractor()

        # Generate polygon data for a cube
        self.cube = vtk.vtkCubeSource()

        # Create a mapper and an actor for the cube data
        self.cube_mapper = vtk.vtkPolyDataMapper()
        self.cube_mapper.SetInput(self.cube.GetOutput())
        self.cube_actor = vtk.vtkActor()
        self.cube_actor.SetMapper(self.cube_mapper)
        self.cube_actor.GetProperty().SetColor(0.0, 1.0, 0.0)  # make the cube red

        # Create a renderer and add the cube actor to it
        self.ren.SetBackground(0.0, 0.0, 0.0)  # make the background black
        self.ren.AddActor(self.cube_actor)

        self.frame.setLayout(self.vl)
        self.setCentralWidget(self.frame)
        self.show()
        self.interactor.Initialize()

 def __init__(self, parent = None):
     QtGui.QMainWindow.__init__(self, parent)
     self.ui = Ui_MainWindow()
     self.ui.setupUi(self)
     self.ren = vtk.vtkRenderer()
     self.ui.vtkWidget.GetRenderWindow().AddRenderer(self.ren)
     self.iren = self.ui.vtkWidget.GetRenderWindow().GetInteractor()
     cube = vtk.vtkCubeSource()
     cube.SetXLength(200)
     cube.SetYLength(200)
     cube.SetZLength(200)
     cube.Update()
     cm = vtk.vtkPolyDataMapper()
     cm.SetInputConnection(cube.GetOutputPort())
     ca = vtk.vtkActor()
     ca.SetMapper(cm)
     self.ren.AddActor(ca)
     self.axesActor = vtk.vtkAnnotatedCubeActor();
     self.axesActor.SetXPlusFaceText('R')
     self.axesActor.SetXMinusFaceText('L')
     self.axesActor.SetYMinusFaceText('H')
     self.axesActor.SetYPlusFaceText('F')
     self.axesActor.SetZMinusFaceText('P')
     self.axesActor.SetZPlusFaceText('A')
     self.axesActor.GetTextEdgesProperty().SetColor(1,1,0)
     self.axesActor.GetTextEdgesProperty().SetLineWidth(2)
     self.axesActor.GetCubeProperty().SetColor(0,0,1)
     self.axes = vtk.vtkOrientationMarkerWidget()
     self.axes.SetOrientationMarker(self.axesActor)
     self.axes.SetInteractor(self.iren)
     self.axes.EnabledOn()
     self.axes.InteractiveOn()
     self.ren.ResetCamera()

def drawVtkSymb(symbType,renderer, RGBcolor, vPos, vDir, scale):
    '''Adds to the renderer a symbol of type 'arrow', 'doubleArrow',
    'cone', 'doubleCone', 'sphere', 'doubleSphere','cube' , 'doubleCube',
    'cylinder', 'doubleCylinder'

    :param symbType: type of symbol (available types: 'arrow', 'doubleArrow',
           'cone', 'doubleCone', 'sphere', 'doubleSphere','cube' ,
           'doubleCube', 'cylinder', 'doubleCylinder')
    :param renderer: vtk renderer
    :param RGBcolor: list [R,G,B] with the 3 components of color
    :param vPos: list [x,y,z] with the 3 coordinates of the point where
           to place the symbol.
    :param vDir: director vector to orient the symbol
    :param scale: scale to be applied to the symbol representation
    '''
    symTpLow=symbType.lower()
    if 'arrow' in symTpLow:
        symbSource=vtk.vtkArrowSource()
    elif 'cone' in symTpLow:
        symbSource=vtk.vtkConeSource()
    elif 'sphere' in symTpLow:
        symbSource=vtk.vtkSphereSource()
    elif 'cube' in symTpLow:
        symbSource=vtk.vtkCubeSource()
    elif 'cylinder' in symTpLow:
        symbSource=vtk.vtkCylinderSource()
    vPosVx=[vPos[i]-scale/2.0*vDir[i] for i in range(3)] #vertex position
    addSymb(symbSource,renderer, RGBcolor, vPosVx, vDir, scale)
    if 'double' in symTpLow:
        vPosVx=[vPosVx[i]-scale*vDir[i] for i in range(3)] #vertex position
        addSymb(symbSource,renderer, RGBcolor, vPosVx, vDir, scale)

def getCell2vtp(vtkObj,ind):
    """
        Function gets a cell by ind and constructs a polydata from it.

    """

    # Get the cell
    cE = vtkObj.GetCell(ind)
    # Make the polygon
    if cE.GetCellType() == 11:
        # Use a cubeSource, much faster
        cube = vtk.vtkCubeSource()
        cube.SetBounds(cE.GetBounds())
        cube.Update()
        vtpObj = cube.GetOutput()
    else:
        polygons = vtk.vtkCellArray()
        for iF in range(cE.GetNumberOfFaces()):
            f = cE.GetFace(iF)
            poly = vtk.vtkPolygon()
            poly.GetPointIds().SetNumberOfIds(f.GetNumberOfPoints())
            for nr in range(f.GetNumberOfPoints()):
                poly.GetPointIds().SetId(nr,f.GetPointId(nr))
            polygons.InsertNextCell(poly)
        # Build the polydata
        vtpObj = vtk.vtkPolyData()
        vtpObj.SetPoints(obj.GetPoints())
        vtpObj.SetPolys(polygons)

    return polydata.normFilter(polydata.triangulatePolyData(vtpObj))

    def __init__(self, renderer):
        Visualizer.__init__(self)

        assert isinstance(renderer, vtk.vtkRenderer)
        self.ren = renderer
    
        # -------- add the beam ----
        # geometry
        self.beam = vtk.vtkCubeSource()
        self.beam.SetXLength(st.visBeamLength)
        self.beam.SetYLength(st.visBeamWidth)
        self.beam.SetZLength(st.visBeamDepth)

        # mapper
        self.beamMapper = vtk.vtkPolyDataMapper()
        self.beamMapper.SetInputConnection(self.beam.GetOutputPort())

        # actor
        self.beamActor = vtk.vtkLODActor()
        self.beamActor.SetMapper(self.beamMapper)

        # make it look nice
        self.beamProp = self.beamActor.GetProperty()
        self.beamProp.SetColor(101 / 255, 123 / 255, 131 / 255)

        self.ren.AddActor(self.beamActor)

        # -------- add the ball ----
        # geometry
        self.ball = vtk.vtkSphereSource()
        self.ball.SetRadius(st.visR)
        self.ball.SetThetaResolution(20)
        self.ball.SetPhiResolution(20)

        # mapper
        self.ballMapper = vtk.vtkPolyDataMapper()
        self.ballMapper.SetInputConnection(self.ball.GetOutputPort())

        # actor
        self.ballActor = vtk.vtkLODActor()
        self.ballActor.SetMapper(self.ballMapper)

        # make it look nice
        self.ballProp = self.ballActor.GetProperty()
        self.ballProp.SetColor(255 / 255, 255 / 255, 0)
        self.ballProp.SetAmbient(0.2)
        self.ballProp.SetDiffuse(0.8)
        self.ballProp.SetSpecular(0.5)
        self.ballProp.SetSpecularPower(0.5)

        self.ren.AddActor(self.ballActor)

        # add background
        self.ren.GradientBackgroundOn()
        self.ren.SetBackground(228 / 255, 232 / 255, 213 / 255)
        self.ren.SetBackground2(38 / 255, 139 / 255, 210 / 255)

        # get everybody into the frame
        self.ren.ResetCamera()
        self.ren.GetActiveCamera().Zoom(1.7)

    def update_viewer(self, event, *args):
        MarkerWindowInteractor.update_viewer(self, event, *args)
        if event=='color marker':
            marker, color = args
            marker.set_color(color)
        elif event=='label marker':
            marker, label = args
            marker.set_label(label)
            
            if shared.debug: print "Create VTK-Text", marker.get_label()
            text = vtk.vtkVectorText()
            text.SetText(marker.get_label())
            textMapper = vtk.vtkPolyDataMapper()
            textMapper.SetInput(text.GetOutput())
            textActor = self.textActors[marker]
            textActor.SetMapper(textMapper)

        elif event=='move marker':
            marker, center = args
            marker.set_center(center)
            #update the select boxes and text actor
            textActor = self.textActors[marker]
            size = marker.get_size()
            textActor.SetScale(size, size, size)
            x,y,z = marker.get_center()
            textActor.SetPosition(x+size, y+size, z+size)

            if self.boxes.has_key(marker):
                selectActor = self.boxes[marker]
                boxSource = vtk.vtkCubeSource()
                boxSource.SetBounds(marker.GetBounds())
                mapper = vtk.vtkPolyDataMapper()
                mapper.SetInput(boxSource.GetOutput())
                selectActor.SetMapper(mapper)
                
        elif event=='labels on':
            actors = self.textActors.values()
            for actor in actors:
                actor.VisibilityOn()
        elif event=='labels off':
            actors = self.textActors.values()
            for actor in actors:
                actor.VisibilityOff()
        #elif event=='select marker':
        #    marker = args[0]
        #    actor = create_box_actor_around_marker(marker)
        #    if shared.debug: print "PlaneWidgetsXYZ.update_viewer(): self.renderer.AddActor(actor)"
        #    self.renderer.AddActor(actor)
        #    self.boxes[marker] = actor
        #elif event=='unselect marker':
        #    marker = args[0]
        #    actor = self.boxes[marker]
        #    print "pwxyz: u m", repr(marker), repr(actor)
        #    self.renderer.RemoveActor(actor)
        #    del self.boxes[marker]
        elif event=="set axes directions":
            self.add_axes_labels()
            EventHandler().notify('observers update plane')
        
        self.Render()

    def __init__(self):

        pypes.pypeScript.__init__(self)

        self.CubeSource = vtk.vtkCubeSource()
        self.CubeActor = vtk.vtkActor()
        
        self.BoxActive = 0
        self.BoxBounds = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
        self.PaintValue = 0.0

        self.vmtkRenderer = None
        self.OwnRenderer = 0

        self.PlaneWidgetX = None
        self.PlaneWidgetY = None
        self.PlaneWidgetZ = None
        self.BoxWidget = None

        self.Image = None

        self.Interactive = 1

        self.SetScriptName('vmtkimagevoipainter')
        self.SetScriptDoc('fill a cubical region of an image with a given gray level')
        self.SetInputMembers([
            ['Image','i','vtkImageData',1,'','the input image','vmtkimagereader'],
            ['Interactive','interactive','bool',1,'','toggle interactivity'],
            ['BoxBounds','boxbounds','float',6,'','bounds of the cubical region for non-interactive mode'],
            ['PaintValue','paintvalue','float',1,'','graylevel to fill the region with'],
            ['vmtkRenderer','renderer','vmtkRenderer',1,'','external renderer']
            ])
        self.SetOutputMembers([
            ['Image','o','vtkImageData',1,'','the output image','vmtkimagewriter']
            ])

 def __init__(self, pos, radius, rgb=[0.62, 0, 0.77]):
     self.source = vtk.vtkCubeSource()
     self.mapper = vtk.vtkPolyDataMapper()
     
     # length of sides
     self.source.SetXLength(radius)
     self.source.SetYLength(radius)
     self.source.SetZLength(radius)
     
     # centre
     self.source.SetCenter(pos)
     
     # edges filter
     edges = vtk.vtkExtractEdges()
     edges.SetInputConnection(self.source.GetOutputPort())
     
     # tube filter
     tubes = vtk.vtkTubeFilter()
     tubes.SetInputConnection(edges.GetOutputPort())
     tubes.SetRadius(0.15)
     tubes.SetNumberOfSides(5)
     tubes.UseDefaultNormalOn()
     tubes.SetDefaultNormal(.577, .577, .577)
     
     # mapper
     self.mapper.SetInputConnection(tubes.GetOutputPort())
     
     # actor
     self.SetMapper(self.mapper)
     self.GetProperty().SetColor(rgb)

def add_tube(prev, x, y):
    cylA = create_cylinder(r=3.155, h=8.6)

    cube = vtk.vtkCubeSource()
    cube.SetXLength(.75)
    cube.SetYLength(6.6)
    cube.SetZLength(13.6)
    cube.SetCenter(0, 1, 0)

    bA = vtkbool.vtkPolyDataBooleanFilter()
    bA.SetInputConnection(cylA.GetOutputPort())
    bA.SetInputConnection(1, cube.GetOutputPort())
    bA.SetOperModeToUnion()

    cylB = create_cylinder(r=2.405, h=8.6)

    bB = vtkbool.vtkPolyDataBooleanFilter()
    bB.SetInputConnection(bA.GetOutputPort())
    bB.SetInputConnection(1, cylB.GetOutputPort())
    bB.SetOperModeToDifference()

    tr = vtk.vtkTransform()
    tr.Translate(x, y, 4.3)
    tr.RotateX(90)

    tf = vtk.vtkTransformPolyDataFilter()
    tf.SetTransform(tr)
    tf.SetInputConnection(bB.GetOutputPort())

    bC = vtkbool.vtkPolyDataBooleanFilter()
    bC.SetInputConnection(prev.GetOutputPort())
    bC.SetInputConnection(1, tf.GetOutputPort())
    bC.SetOperModeToUnion()

    return bC

 def __init__(self, module_manager):
     SimpleVTKClassModuleBase.__init__(
         self, module_manager,
         vtk.vtkCubeSource(), 'Processing.',
         (), ('vtkPolyData',),
         replaceDoc=True,
         inputFunctions=None, outputFunctions=None)

def MkCube( cx, cy, cz, l ):
    CubeModel = vtk.vtkCubeSource()
    CubeModel.SetCenter(cx, cy ,cz)
    CubeModel.SetXLength(l)
    CubeModel.SetYLength(l)
    CubeModel.SetZLength(l)
    return CubeModel

    def render(self, pointsData, scalarsArray, radiusArray, nspecies, colouringOptions, atomScaleFactor, lut):
        """
        Render the given antisites (wire frame).
        
        """
        self._logger.debug("Rendering antisites: colour by '%s'", colouringOptions.colourBy)

        # points
        points = vtk.vtkPoints()
        points.SetData(pointsData.getVTK())

        # poly data
        polydata = vtk.vtkPolyData()
        polydata.SetPoints(points)
        polydata.GetPointData().AddArray(scalarsArray.getVTK())
        polydata.GetPointData().SetScalars(radiusArray.getVTK())

        # source
        cubeSource = vtk.vtkCubeSource()
        edges = vtk.vtkExtractEdges()
        edges.SetInputConnection(cubeSource.GetOutputPort())
        glyphSource = vtk.vtkTubeFilter()
        glyphSource.SetInputConnection(edges.GetOutputPort())
        glyphSource.SetRadius(0.05)
        glyphSource.SetVaryRadius(0)
        glyphSource.SetNumberOfSides(5)
        glyphSource.UseDefaultNormalOn()
        glyphSource.SetDefaultNormal(0.577, 0.577, 0.577)

        # glyph
        glyph = vtk.vtkGlyph3D()
        if vtk.vtkVersion.GetVTKMajorVersion() <= 5:
            glyph.SetSource(glyphSource.GetOutput())
            glyph.SetInput(polydata)
        else:
            glyph.SetSourceConnection(glyphSource.GetOutputPort())
            glyph.SetInputData(polydata)
        glyph.SetScaleFactor(atomScaleFactor * 2.0)
        glyph.SetScaleModeToScaleByScalar()
        glyph.ClampingOff()

        # mapper
        mapper = vtk.vtkPolyDataMapper()
        mapper.SetInputConnection(glyph.GetOutputPort())
        mapper.SetLookupTable(lut)
        mapper.SetScalarModeToUsePointFieldData()
        mapper.SelectColorArray("colours")
        utils.setMapperScalarRange(mapper, colouringOptions, nspecies)

        # actor
        actor = vtk.vtkActor()
        actor.SetMapper(mapper)

        # store attributes
        self._actor = utils.ActorObject(actor)
        self._data["Points"] = pointsData
        self._data["Scalars"] = scalarsArray
        self._data["Radius"] = radiusArray
        self._data["LUT"] = lut
        self._data["Scale factor"] = atomScaleFactor

    def __init__(self, length, position=(0, 0, 0), **kwargs):
        cube = vtk.vtkCubeSource()
        cube.SetXLength(length)
        cube.SetYLength(length)
        cube.SetZLength(length)
        cube.SetCenter(position)
        cube.Update()

        super(Cube, self).__init__(cube, position, **kwargs)

	def __init__(self):
		Model.__init__(self)
		self.source = vtk.vtkCubeSource()
		self.source.SetCenter(0.0, 0.0, 0.0)
		self.source.SetXLength(1.0)
		self.source.SetYLength(1.0)
		self.source.SetZLength(1.0)
		self.source.Update()
		self.Update()

 def render(self, pointsData, scalarsArray, radiusArray, nspecies, colouringOptions, atomScaleFactor, lut, settings):
     """
     Render the given antisites (wire frame).
     
     """
     self._logger.debug("Rendering vacancies: colour by '%s'", colouringOptions.colourBy)
     
     # points
     points = vtk.vtkPoints()
     points.SetData(pointsData.getVTK())
     
     # poly data
     polydata = vtk.vtkPolyData()
     polydata.SetPoints(points)
     polydata.GetPointData().AddArray(scalarsArray.getVTK())
     polydata.GetPointData().SetScalars(radiusArray.getVTK())
     
     # source
     glyphSource = vtk.vtkCubeSource()
     
     # glyph
     glyph = vtk.vtkGlyph3D()
     if vtk.vtkVersion.GetVTKMajorVersion() <= 5:
         glyph.SetSource(glyphSource.GetOutput())
         glyph.SetInput(polydata)
     else:
         glyph.SetSourceConnection(glyphSource.GetOutputPort())
         glyph.SetInputData(polydata)
     scaleVacs = 2.0 * settings.getSetting("vacScaleSize")
     glyph.SetScaleFactor(atomScaleFactor * scaleVacs)
     glyph.SetScaleModeToScaleByScalar()
     glyph.ClampingOff()
       
     # mapper
     mapper = vtk.vtkPolyDataMapper()
     mapper.SetInputConnection(glyph.GetOutputPort())
     mapper.SetLookupTable(lut)
     mapper.SetScalarModeToUsePointFieldData()
     mapper.SelectColorArray("colours")
     utils.setMapperScalarRange(mapper, colouringOptions, nspecies)
     
     # actor
     actor = vtk.vtkActor()
     actor.SetMapper(mapper)
     actor.GetProperty().SetSpecular(settings.getSetting("vacSpecular"))
     actor.GetProperty().SetSpecularPower(settings.getSetting("vacSpecularPower"))
     actor.GetProperty().SetOpacity(settings.getSetting("vacOpacity"))
     
     # store attributes
     self._actor = utils.ActorObject(actor)
     self._data["Points"] = pointsData
     self._data["Scalars"] = scalarsArray
     self._data["Radius"] = radiusArray
     self._data["LUT"] = lut
     self._data["Scale factor"] = atomScaleFactor
     self._data["Vacancy opacity"] = settings.getSetting("vacOpacity")

def load_octomap(octomap_h5_file, conf=0.9, wireframe=False):
    h5f = h5py.File(octomap_h5_file, 'r')
    octree_data = h5f['octree'][...]

    octree_data = octree_data[octree_data[:, 4] > conf]
    pts = vtk.vtkPoints()
    #vtk_pt_data = converter.numpy_to_vtk(np.ascontiguousarray(octree_data[:, 0:3]))
    #pts.SetData(vtk_pt_data)

    use_colors = octree_data.shape[1] > 5
    colors = vtk.vtkUnsignedCharArray()
    colors.SetNumberOfComponents(3)
    #color_data = np.ascontiguousarray(octree_data[:, 5:8])
    #colors = converter.numpy_to_vtk(color_data)
    #colors.SetName('ColorArray')
    #polydata.GetPointData().SetActiveScalars('ColorArray')

    for k in range(octree_data.shape[0]):
        pts.InsertNextPoint(*octree_data[k, 0:3])
        if use_colors:
            r = int(octree_data[k, 5])
            g = int(octree_data[k, 6])
            b = int(octree_data[k, 7])
            colors.InsertNextTupleValue((r, g, b))

    polydata = vtk.vtkPolyData()
    polydata.SetPoints(pts)
    if use_colors:
        polydata.GetPointData().SetScalars(colors)

    cube = vtk.vtkCubeSource()
    cube.SetXLength(octree_data[0, 3])
    cube.SetYLength(octree_data[0, 3])
    cube.SetZLength(octree_data[0, 3])

    glyph = vtk.vtkGlyph3D()
    if use_colors:
        glyph.SetColorModeToColorByScalar()
    glyph.SetSourceConnection(cube.GetOutputPort())
    glyph.SetInput(polydata)
    glyph.ScalingOff()
    glyph.Update()

    mapper = vtk.vtkPolyDataMapper()
    mapper.SetInputConnection(glyph.GetOutputPort())

    actor = vtk.vtkActor()
    actor.SetMapper(mapper)
    if wireframe:
        actor.GetProperty().SetRepresentationToWireframe()
        actor.GetProperty().SetLineWidth(1)
        actor.GetProperty().SetOpacity(0.2)
    actor.GetProperty().LightingOff()

    return actor