def volumeRender(img, tf=[], spacing=[1.0, 1.0, 1.0]):
importer = numpy2VTK(img, spacing)
# Transfer Functions
opacity_tf = vtk.vtkPiecewiseFunction()
color_tf = vtk.vtkColorTransferFunction()
if len(tf) == 0:
tf.append([img.min(), 0, 0, 0, 0])
tf.append([img.max(), 1, 1, 1, 1])
for p in tf:
color_tf.AddRGBPoint(p[0], p[1], p[2], p[3])
opacity_tf.AddPoint(p[0], p[4])
# working on the GPU
volMapper = vtk.vtkGPUVolumeRayCastMapper()
volMapper.SetInputConnection(importer.GetOutputPort())
# The property describes how the data will look
volProperty = vtk.vtkVolumeProperty()
volProperty.SetColor(color_tf)
volProperty.SetScalarOpacity(opacity_tf)
volProperty.ShadeOn()
volProperty.SetInterpolationTypeToLinear()
# working on the CPU
#volMapper = vtk.vtkVolumeRayCastMapper()
#compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
#compositeFunction.SetCompositeMethodToInterpolateFirst()
#volMapper.SetVolumeRayCastFunction(compositeFunction)
#volMapper.SetInputConnection(importer.GetOutputPort())
# The property describes how the data will look
volProperty = vtk.vtkVolumeProperty()
volProperty.SetColor(color_tf)
volProperty.SetScalarOpacity(opacity_tf)
volProperty.ShadeOn()
volProperty.SetInterpolationTypeToLinear()
# Do the lines below speed things up?
# pix_diag = 5.0
# volMapper.SetSampleDistance(pix_diag / 5.0)
# volProperty.SetScalarOpacityUnitDistance(pix_diag)
vol = vtk.vtkVolume()
vol.SetMapper(volMapper)
vol.SetProperty(volProperty)
return [vol]
def MakeVTKColorScheme(ZeroPoint,
MaxScaledVal,
poscolor=(0.95, 0.5, 0.14),
negcolor=(0, 0.23, 0.48)):
#Opacity transfer function
opacitytf = vtk.vtkPiecewiseFunction()
opacitytf.AddPoint(0, 1.0)
opacitytf.AddPoint(ZeroPoint - 1, 0.0)
opacitytf.AddPoint(ZeroPoint + 1, 0.0)
opacitytf.AddPoint(MaxScaledVal, 1.0)
#Color transfer function
colortf = vtk.vtkColorTransferFunction()
colortf.AddRGBPoint(0, *negcolor)
colortf.AddRGBPoint(ZeroPoint - 1, *negcolor)
colortf.AddRGBPoint(ZeroPoint + 1, *poscolor)
colortf.AddRGBPoint(MaxScaledVal, *poscolor)
volprp = vtk.vtkVolumeProperty()
volprp.SetColor(colortf)
volprp.SetScalarOpacity(opacitytf)
volprp.ShadeOn()
volprp.SetInterpolationTypeToLinear()
return volprp
def extractCellsByID(self, idlist, usePointIDs=False):
"""Return a new TetMesh composed of the specified subset of indices."""
selectionNode = vtk.vtkSelectionNode()
if usePointIDs:
selectionNode.SetFieldType(vtk.vtkSelectionNode.POINT)
contcells = vtk.vtkSelectionNode.CONTAINING_CELLS()
selectionNode.GetProperties().Set(contcells, 1)
else:
selectionNode.SetFieldType(vtk.vtkSelectionNode.CELL)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
vidlist = numpy_to_vtkIdTypeArray(np.array(idlist).astype(np.int64))
selectionNode.SetSelectionList(vidlist)
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
es = vtk.vtkExtractSelection()
es.SetInputData(0, self._ugrid)
es.SetInputData(1, selection)
es.Update()
tm_sel = TetMesh(es.GetOutput())
pr = vtk.vtkVolumeProperty()
pr.DeepCopy(self.GetProperty())
tm_sel.SetProperty(pr)
#assign the same transformation to the copy
tm_sel.SetOrigin(self.GetOrigin())
tm_sel.SetScale(self.GetScale())
tm_sel.SetOrientation(self.GetOrientation())
tm_sel.SetPosition(self.GetPosition())
tm_sel._mapper.SetLookupTable(utils.ctf2lut(self))
return tm_sel
def read_images(self, filename, r, g, b, t1=0):
# 2 set up the source
self.reader_src = vtk.vtkNIFTIImageReader()
self.reader_src.SetFileName(filename)
# 3 set up the volume mapper
self.vol_map = vtk.vtkGPUVolumeRayCastMapper()
self.vol_map.SetInputConnection(self.reader_src.GetOutputPort())
# 4 transfer functions for color and opacity
self.funColor = vtk.vtkColorTransferFunction()
self.funColor.AddRGBPoint(0, 0., 0., 0.)
self.funColor.AddRGBPoint(1, r, g, b)
# 5 assign also an alpha (opacity) gradient to the values
if t1 == 1:
self.funAlpha = vtk.vtkPiecewiseFunction()
self.funAlpha.AddPoint(0, 0.)
self.funAlpha.AddPoint(256, 0.01)
else:
self.funAlpha = vtk.vtkPiecewiseFunction()
self.funAlpha.AddPoint(0, 0.)
self.funAlpha.AddPoint(0.01, 0.01)
self.volProp = vtk.vtkVolumeProperty()
self.volProp.SetColor(0, self.funColor)
self.volProp.SetScalarOpacity(0, self.funAlpha)
self.volProp.SetInterpolationTypeToLinear()
self.volActor = vtk.vtkVolume()
self.volActor.SetMapper(self.vol_map)
self.volActor.SetProperty(self.volProp)
return self.volActor, self.funAlpha
def volumeRender(self, img, tf=[], spacing=[1.0, 1.0, 1.0]):
importer = dicomShow.numpy2VTK(img, spacing)
# Transfer Functions
opacity_tf = vtk.vtkPiecewiseFunction()
color_tf = vtk.vtkColorTransferFunction()
if len(tf) == 0:
tf.append([img.min(), 0, 0, 0, 0])
tf.append([img.max(), 1, 1, 1, 1])
for p in tf:
color_tf.AddRGBPoint(p[0], p[1], p[2], p[3])
opacity_tf.AddPoint(p[0], p[4])
# working on the GPU
volMapper = vtk.vtkGPUVolumeRayCastMapper()
volMapper.SetInputConnection(importer.GetOutputPort())
# The property describes how the data will look
volProperty = vtk.vtkVolumeProperty()
volProperty.SetColor(color_tf)
volProperty.SetScalarOpacity(opacity_tf)
volProperty.ShadeOn()
volProperty.SetInterpolationTypeToLinear()
vol = vtk.vtkVolume()
vol.SetMapper(volMapper)
vol.SetProperty(volProperty)
return [vol]
def setup_volume_actor(image, valueRange=None, cmap='jet'):
volumeMapper = vtk.vtkSmartVolumeMapper()
if vtk.VTK_MAJOR_VERSION > 5:
volumeMapper.SetInputData(image)
else:
volumeMapper.SetInput(image)
if not valueRange:
valueRange = image.GetPointData().GetScalars().GetRange()
valueSize = valueRange[1] - valueRange[0]
valueRange = [
valueRange[0] + valueSize * 0.1, valueRange[0] + valueSize * 0.9
]
volumeProperties = vtk.vtkVolumeProperty()
volumeProperties.ShadeOff()
colormap = build_ctf(cmap, valueRange)
volumeProperties.SetColor(colormap)
volumeProperties.SetScalarOpacity(build_opacity_function(valueRange))
scalarOpacityUnitDistance = min(image.GetSpacing()) * 2.0
volumeProperties.SetScalarOpacityUnitDistance(scalarOpacityUnitDistance)
volumeProperties.SetGradientOpacity(default_gradient_opacity())
volumeProperties.SetInterpolationTypeToLinear()
volumeActor = vtk.vtkVolume()
volumeActor.SetMapper(volumeMapper)
volumeActor.SetProperty(volumeProperties)
return volumeMapper, volumeActor
def viz_VisualizeDICOM(self, path):
volume = vtk.vtkVolume()
dc_img_reader = vtk.vtkDICOMImageReader()
dc_img_reader.SetDirectoryName(path)
dc_img_reader.Update()
dc_color_func = vtk.vtkColorTransferFunction()
dc_color_func.AddRGBPoint(-3024, 0.0, 0.0, 0.0)
dc_color_func.AddRGBPoint(-77, 0.55, 0.25, 0.15)
dc_color_func.AddRGBPoint(94, 0.88, 0.60, 0.29)
dc_color_func.AddRGBPoint(179, 1.0, 0.94, 0.95)
dc_color_func.AddRGBPoint(260, 0.62, 0.0, 0.0)
dc_color_func.AddRGBPoint(3071, 0.82, 0.66, 1.0)
dc_alpha_func = vtk.vtkPiecewiseFunction()
dc_alpha_func.AddPoint(-3024, 0.0)
dc_alpha_func.AddPoint(-77, 0.0)
dc_alpha_func.AddPoint(94, 0.29)
dc_alpha_func.AddPoint(179, 0.55)
dc_alpha_func.AddPoint(260, 0.84)
dc_alpha_func.AddPoint(3071, 0.875)
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(dc_color_func)
volumeProperty.SetScalarOpacity(dc_alpha_func)
volumeProperty.ShadeOn()
volumeProperty.SetInterpolationTypeToLinear()
volumeMapper = vtk.vtkGPUVolumeRayCastMapper()
volumeMapper.SetInputConnection(dc_img_reader.GetOutputPort())
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
self.__ren.AddVolume(volume)
def __init__(self, data_reader):
#if vtk_structured_points_data!=None:
# ukosniki=vtk_structured_points_data.count("/")
# etykieta=vtk_structured_points_data.split("/",ukosniki)
# self.WhoAmI=self.WhoAmI+" "+ etykieta[ukosniki]
#def make_name(self,name):
# if name!=None:
# ukosniki=name.count("/")
# etykieta=name.split("/",ukosniki)
# self.WhoAmI=self.WhoAmI+" "+ etykieta[ukosniki]
self.make_color_function(data_reader.get_data_set().GetScalarRange())
# The property describes how the data will look
self.volumeProperty = vtk.vtkVolumeProperty()
self.volumeProperty.SetColor(self.colorTransferFunction)
self.volumeProperty.SetScalarOpacity(self.opacityTransferFunction)
self.volumeProperty.SetGradientOpacity(self.gradientTransferFunction)
# The mapper / ray cast function know how to render the data
self.compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
self.cast = vtk.vtkImageCast()
self.cast.SetInput(data_reader.get_data_set())
self.cast.SetOutputScalarTypeToUnsignedShort()
self.cast.ClampOverflowOff()
self.mapper = vtk.vtkVolumeRayCastMapper()
self.mapper.SetVolumeRayCastFunction(self.compositeFunction)
self.mapper.SetInputConnection(self.cast.GetOutputPort())
self.actor = vtk.vtkVolume()
self.actor.SetMapper(self.mapper)
self.actor.SetProperty(self.volumeProperty)
def create_volume_rendering(self):
opacityfunction=vtk.vtkPiecewiseFunction()
opacityfunction.AddPoint(0,0.0)
opacityfunction.AddPoint(0.1,0.01)
opacityfunction.AddPoint(1,0.02)
opacityfunction.AddPoint(1.5,0.03)
volproperty=vtk.vtkVolumeProperty()
volproperty.SetColor(self.arrowColor)
volproperty.SetScalarOpacity(opacityfunction)
volproperty.ShadeOn()
volproperty.SetInterpolationTypeToLinear()
volumeMapper = vtk.vtkGPUVolumeRayCastMapper()
volumeMapper.SetInputConnection(self.vol_reader.GetOutputPort())
volumeMapper.SetSampleDistance(0.01)
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volproperty)
return volume
def get_volume(self, color_file=None, volume_opacity=0.25):
"""
Default Volume Rendering
Return vtkActor. For volume rendering it is vtkVolume
"""
if not self.flag_read:
sys.stderr.write('No Image Loaded.')
return
# TEST
print self.is_blank_image()
transfer_func = self.get_transfer_functioin(color_file, volume_opacity)
prop_volume = vtk.vtkVolumeProperty()
prop_volume.ShadeOff()
prop_volume.SetColor(transfer_func[0])
prop_volume.SetScalarOpacity(transfer_func[1])
prop_volume.SetGradientOpacity(transfer_func[2])
prop_volume.SetInterpolationTypeToLinear()
prop_volume.SetAmbient(0.4)
prop_volume.SetDiffuse(0.6)
prop_volume.SetSpecular(0.2)
mapper = vtk.vtkSmartVolumeMapper()
mapper.SetRequestedRenderMode(0)
# mapper = vtk.vtkGPUVolumeRayCastMapper()
mapper.SetInputData(self.reader)
actor = vtk.vtkVolume()
actor.SetMapper(mapper)
actor.SetProperty(prop_volume)
return actor
def __init__(self, source):
# 3 set up the volume mapper
volume_mapper = vtk.vtkGPUVolumeRayCastMapper()
volume_mapper.SetInputConnection(source.GetOutputPort())
# 4 transfer functions for color and opacity
self.color_transfer = vtk.vtkColorTransferFunction()
self.alpha_transfer = vtk.vtkPiecewiseFunction()
self.c_map_name = 'copper'
self.c_map = cm.get_cmap(self.c_map_name)
self.init_opacity_points()
self.set_color_transfer() # Fill color transfer function
# 6 set up the volume properties
self.volume_properties = vtk.vtkVolumeProperty()
self.volume_properties.SetColor(0, self.color_transfer)
self.volume_properties.SetScalarOpacity(0, self.alpha_transfer)
self.volume_properties.SetInterpolationTypeToLinear()
self.volume_properties.ShadeOn()
self.volume_properties.SetAmbient(1.0)
self.volume_properties.SetDiffuse(0.7)
self.volume_properties.SetSpecular(0.5)
# 7 set up the actor
self.actor = vtk.vtkVolume()
self.actor.SetMapper(volume_mapper)
self.actor.SetProperty(self.volume_properties)
def test():
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName("C:/Users/Asus/Dropbox/2017-18/ScientificCompAndVisualization/Semana2/SS_2017-master/SS_2017-master/data/wind_image.vti")
volume = vtk.vtkVolume()
#mapper = vtk.vtkFixedPointVolumeRayCastMapper()
mapper = vtk.vtkGPUVolumeRayCastMapper()
mapper.SetBlendModeToMinimumIntensity();
mapper.SetSampleDistance(0.1)
mapper.SetAutoAdjustSampleDistances(0)
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
iRen = vtk.vtkRenderWindowInteractor()
# Set connections
mapper.SetInputConnection(reader.GetOutputPort());
volume.SetMapper(mapper)
ren.AddViewProp(volume)
renWin.AddRenderer(ren)
iRen.SetRenderWindow(renWin)
# Define opacity transfer function and color functions
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint(0.1, 1.0)
opacityTransferFunction.AddPoint(14, 0.5)
# Create transfer mapping scalar value to color
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.AddRGBPoint(1.5, 1.0, 1.0, 0.0)
colorTransferFunction.AddRGBPoint(0.5, 1.0, 0.0, 0.0)
colorTransferFunction.AddRGBPoint(3.0, 0.0, 1.0, 0.0)
colorTransferFunction.AddRGBPoint(6.0, 0.0, 1.0, 1.0)
colorTransferFunction.AddRGBPoint(14.0, 0.0, 0.0, 1.0)
# Now set the opacity and the color
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorTransferFunction)
volumeProperty.SetScalarOpacity(opacityTransferFunction)
volumeProperty.ShadeOff()
volumeProperty.SetInterpolationTypeToLinear()
volume.SetProperty(volumeProperty)
renderer = vtk.vtkRenderer()
renderer.SetBackground(0.5, 0.5, 0.5)
renderer.AddVolume(volume)
renderer.ResetCamera()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindow.SetSize(500, 500)
renderWindow.Render()
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renderWindow)
iren.Start()
def _initialize (self):
debug ("In Volume::_initialize ()")
self.data_range = dr = self.mod_m.get_scalar_data_range ()
ctf = default_color_transfer_function(dr[0], dr[1])
otf = default_opacity_transfer_function(dr[0], dr[1])
self.rc_func = 0 # 0 - composite, 1 - MIP, 2 - Isosurface
self.ray_cast_func = self.get_ray_cast_function()
self.vp_func = 0 # 0 - composite, 1 - MAXIP, 2 - MINIP
# 0 - Ray cast, 1 - TextureMapper, 2 -- VolumeProMapper
self.map_type = -1 # Uninitialized
map_type = 0 # default to ray cast.
self.set_map_type(map_type)
self.map.SetInput (self.mod_m.GetOutput ())
# The property describes how the data will look
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(ctf)
volumeProperty.SetScalarOpacity(otf)
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.ShadeOn()
self.act.SetMapper (self.map)
self.act.SetProperty (volumeProperty)
self.renwin.add_actors (self.act)
# used for the pipeline browser
self.pipe_objs = self.act
def __init__(self):
super(VolumeVisualizationSimple, self).__init__()
self.visualizationType = VisualizationTypeSimple
# Create the volume property
self.volProp = vtkVolumeProperty()
self.volProp.SetIndependentComponents(True)
self.volProp.SetInterpolationTypeToLinear()
self.volProp.ShadeOn()
self.volProp.SetAmbient(0.3)
self.volProp.SetDiffuse(0.8)
self.volProp.SetSpecular(0.2)
self.volProp.SetSpecularPower(10.0)
self.volProp.SetScalarOpacityUnitDistance(0.8919)
self.minimum = 0
self.maximum = 1
self.lowerBound = 0
self.upperBound = 1
colors = [[255, 139, 0], [0, 147, 255], [0, 255, 147], [213, 100, 255],
[255, 75, 75]]
self.colors = map(lambda x: [x[0] / 255.0, x[1] / 255.0, x[2] / 255.0],
colors)
self.color = self.colors[0]
self.opacity = 1.0
self.colorFunction = None
self.opacityFunction = None
def __init__(self, name, image_data):
if not isinstance(image_data, vtk.vtkImageData):
raise TypeError("input has to be vtkImageData")
self.name = name
# Create transfer mapping scalar value to opacity.
opacity_function = vtk.vtkPiecewiseFunction()
opacity_function.AddPoint(0, 0.0)
opacity_function.AddPoint(127, 0.0)
opacity_function.AddPoint(128, 0.2)
opacity_function.AddPoint(255, 0.2)
# Create transfer mapping scalar value to color.
color_function = vtk.vtkColorTransferFunction()
color_function.SetColorSpaceToHSV()
color_function.AddHSVPoint(0, 0.0, 0.0, 0.0)
color_function.AddHSVPoint(127, 0.0, 0.0, 0.0)
color_function.AddHSVPoint(128, 0.0, 0.0, 1.0)
color_function.AddHSVPoint(255, 0.0, 0.0, 1.0)
volume_property = vtk.vtkVolumeProperty()
volume_property.SetColor(color_function)
volume_property.SetScalarOpacity(opacity_function)
volume_property.ShadeOn()
volume_property.SetInterpolationTypeToLinear()
volume_mapper = vtk.vtkSmartVolumeMapper()
volume_mapper.SetInputData(image_data)
self.volume = vtk.vtkVolume()
self.volume.SetMapper(volume_mapper)
self.volume.SetProperty(volume_property)
def __init__(self, input=None, MinOpacity=0.0, MaxOpacity=0.1):
import qt
import vtk
from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
self.__MinOpacity__ = MinOpacity
self.__MaxOpacity__ = MaxOpacity
# every QT app needs an app
self.__app__ = qt.QApplication(['itkviewer'])
# create the widget
self.__widget__ = QVTKRenderWindowInteractor()
self.__ren__ = vtk.vtkRenderer()
self.__widget__.GetRenderWindow().AddRenderer(self.__ren__)
self.__itkvtkConverter__ = None
self.__volumeMapper__ = vtk.vtkVolumeTextureMapper2D()
self.__volume__ = vtk.vtkVolume()
self.__volumeProperty__ = vtk.vtkVolumeProperty()
self.__volume__.SetMapper(self.__volumeMapper__)
self.__volume__.SetProperty(self.__volumeProperty__)
self.__ren__.AddVolume(self.__volume__)
self.__outline__ = None
self.__outlineMapper__ = None
self.__outlineActor__ = None
self.AdaptColorAndOpacity(0, 255)
if input:
self.SetInput(input)
self.AdaptColorAndOpacity()
def _createPipeline(self):
# setup our pipeline
self._splatMapper = vtkdevide.vtkOpenGLVolumeShellSplatMapper()
self._splatMapper.SetOmegaL(0.9)
self._splatMapper.SetOmegaH(0.9)
# high-quality rendermode
self._splatMapper.SetRenderMode(0)
self._otf = vtk.vtkPiecewiseFunction()
self._otf.AddPoint(0.0, 0.0)
self._otf.AddPoint(0.9, 0.0)
self._otf.AddPoint(1.0, 1.0)
self._ctf = vtk.vtkColorTransferFunction()
self._ctf.AddRGBPoint(0.0, 0.0, 0.0, 0.0)
self._ctf.AddRGBPoint(0.9, 0.0, 0.0, 0.0)
self._ctf.AddRGBPoint(1.0, 1.0, 0.937, 0.859)
self._volumeProperty = vtk.vtkVolumeProperty()
self._volumeProperty.SetScalarOpacity(self._otf)
self._volumeProperty.SetColor(self._ctf)
self._volumeProperty.ShadeOn()
self._volumeProperty.SetAmbient(0.1)
self._volumeProperty.SetDiffuse(0.7)
self._volumeProperty.SetSpecular(0.2)
self._volumeProperty.SetSpecularPower(10)
self._volume = vtk.vtkVolume()
self._volume.SetProperty(self._volumeProperty)
self._volume.SetMapper(self._splatMapper)
def _createPipeline(self):
# setup our pipeline
self._splatMapper = vtkdevide.vtkOpenGLVolumeShellSplatMapper()
self._splatMapper.SetOmegaL(0.9)
self._splatMapper.SetOmegaH(0.9)
# high-quality rendermode
self._splatMapper.SetRenderMode(0)
self._otf = vtk.vtkPiecewiseFunction()
self._otf.AddPoint(0.0, 0.0)
self._otf.AddPoint(0.9, 0.0)
self._otf.AddPoint(1.0, 1.0)
self._ctf = vtk.vtkColorTransferFunction()
self._ctf.AddRGBPoint(0.0, 0.0, 0.0, 0.0)
self._ctf.AddRGBPoint(0.9, 0.0, 0.0, 0.0)
self._ctf.AddRGBPoint(1.0, 1.0, 0.937, 0.859)
self._volumeProperty = vtk.vtkVolumeProperty()
self._volumeProperty.SetScalarOpacity(self._otf)
self._volumeProperty.SetColor(self._ctf)
self._volumeProperty.ShadeOn()
self._volumeProperty.SetAmbient(0.1)
self._volumeProperty.SetDiffuse(0.7)
self._volumeProperty.SetSpecular(0.2)
self._volumeProperty.SetSpecularPower(10)
self._volume = vtk.vtkVolume()
self._volume.SetProperty(self._volumeProperty)
self._volume.SetMapper(self._splatMapper)
def CreateVolumeProperty(self):
volumeColor = vtk.vtkColorTransferFunction()
volumeColor.AddRGBPoint(0, 0.0, 0.0, 0.0)
volumeColor.AddRGBPoint(71.78, 0.25, 0.25, 0.25)
volumeColor.AddRGBPoint(143.56, 0.5, 0.5, 0.5)
volumeColor.AddRGBPoint(215.34, 0.75, 0.75, 0.75)
volumeColor.AddRGBPoint(286.00, 1.0, 1.0, 1.0)
volumeColor.AddRGBPoint(512, 1.0, 1.0, 1.0)
volumeScalarOpacity = vtk.vtkPiecewiseFunction()
volumeScalarOpacity.AddPoint(0, 0.0)
volumeScalarOpacity.AddPoint(512, 1.0)
volumeGradientOpacity = vtk.vtkPiecewiseFunction()
volumeGradientOpacity.AddPoint(0, 1.0)
volumeGradientOpacity.AddPoint(512, 1.0)
volumeProp = vtk.vtkVolumeProperty()
volumeProp.SetColor(volumeColor)
volumeProp.SetScalarOpacity(volumeScalarOpacity)
volumeProp.SetGradientOpacity(volumeGradientOpacity)
volumeProp.SetInterpolationTypeToLinear()
volumeProp.ShadeOn()
volumeProp.SetAmbient(0.30)
volumeProp.SetDiffuse(0.60)
volumeProp.SetSpecular(0.20)
return volumeProp
def __init__(self, input=None, MinOpacity=0.0, MaxOpacity=0.1) :
import qt
import vtk
from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
self.__MinOpacity__ = MinOpacity
self.__MaxOpacity__ = MaxOpacity
# every QT app needs an app
self.__app__ = qt.QApplication(['itkviewer'])
# create the widget
self.__widget__ = QVTKRenderWindowInteractor()
self.__ren__ = vtk.vtkRenderer()
self.__widget__.GetRenderWindow().AddRenderer(self.__ren__)
self.__itkvtkConverter__ = None
self.__volumeMapper__ = vtk.vtkVolumeTextureMapper2D()
self.__volume__ = vtk.vtkVolume()
self.__volumeProperty__ = vtk.vtkVolumeProperty()
self.__volume__.SetMapper(self.__volumeMapper__)
self.__volume__.SetProperty(self.__volumeProperty__)
self.__ren__.AddVolume(self.__volume__)
self.__outline__ = None
self.__outlineMapper__ = None
self.__outlineActor__ = None
self.AdaptColorAndOpacity(0, 255)
if input :
self.SetInput(input)
self.AdaptColorAndOpacity()
def reader(self,filename,r,g,b):
self.reader_src = vtk.vtkNIFTIImageReader()
self.reader_src.SetFileName(filename)
self.vol_map = vtk.vtkGPUVolumeRayCastMapper()
self.vol_map.SetInputConnection(self.reader_src.GetOutputPort())
# transfer functions for color and opacity
self.funColor = vtk.vtkColorTransferFunction()
self.funColor.AddRGBPoint(0, 0., 0., 0.)
self.funColor.AddRGBPoint(1, r, g, b)
# for the T1
if filename == self.filename1:
self.funAlpha = vtk.vtkPiecewiseFunction()
self.funAlpha.AddPoint(0, 0.)
self.funAlpha.AddPoint(256, .003)
# for the masks
else:
self.funAlpha = vtk.vtkPiecewiseFunction()
self.funAlpha.AddPoint(0, 0.)
self.funAlpha.AddPoint(1, 0.00003)
self.volProp = vtk.vtkVolumeProperty()
self.volProp.SetColor(0, self.funColor)
self.volProp.SetScalarOpacity(0, self.funAlpha)
self.volProp.SetInterpolationTypeToLinear()
self.actor = vtk.vtkVolume()
self.actor.SetMapper(self.vol_map)
self.actor.SetProperty(self.volProp)
return self.actor
def axonComparison(axons, N):
axonsToRender = []
for i in range(N):
axon = axons.pop(random.randrange(len(axons)))
axonsToRender.append(axon)
bins = main.BINS
data_matrix = numpy.zeros([500, 500, 500], dtype=numpy.uint16)
dataImporter = vtk.vtkImageImport()
data_string = data_matrix.tostring()
dataImporter.CopyImportVoidPointer(data_string, len(data_string))
dataImporter.SetDataScalarTypeToUnsignedChar()
dataImporter.SetNumberOfScalarComponents(1)
dataImporter.SetDataExtent(0, 500, 0, 500, 0, 500)
dataImporter.SetWholeExtent(0, 500, 0, 500, 0, 500)
volumeProperty = vtk.vtkVolumeProperty()
compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
volumeMapper = vtk.vtkVolumeRayCastMapper()
volumeMapper.SetVolumeRayCastFunction(compositeFunction)
volumeMapper.SetInputConnection(dataImporter.GetOutputPort())
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
renderer = vtk.vtkRenderer()
renderWin = vtk.vtkRenderWindow()
renderWin.AddRenderer(renderer)
renderInteractor = vtk.vtkRenderWindowInteractor()
renderInteractor.SetRenderWindow(renderWin)
renderer.SetBackground(1, 1, 1)
renderWin.SetSize(400, 400)
for axon in axonsToRender:
renderer = Utils.renderSingleAxon(axon, renderer, [random.random(), random.random(), random.random()])
renderWin.AddObserver("AbortCheckEvent", exitCheck)
renderInteractor.Initialize()
renderWin.Render()
renderInteractor.Start()
def __init__(self, img, color):
self.volume = vtk.vtkVolume()
self.__color = color
dataImporter = vtk.vtkImageImport()
simg = np.ascontiguousarray(img, np.uint8)
dataImporter.CopyImportVoidPointer(simg.data, len(simg.data))
dataImporter.SetDataScalarTypeToUnsignedChar()
dataImporter.SetNumberOfScalarComponents(1)
dataImporter.SetDataExtent(0, simg.shape[2]-1, 0, simg.shape[1]-1, 0, simg.shape[0]-1)
dataImporter.SetWholeExtent(0, simg.shape[2]-1, 0, simg.shape[1]-1, 0, simg.shape[0]-1)
self.__smoother = vtk.vtkImageGaussianSmooth()
self.__smoother.SetStandardDeviation(1, 1, 1)
self.__smoother.SetInputConnection(dataImporter.GetOutputPort())
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputConnection(self.__smoother.GetOutputPort())
self.__volumeProperty = vtk.vtkVolumeProperty()
self.__colorFunc = vtk.vtkColorTransferFunction()
self.__alpha = vtk.vtkPiecewiseFunction()
for i in range(256):
self.__colorFunc.AddRGBPoint(i, i * color[0], i * color[1], i * color[2])
self.__alpha.AddPoint(5, .01)
self.__alpha.AddPoint(10, .03)
self.__alpha.AddPoint(50, .1)
self.__alpha.AddPoint(150, .2)
self.__volumeProperty.SetColor(self.__colorFunc)
self.__volumeProperty.SetScalarOpacity(self.__alpha)
self.volume.SetMapper(volumeMapper)
self.volume.SetProperty(self.__volumeProperty)
def __init__(self): super(VolumeVisualizationCT, self).__init__() self.visualizationType = VisualizationTypeCT # Cloth, Skin, Muscle, Vascular stuff, Cartilage, Bones self.sections = [-3000.0, -964.384, -656.56, 20.144, 137.168, 233.84, 394.112, 6000.0] self.sectionsOpacity = [0.0, 0.0, 0.0, 0.0, 0.07, 0.1, 0.2] self.sectionNames = ["Air:", "Cloth:", "Skin:", "Muscle:", "Blood vessels:", "Cartilage:", "Bones:"] # sectionColors should be specified for each boundary # Just like opacity should be tweaked. A section can have any slope / configuration self.sectionColors = [(1.0, 1.0, 1.0), (0.0, 1.0, 0.0), (1.0, 0.9, 0.8), (1.0, 0.7, 0.6), (1.0, 0.2, 0.2), (1.0, 0.9, 0.7), (0.9, 1.0, 0.9)] # Create property and attach the transfer function self.volProp = vtkVolumeProperty() self.volProp.SetIndependentComponents(True) self.volProp.SetInterpolationTypeToLinear() self.volProp.ShadeOn() self.volProp.SetAmbient(0.1) self.volProp.SetDiffuse(0.9) self.volProp.SetSpecular(0.2) self.volProp.SetSpecularPower(10.0) self.volProp.SetScalarOpacityUnitDistance(0.8919)
def init_all_VolumeRendering_component(self, flagMesh):
self.flagMesh = flagMesh
self.ren= vtk.vtkRenderer()
self.renWin.AddRenderer(self.ren)
self.iren = vtk.vtkXRenderWindowInteractor()
self.iren.SetRenderWindow(self.renWin)
self.ren.GetVolumes()
self.alpha_channel_function = vtk.vtkPiecewiseFunction()
self.alpha_channel_function.AddPoint(0, 0.0, 0.5, 0.0)
self.alpha_channel_function.AddPoint(255, 1, 0.5, 0.0)
self.color_function = vtk.vtkColorTransferFunction()
self.color_function.AddRGBPoint(0, 0, 0.0, 0.0, 0.5, 0.0)
self.color_function.AddRGBPoint(255, 1, 1, 1, 0.5, 0.0)
self.volume_property = vtk.vtkVolumeProperty()
self.volume_property.SetColor(self.color_function)
self.volume_property.SetScalarOpacity(self.alpha_channel_function)
self.data_importer = vtk.vtkImageImport()
if self.flagMesh :
self.volume_mapper = vtk.vtkPolyDataMapper()
else:
self.volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
self.volume = vtk.vtkVolume()
def initRenderWindow(self):
pix_diag = 5.0
self.nVolumes = 0
self.vtkWidget = QVTKRenderWindowInteractor(self.frame)
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(1.0, 1.0, 1.0)
self.vtkWidget.GetRenderWindow().AddRenderer(self.ren)
self.window = self.vtkWidget.GetRenderWindow()
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
drange = [0,400]
self.vtkWidget.opacity_tf = vtk.vtkPiecewiseFunction()
self.vtkWidget.opacity_tf.AddPoint(drange[0],0.0)
self.vtkWidget.opacity_tf.AddPoint(drange[1],0.0)
self.vtkWidget.color_tf = vtk.vtkColorTransferFunction()
self.vtkWidget.color_tf.AddRGBPoint(drange[0], 0.0, 0.0, 0.0)
self.vtkWidget.color_tf.AddRGBPoint(drange[1], 1.0, 1.0, 1.0)
self.vtkWidget.volProperty = vtk.vtkVolumeProperty()
self.vtkWidget.volProperty.SetColor(self.vtkWidget.color_tf);
self.vtkWidget.volProperty.SetScalarOpacity(self.vtkWidget.opacity_tf)
self.vtkWidget.volProperty.ShadeOn()
self.vtkWidget.volProperty.SetInterpolationTypeToLinear()
self.vtkWidget.volProperty.SetScalarOpacityUnitDistance(pix_diag)
def __init__(self):
super(VolumeVisualizationCT, self).__init__()
self.visualizationType = VisualizationTypeCT
# Cloth, Skin, Muscle, Vascular stuff, Cartilage, Bones
self.sections = [
-3000.0, -964.384, -656.56, 20.144, 137.168, 233.84, 394.112,
6000.0
]
self.sectionsOpacity = [0.0, 0.0, 0.0, 0.0, 0.07, 0.1, 0.2]
self.sectionNames = [
"Air:", "Cloth:", "Skin:", "Muscle:", "Blood vessels:",
"Cartilage:", "Bones:"
]
# sectionColors should be specified for each boundary
# Just like opacity should be tweaked. A section can have any slope / configuration
self.sectionColors = [
(1.0, 1.0, 1.0), (0.0, 1.0, 0.0), (1.0, 0.9, 0.8), (1.0, 0.7, 0.6),
(1.0, 0.2, 0.2), (1.0, 0.9, 0.7), (0.9, 1.0, 0.9)
]
# Create property and attach the transfer function
self.volProp = vtkVolumeProperty()
self.volProp.SetIndependentComponents(True)
self.volProp.SetInterpolationTypeToLinear()
self.volProp.ShadeOn()
self.volProp.SetAmbient(0.1)
self.volProp.SetDiffuse(0.9)
self.volProp.SetSpecular(0.2)
self.volProp.SetSpecularPower(10.0)
self.volProp.SetScalarOpacityUnitDistance(0.8919)
def _create_pipeline(self):
# setup our pipeline
self._otf = vtk.vtkPiecewiseFunction()
self._ctf = vtk.vtkColorTransferFunction()
self._volume_property = vtk.vtkVolumeProperty()
self._volume_property.SetScalarOpacity(self._otf)
self._volume_property.SetColor(self._ctf)
self._volume_property.ShadeOn()
self._volume_property.SetAmbient(0.1)
self._volume_property.SetDiffuse(0.7)
self._volume_property.SetSpecular(0.2)
self._volume_property.SetSpecularPower(10)
self._volume_raycast_function = vtk.vtkVolumeRayCastMIPFunction()
self._volume_mapper = vtk.vtkVolumeRayCastMapper()
# can also used FixedPoint, but then we have to use:
# SetBlendModeToMaximumIntensity() and not SetVolumeRayCastFunction
#self._volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
self._volume_mapper.SetVolumeRayCastFunction(
self._volume_raycast_function)
module_utils.setup_vtk_object_progress(self, self._volume_mapper,
'Preparing render.')
self._volume = vtk.vtkVolume()
self._volume.SetProperty(self._volume_property)
self._volume.SetMapper(self._volume_mapper)
def get_volume(self, color_file=None, volume_opacity=0.25):
"""
Default Volume Rendering
Return vtkActor. For volume rendering it is vtkVolume
"""
if not self.flag_read:
sys.stderr.write('No Image Loaded.')
return
# TEST
print self.is_blank_image()
transfer_func = self.get_transfer_functioin(color_file, volume_opacity)
prop_volume = vtk.vtkVolumeProperty()
prop_volume.ShadeOff()
prop_volume.SetColor(transfer_func[0])
prop_volume.SetScalarOpacity(transfer_func[1])
prop_volume.SetGradientOpacity(transfer_func[2])
prop_volume.SetInterpolationTypeToLinear()
prop_volume.SetAmbient(0.4)
prop_volume.SetDiffuse(0.6)
prop_volume.SetSpecular(0.2)
mapper = vtk.vtkSmartVolumeMapper()
mapper.SetRequestedRenderMode(0)
# mapper = vtk.vtkGPUVolumeRayCastMapper()
mapper.SetInputData(self.reader)
actor = vtk.vtkVolume()
actor.SetMapper(mapper)
actor.SetProperty(prop_volume)
return actor
def volumeRender(reader,ren,renWin): #Create transfer mapping scalar value to opacity opacityTransferFunction = vtk.vtkPiecewiseFunction() opacityTransferFunction.AddPoint(1, 0.0) opacityTransferFunction.AddPoint(100, 0.1) opacityTransferFunction.AddPoint(255,1.0) colorTransferFunction = vtk.vtkColorTransferFunction() colorTransferFunction.AddRGBPoint(0.0,0.0,0.0,0.0) colorTransferFunction.AddRGBPoint(64.0,1.0,0.0,0.0) colorTransferFunction.AddRGBPoint(128.0,0.0,0.0,1.0) colorTransferFunction.AddRGBPoint(192.0,0.0,1.0,0.0) colorTransferFunction.AddRGBPoint(255.0,0.0,0.2,0.0) volumeProperty = vtk.vtkVolumeProperty() volumeProperty.SetColor(colorTransferFunction) volumeProperty.SetScalarOpacity(opacityTransferFunction) volumeProperty.ShadeOn() volumeProperty.SetInterpolationTypeToLinear() compositeFunction = vtk.vtkVolumeRayCastCompositeFunction() volumeMapper = vtk.vtkFixedPointVolumeRayCastMapper() volumeMapper.SetInputConnection(reader.GetOutputPort()) volume = vtk.vtkVolume() volume.SetMapper(volumeMapper) volume.SetProperty(volumeProperty) ren.RemoveAllViewProps() ren.AddVolume(volume) ren.SetBackground(1,1,1) renWin.Render()
def __init__(self): super(VolumeVisualizationSimple, self).__init__() self.visualizationType = VisualizationTypeSimple # Create the volume property self.volProp = vtkVolumeProperty() self.volProp.SetIndependentComponents(True) self.volProp.SetInterpolationTypeToLinear() self.volProp.ShadeOn() self.volProp.SetAmbient(0.3) self.volProp.SetDiffuse(0.8) self.volProp.SetSpecular(0.2) self.volProp.SetSpecularPower(10.0) self.volProp.SetScalarOpacityUnitDistance(0.8919) self.minimum = 0 self.maximum = 1 self.lowerBound = 0 self.upperBound = 1 colors = [[255, 139, 0], [0, 147, 255], [0, 255, 147], [213, 100, 255], [255, 75, 75]] self.colors = map(lambda x: [x[0] / 255.0, x[1] / 255.0, x[2] / 255.0], colors) self.color = self.colors[0] self.opacity = 1.0 self.colorFunction = None self.opacityFunction = None
def _create_pipeline(self):
# setup our pipeline
self._otf = vtk.vtkPiecewiseFunction()
self._ctf = vtk.vtkColorTransferFunction()
self._volume_property = vtk.vtkVolumeProperty()
self._volume_property.SetScalarOpacity(self._otf)
self._volume_property.SetColor(self._ctf)
self._volume_property.ShadeOn()
self._volume_property.SetAmbient(0.1)
self._volume_property.SetDiffuse(0.7)
self._volume_property.SetSpecular(0.2)
self._volume_property.SetSpecularPower(10)
self._volume_raycast_function = vtk.vtkVolumeRayCastMIPFunction()
self._volume_mapper = vtk.vtkVolumeRayCastMapper()
# can also used FixedPoint, but then we have to use:
# SetBlendModeToMaximumIntensity() and not SetVolumeRayCastFunction
#self._volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
self._volume_mapper.SetVolumeRayCastFunction(
self._volume_raycast_function)
module_utils.setup_vtk_object_progress(self, self._volume_mapper,
'Preparing render.')
self._volume = vtk.vtkVolume()
self._volume.SetProperty(self._volume_property)
self._volume.SetMapper(self._volume_mapper)
def __init__(self):
# Objects for volume rendering
self.volume = vtk.vtkVolume()
self.volumeMapper = vtk.vtkSmartVolumeMapper()
self.volumeProperty = vtk.vtkVolumeProperty()
# Objects for slice rendering
self.sliceActor = vtk.vtkImageActor()
self.sliceMapper = vtk.vtkImageResliceMapper()
self.sliceProperty = vtk.vtkImageProperty()
# Objects for importing and reslicing the data
self.importer = [vtk.vtkImageImport()]
self.slice = [vtk.vtkImageResliceToColors()]
# Objects that point to the output algorithms
# These must be specified at run time by the implementing class
self.output = None
self.sliceOutput = None
# Some properties of the data
self.numberOfDataSets = 0
self.numberOfTimeFrames = 0
self.currentTimeFrame = 0
self.dimensions = [0, 0, 0]
def volumeRender(img, tf=[],spacing=[1.0,1.0,1.0]):
importer = numpy2VTK(img,spacing)
# Transfer Functions
opacity_tf = vtk.vtkPiecewiseFunction()
color_tf = vtk.vtkColorTransferFunction()
if len(tf) == 0:
tf.append([img.min(),0,0,0,0])
tf.append([img.max(),1,1,1,1])
for p in tf:
color_tf.AddRGBPoint(p[0], p[1], p[2], p[3])
opacity_tf.AddPoint(p[0], p[4])
volMapper = vtk.vtkGPUVolumeRayCastMapper()
volMapper.SetInputConnection(importer.GetOutputPort())
# The property describes how the data will look
volProperty = vtk.vtkVolumeProperty()
volProperty.SetColor(color_tf)
volProperty.SetScalarOpacity(opacity_tf)
volProperty.ShadeOn()
volProperty.SetInterpolationTypeToLinear()
vol = vtk.vtkVolume()
vol.SetMapper(volMapper)
vol.SetProperty(volProperty)
return [vol]
def __init__(self, Mgr):
self.Mgr = Mgr
self.m_volumeInfo = None
self.m_selectedIdx = None
self.m_selectedImage = None
# self.m_reverseSagittal = False
# self.m_reverseAxial = False
self.m_shoulderSide = 'L'
self.m_orientation = None ##AXL:1, COR:0, SAG:2
#Selected Volume CFGS
self.m_colorFunction = vtk.vtkColorTransferFunction()
self.m_opacityFunction = vtk.vtkPiecewiseFunction()
self.m_scalarRange = [0.0, 1.0]
self.m_volumeProperty = vtk.vtkVolumeProperty()
self.m_imageProperty = vtk.vtkImageProperty()
self.m_imageProperty.SetInterpolationTypeToLinear()
#Volume
self.volume_data = vtk.vtkImageData()
self.volume_cropper = vtk.vtkImageData()
self.m_volumeMapper = vtk.vtkSmartVolumeMapper()
self.m_volume = vtk.vtkVolume()
self.m_resliceMapper = [0, 0, 0]
self.m_resliceActor = [0, 0, 0]
#Color MAp Volume
self.m_bShowCAM = False
self.m_bShowVolume = False
self.m_colorMapMapper = vtk.vtkSmartVolumeMapper()
self.m_colorMapVolume = vtk.vtkVolume()
self.m_colorMapResliceMapper = [None, None, None]
self.m_colorMapResliceActor = [None, None, None]
self.resolution = 64
#Crop View
self.croppingMapper = vtk.vtkImageSliceMapper()
self.croppingActor = vtk.vtkImageSlice()
for i in range(3):
self.m_resliceMapper[i] = vtk.vtkImageSliceMapper()
self.m_resliceActor[i] = vtk.vtkImageSlice()
self.m_colorMapResliceMapper[i] = vtk.vtkImageSliceMapper()
self.m_colorMapResliceActor[i] = vtk.vtkImageSlice()
self.m_resliceActor[0].RotateY(90)
self.m_resliceActor[1].RotateX(-90)
self.m_colorMapResliceActor[0].RotateY(90)
self.m_colorMapResliceActor[1].RotateX(-90)
#Initialize
self.SetPresetFunctions(
self.Mgr.mainFrm.volumeWidget.GetCurrentColorIndex())
self.InitializeVolumeFunctions()
self.InitializeClassActivationMap()
def vtkKWVolumeMaterialPropertyWidgetEntryPoint(parent, win):
app = parent.GetApplication()
# -----------------------------------------------------------------------
# Create the volume property that will be modified by the widget
volprop1 = vtkVolumeProperty()
# -----------------------------------------------------------------------
# Create the material widget
# Assign our volume property to the editor
volprop1_widget = vtkKWVolumeMaterialPropertyWidget()
volprop1_widget.SetParent(parent)
volprop1_widget.Create()
volprop1_widget.SetBalloonHelpString(
"A volume material property widget.")
volprop1_widget.SetVolumeProperty(volprop1)
app.Script(
"pack %s -side top -anchor nw -expand n -padx 2 -pady 2",
volprop1_widget.GetWidgetName())
# -----------------------------------------------------------------------
# Create another material widget, in popup mode
# Assign our volume property to the editor
volprop2_widget = vtkKWVolumeMaterialPropertyWidget()
volprop2_widget.SetParent(parent)
volprop2_widget.PopupModeOn()
volprop2_widget.Create()
volprop2_widget.SetMaterialColor(0.3, 0.4, 1.0)
volprop2_widget.SetBalloonHelpString(
"A volume material property widget, created in popup mode. Note that "
"it edits the same volume property object as the first widget.")
volprop2_widget.SetVolumeProperty(volprop1)
app.Script(
"pack %s -side top -anchor nw -expand n -padx 2 -pady 15",
volprop2_widget.GetWidgetName())
# Both editor are linked to the same vol prop, so they should notify
# each other of any changes to refresh the preview nicely
volprop2_widget.SetPropertyChangingCommand(volprop1_widget, "Update")
volprop2_widget.SetPropertyChangedCommand(volprop1_widget, "Update")
volprop1_widget.SetPropertyChangingCommand(volprop2_widget, "Update")
volprop1_widget.SetPropertyChangedCommand(volprop2_widget, "Update")
return "TypeVTK"
def __init__(self, default = '', color = [1.0, 0.766, 0.336], singleview = True):
# Create the importer and load a volume (gets things warmed up)
self.dataImporter = vtk.vtkImageImport()
if len(default) == 0:
# a dataset's config.yaml will specify the name of the default volume and it'll be included
default = '/Users/cam/data/dSpaceX/latest/nanoparticles_volume/unprocessed_data/shape_representations/Images.0002.nrrd'
self.loadNewVolume(default)
# colors
colors = vtk.vtkNamedColors()
# volume properties
volumeProperty = vtk.vtkVolumeProperty()
alphaChannelFunc = vtk.vtkPiecewiseFunction()
alphaChannelFunc.AddPoint(0, 0.0)
alphaChannelFunc.AddPoint(228, 0.0)
alphaChannelFunc.AddPoint(255, 0.25)
colorFunc = vtk.vtkColorTransferFunction()
colorFunc.AddRGBPoint(0, color[0]/2.0, color[1]/2.0, color[2]/2.0)
colorFunc.AddRGBPoint(255, color[0], color[1], color[2])
volumeProperty.SetColor(colorFunc)
volumeProperty.SetScalarOpacity(alphaChannelFunc)
volumeProperty.ShadeOn()
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.SetDiffuse(2.0)
volumeProperty.SetSpecular(1.5)
volumeProperty.SetSpecularPower(15)
# volume
volumeMapper = vtk.vtkGPUVolumeRayCastMapper()
volumeMapper.SetInputConnection(self.dataImporter.GetOutputPort())
self.volume = vtk.vtkVolume()
self.volume.SetMapper(volumeMapper)
self.volume.SetProperty(volumeProperty)
# renderer
self.ren = vtk.vtkRenderer()
self.renWin = vtk.vtkRenderWindow()
self.renWin.AddRenderer(self.ren)
self.renWin.OffScreenRenderingOn() # ***** don't open a window *****
# add volume, set background and size
self.ren.AddVolume(self.volume)
self.ren.SetBackground(colors.GetColor3d("Wheat"))
# camera
self.resetCamera()
self.renWin.SetWindowName('TwistyTurnyNanoparticle')
# screenshot filter
self.w2if = vtk.vtkWindowToImageFilter()
self.w2if.SetInput(self.renWin)
self.w2if.SetInputBufferTypeToRGB()
self.w2if.ReadFrontBufferOff()
def __init__(self, volume_data, genren):
self.volume_data = volume_data
self.genren = genren
self.vtk_renderer = vtk.vtkRenderer()
self.vtk_renderer.SetBackground(0.310999694819562063,0.3400015259021897,0.4299992370489052)
self.renWin = vtk.vtkRenderWindow()
self.renWin.SetSize(256,256)
self.renWin.AddRenderer(self.vtk_renderer)
self.renWin.SetWindowName('VTK Renderer')
self.iren = vtk.vtkRenderWindowInteractor()
self.iren.SetRenderWindow(self.renWin)
# compute volume center
volume_spacing = np.array(self.volume_data.GetSpacing())
volume_origin = np.array(self.volume_data.GetOrigin())
volume_dimensions = np.array(self.volume_data.GetDimensions())
volume_max = volume_origin+volume_spacing*volume_dimensions
volume_center = 0.5*(volume_origin+volume_max)
volume_diag = volume_max-volume_origin
#offset_scale = 2.25
offset_scale = 2.0
# camera
self.camera = self.vtk_renderer.MakeCamera()
self.camera.SetClippingRange(0.01,offset_scale*2.0*np.linalg.norm(volume_diag))
self.camera.SetPosition(volume_center[0],volume_center[1],volume_center[2]+offset_scale*np.linalg.norm(volume_diag))
self.camera.SetFocalPoint(volume_center[0],volume_center[1],volume_center[2])
self.camera.Elevation(-85)
self.vtk_renderer.SetActiveCamera(self.camera)
# color map, opacity map
self.vtk_color_map = vtk.vtkColorTransferFunction()
for color_val in self.genren.color_tf:
self.vtk_color_map.AddRGBPoint(color_val[0],color_val[1],color_val[2],color_val[3])
vtk_opacity_map = vtk.vtkPiecewiseFunction()
for op_val in self.genren.opacity_tf:
vtk_opacity_map.AddPoint(op_val[0],op_val[1])
# volume properties
self.prop_volume = vtk.vtkVolumeProperty()
self.prop_volume.ShadeOff()
self.prop_volume.SetColor(self.vtk_color_map)
self.prop_volume.SetScalarOpacity(vtk_opacity_map)
self.prop_volume.SetInterpolationTypeToLinear()
# vtk volume render
self.mapperVolume = vtk.vtkSmartVolumeMapper()
self.mapperVolume = vtk.vtkGPUVolumeRayCastMapper()
self.mapperVolume.SetBlendModeToComposite()
self.mapperVolume.SetInputData(self.volume_data)
self.actorVolume = vtk.vtkVolume()
self.actorVolume.SetMapper(self.mapperVolume)
self.actorVolume.SetProperty(self.prop_volume)
self.vtk_renderer.AddActor(self.actorVolume)
self.iren.Initialize()
def volumeRender():
# Create the standard renderer, render window and interactor.
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Create the reader for the data.
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName('./image/ironProt.vtk')
# Create transfer mapping scalar value to opacity.
volumeOpacity = vtk.vtkPiecewiseFunction()
volumeOpacity.AddPoint(50, 0)
volumeOpacity.AddPoint(150, 0.4)
volumeOpacity.AddPoint(200, 0.7)
volumeOpacity.AddPoint(255, 1)
# Create transfer mapping scalar value to color.
volumeColor = vtk.vtkColorTransferFunction()
volumeColor.AddRGBPoint(0.0, 25.0, 25.0, 25.0)
volumeColor.AddRGBPoint(64.0, 100.0, 100.0, 100.0)
volumeColor.AddRGBPoint(128.0, 150.0, 150.0, 150.0)
volumeColor.AddRGBPoint(192.0, 200.0, 200.0, 200.0)
# The property describes how the data will look.
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(volumeColor)
volumeProperty.SetScalarOpacity(volumeOpacity)
volumeProperty.ShadeOn()
volumeProperty.SetInterpolationTypeToLinear()
# The mapper / ray cast function know how to render the data.
volumeMapper = vtk.vtkFixedPointVolumeRayCastMapper()
volumeMapper.SetInputConnection(reader.GetOutputPort())
# The volume holds the mapper and the property and
# can be used to position/orient the volume.
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
colors = vtk.vtkNamedColors()
ren1.AddVolume(volume)
ren1.SetBackground(colors.GetColor3d("White"))
ren1.GetActiveCamera().Azimuth(0)
ren1.GetActiveCamera().Elevation(15)
ren1.ResetCameraClippingRange()
ren1.ResetCamera()
renWin.SetSize(600, 600)
renWin.Render()
iren.Start()
def create_volume(self, time_step):
# Get data
npdatauchar = list()
vtk_volume_prop = vtk.vtkVolumeProperty()
vtk_volume_prop.IndependentComponentsOn()
vtk_volume_prop.SetInterpolationTypeToLinear()
for i, volume in enumerate(self.volume_list):
npdatauchar.append(volume.get_data(time_step, 200, 300, 0.5))
vtk_volume_prop.SetColor(i, volume.vtk_color)
vtk_volume_prop.SetScalarOpacity(i, volume.vtk_opacity)
vtk_volume_prop.ShadeOff(i)
npdatamulti = np.concatenate(
[aux[..., np.newaxis] for aux in npdatauchar], axis=3)
axes = self.volume_list[0].get_axes(time_step)
axes_spacing = self.volume_list[0].get_axes_spacing(
time_step, 200, 300, 0.5)
# Normalize spacing. Too small values lead to ghost volumes.
max_sp = max(axes_spacing["x"], axes_spacing["y"], axes_spacing["z"])
# Too big cells turn opaque, too small become transparent.
# max_cell_size normalizes the cell size
max_cell_size = 0.1
norm_factor = max_cell_size / max_sp
axes_spacing["x"] = axes_spacing["x"] * norm_factor
axes_spacing["y"] = axes_spacing["y"] * norm_factor
axes_spacing["z"] = axes_spacing["z"] * norm_factor
# Put data in VTK format
vtk_data_import = vtk.vtkImageImport()
vtk_data_import.SetImportVoidPointer(npdatamulti)
vtk_data_import.SetDataScalarTypeToUnsignedChar()
vtk_data_import.SetNumberOfScalarComponents(len(self.volume_list))
vtk_data_import.SetDataExtent(0, npdatamulti.shape[2] - 1, 0,
npdatamulti.shape[1] - 1, 0,
npdatamulti.shape[0] - 1)
vtk_data_import.SetWholeExtent(0, npdatamulti.shape[2] - 1, 0,
npdatamulti.shape[1] - 1, 0,
npdatamulti.shape[0] - 1)
vtk_data_import.SetDataSpacing(axes_spacing["x"], axes_spacing["y"],
axes_spacing["z"])
# data origin is also changed by the normalization
vtk_data_import.SetDataOrigin(axes["x"][0] * norm_factor,
axes["y"][0] * norm_factor,
axes["z"][0] * norm_factor)
vtk_data_import.Update()
# Create the mapper
vtk_volume_mapper = vtk.vtkGPUVolumeRayCastMapper()
vtk_volume_mapper.SetInputConnection(vtk_data_import.GetOutputPort())
vtk_volume_mapper.Update()
# Add to volume
self.vtk_volume.SetMapper(vtk_volume_mapper)
self.vtk_volume.SetProperty(vtk_volume_prop)
# Set visualization parameters
self.set_render_quality(self.render_quality)
self.set_color_level(self.volume_color_level)
self.set_color_window(self.volume_color_window)
# Add to render
self.renderer.AddVolume(self.vtk_volume)
self.renderer.ResetCamera()
self.interactor.Render()
def InitializeClassActivationMap(self):
self.cam_data = vtk.vtkImageData()
self.cam_data.SetOrigin([0, 0, 0])
self.cam_data.SetDimensions(
64,
64,
64,
)
self.cam_data.AllocateScalars(vtk.VTK_UNSIGNED_INT, 1)
self.cam_data.SetSpacing([1.0, 1.0, 1.0])
#set Class Activation Map
cam_color_function = vtk.vtkColorTransferFunction()
cam_opacity_function = vtk.vtkPiecewiseFunction()
scalarRange = [0.0, 255.0]
cam_volume_property = vtk.vtkVolumeProperty()
cam_color_function.AddRGBPoint((scalarRange[0] + scalarRange[1]) * 0.4,
0.0, 0.0, 1.0)
cam_color_function.AddRGBPoint((scalarRange[0] + scalarRange[1]) * 0.7,
0.0, 1.0, 0.0)
cam_color_function.AddRGBPoint(scalarRange[1], 1.0, 0.0, 0.0)
cam_opacity_function.AddPoint((scalarRange[0] + scalarRange[1]) * 0.0,
0.3)
cam_opacity_function.AddPoint(scalarRange[1], 0.3)
cam_volume_property.SetColor(cam_color_function)
cam_volume_property.SetScalarOpacity(cam_opacity_function)
cam_volume_property.ShadeOff()
cam_volume_property.SetInterpolationTypeToLinear()
self.m_colorMapMapper.SetInputData(self.cam_data)
self.m_colorMapMapper.SetBlendModeToMaximumIntensity()
#Actor
self.m_colorMapVolume.SetMapper(self.m_colorMapMapper)
self.m_colorMapVolume.SetProperty(cam_volume_property)
self.m_colorMapVolume.SetPosition([0, 0, 0])
lookupTable = vtk.vtkLookupTable()
lookupTable.SetTableRange(0.0, 255.0)
lookupTable.SetHueRange(0.7, 0.0)
lookupTable.Build()
imageProperty = vtk.vtkImageProperty()
imageProperty.SetInterpolationTypeToLinear()
imageProperty.SetLookupTable(lookupTable)
imageProperty.SetOpacity(0.3)
#Slice
for i in range(3):
self.m_colorMapResliceMapper[i].SetInputData(self.cam_data)
self.m_colorMapResliceMapper[i].SetOrientation(i)
self.m_colorMapResliceActor[i].SetMapper(
self.m_colorMapResliceMapper[i])
self.m_colorMapResliceActor[i].SetProperty(imageProperty)
def defaultEnvironment(environment, attribute):
"""
Default 3d environment renderer. White is the highest value in the frame and black is the lowest value.
"""
xbounds = environment.mesh.boundsX
ybounds = environment.mesh.boundsY
zbounds = environment.mesh.boundsZ
attributeIndex = environment.current.variables[attribute]
positions = environment.mesh.voxels
data = environment.current.data[attributeIndex]
xCount = np.unique(environment.mesh.voxels[environment.mesh.variables['x']]).shape[0]
yCount = np.unique(environment.mesh.voxels[environment.mesh.variables['y']]).shape[0]
zCount = np.unique(environment.mesh.voxels[environment.mesh.variables['z']]).shape[0]
minimum = np.min(data)
maximum = np.max(data)
if not maximum == 0:
data = data / maximum
data = np.reshape(data, (xCount, yCount, zCount))
imdata = vtk.vtkImageData()
depthArray = numpy_support.numpy_to_vtk(data.ravel(), deep=True, array_type=vtk.VTK_DOUBLE)
imdata.SetDimensions(data.shape)
imdata.SetSpacing([(xbounds[1] - xbounds[0]) / xCount, (ybounds[1] - ybounds[0]) / yCount, (zbounds[1] - zbounds[0]) / zCount])
imdata.SetOrigin([xbounds[0], ybounds[0], zbounds[0]])
imdata.GetPointData().SetScalars(depthArray)
colorFunc = vtk.vtkColorTransferFunction()
colorFunc.AddRGBPoint(0.0, 0.0, 0.0, 0.0)
colorFunc.AddRGBPoint(1.0, 1.0, 1.0, 1.0)
opacity = vtk.vtkPiecewiseFunction()
opacity.AddPoint(0.0, 0.0)
opacity.AddPoint(1, 0.8)
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorFunc)
volumeProperty.SetScalarOpacity(opacity)
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.SetIndependentComponents(2)
volumeMapper = vtk.vtkFixedPointVolumeRayCastMapper()
volumeMapper.SetInputData(imdata)
volumeMapper.SetBlendModeToMaximumIntensity()
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
return volume
def _createVolPropFromImageData(self, imageData, color):
volProp = vtkVolumeProperty()
if imageData is not None:
color, opacityFunction = CreateRangeFunctions(imageData, color)
else:
color, opacityFunction = CreateEmptyFunctions()
volProp.SetColor(color)
volProp.SetScalarOpacity(opacityFunction)
return volProp
def _createVolPropFromImageData(self, imageData): volProp = vtkVolumeProperty() if imageData is not None: color, opacityFunction = CreateRangeFunctions(imageData) else: color, opacityFunction = CreateEmptyFunctions() volProp.SetColor(color) volProp.SetScalarOpacity(opacityFunction) return volProp
def SetPresetVolumeProperty(self):
'''Create the transfer functions and set volume properties in a vtkVolumeProperty object'''
# parse the xml file which is loaded in the same path as the vmtkimagevolumeviewer.py file at runtime
presetElementTree = ET.parse(os.path.join(os.path.dirname(__file__), 'share', 'vmtkimagevolumeviewerpresets.xml'))
presetRoot = presetElementTree.getroot()
volProperties = presetRoot.findall('VolumeProperty[@name="' + self.Preset + '"]') # should return a list with only one element
volPropertiesDict = volProperties[0].attrib
def _chunks(l, n):
"""Yield successive n-sized chunks from l."""
PY3 = sys.version_info[0] == 3
if PY3:
range_func = range
else:
range_func = xrange
for i in range_func(0, len(l), n):
yield l[i:i + n]
# need to convert the space seperated string displaying values into a list of floats
colorList = [float(i) for i in volPropertiesDict['colorTransfer'].split()]
gradientOpacityList = [float(i) for i in volPropertiesDict['gradientOpacity'].split()]
opacityList = [float(i) for i in volPropertiesDict['scalarOpacity'].split()]
# create an array of arrays with each list split into subarrays of desired size
colorMapList = _chunks(colorList, 4)
gradientOpacityMapList = _chunks(gradientOpacityList, 2)
opacityMapList = _chunks(opacityList, 2)
# create vtk objects from the mapped lists (now arrays of arrays)
self.ColorTransferFunction = self.BuildVTKColorTransferFunction(colorMapList)
self.GradientOpacityTransferFunction = self.BuildVTKPiecewiseFunction(gradientOpacityMapList)
self.OpacityTransferFunction = self.BuildVTKPiecewiseFunction(opacityMapList)
# assign other properties from the element tree to variables with the appropriate type
self.InterpolationType = int(volPropertiesDict['interpolation'])
self.Shade = int(volPropertiesDict['shade'])
self.SpecularPower = float(volPropertiesDict['specularPower'])
self.Specular = float(volPropertiesDict['specular'])
self.Diffuse = float(volPropertiesDict['diffuse'])
self.Ambient = float(volPropertiesDict['ambient'])
# set transfer function and lighting properties of the vtk volume object
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetScalarOpacity(self.OpacityTransferFunction)
volumeProperty.SetGradientOpacity(self.GradientOpacityTransferFunction)
volumeProperty.SetColor(self.ColorTransferFunction)
volumeProperty.SetInterpolationType(self.InterpolationType)
volumeProperty.SetShade(self.Shade)
volumeProperty.SetSpecularPower(self.SpecularPower)
volumeProperty.SetSpecular(self.Specular)
volumeProperty.SetDiffuse(self.Diffuse)
volumeProperty.SetAmbient(self.Ambient)
self.VolumeProperty = volumeProperty
def setVolumeVisualization(self, visualization): self.visualization = visualization if self.visualization is None: color, opacityFunction = CreateEmptyFunctions() self.fixedVolumeProperty = vtkVolumeProperty() self.fixedVolumeProperty.SetColor(color) self.fixedVolumeProperty.SetScalarOpacity(opacityFunction) self.movingVolumeProperty = vtkVolumeProperty() self.movingVolumeProperty.SetColor(color) self.movingVolumeProperty.SetScalarOpacity(opacityFunction) else: self.fixedVolumeProperty = self.visualization.fixedVolProp self.movingVolumeProperty = self.visualization.movingVolProp self.visualization.setMapper(self.mapper) if self.visualization.fixedVisualization: self._updateMapper(self.visualization.fixedVisualization, 1) if self.visualization.movingVisualization: self._updateMapper(self.visualization.movingVisualization, 2) self._updateVolumeProperties()
def _create_pipeline(self):
# setup our pipeline
self._volume_property = vtk.vtkVolumeProperty()
self._volume_property.ShadeOn()
self._volume_mapper = None
self._volume = vtk.vtkVolume()
self._volume.SetProperty(self._volume_property)
self._volume.SetMapper(self._volume_mapper)
def originalObject(self): volumeProperty = vtkVolumeProperty() volumeProperty.SetIndependentComponents(self.independentComponents) volumeProperty.SetInterpolationType(self.interpolationType) volumeProperty.SetShade(self.shade) volumeProperty.SetAmbient(self.ambient) volumeProperty.SetDiffuse(self.diffuse) volumeProperty.SetSpecular(self.specular) volumeProperty.SetSpecularPower(self.specularPower) volumeProperty.SetScalarOpacityUnitDistance(self.scalarOpacityUnitDistance) return volumeProperty
def __init__(self): super(VolumeVisualizationMIDA, self).__init__() self.visualizationType = VisualizationTypeMIDA self.mapper = None # TODO: add two sliders with which to threshold the data # Create property and attach the transfer function self.volProp = vtkVolumeProperty() self.volProp.SetIndependentComponents(True) self.volProp.SetInterpolationTypeToLinear()
def vtkKWVolumePropertyWidgetEntryPoint(parent, win):
app = parent.GetApplication()
# -----------------------------------------------------------------------
# This is a faily big widget, so create a scrolled frame
vpw_frame = vtkKWFrameWithScrollbar()
vpw_frame.SetParent(parent)
vpw_frame.Create()
app.Script("pack %s -side top -fill both -expand y", vpw_frame.GetWidgetName())
# -----------------------------------------------------------------------
# Create a volume property widget
vpw = vtkKWVolumePropertyWidget()
vpw.SetParent(vpw_frame.GetFrame())
vpw.Create()
app.Script("pack %s -side top -anchor nw -expand y -padx 2 -pady 2", vpw.GetWidgetName())
# Create a volume property and assign it
# We need color tfuncs, opacity, and gradient
vpw_vp = vtkVolumeProperty()
vpw_vp.SetIndependentComponents(1)
vpw_cfun = vtkColorTransferFunction()
vpw_cfun.SetColorSpaceToHSV()
vpw_cfun.AddHSVSegment(0.0, 0.2, 1.0, 1.0, 255.0, 0.8, 1.0, 1.0)
vpw_cfun.AddHSVSegment(80, 0.8, 1.0, 1.0, 130.0, 0.1, 1.0, 1.0)
vpw_ofun = vtkPiecewiseFunction()
vpw_ofun.AddSegment(0.0, 0.2, 255.0, 0.8)
vpw_ofun.AddSegment(40, 0.9, 120.0, 0.1)
vpw_gfun = vtkPiecewiseFunction()
vpw_gfun.AddSegment(0.0, 0.2, 60.0, 0.4)
vpw_vp.SetColor(0, vpw_cfun)
vpw_vp.SetScalarOpacity(0, vpw_ofun)
vpw_vp.SetGradientOpacity(0, vpw_gfun)
vpw.SetVolumeProperty(vpw_vp)
vpw.SetWindowLevel(128, 128)
# vpw.MergeScalarOpacityAndColorEditors()
return "TypeVTK"
def volumeRender(img, tf=[],spacing=[1.0,1.0,1.0]):
importer = numpy2VTK(img,spacing)
# Transfer Functions
opacity_tf = vtk.vtkPiecewiseFunction()
color_tf = vtk.vtkColorTransferFunction()
if len(tf) == 0:
tf.append([img.min(),0,0,0,0])
tf.append([img.max(),1,1,1,1])
for p in tf:
color_tf.AddRGBPoint(p[0], p[1], p[2], p[3])
opacity_tf.AddPoint(p[0], p[4])
# working on the GPU
# volMapper = vtk.vtkGPUVolumeRayCastMapper()
# volMapper.SetInputConnection(importer.GetOutputPort())
# # The property describes how the data will look
# volProperty = vtk.vtkVolumeProperty()
# volProperty.SetColor(color_tf)
# volProperty.SetScalarOpacity(opacity_tf)
# volProperty.ShadeOn()
# volProperty.SetInterpolationTypeToLinear()
# working on the CPU
volMapper = vtk.vtkVolumeRayCastMapper()
compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
compositeFunction.SetCompositeMethodToInterpolateFirst()
volMapper.SetVolumeRayCastFunction(compositeFunction)
volMapper.SetInputConnection(importer.GetOutputPort())
# The property describes how the data will look
volProperty = vtk.vtkVolumeProperty()
volProperty.SetColor(color_tf)
volProperty.SetScalarOpacity(opacity_tf)
volProperty.ShadeOn()
volProperty.SetInterpolationTypeToLinear()
# Do the lines below speed things up?
# pix_diag = 5.0
# volMapper.SetSampleDistance(pix_diag / 5.0)
# volProperty.SetScalarOpacityUnitDistance(pix_diag)
vol = vtk.vtkVolume()
vol.SetMapper(volMapper)
vol.SetProperty(volProperty)
return [vol]
def BuildView(self):
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if self.Volume:
self.vmtkRenderer.Renderer.RemoveVolume(self.Volume)
if (self.ArrayName != ''):
self.Image.GetPointData().SetActiveScalars(self.ArrayName)
scalarRange = [0.0, 0.0]
if self.WindowLevel[0] > 0.0:
scalarRange = [self.WindowLevel[1] - self.WindowLevel[0]/2.0, self.WindowLevel[1] + self.WindowLevel[0]/2.0]
else:
scalarRange = self.Image.GetScalarRange()
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.AddRGBPoint(scalarRange[0], 0.0, 0.0, 0.0)
colorTransferFunction.AddRGBPoint(scalarRange[1], 1.0, 1.0, 1.0)
volumeMapper = vtk.vtkFixedPointVolumeRayCastMapper()
volumeMapper.SetInput(self.Image)
volumeMapper.SetBlendModeToMaximumIntensity()
if self.AutoSampleDistance:
volumeMapper.AutoAdjustSampleDistancesOn()
else:
volumeMapper.SetSampleDistance(self.SampleDistance)
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.ShadeOn()
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.SetColor(colorTransferFunction)
self.Volume = vtk.vtkVolume()
self.Volume.SetMapper(volumeMapper)
self.Volume.SetProperty(volumeProperty)
self.vmtkRenderer.Renderer.AddVolume(self.Volume)
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def __init__(self): super(VolumeVisualizationRamp, self).__init__() self.visualizationType = VisualizationTypeRamp self.volProp = vtkVolumeProperty() self.volProp.SetIndependentComponents(True) self.volProp.SetInterpolationTypeToLinear() self.volProp.ShadeOn() self.volProp.SetAmbient(0.1) self.volProp.SetDiffuse(0.9) self.volProp.SetSpecular(0.2) self.volProp.SetSpecularPower(10.0) self.volProp.SetScalarOpacityUnitDistance(0.8919)
def save_vtk_image(images, dst, i):
image_import = vtk.vtkImageImport()
image_import.CopyImportVoidPointer(images.tostring(), len(images.tostring()))
image_import.SetDataScalarTypeToUnsignedChar()
image_import.SetNumberOfScalarComponents(1)
image_import.SetDataExtent(0, images.shape[2] - 1, 0, images.shape[1] - 1, 0, images.shape[0] - 1)
image_import.SetWholeExtent(0, images.shape[2] - 1, 0, images.shape[1] - 1, 0, images.shape[0] - 1)
volume = vtk.vtkVolume()
volume_mapper = vtk.vtkVolumeRayCastMapper()
alpha_channel_func = vtk.vtkPiecewiseFunction()
alpha_channel_func.AddPoint(0, 0.0)
# alpha_channel_func.AddPoint(64, 0.3)
# alpha_channel_func.AddPoint(128, 0.5)
alpha_channel_func.AddPoint(100, 1.0)
alpha_channel_func.ClampingOn()
color_func = vtk.vtkPiecewiseFunction()
color_func.AddPoint(5, 0.3)
color_func.AddPoint(25, 0.5)
color_func.AddPoint(125, 0.7)
color_func.AddPoint(255, 1.0)
volume_property = vtk.vtkVolumeProperty()
volume_property.SetColor(color_func)
volume_property.SetInterpolationTypeToLinear()
volume_property.SetScalarOpacity(alpha_channel_func)
volume.SetProperty(volume_property)
volume_ray_cast_func = vtk.vtkVolumeRayCastMIPFunction()
volume_mapper.SetInputConnection(image_import.GetOutputPort())
volume_mapper.SetVolumeRayCastFunction(volume_ray_cast_func)
# volume_mapper.SetSampleDistance(1)
# volume_mapper.SetAutoAdjustSampleDistances(0)
# volume_mapper.SetImageSampleDistance(1)
volume.SetMapper(volume_mapper)
ren = vtk.vtkRenderer()
ren.AddVolume(volume)
ren.SetBackground(0, 0, 0)
renWin = vtk.vtkRenderWindow()
renWin.SetSize(1024, 1024)
renWin.AddRenderer(ren)
renWin.Render()
window_2_image = vtk.vtkWindowToImageFilter()
window_2_image.SetInput(renWin)
window_2_image.Update()
png_writer = vtk.vtkPNGWriter()
png_writer.SetFileName(dst + '%05d'%(i) + '.png')
png_writer.SetInput(window_2_image.GetOutput())
png_writer.Write()
def load_atlas(path, intensities, signs):
'''
path: path to atlas file
opacity: opacity of overlayed atlas brain
'''
nifti_reader = vtk.vtkNIFTIImageReader()
nifti_reader.SetFileName(path)
nifti_reader.Update()
# intensities = intensities/math.sqrt(np.mean(intensities**2))
# The following class is used to store transparencyv-values for later
# retrival. In our case, we want the value 0 to be completly opaque
alphaChannelFunc = vtk.vtkPiecewiseFunction()
alphaChannelFunc.AddPoint(0, 0.0)
for i in range(len(intensities)):
alphaChannelFunc.AddPoint(i+1, intensities[i])
# 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(0, 0.0, 0.0, 0.0)
for i in range(len(signs)):
if signs[i] < 0: colorFunc.AddRGBPoint(i+1, 0.0, 0.0, intensities[i])
elif signs[i] > 0: colorFunc.AddRGBPoint(i+1, intensities[i], 0.0, 0.0)
else: colorFunc.AddRGBPoint(i+1, 1.0, 1.0, 1.0)
# 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 prpoperties.
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorFunc)
volumeProperty.SetScalarOpacity(alphaChannelFunc)
volumeProperty.ShadeOn()
# 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.vtkSmartVolumeMapper()
volumeMapper.SetInputDataObject(nifti_reader.GetOutput())
# 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)
return volume
def main(argv):
if len(argv) < 2:
print "usage:",argv[0]," data.nrrd data.cmap"
exit(1)
data_fn = argv[1]
cmap_fn = argv[2]
reader = vtk.vtkPNrrdReader()
reader.SetFileName(data_fn)
reader.Update()
data = reader.GetOutput()
# opacity function
opacityFunction = vtk.vtkPiecewiseFunction()
# color function
colorFunction = vtk.vtkColorTransferFunction()
cmap = open(cmap_fn, 'r')
for line in cmap.readlines():
parts = line.split()
value = float(parts[0])
r = float(parts[1])
g = float(parts[2])
b = float(parts[3])
a = float(parts[4])
opacityFunction.AddPoint(value, a)
colorFunction.AddRGBPoint(value, r, g, b)
# volume setup:
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorFunction)
volumeProperty.SetScalarOpacity(opacityFunction)
# composite function (using ray tracing)
compositeFunction = vtk.vtkVolumeRayCastMIPFunction()
volumeMapper = vtk.vtkVolumeRayCastMapper()
volumeMapper.SetVolumeRayCastFunction(compositeFunction)
volumeMapper.SetInput(data)
# make the volume
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
# renderer
renderer = vtk.vtkRenderer()
renderWin = vtk.vtkRenderWindow()
renderWin.AddRenderer(renderer)
renderInteractor = vtk.vtkRenderWindowInteractor()
renderInteractor.SetRenderWindow(renderWin)
renderer.AddVolume(volume)
renderer.SetBackground(0,0,0)
renderWin.SetSize(400, 400)
renderInteractor.Initialize()
renderWin.Render()
renderInteractor.Start()
def __init__(self):
'''
Constructor
'''
vtkPythonViewImage.__init__(self)
# texture mapper in 3D: vtkVolumeMapper
self.__VolumeMapper = None
# texture mapper in 3D: vtkVolumeTextureMapper3D
self.__VolumeTextureMapper = vtk.vtkVolumeTextureMapper3D()
# volume ray cast mapper vtkFixedPointVolumeRayCastMapper
self.__VolumeRayCastMapper = vtk.vtkFixedPointVolumeRayCastMapper()
# volume property: vtkVolumeProperty
self.__VolumeProperty = vtk.vtkVolumeProperty()
# volume actor: vtkVolume
self.__VolumeActor = vtk.vtkVolume()
# opacity transfer function: vtkPiecewiseFunction
self.__OpacityFunction = vtk.vtkPiecewiseFunction()
# color transfer function: vtkColorTransferFunction
self.__ColorFunction = vtk.vtkColorTransferFunction()
# vtkProp3DCollection
self.__PhantomCollection = vtk.vtkProp3DCollection()
# blender: vtkImageBlend
self.__Blender = None
# image 3D cropping box callback: vtkImage3DCroppingBoxCallback
self.__Callback = vtkPythonImage3DCroppingBoxCallback()
# box widget: vtkOrientedBoxWidget
# self.__BoxWidget = vtkOrientedBoxWidget() # Now I could not wrap vtkOrientedBoxWidget
self.__BoxWidget = vtk.vtkBoxWidget()
# vtkPlane widget: vtkPlaneWidget
self.__PlaneWidget = vtk.vtkPlaneWidget()
# annotated cube actor: vtkAnnotatedCubeActor, vtkOrientationMarkerWidget
self.__Cube = vtk.vtkAnnotatedCubeActor()
self.__Marker = vtk.vtkOrientationMarkerWidget()
self.SetupVolumeRendering()
self.SetupWidgets()
self.ShowAnnotationsOn()
self.getTextProperty().SetColor(0, 0, 0)
self.SetBackground(0.9, 0.9, 0.9) # white
self.__FirstRender = 1
self.__RenderingMode = self.PLANAR_RENDERING
self.__VRQuality = 1
self.__InteractorStyleSwitcher = None
def __init__(self, parent): wx.SplitterWindow.__init__(self, parent) # # setup the control panel # self.controlPanel = wx.lib.scrolledpanel.ScrolledPanel( self ) vBox = wx.BoxSizer( wx.VERTICAL ) self.mode = wx.RadioBox( self.controlPanel, label="Mode", choices=["2D", "3D"] ) vBox.Add( self.mode, 0, wx.EXPAND ) self.colorAndOpacityEditor = WrapITKColorAndOpacityEditor( self.controlPanel ) vBox.Add( self.colorAndOpacityEditor, 0, wx.EXPAND ) self.controlPanel.SetSizer( vBox ) self.controlPanel.SetupScrolling() # # setup the render window # from vtk.wx.wxVTKRenderWindowInteractor import wxVTKRenderWindowInteractor from vtk import vtkRenderer, vtkVolumeTextureMapper2D, vtkVolumeProperty, vtkVolume self.rendererWindow = wxVTKRenderWindowInteractor(self, -1) self.renderer = vtkRenderer() self.rendererWindow.GetRenderWindow().AddRenderer(self.renderer) self.volumeMapper = vtkVolumeTextureMapper2D() self.volume = vtkVolume() self.volumeProperty = vtkVolumeProperty() self.volumeProperty.SetScalarOpacity( self.colorAndOpacityEditor.opacityTransferFunction ) self.volumeProperty.SetColor( self.colorAndOpacityEditor.colorTransferFunction ) self.volume.SetMapper( self.volumeMapper ) self.volume.SetProperty( self.volumeProperty ) self.renderer.AddVolume( self.volume ) self.outline = None self.outlineMapper = None self.outlineActor = None # fill the split pane self.SplitVertically( self.controlPanel, self.rendererWindow ) # avoid loosing on panel or the other self.SetMinimumPaneSize( 1 ) # to manage update event correctly self.updateInProgress = False
def opImplement(self):
opacity = vtk.vtkPiecewiseFunction();
#x is scaler value , y is opacity value
opacity.AddPoint(IMAGEOUT,0.0);
opacity.AddPoint(IMAGEIN ,1.0);
#x is scaler value , other is rgb value
color = vtk.vtkColorTransferFunction();
color.AddRGBPoint(IMAGEIN ,255.0/255.0,255.0/255.0,255.0/255.0);
volumeProperty = vtk.vtkVolumeProperty();
volumeProperty.ShadeOn();
volumeProperty.SetScalarOpacity(opacity)
volumeProperty.SetColor(color);
mapper = vtk.vtkSmartVolumeMapper();
mapper.SetInputData(self.data);
volume = vtk.vtkVolume();
volume.SetMapper(mapper);
volume.SetProperty(volumeProperty);
return volume;