def _volume(dimensions, origin, spacing, scalars,
surface_alpha, resolution, blending, center):
# Now we can actually construct the visualization
grid = pyvista.UniformGrid()
grid.dimensions = dimensions + 1 # inject data on the cells
grid.origin = origin
grid.spacing = spacing
grid.cell_arrays['values'] = scalars
# Add contour of enclosed volume (use GetOutput instead of
# GetOutputPort below to avoid updating)
grid_alg = vtk.vtkCellDataToPointData()
grid_alg.SetInputDataObject(grid)
grid_alg.SetPassCellData(False)
grid_alg.Update()
if surface_alpha > 0:
grid_surface = vtk.vtkMarchingContourFilter()
grid_surface.ComputeNormalsOn()
grid_surface.ComputeScalarsOff()
grid_surface.SetInputData(grid_alg.GetOutput())
grid_surface.SetValue(0, 0.1)
grid_surface.Update()
grid_mesh = vtk.vtkPolyDataMapper()
grid_mesh.SetInputData(grid_surface.GetOutput())
else:
grid_mesh = None
mapper = vtk.vtkSmartVolumeMapper()
if resolution is None: # native
mapper.SetScalarModeToUseCellData()
mapper.SetInputDataObject(grid)
else:
upsampler = vtk.vtkImageReslice()
upsampler.SetInterpolationModeToLinear() # default anyway
upsampler.SetOutputSpacing(*([resolution] * 3))
upsampler.SetInputConnection(grid_alg.GetOutputPort())
mapper.SetInputConnection(upsampler.GetOutputPort())
# Additive, AverageIntensity, and Composite might also be reasonable
remap = dict(composite='Composite', mip='MaximumIntensity')
getattr(mapper, f'SetBlendModeTo{remap[blending]}')()
volume_pos = vtk.vtkVolume()
volume_pos.SetMapper(mapper)
dist = grid.length / (np.mean(grid.dimensions) - 1)
volume_pos.GetProperty().SetScalarOpacityUnitDistance(dist)
if center is not None and blending == 'mip':
# We need to create a minimum intensity projection for the neg half
mapper_neg = vtk.vtkSmartVolumeMapper()
if resolution is None: # native
mapper_neg.SetScalarModeToUseCellData()
mapper_neg.SetInputDataObject(grid)
else:
mapper_neg.SetInputConnection(upsampler.GetOutputPort())
mapper_neg.SetBlendModeToMinimumIntensity()
volume_neg = vtk.vtkVolume()
volume_neg.SetMapper(mapper_neg)
volume_neg.GetProperty().SetScalarOpacityUnitDistance(dist)
else:
volume_neg = None
return grid, grid_mesh, volume_pos, volume_neg
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 __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 __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 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, 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 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 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 __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 CreateVolumeRayCastMapper(self, volumeSrc):
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputConnection(volumeSrc.GetOutputPort())
volumeMapper.SetRequestedRenderModeToRayCast()
volumeMapper.SetBlendModeToMaximumIntensity()
volumeMapper.SetInterpolationModeToNearestNeighbor()
return volumeMapper
def viz_visualize(self):
volume = vtk.vtkVolume()
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(self.__colorFunc)
volumeProperty.SetScalarOpacity(self.__alphaChannelFunc)
volumeProperty.ShadeOn()
volumeProperty.SetInterpolationTypeToLinear()
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputConnection(self.__dataImporter.GetOutputPort())
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
self.__ren.AddVolume(volume)
def render_p(self):
self.ren.RemoveVolume(self.P_volume)
if not self.config["P"][0]:
return
# input: file containing all data for P.vti
# output: actor for current timestep
data_path = compose_file_name(self.base_dir, "/P",
self.data_folders["P"], self.time_step)
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(data_path)
reader.Update()
spacing = reader.GetOutput().GetSpacing()
reader.GetOutput().SetSpacing(spacing[0], spacing[1], spacing[2] * 30)
myrange = reader.GetOutput().GetPointData().GetScalars().GetRange()
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint(-3781, 0.3)
opacityTransferFunction.AddPoint(-3097, 0.3)
opacityTransferFunction.AddPoint(-2488, 0)
opacityTransferFunction.AddPoint(-1334, 0)
opacityTransferFunction.AddPoint(-661, 0.001)
opacityTransferFunction.AddPoint(-354, 0)
opacityTransferFunction.AddPoint(787, 0.0021)
opacityTransferFunction.AddPoint(1225, 0.0062)
opacityTransferFunction.AddPoint(2010, 0.1)
opacityTransferFunction.AddPoint(2329, 0.1)
color = vtk.vtkColorTransferFunction()
# Blue
color.AddRGBPoint(myrange[0], 0., 1., 0)
color.AddRGBPoint((myrange[0] + myrange[1]) / 2, 1., 1., 0)
color.AddRGBPoint(myrange[1], 1., 0., 0.)
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(color)
volumeProperty.SetScalarOpacity(opacityTransferFunction)
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.ShadeOff()
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetBlendModeToComposite()
volumeMapper.SetAutoAdjustSampleDistances(0)
volumeMapper.SetSampleDistance(0.5)
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)
self.P_volume = volume
self.ren.AddVolume(volume)
def RenderImage(self, origImg):
self.ren[0].RemoveVolume(self.volume)
self.ren[0].RemoveActor(self.outLine)
# create volume
volumeImport = vtk.vtkImageImport()
data_string = origImg.tostring()
if origImg.dtype == np.uint16:
volumeImport.CopyImportVoidPointer(data_string, len(data_string))
volumeImport.SetDataScalarTypeToUnsignedShort()
else:
volumeImport.CopyImportVoidPointer(data_string, len(data_string))
volumeImport.SetDataScalarTypeToUnsignedChar()
volumeImport.SetNumberOfScalarComponents(1)
sz = origImg.shape
volumeImport.SetDataExtent(0, sz[2] - 1, 0, sz[1] - 1, 0, sz[0] - 1)
volumeImport.SetWholeExtent(0, sz[2] - 1, 0, sz[1] - 1, 0, sz[0] - 1)
volumeImport.Update()
self.importData.DeepCopy(volumeImport.GetOutput())
self.volumeSize = sz
#
alphaChannelFunc = vtk.vtkPiecewiseFunction()
alphaChannelFunc.AddPoint(0, 0.0)
alphaChannelFunc.AddPoint(10, 0.9)
#
self.colorFunc.AddRGBPoint(1, 0.0, 0.0, 0.0)
self.colorFunc.AddRGBPoint(255, 1.0, 1.0, 1.0)
#
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(self.colorFunc)
volumeProperty.SetScalarOpacity(alphaChannelFunc)
volumeProperty.SetInterpolationType(3)
#
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetBlendModeToMaximumIntensity()
# volumeMapper.SetVolumeRayCastFunction(compositeFunction)
volumeMapper.SetInterpolationModeToCubic()
volumeMapper.SetInputConnection(volumeImport.GetOutputPort())
self.volume.SetMapper(volumeMapper)
self.volume.SetProperty(volumeProperty)
self.volume.SetUserTransform(self.transform)
#
outLineSource = vtk.vtkVolumeOutlineSource()
outLineSource.SetVolumeMapper(volumeMapper)
outLineMapper = vtk.vtkPolyDataMapper()
outLineMapper.SetInputConnection(outLineSource.GetOutputPort())
self.outLine.SetMapper(outLineMapper)
self.outLine.GetProperty().SetColor(0, 1, 1)
self.outLine.SetUserTransform(self.transform)
self.ren[0].AddVolume(self.volume)
self.ren[0].AddActor(self.outLine)
self.ren[0].ResetCamera()
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 __init__(self, data_dir, opacityL, opacityH):
# Read the data
filename = "vol_t00_x5_70_d4pt5_inner.vti"
vSource = vtk.vtkXMLImageDataReader()
vSource.SetFileName(filename)
vSource.Update()
#blocks = reader1.GetOutput()
#b0 = blocks.GetBlock(0)
# Setup VTK environment
#Create a mapper and actor
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint(opacityL, 0.0)
opacityTransferFunction.AddPoint(opacityH, 0.8)
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.AddRGBPoint(0.0, 0.0, 0.0, 0.0)
colorTransferFunction.AddRGBPoint(64.0, 1.0, 0.2, 0.4)
#colorTransferFunction.AddRGBPoint(128.0, 0.0, 0.0, 1.0)
#colorTransferFunction.AddRGBPoint(192.0, 0.0, 1.0, 0.0)
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorTransferFunction)
#volumeProperty.SetGradientOpacity(gradientTransferFunction)
volumeProperty.SetScalarOpacity(opacityTransferFunction)
#volumeProperty.ShadeOn()
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.SetAmbient(1.0)
volumeProperty.SetDiffuse(0.7)
volumeProperty.SetSpecular(0.5)
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputConnection(vSource.GetOutputPort())
#volumeMapper.CroppingOn()
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
volume.Update()
#renderer.AddVolume(volume)
# Mapper
#glyph_mapper = vtk.vtkPolyDataMapper()
#glyph_mapper.SetInputConnection(glyphs.GetOutputPort())
#glyph_actor = vtk.vtkActor()
#glyph_actor.SetMapper(glyph_mapper)
#self.b0 = b0
self.volume = volume
self.vSource = vSource
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 __init__(self):
super().__init__()
self.vtk_widget = QVTKRenderWindowInteractor(self)
self.main_layout = QGridLayout()
self.main_layout.addWidget(self.vtk_widget)
self.setLayout(self.main_layout)
self.vtk_renderer = vtk.vtkRenderer()
self.vtk_render_win = self.vtk_widget.GetRenderWindow()
self.vtk_render_win.AddRenderer(self.vtk_renderer)
self.vtk_interactor = self.vtk_render_win.GetInteractor()
self.vtk_interactor.Initialize()
self.vtk_volume_mapper = vtk.vtkSmartVolumeMapper()
pass
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;
def render_cloud(self):
self.ren.RemoveVolume(self.cloud_volume)
if not self.config["CLOUD"][0]:
return
data_path = compose_file_name(self.base_dir, "/CLOUD",
self.data_folders["CLOUD"],
self.time_step)
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(data_path)
reader.Update()
spacing = reader.GetOutput().GetSpacing()
reader.GetOutput().SetSpacing(spacing[0], spacing[1], spacing[2] * 30)
myrange = reader.GetOutput().GetPointData().GetScalars().GetRange()
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint(myrange[0], 0.0)
opacityTransferFunction.AddPoint(myrange[1], 0.1)
color = vtk.vtkColorTransferFunction()
# Blue
color.AddRGBPoint(myrange[0], 0.8, 0.8, 0.8)
color.AddRGBPoint((myrange[0] + myrange[1]) / 2, 1., 1., 1)
color.AddRGBPoint(myrange[1], 0.8, 0.8, 0.8)
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(color)
volumeProperty.SetScalarOpacity(opacityTransferFunction)
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.ShadeOff()
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetBlendModeToComposite()
volumeMapper.SetAutoAdjustSampleDistances(0)
volumeMapper.SetSampleDistance(0.5)
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)
self.cloud_volume = volume
self.ren.AddVolume(volume)
def makeVolumeRenderingPipeline(in_volume):
dataImporter = vtk.vtkImageImport()
if in_volume.dtype == numpy.uint8:
dataImporter.SetDataScalarTypeToUnsignedChar()
elif in_volume.dtype == numpy.uint16:
dataImporter.SetDataScalarTypeToUnsignedShort()
elif in_volume.dtype == numpy.int32:
dataImporter.SetDataScalarTypeToInt()
elif in_volume.dtype == numpy.int16:
dataImporter.SetDataScalarTypeToShort()
else:
raise RuntimeError("unknown data type %r of volume" %
(in_volume.dtype, ))
dataImporter.SetImportVoidPointer(in_volume, len(in_volume))
dataImporter.SetNumberOfScalarComponents(1)
extent = [
0, in_volume.shape[2] - 1, 0, in_volume.shape[1] - 1, 0,
in_volume.shape[0] - 1
]
dataImporter.SetDataExtent(*extent)
dataImporter.SetWholeExtent(*extent)
alphaChannelFunc = vtk.vtkPiecewiseFunction()
alphaChannelFunc.AddPoint(0, 0.0)
for i in range(1, NOBJECTS):
alphaChannelFunc.AddPoint(i, 1.0)
colorFunc = vtk.vtkColorTransferFunction()
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputConnection(dataImporter.GetOutputPort())
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorFunc)
volumeProperty.SetScalarOpacity(alphaChannelFunc)
volumeProperty.ShadeOn()
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
return dataImporter, colorFunc, volume, volumeMapper
def showVolume(self, vtkImageData, preserveState):
'''Shows volume of image.'''
producer = vtk.vtkTrivialProducer()
producer.SetOutput(vtkImageData)
flip = vtk.vtkImageFlip()
# flip over y axis
flip.SetFilteredAxis(1)
flip.SetInputConnection(producer.GetOutputPort())
mapper = vtk.vtkSmartVolumeMapper()
mapper.SetInputConnection(flip.GetOutputPort())
scalarRange = vtkImageData.GetScalarRange()
opacity = vtk.vtkPiecewiseFunction()
opacity.AddPoint(scalarRange[0], 0.2)
opacity.AddPoint(scalarRange[1], 0.9)
color = vtk.vtkColorTransferFunction()
color.AddRGBPoint(scalarRange[0], 0, 0, 0)
color.AddRGBPoint(scalarRange[1], 1, 1, 1)
prop = vtk.vtkVolumeProperty()
prop.ShadeOff()
prop.SetInterpolationType(vtk.VTK_LINEAR_INTERPOLATION)
prop.SetColor(color)
prop.SetScalarOpacity(opacity)
# save tubes and property if preserving state
if preserveState and self.volume:
prop = self.volume.GetProperty()
self.volumeRenderer.RemoveViewProp(self.volume)
else:
self.volumeRenderer.RemoveAllViewProps()
self.volume = vtk.vtkVolume()
self.volume.SetMapper(mapper)
self.volume.SetProperty(prop)
self.volumeRenderer.AddViewProp(self.volume)
self.volumeRenderer.ResetCamera()
def makeVolumeRenderingPipeline(in_volume):
dataImporter = vtk.vtkImageImport()
if in_volume.dtype == numpy.uint8:
dataImporter.SetDataScalarTypeToUnsignedChar()
elif in_volume.dtype == numpy.uint16:
dataImporter.SetDataScalarTypeToUnsignedShort()
elif in_volume.dtype == numpy.int32:
dataImporter.SetDataScalarTypeToInt()
elif in_volume.dtype == numpy.int16:
dataImporter.SetDataScalarTypeToShort()
else:
raise RuntimeError("unknown data type %r of volume" % (in_volume.dtype,))
dataImporter.SetImportVoidPointer(in_volume, len(in_volume))
dataImporter.SetNumberOfScalarComponents(1)
extent = [0, in_volume.shape[2]-1, 0, in_volume.shape[1]-1, 0, in_volume.shape[0]-1]
dataImporter.SetDataExtent(*extent)
dataImporter.SetWholeExtent(*extent)
alphaChannelFunc = vtk.vtkPiecewiseFunction()
alphaChannelFunc.AddPoint(0, 0.0)
for i in range(1, NOBJECTS):
alphaChannelFunc.AddPoint(i, 1.0)
colorFunc = vtk.vtkColorTransferFunction()
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputConnection(dataImporter.GetOutputPort())
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorFunc)
volumeProperty.SetScalarOpacity(alphaChannelFunc)
volumeProperty.ShadeOn()
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
return dataImporter, colorFunc, volume, volumeMapper
def __init__(self, data_dir, opacityL, opacityH):
# Read the data
filename = "inclusions_all.vti"
vSource = vtk.vtkXMLImageDataReader()
vSource.SetFileName(filename)
vSource.Update()
#Create a mapper and actor
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint(opacityL, 0.0)
opacityTransferFunction.AddPoint(opacityH, 0.8)
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.AddRGBPoint(0.0, 0.0, 0.0, 0.0)
colorTransferFunction.AddRGBPoint(64.0, 1.0, 0.2, 0.4)
colorTransferFunction.AddRGBPoint(128.0, 0.0, 0.0, 1.0)
colorTransferFunction.AddRGBPoint(192.0, 0.0, 1.0, 0.0)
volumeProperty = vtk.vtkVolumeProperty()
#volumeProperty.SetColor(colorTransferFunction)
#volumeProperty.SetGradientOpacity(gradientTransferFunction)
volumeProperty.SetScalarOpacity(opacityTransferFunction)
#volumeProperty.ShadeOn()
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.SetAmbient(1.0)
volumeProperty.SetDiffuse(0.7)
volumeProperty.SetSpecular(0.5)
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputConnection(vSource.GetOutputPort())
#volumeMapper.CroppingOn()
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
volume.Update()
#renderer.AddVolume(volume)
#self.b0 = b0
self.volume = volume
self.vSource = vSource
def __init__(self, cmData, reslice=None):
self.cmData = cmData
self._min = 0
self._max = 255
self.dataImport = vtk.vtkImageImport()
self.dataImport.SetDataScalarTypeToUnsignedChar()
self.dataImport.SetNumberOfScalarComponents(1)
self.alphaFunc = vtk.vtkPiecewiseFunction()
self.colorFunc = vtk.vtkColorTransferFunction()
self.setupColorFunc()
self.prop = vtk.vtkVolumeProperty()
self.prop.SetColor(self.colorFunc)
self.prop.SetScalarOpacity(self.alphaFunc)
self.mapper = vtk.vtkSmartVolumeMapper()
self.mapper.SetBlendModeToMaximumIntensity()
if reslice is not None:
reslice.SetInputConnection(self.dataImport.GetOutputPort())
self.mapper.SetInputConnection(reslice.GetOutputPort())
else:
self.mapper.SetInputConnection(self.dataImport.GetOutputPort())
self.volume = vtk.vtkVolume()
self.volume.SetMapper(self.mapper)
self.volume.SetProperty(self.prop)
def _from_itk_to_vtk(image_type,
image_data,
color_func=None,
opacity_func=None):
# convert itk to vtk image data
itk_to_vtk = itk.ImageToVTKImageFilter[image_type].New()
itk_to_vtk.SetInput(image_data)
itk_to_vtk.Update()
vtk_image_data = itk_to_vtk.GetOutput()
# convert vtk image data to vtk object for slicer rendering
cast_filter = vtk.vtkImageCast()
cast_filter.SetInputData(vtk_image_data)
cast_filter.Update()
# convert vtk image data to vtk volume for volume rendering
vol = vtk.vtkVolume()
mapper = vtk.vtkSmartVolumeMapper()
mapper.SetInputData(vtk_image_data)
vol.SetMapper(mapper)
if color_func is None:
color_func = vtk.vtkColorTransferFunction()
if opacity_func is None:
opacity_func = vtk.vtkPiecewiseFunction()
volume_property = vtk.vtkVolumeProperty()
volume_property.SetColor(color_func)
volume_property.SetScalarOpacity(opacity_func)
volume_property.SetInterpolationTypeToLinear()
vol.SetProperty(volume_property)
vol.SetMapper(mapper)
return cast_filter, vol
colorFunc = vtk.vtkColorTransferFunction()
colorFunc.AddRGBPoint(0, 0.75, 0.75, 0.75)
colorFunc.AddRGBPoint(128, 0.75, 0.75, 0.75)
colorFunc.AddRGBPoint(255, 0.5, 0.5, 0.5)
volProp = vtk.vtkVolumeProperty()
volProp.SetColor(colorFunc)
volProp.ShadeOn()
volProp.SetAmbient(0.25)
volProp.SetDiffuse(0.75)
volProp.SetSpecular(0)
volProp.SetScalarOpacity(alphaFunc)
volProp.SetInterpolationTypeToLinear()
# volMapper = vtk.vtkFixedPointVolumeRayCastMapper()
volMapper = vtk.vtkSmartVolumeMapper()
volMapper.SetInputConnection(reader.GetOutputPort())
vol = vtk.vtkVolume()
vol.SetMapper(volMapper)
vol.SetProperty(volProp)
renderer = vtk.vtkRenderer()
renderer.AddVolume(vol)
renderer.SetBackground(colors.GetColor3d('White'))
renderer.ResetCamera()
renderer.GetActiveCamera().Azimuth(-90)
renderer.GetActiveCamera().Elevation(-90)
# renderer.GetActiveCamera().Roll(180)
renderer.GetActiveCamera().Zoom(1.5)
def initialize(self):
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(
protocols.vtkWebPublishImageDelivery(decode=False))
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(_WebCone.authKey)
# tell the C++ web app to use no encoding.
# ParaViewWebPublishImageDelivery must be set to decode=False to match.
self.getApplication().SetImageEncoding(0)
# Create default pipeline (Only once for all the session)
if not _WebCone.view:
# VTK specific code
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderWindowInteractor.GetInteractorStyle(
).SetCurrentStyleToTrackballCamera()
# cone = vtk.vtkConeSource()
# mapper = vtk.vtkPolyDataMapper()
# actor = vtk.vtkActor()
# mapper.SetInputConnection(cone.GetOutputPort())
# actor.SetMapper(mapper)
# renderer.AddActor(actor)
# load nrrd
reader = vtk.vtkNrrdReader()
reader.SetFileName('C:\\Users\\Mat\\Desktop\\tardiva3.0.nrrd')
reader.Update()
# The volume will be displayed by ray-cast alpha compositing.
# A ray-cast mapper is needed to do the ray-casting.
# volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
volume_mapper = vtk.vtkSmartVolumeMapper()
volume_mapper.SetInputConnection(reader.GetOutputPort())
volume_mapper.SetSampleDistance(0.5)
# The color transfer function maps voxel intensities to colors.
# It is modality-specific, and often anatomy-specific as well.
# The goal is to one color for flesh (between 500 and 1000)
# and another color for bone (1150 and over).
volume_color = vtk.vtkColorTransferFunction()
volume_color.AddRGBPoint(0, 0.2, 0.2, 0.7)
volume_color.AddRGBPoint(500, 240.0 / 255.0, 184.0 / 255.0,
160.0 / 255.0)
volume_color.AddRGBPoint(1000, 240.0 / 255.0, 184.0 / 255.0,
160.0 / 255.0)
volume_color.AddRGBPoint(1150, 1.0, 1.0, 240.0 / 255.0) # Ivory
# The opacity transfer function is used to control the opacity
# of different tissue types.
volume_scalar_opacity = vtk.vtkPiecewiseFunction()
volume_scalar_opacity.AddPoint(0, 0.00)
volume_scalar_opacity.AddPoint(500, 0.15)
volume_scalar_opacity.AddPoint(1000, 0.15)
volume_scalar_opacity.AddPoint(1150, 0.85)
# The gradient opacity function is used to decrease the opacity
# in the 'flat' regions of the volume while maintaining the opacity
# at the boundaries between tissue types. The gradient is measured
# as the amount by which the intensity changes over unit distance.
# For most medical data, the unit distance is 1mm.
volume_gradient_opacity = vtk.vtkPiecewiseFunction()
volume_gradient_opacity.AddPoint(0, 0.0)
volume_gradient_opacity.AddPoint(90, 0.5)
volume_gradient_opacity.AddPoint(100, 1.0)
# The VolumeProperty attaches the color and opacity functions to the
# volume, and sets other volume properties. The interpolation should
# be set to linear to do a high-quality rendering. The ShadeOn option
# turns on directional lighting, which will usually enhance the
# appearance of the volume and make it look more '3D'. However,
# the quality of the shading depends on how accurately the gradient
# of the volume can be calculated, and for noisy data the gradient
# estimation will be very poor. The impact of the shading can be
# decreased by increasing the Ambient coefficient while decreasing
# the Diffuse and Specular coefficient. To increase the impact
# of shading, decrease the Ambient and increase the Diffuse and Specular.
volume_property = vtk.vtkVolumeProperty()
volume_property.SetColor(volume_color)
volume_property.SetScalarOpacity(volume_scalar_opacity)
volume_property.SetGradientOpacity(volume_gradient_opacity)
volume_property.SetInterpolationTypeToLinear()
volume_property.ShadeOn()
volume_property.SetAmbient(0.4)
volume_property.SetDiffuse(0.6)
volume_property.SetSpecular(0.2)
# The vtkVolume is a vtkProp3D (like a vtkActor) and controls the position
# and orientation of the volume in world coordinates.
volumeActor = vtk.vtkVolume()
volumeActor.SetMapper(volume_mapper)
volumeActor.SetProperty(volume_property)
# Finally, add the volume to the renderer
renderer.AddActor(volumeActor)
##########################
# renderer.AddActor(actor)
# render
renderer.ResetCamera()
renderWindow.Render()
# VTK Web application specific
_WebCone.view = renderWindow
self.getApplication().GetObjectIdMap().SetActiveObject(
"VIEW", renderWindow)
camera = renderer.MakeCamera()
camera.SetPosition(
volume_center[0], volume_center[1],
volume_center[2] + offset_scale * np.linalg.norm(volume_diag))
camera.SetFocalPoint(volume_center[0], volume_center[1], volume_center[2])
#camera.SetParallelScale(135.24329927948372)
camera.Elevation(-85)
renderer.SetActiveCamera(camera)
# volume properties
prop_volume = vtk.vtkVolumeProperty()
prop_volume.ShadeOff()
prop_volume.SetInterpolationTypeToLinear()
# vtk volume renderer
mapperVolume = vtk.vtkSmartVolumeMapper()
mapperVolume.SetRequestedRenderModeToGPU()
#mapperVolume.SetRequestedRenderModeToRayCast()
mapperVolume.SetBlendModeToComposite()
mapperVolume.SetInputData(volume_data)
actorVolume = vtk.vtkVolume()
actorVolume.SetMapper(mapperVolume)
actorVolume.SetProperty(prop_volume)
renderer.AddActor(actorVolume)
if not os.path.exists(base_dir + 'imgs'):
os.makedirs(base_dir + 'imgs')
if not os.path.exists(base_dir + 'inputs'):
os.makedirs(base_dir + 'inputs')
output_img_dir = base_dir + 'imgs/'
def main(argv):
if len(argv) < 3:
sys.stderr.write("Usage: %s <volume.mhd> <trace.vtk>\n" % argv[0])
return 1
segmented_volume_filename, trace_filename = argv[1:3]
for filename in [ segmented_volume_filename, trace_filename ]:
if not os.path.exists(filename):
sys.stderr.write("file '%s' not found\n" % filename)
return 1
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(WIDTH, HEIGHT)
# create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
antique_white = [ 0.9804, 0.9216, 0.8431 ]
line_width = 5
centerline = vtk.vtkPolyDataReader()
for centerline in [centerline]:
for r in [centerline]:
r.SetFileName( trace_filename )
r.ReadAllVectorsOn()
r.ReadAllScalarsOn()
r.Update()
centerline_mapper = vtk.vtkPolyDataMapper()
for m in [centerline_mapper]:
m.SetInput( centerline.GetOutput() )
centreline_actor = vtk.vtkActor()
for a in [centreline_actor]:
a.SetMapper( centerline_mapper )
a.GetProperty().SetColor( *antique_white )
a.GetProperty().SetLineWidth( line_width );
# Create transfer mapping scalar value to opacity
opacity_transfer_function = vtk.vtkPiecewiseFunction()
for tf in [opacity_transfer_function]:
tf.AddPoint( 20 , 0.0)
tf.AddPoint( 255 , 0.2)
# Create transfer mapping scalar value to color
color_transfer_function = vtk.vtkColorTransferFunction()
for tf in [color_transfer_function]:
tf.AddRGBPoint(0.0, 0.0, 0.0, 0.0)
tf.AddRGBPoint(64.0, 0.2, 0.0, 0.0)
tf.AddRGBPoint(128.0, 0.0, 0.0, 1.0)
tf.AddRGBPoint( 192.0, 0.0, 1.0, 0.0)
tf.AddRGBPoint( 255.0, 0.0, 0.2, 0.0)
tf.SetColorSpaceToDiverging()
# The property describes how the data will look
volume_property = vtk.vtkVolumeProperty()
for vp in [volume_property]:
vp.SetColor(color_transfer_function)
vp.SetScalarOpacity(opacity_transfer_function)
segmentation = vtk.vtkMetaImageReader()
for segmentation in [segmentation]:
for r in [segmentation]:
r.SetFileName( segmented_volume_filename )
r.Update()
segmentation_outline_filter = vtk.vtkOutlineFilter()
for f in [segmentation_outline_filter]:
f.SetInput( segmentation.GetOutput() )
segmentation_outline_mapper = vtk.vtkPolyDataMapper()
for m in [segmentation_outline_mapper]:
m.SetInputConnection( segmentation_outline_filter.GetOutputPort() )
segmentation_outline_actor = vtk.vtkActor()
for a in [segmentation_outline_actor]:
a.SetMapper( segmentation_outline_mapper )
segmentation_mapper = vtk.vtkSmartVolumeMapper()
for m in [segmentation_mapper]:
m.SetInput( segmentation.GetOutput() )
segmentation_actor = vtk.vtkVolume()
for a in [segmentation_actor]:
a.SetMapper( segmentation_mapper )
a.SetProperty( volume_property )
for actor in [ centreline_actor, segmentation_actor, segmentation_outline_actor]:
ren.AddActor( actor )
iren.Initialize()
renWin.Render()
iren.Start()
iren = vtk.vtkRenderWindowInteractor() iren.SetRenderWindow(renWin) #--------------------------------------------------------- # read the volume reader = vtk.vtkImageReader2() reader.SetDataExtent(0,63,0,63,0,92) reader.SetFileNameSliceOffset(1) reader.SetDataScalarTypeToUnsignedShort() reader.SetDataByteOrderToLittleEndian() reader.SetFilePrefix(str(VTK_DATA_ROOT) + "/Data/headsq/quarter") reader.SetDataSpacing(3.2,3.2,1.5) #--------------------------------------------------------- # set up the volume rendering volumeMapper = vtk.vtkSmartVolumeMapper()#vtk.vtkVolumeTextureMapper3D() volumeMapper.SetInputConnection(reader.GetOutputPort()) volumeMapper.CroppingOn() volumeMapper.SetCroppingRegionPlanes((0.0, 141.6, 0.0, 201.6, 0.0, 138.0)) volumeColor = vtk.vtkColorTransferFunction() volumeColor.AddRGBPoint(0,0.0,0.0,0.0) volumeColor.AddRGBPoint(180,0.3,0.1,0.2) volumeColor.AddRGBPoint(1000,1.0,0.7,0.6) volumeColor.AddRGBPoint(2000,1.0,1.0,0.9) volumeScalarOpacity = vtk.vtkPiecewiseFunction() volumeScalarOpacity.AddPoint(0,0.0) volumeScalarOpacity.AddPoint(180,0.0) volumeScalarOpacity.AddPoint(1000,0.2) volumeScalarOpacity.AddPoint(2000,0.8)
def BuildView(self):
# ensure python 2-3 compatibility for checking string type (difference with unicode str handeling)
PY3 = sys.version_info[0] == 3
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if (self.ArrayName != ''):
self.Image.GetPointData().SetActiveScalars(self.ArrayName)
if PY3:
string_types = str,
else:
string_types = basestring,
if not isinstance(self.VolumeRenderingMethod, string_types):
self.PrintError(
'Specified Rendering Method is not of required "string" type')
# create volume mapper and apply requested volume rendering method
volumeMapper = vtk.vtkSmartVolumeMapper()
if self.VolumeRenderingMethod.lower() == 'default':
volumeMapper.SetRequestedRenderModeToDefault()
elif self.VolumeRenderingMethod.lower() == 'gpu':
volumeMapper.SetRequestedRenderModeToGPU()
elif self.VolumeRenderingMethod.lower() == 'ospray':
volumeMapper.SetRequestedRenderModeToOSPRay()
elif self.VolumeRenderingMethod.lower() == 'raycast':
volumeMapper.SetRequestedRenderModeToRayCast()
else:
self.PrintError(
'Specified Rendering Method: ' + self.VolumeRenderingMethod +
' not supported. Please choose from ["default", "gpu", "ospray", "raycast"]'
)
volumeMapper.SetInputData(self.Image)
volumeMapper.SetBlendModeToComposite()
# 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."""
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)
# create the volume from the mapper (defining image data and render mode) with the defined properties
# this is the last pipeline step applied. self.Volume just needs to now be added to the Renderer
self.Volume = vtk.vtkVolume()
self.Volume.SetMapper(volumeMapper)
self.Volume.SetProperty(volumeProperty)
# add the actors to the renderer
self.vmtkRenderer.Renderer.AddVolume(self.Volume)
# This next section is responsible for creating the box outline around the volume's data extent.
if self.BoxOutline:
outline = vtk.vtkOutlineFilter()
outline.SetInputData(self.Image)
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
# The SetInteractor method is how 3D widgets are associated with the
# render window interactor. Internally, SetInteractor sets up a bunch
# of callbacks using the Command/Observer mechanism (AddObserver()).
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
boxWidget.SetPlaceFactor(1.0)
# Place the interactor initially. The output of the reader is used to
# place the box widget.
boxWidget.SetInputData(self.Image)
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
# Add the actors to the renderer
self.vmtkRenderer.Renderer.AddActor(outlineActor)
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def actor_volume(volume,
what,
origin=(0, 0, 0),
c=(1, 1, 1),
tb_colors=None,
tb_opacity=.05):
imagedata = volume_to_imagedata(volume, origin=origin)
volumeMapper = vtk.vtkSmartVolumeMapper()
# volumeMapper.SetBlendModeToComposite()
volumeMapper.SetInputData(imagedata)
volumeProperty = vtk.vtkVolumeProperty()
# volumeProperty.ShadeOff()
# volumeProperty.SetInterpolationType(vtk.VTK_LINEAR_INTERPOLATION)
if what == 'tb':
compositeOpacity = vtk.vtkPiecewiseFunction()
compositeOpacity.AddPoint(0.0, 0.)
if tb_colors is not None:
for v, c in sorted(tb_colors.items()):
vl = v - .5
vr = v + .5
cp1 = vl - .25
cp2 = vr - .25
compositeOpacity.AddPoint(cp1, .5 * cp1 / 200., .5, 1.)
compositeOpacity.AddPoint(v, 1., .5, 1.)
compositeOpacity.AddPoint(cp2, .5 * cp2 / 200., .5, 1.)
compositeOpacity.AddPoint(vr, .5 * vr / 200.)
compositeOpacity.AddPoint(240., tb_opacity)
compositeOpacity.AddPoint(255.0, tb_opacity)
# compositeOpacity.AddPoint(240., .5)
# compositeOpacity.AddPoint(255.0, .5)
color = vtk.vtkColorTransferFunction()
color.AddRGBPoint(0.0, 0, 0, 0)
if tb_colors is not None:
for v, c in sorted(tb_colors.items()):
vl = v - .5
vr = v + .5
cp1 = vl - .25
cp2 = vr - .25
color.AddRGBPoint(cp1, .5 * cp1 / 200., .5 * cp1 / 200.,
.5 * cp1 / 200., .5, 1.)
color.AddRGBPoint(v, c[0], c[1], c[2], .5, 1.)
color.AddRGBPoint(cp2, .5 * cp2 / 200., .5 * cp2 / 200.,
.5 * cp2 / 200., .5, 1.)
color.AddRGBPoint(vr, .5 * vr / 200., .5 * vr / 200.,
.5 * vr / 200.)
color.AddRGBPoint(200.0, .5, .5, .5)
color.AddRGBPoint(255.0, 1, 1, 1)
# volumeGradientOpacity = vtk.vtkPiecewiseFunction()
# volumeGradientOpacity.AddPoint(0, 0.0)
# volumeGradientOpacity.AddPoint(1, 0.5)
# volumeGradientOpacity.AddPoint(2, 1.0)
elif what == 'score':
compositeOpacity = vtk.vtkPiecewiseFunction()
compositeOpacity.AddPoint(0.0, 0.0)
# compositeOpacity.AddPoint(0.95, .0)
# compositeOpacity.AddPoint(0.96, .2)
compositeOpacity.AddPoint(0.9999, .0)
compositeOpacity.AddPoint(1.0, .2)
volumeProperty.SetScalarOpacity(compositeOpacity)
color = vtk.vtkColorTransferFunction()
color.AddRGBPoint(0.0, 1, 1, 1)
color.AddRGBPoint(0.95, 1, 1, 1)
color.AddRGBPoint(1.0, 1, 1, 1)
elif what == 'probability':
compositeOpacity = vtk.vtkPiecewiseFunction()
compositeOpacity.AddPoint(0.0, 0.)
compositeOpacity.AddPoint(.9, 0.05)
compositeOpacity.AddPoint(1., 0.05)
r, g, b = c
color = vtk.vtkColorTransferFunction()
color.AddRGBPoint(0.0, r, g, b)
# color.AddRGBPoint(.95, .5,.5,.5)
color.AddRGBPoint(1., r, g, b)
# lookupTable = vtkLookupTable()
# lookupTable.SetNumberOfTableValues(2);
# lookupTable.SetRange(0.0,1.0);
# lookupTable.SetTableValue( 0, 0.0, 0.0, 0.0, 0.0 ); #label 0 is transparent
# lookupTable.SetTableValue( 1, 0.0, 1.0, 0.0, 1.0 ); #label 1 is opaque and green
# lookupTable.Build()
#
# mapTransparency = vtkImageMapToColors()
# mapTransparency.SetLookupTable(lookupTable)
# mapTransparency.PassAlphaToOutputOn()
# mapTransparency.SetInputData(maskImage)
#
# maskActor = vtkImageActor()
# maskActor.GetMapper().SetInputConnection(mapTransparency.GetOutputPort())
#
#
# volumeProperty.SetScalarOpacity(compositeOpacity)
# volumeProperty.SetColor(color)
#
# volume = vtk.vtkVolume()
# volume.SetMapper(volumeMapper)
# volume.SetProperty(volumeProperty)
#
# return volume
else:
sys.stderr.write('Color/opacity profile not recognized.\n')
volumeProperty.SetScalarOpacity(compositeOpacity)
volumeProperty.SetColor(color)
# volumeProperty.SetGradientOpacity(volumeGradientOpacity)
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
return volume
def show_3D_array(self, in_array):
"""
displays a numpy.ndarray as a 3D-Volume that can be interactively inspected
:param in_array: the input 3D-array to be displayed
"""
data_type = in_array.dtype
dims = in_array.shape
data_min, data_max = (np.min(in_array), np.max(in_array))
renderer = vtk.vtkRenderer()
window = vtk.vtkRenderWindow()
window.AddRenderer(renderer)
interactor = vtk.vtkRenderWindowInteractor()
style = vtk.vtkInteractorStyleTrackballCamera()
interactor.SetInteractorStyle(style)
interactor.SetRenderWindow(window)
renderer.SetBackground(0, 0, 0)
window.SetSize(800, 600)
importer = vtk.vtkImageImport()
if data_type == 'uint8':
importer.SetDataScalarTypeToUnsignedChar()
elif data_type == 'uint16':
importer.SetDataScalarTypeToShort()
else:
self.logger.log_error(
f"unsupported data type ({data_type}) for image display, exiting!"
)
importer.SetNumberOfScalarComponents(1)
importer.SetDataExtent(0, dims[2] - 1, 0, dims[1] - 1, 0, dims[0] - 1)
importer.SetWholeExtent(0, dims[2] - 1, 0, dims[1] - 1, 0, dims[0] - 1)
importer.CopyImportVoidPointer(in_array, in_array.nbytes)
acf = vtk.vtkPiecewiseFunction()
acf.AddPoint(data_min, 0.0)
acf.AddPoint(data_max, 1.0)
color_func = vtk.vtkColorTransferFunction()
color_func.AddRGBPoint(data_min, 0.0, 0.0, 0.0)
color_func.AddRGBPoint(data_max, 1.0, 1.0, 1.0)
volume_property = vtk.vtkVolumeProperty()
volume_property.SetColor(color_func)
volume_property.SetScalarOpacity(acf)
volume_property.ShadeOn()
volume_property.SetInterpolationTypeToLinear()
volume_mapper = vtk.vtkSmartVolumeMapper()
volume_mapper.SetInputConnection(importer.GetOutputPort())
volume = vtk.vtkVolume()
volume.SetMapper(volume_mapper)
volume.SetProperty(volume_property)
renderer.AddVolume(volume)
renderer.SetBackground(
255, 255, 255) # (25.0 / 255.0, 51.0 / 255.0, 102.0 / 255.0)
axes = vtk.vtkAxesActor()
# swap X and Z-Axes due to VTKs inverted indexing
axes.SetXAxisLabelText('Z')
axes.SetZAxisLabelText('X')
widget = vtk.vtkOrientationMarkerWidget()
widget.SetOutlineColor(0.9300, 0.5700, 0.1300)
widget.SetOrientationMarker(axes)
widget.SetInteractor(interactor)
# widget.SetViewport(0.0, 0.0, 0.4, 0.4)
widget.SetEnabled(1)
widget.InteractiveOn()
window.Render()
interactor.Initialize()
interactor.Start()
def renderFig(self, direction):
print "cool, it is done"
fr=gzip.open(self.fname[:-3]+"voxr","rb")
dataRed=pickle.load(fr)
self.data_matrix_red=numpy.uint8(dataRed)
self.dataImporterR = vtk.vtkImageImport()
data_string = self.data_matrix_red.tostring()
self.dataImporterR.CopyImportVoidPointer(data_string, len(data_string))
self.dataImporterR.SetDataScalarTypeToUnsignedChar()
self.dataImporterR.SetNumberOfScalarComponents(1)
xdim,ydim,zdim=self.data_matrix_red.shape
#self.dataImporter.SetDataExtent(0, zdim-1, 0, vtkPiecewiseFunctionb-1, 0, xdim-1)
self.dataImporterR.SetDataExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
#self.dataImporter.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
self.dataImporterR.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
fg=gzip.open(self.fname[:-3]+"voxg","rb")
dataGreen=pickle.load(fg)
self.data_matrix_green=numpy.uint8(dataGreen)
self.dataImporterG = vtk.vtkImageImport()
data_string = self.data_matrix_green.tostring()
self.dataImporterG.CopyImportVoidPointer(data_string, len(data_string))
self.dataImporterG.SetDataScalarTypeToUnsignedChar()
self.dataImporterG.SetNumberOfScalarComponents(1)
xdim,ydim,zdim=self.data_matrix_green.shape
#self.dataImporter.SetDataExtent(0, zdim-1, 0, vtkPiecewiseFunctionb-1, 0, xdim-1)
self.dataImporterG.SetDataExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
#self.dataImporter.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
self.dataImporterG.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
fb=gzip.open(self.fname[:-3]+"voxb","rb")
dataBlue=pickle.load(fb)
self.data_matrix_blue=numpy.uint8(dataBlue)
self.dataImporterB = vtk.vtkImageImport()
data_string = self.data_matrix_blue.tostring()
self.dataImporterB.CopyImportVoidPointer(data_string, len(data_string))
self.dataImporterB.SetDataScalarTypeToUnsignedChar()
self.dataImporterB.SetNumberOfScalarComponents(1)
xdim,ydim,zdim=self.data_matrix_blue.shape
#self.dataImporter.SetDataExtent(0, zdim-1, 0, vtkPiecewiseFunctionb-1, 0, xdim-1)
self.dataImporterB.SetDataExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
#self.dataImporter.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
self.dataImporterB.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
"""Append the output to VTK"""
self.append = vtk.vtkImageAppendComponents()
self.append.SetInputConnection(self.dataImporterR.GetOutputPort())
self.append.AddInputConnection(self.dataImporterG.GetOutputPort())
self.append.AddInputConnection(self.dataImporterB.GetOutputPort())
self.append.Update()
"""Set the mapper in VTK"""
# This class describes how the volume is rendered (through ray tracing).
#compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
# We can finally create our volume. We also have to specify the data for it, as well as how the data will be rendered.
#volumeMapper = vtk.vtkVolumeRayCastMapper()
volumeMapper = vtk.vtkSmartVolumeMapper()
#volumeMapper.SetVolumeRayCastFunction(compositeFunction)
#volumeMapper.SetBlendModeToComposite()
#volumeMapper = vtk.vtkFixedPointVolumeRayCastMapper()
volumeMapper.SetInputConnection(self.append.GetOutputPort())
"""Set the property of the volume"""
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.ShadeOff()
volumeProperty.SetInterpolationTypeToLinear()
#volumeProperty.SetIndependentComponents(3)
volumeProperty.IndependentComponentsOn()
"""Set the color and opacity of each output"""
opacityTF1 = vtk.vtkPiecewiseFunction()
opacityTF1.AddPoint( 0.0, 0.0 )
opacityTF1.AddPoint( 1.0, 0.33)
opacityTF1.AddPoint( 128.0, 0.33)
opacityTF1.AddPoint( 255.0, 0.33 )
volumeProperty.SetScalarOpacity(0,opacityTF1)
colourTF1 = vtk.vtkColorTransferFunction()
colourTF1.AddRGBPoint( 0.0, 0.0, 0.0, 0.0 )
colourTF1.AddRGBPoint( 1.0, 0.0, 0.0, 0.1 )
colourTF1.AddRGBPoint( 128.0, 0.0, 0.0, 0.5 )
colourTF1.AddRGBPoint( 255.0, 0.0, 0.0, 1.0 )
volumeProperty.SetColor(0,colourTF1)
opacityTF2 = vtk.vtkPiecewiseFunction()
opacityTF2.AddPoint( 0.0, 0.0 )
opacityTF2.AddPoint( 1.0, 0.33 )
opacityTF2.AddPoint( 128.0, 0.33)
opacityTF2.AddPoint( 255.0, 0.33 )
volumeProperty.SetScalarOpacity(1,opacityTF2)
colourTF2 = vtk.vtkColorTransferFunction()
colourTF2.AddRGBPoint( 0.0, 0.0, 0.0, 0.0 )
colourTF2.AddRGBPoint( 1.0, 0.0, 0.1, 0.0 )
colourTF2.AddRGBPoint( 128.0, 0.0, 0.5, 0.0 )
colourTF2.AddRGBPoint( 255.0, 0.0, 1.0, 0.0 )
volumeProperty.SetColor(1,colourTF2)
opacityTF3 = vtk.vtkPiecewiseFunction()
opacityTF3.AddPoint( 0.0, 0.0 )
opacityTF3.AddPoint( 1.0, 0.33 )
opacityTF3.AddPoint( 128.0, 0.33)
opacityTF3.AddPoint( 255.0, 0.33 )
volumeProperty.SetScalarOpacity(2,opacityTF3)
colourTF3 = vtk.vtkColorTransferFunction()
colourTF3.AddRGBPoint( 0.0, 0.0, 0.0, 0.0 )
colourTF3.AddRGBPoint( 1.0, 0.1, 0.0, 0.0 )
colourTF3.AddRGBPoint( 128.0, 0.5, 0.0, 0.0 )
colourTF3.AddRGBPoint( 255.0, 1.0, 0.0, 0.0 )
volumeProperty.SetColor(2,colourTF3)
#volumeProperty.SetIndependentComponents(4)
#volumeProperty = vtk.vtkVolumeProperty()
#volprop.SetColor(colourTF)
#volprop.SetScalarOpacity(alphaChannelFunc)
self.volume.SetMapper(volumeMapper)
self.volume.SetProperty(volumeProperty)
self.ren.RemoveActor(self.actor)
self.ren.AddVolume(self.volume)
self.ren.SetBackground(1, 1, 1)
self.addPicker()
# A simple function to be called when the user decides to quit the application.
def exitCheck(obj, event):
if obj.GetEventPending() != 0:
obj.SetAbortRender(1)
# Tell the application to use the function as an exit check.
renderWin = self.vtkWidget.GetRenderWindow()
renderWin.AddObserver("AbortCheckEvent", exitCheck)
self.iren.Initialize()
# Initially pick the cell at this location.
self.picker.Pick(85, 126, 0, self.ren)
self.iren.Start()
def Add_MomActors(self,ren,renWin,iren,ASDdata,window):
"""Main wrapper to add the needed actors for visualization of the moments.
Class that contains the data structures for creation of the glyphs or the
visualization of the magnetic moments. It also has the capacity to create
tessellations for the visualization of volume vendering.
Args:
ren: current renderer.
renWin: current rendering window.
iren: current interactor for the renderer.
ASDdata: class where the data read from the ASD simulations is stored.
window: QMainWindow object where the visualization is performed.
Author
----------
Jonathan Chico
"""
import vtk
import numpy as np
ASDMomActors.timer_count=0
ASDMomActors.camera_pos=np.zeros(3,dtype=np.float32)
ASDMomActors.camera_focal=np.zeros(3,dtype=np.float32)
ASDMomActors.camera_yaw=0.0
ASDMomActors.camera_roll=0.0
ASDMomActors.camera_pitch=0.0
ASDMomActors.camera_azimuth=0.0
ASDMomActors.camera_elevation=0.0
ASDMomActors.kmc_disp=ASDdata.kmc_flag
ASDMomActors.cluster_disp=ASDdata.cluster_flag
ASDMomActors.glob_color=ASDdata.colors
#-----------------------------------------------------------------------
# Look up tables for colors
#-----------------------------------------------------------------------
# This is a diverging RWB color mapping based on the work of Kenneth
# Moreland and with the vtk examples provided by Andrew Maclean
if ASDdata.flag2D:
ASDMomActors.lut = vtk.vtkLookupTable()
num_colors = 256
ASDMomActors.lut.SetNumberOfTableValues(num_colors)
ASDMomActors.transfer_func = vtk.vtkColorTransferFunction()
ASDMomActors.transfer_func.SetColorSpaceToDiverging()
ASDMomActors.transfer_func.AddRGBPoint(0, 0.230, 0.299, 0.754)
ASDMomActors.transfer_func.AddRGBPoint(1, 0.706, 0.016, 0.150)
for ii,ss in enumerate([float(xx)/float(num_colors) for xx in range(num_colors)]):
cc = ASDMomActors.transfer_func.GetColor(ss)
ASDMomActors.lut.SetTableValue(ii, cc[0], cc[1], cc[2], 1.0)
ASDMomActors.lut.Build()
else:
ASDMomActors.lut = vtk.vtkLookupTable()
num_colors = 256
ASDMomActors.lut.SetNumberOfTableValues(num_colors)
ASDMomActors.transfer_func = vtk.vtkColorTransferFunction()
ASDMomActors.transfer_func.SetColorSpaceToDiverging()
ASDMomActors.transfer_func.AddRGBPoint(-0, 0.230, 0.299, 0.754)
ASDMomActors.transfer_func.AddRGBPoint( 1, 0.706, 0.016, 0.150)
for ii,ss in enumerate([float(xx)/float(num_colors) for xx in range(num_colors)]):
cc = ASDMomActors.transfer_func.GetColor(ss)
ASDMomActors.lut.SetTableValue(ii, cc[0], cc[1], cc[2], 1.0)
ASDMomActors.lut.Build()
#-----------------------------------------------------------------------
# Data structures for the generation of the smooth grid
#-----------------------------------------------------------------------
# Passing the data from the full system to the PolyData
ASDMomActors.src=vtk.vtkPolyData()
ASDMomActors.src.SetPoints(ASDdata.coord)
ASDMomActors.src.GetPointData().SetScalars(ASDdata.colors[2])
ASDMomActors.src.GetPointData().SetVectors(ASDdata.moments)
scalar_range = ASDMomActors.src.GetScalarRange()
#-----------------------------------------------------------------------
# Finding useful geometrical information of the sample
#-----------------------------------------------------------------------
# Finding the middle of the sample
# Also making sure that if the sample is 2D one has no problem with bounds
# this is mostly useful if splatters are used
(ASDMomActors.xmin,ASDMomActors.xmax,ASDMomActors.ymin,ASDMomActors.ymax,\
ASDMomActors.zmin,ASDMomActors.zmax)= ASDMomActors.src.GetBounds()
if ASDMomActors.xmin==ASDMomActors.xmax:
ASDMomActors.xmin=0.0
ASDMomActors.xmax=1.0
if ASDMomActors.ymin==ASDMomActors.ymax:
ASDMomActors.ymin=0.0
ASDMomActors.ymax=1.0
if ASDMomActors.zmin==ASDMomActors.zmax:
ASDMomActors.zmin=0.0
ASDMomActors.zmax=1.0
ASDMomActors.xmid = (ASDMomActors.xmin+ASDMomActors.xmax)*0.5
ASDMomActors.ymid = (ASDMomActors.ymin+ASDMomActors.ymax)*0.5
ASDMomActors.zmid = (ASDMomActors.zmin+ASDMomActors.zmax)*0.5
ASDMomActors.height=max(ASDMomActors.xmax,ASDMomActors.ymax,ASDMomActors.zmax)*1.75
self.dist_x=np.absolute(ASDMomActors.xmax-ASDMomActors.xmin)
self.dist_y=np.absolute(ASDMomActors.ymax-ASDMomActors.ymin)
self.dist_z=np.absolute(ASDMomActors.zmax-ASDMomActors.zmin)
ASDMomActors.camera_pos[0]=ASDMomActors.xmid
ASDMomActors.camera_pos[1]=ASDMomActors.ymid
ASDMomActors.camera_pos[2]=ASDMomActors.height
ASDMomActors.camera_focal[0]=ASDMomActors.xmid
ASDMomActors.camera_focal[1]=ASDMomActors.ymid
ASDMomActors.camera_focal[2]=ASDMomActors.zmid
# The delaunay tessellation seems to be the best way to transform the point cloud
# to a surface for volume rendering, the problem is that it is too slow for large
# data sets, meaning that the best option is first to prune out the data to ensure
# that one has a manageable number of data points over which to do the construction
# surface reconstruction and splatter techniques also can be used to generate something
# akin to the kind of surfaces we want. The issue is that they transform the data to a
# regular mesh by default. And thus it is a problem for most kind of systems
if ASDdata.flag2D:
# Passing the data to generate a triangulation of the data
ASDMomActors.MagDensMethod = vtk.vtkDelaunay2D()
ASDMomActors.MagDensMethod.SetInputData(ASDMomActors.src)
ASDMomActors.MagDensMethod.BoundingTriangulationOff()
ASDMomActors.MagDensMethod.SetTolerance(0.005)
# Time the execution of the delaunay tessellation
SM_timer = vtk.vtkExecutionTimer()
SM_timer.SetFilter(ASDMomActors.MagDensMethod)
ASDMomActors.MagDensMethod.Update()
SM = SM_timer.GetElapsedWallClockTime()
print ("2D Delaunay:", SM)
# Creating the mapper for the smooth surfaces
ASDMomActors.MagDensMap = vtk.vtkDataSetMapper()
ASDMomActors.MagDensMap.SetScalarRange(scalar_range)
ASDMomActors.MagDensMap.SetInputConnection(ASDMomActors.MagDensMethod.GetOutputPort())
ASDMomActors.MagDensMap.SetLookupTable(ASDMomActors.lut)
ASDMomActors.MagDensMap.SetColorModeToMapScalars()
ASDMomActors.MagDensMap.Update()
# Creating the actor for the smooth surfaces
ASDMomActors.MagDensActor = vtk.vtkLODActor()
ASDMomActors.MagDensActor.SetMapper(ASDMomActors.MagDensMap)
ASDMomActors.MagDensActor.GetProperty().SetOpacity(0.75)
ASDMomActors.MagDensActor.GetProperty().EdgeVisibilityOff()
if window.DensBox.isChecked():
ASDMomActors.MagDensActor.VisibilityOn()
else:
ASDMomActors.MagDensActor.VisibilityOff()
else:
#-------------------------------------------------------------------
# Setting the parameters for the visualization of 3D structures with
# splatters
#-------------------------------------------------------------------
ASDMomActors.MagDensMethod = vtk.vtkGaussianSplatter()
ASDMomActors.MagDensMethod.SetInputData(ASDMomActors.src)
#-------------------------------------------------------------------
# Options for the Gaussian splatter. These determine the quality of the
# rendering, increasing the radius smoothens out the volume but performance
# decreases rapidly
#-------------------------------------------------------------------
dist=(np.asarray(ASDMomActors.src.GetPoint(0))-np.asarray(ASDMomActors.src.GetPoint(1)))
norm=np.sqrt(dist.dot(dist))
if norm<1:
rad_fac=0.040
else:
rad_fac=0.40
ASDMomActors.MagDensMethod.SetRadius(rad_fac)
ASDMomActors.MagDensMethod.ScalarWarpingOn()
#-------------------------------------------------------------------
# The exponent factor determines how fast the gaussian splatter decay
# they again can be used to improve quality at the sake of rendering time
#-------------------------------------------------------------------
ASDMomActors.MagDensMethod.SetExponentFactor(-10)
ASDMomActors.MagDensMethod.NormalWarpingOn()
ASDMomActors.MagDensMethod.SetEccentricity(10)
#-------------------------------------------------------------------
# The Null value can be used to try to eliminate contributions not belonging
# to the actual sample
#-------------------------------------------------------------------
ASDMomActors.MagDensMethod.SetNullValue(-10)
#-------------------------------------------------------------------
# Set the actual size of the rendering model
#-------------------------------------------------------------------
ASDMomActors.MagDensMethod.SetModelBounds(ASDMomActors.xmin,ASDMomActors.xmax,\
ASDMomActors.ymin,ASDMomActors.ymax,ASDMomActors.zmin,ASDMomActors.zmax)
# This should get rid of the problems when trying to map very thin structures in 2D
if self.dist_x==min(self.dist_x,self.dist_y,self.dist_z) and self.dist_x<3:
ASDMomActors.MagDensMethod.SetSampleDimensions(3,int(ASDMomActors.ymax),int(ASDMomActors.zmax))
elif self.dist_y==min(self.dist_x,self.dist_y,self.dist_z) and self.dist_y<3:
ASDMomActors.MagDensMethod.SetSampleDimensions(int(ASDMomActors.xmax),3,int(ASDMomActors.zmax))
elif self.dist_z==min(self.dist_x,self.dist_y,self.dist_z) and self.dist_z<3:
ASDMomActors.MagDensMethod.SetSampleDimensions(int(ASDMomActors.xmax),int(ASDMomActors.ymax),3)
# Timming for the execution of the volume creation
SP_timer = vtk.vtkExecutionTimer()
SP_timer.SetFilter(ASDMomActors.MagDensMethod)
ASDMomActors.MagDensMethod.Update()
SP = SP_timer.GetElapsedWallClockTime()
print ("3D vtkGaussianSplatter Method:", SP)
# Scalar opacities
funcOpacityScalar = vtk.vtkPiecewiseFunction()
funcOpacityScalar.AddPoint(-1.00,0.00)
funcOpacityScalar.AddPoint( 0.00,0.05)
funcOpacityScalar.AddPoint( 0.50,0.50)
funcOpacityScalar.AddPoint( 0.75,1.00)
# Gradient opacities
volumeGradientOpacity = vtk.vtkPiecewiseFunction()
volumeGradientOpacity.AddPoint(0.000,0.0)
volumeGradientOpacity.AddPoint(0.001,1.0)
volumeGradientOpacity.AddPoint(1.000,1.0)
# Volume properties
ASDMomActors.volumeProperty = vtk.vtkVolumeProperty()
ASDMomActors.volumeProperty.SetColor(ASDMomActors.transfer_func)
ASDMomActors.volumeProperty.SetInterpolationTypeToLinear()
ASDMomActors.volumeProperty.SetAmbient(0.6)
ASDMomActors.volumeProperty.SetDiffuse(0.6)
ASDMomActors.volumeProperty.SetSpecular(0.1)
ASDMomActors.volumeProperty.SetGradientOpacity(volumeGradientOpacity)
ASDMomActors.volumeProperty.SetScalarOpacity(funcOpacityScalar)
# Volume Mapper
ASDMomActors.MagDensMap = vtk.vtkSmartVolumeMapper()
ASDMomActors.MagDensMap.SetInputConnection(ASDMomActors.MagDensMethod.GetOutputPort())
# Volume Actor
ASDMomActors.MagDensActor = vtk.vtkVolume()
ASDMomActors.MagDensActor.SetMapper(ASDMomActors.MagDensMap)
ASDMomActors.MagDensActor.SetProperty(self.volumeProperty)
if window.DensBox.isChecked():
ASDMomActors.MagDensActor.VisibilityOn()
else:
ASDMomActors.MagDensActor.VisibilityOff()
#-----------------------------------------------------------------------
# Data structures for the spins
#-----------------------------------------------------------------------
# Passing the data from the full system to the PolyData
ASDMomActors.src_spins=vtk.vtkPolyData()
ASDMomActors.src_spins.SetPoints(ASDdata.coord)
ASDMomActors.src_spins.GetPointData().SetScalars(ASDdata.colors[2])
ASDMomActors.src_spins.GetPointData().SetVectors(ASDdata.moments)
scalar_range_spins = ASDMomActors.src_spins.GetScalarRange()
#-----------------------------------------------------------------------
# Data structures for the contours
#-----------------------------------------------------------------------
# Define the contour filters
contours = vtk.vtkContourFilter()
contours.SetInputConnection(ASDMomActors.MagDensMethod.GetOutputPort())
# This generates the contours, it will do 5 between the -1 and 0.5 range
cont_num=5
range_cont=(-1,0.5)
contours.GenerateValues(cont_num,range_cont)
# Map the contours to graphical primitives
contMapper = vtk.vtkPolyDataMapper()
contMapper.SetInputConnection(contours.GetOutputPort())
contMapper.SetScalarVisibility(False) # colored contours
contMapper.SetScalarRange(scalar_range)
# Create an actor for the contours
ASDMomActors.contActor = vtk.vtkLODActor()
ASDMomActors.contActor.SetMapper(contMapper)
ASDMomActors.contActor.GetProperty().SetColor(0, 0, 0)
ASDMomActors.contActor.GetProperty().SetLineWidth(1.0)
ASDMomActors.contActor.VisibilityOff()
#-----------------------------------------------------------------------
# Setting information of the directions
#-----------------------------------------------------------------------
# Create vectors
arrow = vtk.vtkArrowSource()
arrow.SetTipRadius(0.20)
arrow.SetShaftRadius(0.10)
arrow.SetTipResolution(20)
arrow.SetShaftResolution(20)
# Create the mapper for the spins
arrowMapper = vtk.vtkGlyph3DMapper()
arrowMapper.SetSourceConnection(arrow.GetOutputPort())
arrowMapper.SetInputData(ASDMomActors.src)
arrowMapper.SetScaleFactor(0.50)
arrowMapper.SetScalarVisibility(False)
arrowMapper.SetScaleModeToNoDataScaling()
arrowMapper.Update()
# Define the vector actor for the spins
ASDMomActors.vector = vtk.vtkLODActor()
ASDMomActors.vector.SetMapper(arrowMapper)
ASDMomActors.vector.GetProperty().SetSpecular(0.3)
ASDMomActors.vector.GetProperty().SetSpecularPower(60)
ASDMomActors.vector.GetProperty().SetAmbient(0.2)
ASDMomActors.vector.GetProperty().SetDiffuse(0.8)
ASDMomActors.vector.GetProperty().SetColor(0, 0, 0)
ASDMomActors.vector.VisibilityOff()
#-----------------------------------------------------------------------
# Setting information of the spins
#-----------------------------------------------------------------------
# Create vectors
ASDMomActors.spinarrow = vtk.vtkArrowSource()
ASDMomActors.spinarrow.SetTipRadius(0.20)
ASDMomActors.spinarrow.SetShaftRadius(0.10)
ASDMomActors.spinarrow.SetTipResolution(20)
ASDMomActors.spinarrow.SetShaftResolution(20)
# Create the mapper for the spins
ASDMomActors.SpinMapper = vtk.vtkGlyph3DMapper()
ASDMomActors.SpinMapper.SetSourceConnection(ASDMomActors.spinarrow.GetOutputPort())
ASDMomActors.SpinMapper.SetInputData(ASDMomActors.src_spins)
ASDMomActors.SpinMapper.SetScalarRange(scalar_range_spins)
ASDMomActors.SpinMapper.SetScaleFactor(0.50)
ASDMomActors.SpinMapper.SetScaleModeToNoDataScaling()
ASDMomActors.SpinMapper.SetLookupTable(self.lut)
ASDMomActors.SpinMapper.SetColorModeToMapScalars()
ASDMomActors.SpinMapper.Update()
# Define the vector actor for the spins
ASDMomActors.Spins = vtk.vtkLODActor()
ASDMomActors.Spins.SetMapper(ASDMomActors.SpinMapper)
ASDMomActors.Spins.GetProperty().SetSpecular(0.3)
ASDMomActors.Spins.GetProperty().SetSpecularPower(60)
ASDMomActors.Spins.GetProperty().SetAmbient(0.2)
ASDMomActors.Spins.GetProperty().SetDiffuse(0.8)
if window.SpinsBox.isChecked():
ASDMomActors.Spins.VisibilityOn()
else:
ASDMomActors.Spins.VisibilityOff()
if (ASDdata.kmc_flag):
#-------------------------------------------------------------------
# Setting data structures for the KMC particle visualization
#-------------------------------------------------------------------
ASDMomActors.KMC_src=vtk.vtkPolyData()
ASDMomActors.KMC_src.SetPoints(ASDdata.coord_KMC)
# Atom sphere
KMC_part = vtk.vtkSphereSource()
KMC_part.SetRadius(1.75)
KMC_part.SetThetaResolution(40)
KMC_part.SetPhiResolution(40)
# Atom glyph
KMC_part_mapper = vtk.vtkGlyph3DMapper()
KMC_part_mapper.SetInputData(ASDMomActors.KMC_src)
KMC_part_mapper.SetSourceConnection(KMC_part.GetOutputPort())
KMC_part_mapper.SetScaleFactor(0.5)
KMC_part_mapper.ClampingOn()
KMC_part_mapper.SetScaleModeToNoDataScaling()
KMC_part_mapper.SetColorModeToMapScalars()
KMC_part_mapper.Update()
# Atoms actors
ASDMomActors.KMC_part_actor = vtk.vtkLODActor()
ASDMomActors.KMC_part_actor.SetMapper(KMC_part_mapper)
ASDMomActors.KMC_part_actor.GetProperty().SetOpacity(0.9)
ASDMomActors.KMC_part_actor.GetProperty().SetColor(0.0, 0.0, 1.0)
ASDMomActors.KMC_part_actor.GetProperty().EdgeVisibilityOn()
ASDMomActors.KMC_part_actor.GetProperty().SetEdgeColor(0,0,0)
#-----------------------------------------------------------------------
# Setting information of the renderer
#-----------------------------------------------------------------------
# Define the renderer
# Add the actors to the scene
if ASDdata.flag2D:
ren.AddActor(ASDMomActors.MagDensActor)
else:
ren.AddViewProp(ASDMomActors.MagDensActor)
ren.AddActor(ASDMomActors.Spins)
ren.AddActor(ASDMomActors.vector)
ren.AddActor(ASDMomActors.contActor)
#If the KMC particles are present add them to the renderer
if ASDdata.kmc_flag:
ren.AddActor(ASDMomActors.KMC_part_actor)
# Defining the camera directions
ren.GetActiveCamera().Azimuth(ASDMomActors.camera_azimuth)
ren.GetActiveCamera().Elevation(ASDMomActors.camera_elevation)
ren.GetActiveCamera().Yaw(ASDMomActors.camera_yaw)
ren.GetActiveCamera().Roll(ASDMomActors.camera_roll)
ren.GetActiveCamera().Pitch(ASDMomActors.camera_pitch)
ren.GetActiveCamera().SetFocalPoint(ASDMomActors.camera_focal)
ren.GetActiveCamera().SetPosition(ASDMomActors.camera_pos)
ren.GetActiveCamera().SetViewUp(0,1,0)
#-----------------------------------------------------------------------
# Start the renderer
#-----------------------------------------------------------------------
iren.Start()
renWin.Render()
return;
def showLayer(self):
if self.volume != Null:
self.ren.RemoveVolume(self.volume)
sliceNumber = self.sliceNumber.text()
sliceIntArray = sliceNumber.toUInt()
sliceInt = sliceIntArray[0]
print "cool, it is done"
fr=gzip.open(self.fname[:-3]+"voxr","rb")
dataRed=pickle.load(fr)
self.data_matrix_red=numpy.uint8(dataRed)
self.data_matrix_red=self.data_matrix_red[sliceInt-1:sliceInt+1,:,:]
with file('layerView.txt', 'w') as outfile:
for data_slice in self.data_matrix_red:
# The formatting string indicates that I'm writing out
# the values in left-justified columns 7 characters in width
# with 2 decimal places.
numpy.savetxt(outfile, data_slice,fmt='%-7.1f')
# Writing out a break to indicate different slices...
outfile.write('# New slice\n')
self.dataImporterR = vtk.vtkImageImport()
data_string = self.data_matrix_red.tostring()
self.dataImporterR.CopyImportVoidPointer(data_string, len(data_string))
self.dataImporterR.SetDataScalarTypeToUnsignedChar()
self.dataImporterR.SetNumberOfScalarComponents(1)
xdim,ydim,zdim=self.data_matrix_red.shape
#self.dataImporter.SetDataExtent(0, zdim-1, 0, vtkPiecewiseFunctionb-1, 0, xdim-1)
self.dataImporterR.SetDataExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
#self.dataImporter.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
self.dataImporterR.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
fg=gzip.open(self.fname[:-3]+"voxg","rb")
dataGreen=pickle.load(fg)
self.data_matrix_green=numpy.uint8(dataGreen)
self.data_matrix_green = self.data_matrix_green[sliceInt-1:sliceInt+1,:,:]
self.dataImporterG = vtk.vtkImageImport()
data_string = self.data_matrix_green.tostring()
self.dataImporterG.CopyImportVoidPointer(data_string, len(data_string))
self.dataImporterG.SetDataScalarTypeToUnsignedChar()
self.dataImporterG.SetNumberOfScalarComponents(1)
xdim,ydim,zdim=self.data_matrix_green.shape
#self.dataImporter.SetDataExtent(0, zdim-1, 0, vtkPiecewiseFunctionb-1, 0, xdim-1)
self.dataImporterG.SetDataExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
#self.dataImporter.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
self.dataImporterG.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
fb=gzip.open(self.fname[:-3]+"voxb","rb")
dataBlue=pickle.load(fb)
self.data_matrix_blue=numpy.uint8(dataBlue)
self.data_matrix_blue = self.data_matrix_blue[sliceInt-1:sliceInt+1,:,:]
self.dataImporterB = vtk.vtkImageImport()
data_string = self.data_matrix_blue.tostring()
self.dataImporterB.CopyImportVoidPointer(data_string, len(data_string))
self.dataImporterB.SetDataScalarTypeToUnsignedChar()
self.dataImporterB.SetNumberOfScalarComponents(1)
xdim,ydim,zdim=self.data_matrix_blue.shape
#self.dataImporter.SetDataExtent(0, zdim-1, 0, vtkPiecewiseFunctionb-1, 0, xdim-1)
self.dataImporterB.SetDataExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
#self.dataImporter.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
self.dataImporterB.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
self.append = vtk.vtkImageAppendComponents()
self.append.SetInputConnection(self.dataImporterR.GetOutputPort())
self.append.AddInputConnection(self.dataImporterG.GetOutputPort())
self.append.AddInputConnection(self.dataImporterB.GetOutputPort())
self.append.Update()
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputConnection(self.append.GetOutputPort())
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.ShadeOff()
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.IndependentComponentsOn()
opacityTF1 = vtk.vtkPiecewiseFunction()
opacityTF1.AddPoint( 0.0, 0.0 )
opacityTF1.AddPoint( 1.0, 0.33)
opacityTF1.AddPoint( 128.0, 0.33)
opacityTF1.AddPoint( 255.0, 0.33 )
volumeProperty.SetScalarOpacity(0,opacityTF1)
colourTF1 = vtk.vtkColorTransferFunction()
colourTF1.AddRGBPoint( 0.0, 0.0, 0.0, 0.0 )
colourTF1.AddRGBPoint( 1.0, 0.0, 0.0, 0.1 )
colourTF1.AddRGBPoint( 128.0, 0.0, 0.0, 0.5 )
colourTF1.AddRGBPoint( 255.0, 0.0, 0.0, 1.0 )
volumeProperty.SetColor(0,colourTF1)
opacityTF2 = vtk.vtkPiecewiseFunction()
opacityTF2.AddPoint( 0.0, 0.0 )
opacityTF2.AddPoint( 1.0, 0.33 )
opacityTF2.AddPoint( 128.0, 0.33)
opacityTF2.AddPoint( 255.0, 0.33 )
volumeProperty.SetScalarOpacity(1,opacityTF2)
colourTF2 = vtk.vtkColorTransferFunction()
colourTF2.AddRGBPoint( 0.0, 0.0, 0.0, 0.0 )
colourTF2.AddRGBPoint( 1.0, 0.0, 0.1, 0.0 )
colourTF2.AddRGBPoint( 128.0, 0.0, 0.5, 0.0 )
colourTF2.AddRGBPoint( 255.0, 0.0, 1.0, 0.0 )
volumeProperty.SetColor(1,colourTF2)
opacityTF3 = vtk.vtkPiecewiseFunction()
opacityTF3.AddPoint( 0.0, 0.0 )
opacityTF3.AddPoint( 1.0, 0.33 )
opacityTF3.AddPoint( 128.0, 0.33)
opacityTF3.AddPoint( 255.0, 0.33 )
volumeProperty.SetScalarOpacity(2,opacityTF3)
colourTF3 = vtk.vtkColorTransferFunction()
colourTF3.AddRGBPoint( 0.0, 0.0, 0.0, 0.0 )
colourTF3.AddRGBPoint( 1.0, 0.1, 0.0, 0.0 )
colourTF3.AddRGBPoint( 128.0, 0.5, 0.0, 0.0 )
colourTF3.AddRGBPoint( 255.0, 1.0, 0.0, 0.0 )
volumeProperty.SetColor(2,colourTF3)
self.volume.SetMapper(volumeMapper)
self.volume.SetProperty(volumeProperty)
#self.ren.RemoveActor(self.actor)
self.ren.AddVolume(self.volume)
self.ren.SetBackground(0, 0, 0)
# A simple function to be called when the user decides to quit the application.
def exitCheck(obj, event):
if obj.GetEventPending() != 0:
obj.SetAbortRender(1)
# Tell the application to use the function as an exit check.
light = vtk.vtkLight()
#light.SetColor(1, 1, 1)
light.SwitchOff()
self.ren.AddLight(light)
renderWin = self.vtkWidget.GetRenderWindow()
renderWin.AddObserver("AbortCheckEvent", exitCheck)
self.iren.Initialize()
self.iren.Start()
def assignVolumeProperties(self, recomp=False):
''' Configures Transfer Functions for Volume Render. '''
self.chart = vtk.vtkChartXY()
# remove previous volume / scalarbar if there was one
if self.actorVolume != None:
self.renderer.RemoveActor(self.actorVolume)
self.renderer.RemoveActor(self.scalarBar)
if recomp:
self.colorfunctions.clear()
if self.curr_statistic not in self.colorfunctions.keys():
self.colorfunctions[self.curr_statistic] = vtk.vtkColorTransferFunction()
self.opacityfunctions[self.curr_statistic] = vtk.vtkPiecewiseFunction()
cfn = self.colorfunctions[self.curr_statistic]
ofn = self.opacityfunctions[self.curr_statistic]
self.setColorOpacityDataPoints(cfn, ofn)
self.opacityfunctions[self.curr_statistic].ClampingOn()
cfn = self.colorfunctions[self.curr_statistic]
ofn = self.opacityfunctions[self.curr_statistic]
self.__buildTransFuncChart(cfn, ofn)
self.__buildScalarBar(self.curr_statistic)
self.mapperVolume2 = vtk.vtkSmartVolumeMapper()
img = self.images[self.curr_statistic]
self.mapperVolume2.SetInputData( img )
self.mapperVolume2.CroppingOff()
self.addClippingPlanes(self.mapperVolume2, recomp)
self.mapperVolume2.SetBlendModeToComposite()
'''
virtual void SetBlendMode (int)
void SetBlendModeToComposite ()
void SetBlendModeToMaximumIntensity ()
void SetBlendModeToMinimumIntensity ()
void SetBlendModeToAdditive ()
virtual int GetBlendMode ()
'''
self.propVolume = vtk.vtkVolumeProperty()
self.propVolume.ShadeOff()
self.propVolume.SetColor(cfn)
self.propVolume.SetScalarOpacity(ofn)
#self.propVolume.SetInterpolationTypeToLinear()
self.actorVolume = vtk.vtkVolume()
self.actorVolume.SetMapper(self.mapperVolume2)
self.actorVolume.SetProperty(self.propVolume)
self.renderer.AddActor(self.actorVolume)
self.renderer.AddActor(self.scalarBar)
# set TF chart labels
stat = self.curr_statistic
if stat == 'Mean' or stat =='Var' or stat =='Min' or \
stat =='Max' or stat =='NumSamples':
self.setTFAxisLabels(self.curr_statistic, \
self.curr_statistic, \
self.curr_statistic)
elif self.curr_statistic == 'Mean-Var':
self.setTFAxisLabels(self.curr_statistic, \
xlabel = 'Mean', \
ylabel = '1.0 - Normalized Mean-Var')
elif self.curr_statistic == 'Min-Var':
self.setTFAxisLabels(self.curr_statistic, \
xlabel = 'Min', \
ylabel = '1.0 - Normalized Min-Var')
elif self.curr_statistic == 'Max-Var':
self.setTFAxisLabels(self.curr_statistic, \
xlabel = 'Max', \
ylabel = '1.0 - Normalized Max-Var')
def buildPipeline(self):
""" execute() -> None
Dispatch the vtkRenderer to the actual rendering widget
"""
extent = self.input().GetExtent()
rangeBounds = self.getRangeBounds()
self.sliceCenter = [ (extent[2*i+1]-extent[2*i])/2 for i in range(3) ]
spacing = self.input().GetSpacing()
sx, sy, sz = spacing
origin = self.input().GetOrigin()
ox, oy, oz = origin
self._range = [ rangeBounds[0], rangeBounds[1], rangeBounds[0], 0 ]
dataType = self.input().GetScalarTypeAsString()
self.setMaxScalarValue( self.input().GetScalarType() )
self.pos = [ spacing[i]*extent[2*i] for i in range(3) ]
# if ( (origin[0] + self.pos[0]) < 0.0): self.pos[0] = self.pos[0] + 360.0
bounds = [0]*6
for i in range(6):
io2 = int(i/2)
bounds[i] = origin[io2] + spacing[io2]*extent[i]
print " --VolumeRenderer-- Data Type = %s, range = (%f,%f), max_scalar = %s" % ( dataType, rangeBounds[0], rangeBounds[1], self._max_scalar_value )
print "Extent: %s " % str( self.input().GetWholeExtent() )
print "Spacing: %s " % str( spacing )
print "Origin: %s " % str( origin )
print "Dimensions: %s " % str( self.input().GetDimensions() )
print "Bounds: %s " % str( bounds )
print "Input Bounds: %s " % str( self.input().GetBounds() )
print "VolumePosition: %s " % str( self.pos )
# self.inputInfo = self.inputPort.GetInformation()
# translation = inputInfo.Get( ResampleTranslationKey )
# Create transfer mapping scalar value to color
self.colorTransferFunction = vtk.vtkColorTransferFunction()
# Create transfer mapping scalar value to opacity
self.opacityTransferFunction = vtk.vtkPiecewiseFunction()
# The property describes how the data will look
self.volumeProperty = vtk.vtkVolumeProperty()
self.volumeProperty.SetInterpolationType( vtk.VTK_LINEAR_INTERPOLATION )
self.volumeProperty.SetColor(self.colorTransferFunction)
self.volumeProperty.SetScalarOpacity(self.opacityTransferFunction)
# self.volumeProperty.SetGradientOpacity(self.opacityTransferFunction)
# The mapper knows how to render the data
# self.volumeMapperTexture2D = vtk.vtkVolumeTextureMapper2D()
self.volumeMapper = vtk.vtkSmartVolumeMapper()
self.volumeMapper.SetBlendModeToComposite()
self.volumeMapper.CroppingOff()
self.clipper = vtk.vtkBoxWidget()
self.clipper.RotationEnabledOff()
self.clipper.SetPlaceFactor( 1.0 )
self.clipper.AddObserver( 'StartInteractionEvent', self.startClip )
self.clipper.AddObserver( 'EndInteractionEvent', self.endClip )
self.clipper.AddObserver( 'InteractionEvent', self.executeClip )
# self.clipper.AddObserver( 'AnyEvent', self.clipObserver )
# self.volumeMapper.SetScalarModeToUsePointFieldData()
# if vtk.VTK_MAJOR_VERSION <= 5: self.volumeMapper.SetInput(self.input())
# else: self.volumeMapper.SetInputData(self.input())
# The volume holds the mapper and the property and can be used to
# position/orient the volume
self.volume = vtk.vtkVolume()
self.volume.SetScale( 1.0, 1.0, 1.0 )
self.volume.SetMapper( self.volumeMapper )
# self.volume.SetScale( spacing[0], spacing[1], spacing[2] )
self.setVolRenderCfg( None, False )
self.volume.SetProperty(self.volumeProperty)
# self.clipper.AddObserver( 'AnyEvent', self.EventWatcher )
# self.input().AddObserver( 'AnyEvent', self.EventWatcher )
self.volume.SetPosition( self.pos )
self.renderer.AddVolume( self.volume )
self.renderer.SetBackground( VTK_BACKGROUND_COLOR[0], VTK_BACKGROUND_COLOR[1], VTK_BACKGROUND_COLOR[2] )
self.setColormap( [ 'jet', 1, 0, 0 ] )
def vis_volRepos(ren, objName):
if Repository.Exists(objName)==0:
raise ValueError("ERROR: Object does not exist.")
return
if Repository.Type(objName) != "StructuredPts":
raise TypeError("Incorrect object type.")
return
caster = [None]*2
opacityTransferFunction = [None]*2
colorTransferFunction = [None]*2
gradientTransferFunction = [None]*2
volumeProperty = [None]*2
volumeMapper = [None]*2
compositeFunction = [None]*2
outline = [None]*2
outlineMapper = [None]*2
outlineProperty = [None]*2
lod = [None]*2
caster[0] = "vis_vol_caster_"+objName
opacityTransferFunction[0] = "vis_vol_opacityTransferFunction_"+objName
colorTransferFunction[0] = "vis_vol_colorTransferFunction_"+objName
gradientTransferFunction[0] = "vis_vol_gradientTransferFunction_"+objName
volumeProperty[0] = "vis_vol_volumeProperty_"+objName
volumeMapper[0] = "vis_vol_volumeMapper_"+objName
compositeFunction[0] = "vis_vol_compositeFunction_"+objName
outline[0] = "vis_vol_outline_"+objName
outlineMapper[0] = "vis_vol_outlineMapper_"+objName
outlineProperty[0] = "vis_vol_outlineProperty_"+objName
lod[0] = "vis_vol_lod_" + objName
caster[1] = vtk.vtkImageCast()
caster[1].SetOutputScalarTypeToUnsignedShort()
caster[1].SetInputDataObject(Repository.ExportToVtk(objName))
caster[1].Update()
# Create transfer functions for opacity and color
opacityTransferFunction[1] = vtk.vtkPiecewiseFunction()
opacityTransferFunction[1].AddPoint(0,0.)
opacityTransferFunction[1].AddPoint(80,0.)
opacityTransferFunction[1].AddPoint(128,0.5)
opacityTransferFunction[1].AddPoint(150,0.9)
opacityTransferFunction[1].AddPoint(350,1.0)
colorTransferFunction[1] = vtk.vtkColorTransferFunction()
colorTransferFunction[1].AddRGBPoint(0,0,0,0)
colorTransferFunction[1].AddRGBPoint(350,1,1,1)
gradientTransferFunction[1] = vtk.vtkPiecewiseFunction()
gradientTransferFunction[1].AddPoint(0,1.0)
gradientTransferFunction[1].AddPoint(1,1.0)
gradientTransferFunction[1].AddPoint(255,1.0)
gradientTransferFunction[1].AddPoint(512,1.0)
# Create properties, mappers, volume actors, and ray cast function
volumeProperty[1] = vtk.vtkVolumeProperty()
volumeProperty[1].SetColor(colorTransferFunction[1])
volumeProperty[1].SetScalarOpacity(opacityTransferFunction[1])
volumeProperty[1].SetGradientOpacity(gradientTransferFunction[1])
volumeProperty[1].SetInterpolationTypeToLinear()
volumeMapper[1] = vtk.vtkSmartVolumeMapper()
volumeMapper[1].SetInputDataObject(caster[1].GetOutput())
lod[1] = vtk.vtkVolume()
lod[1].SetProperty(volumeProperty[1])
lod[1].SetMapper(volumeMapper[1])
ren[1].AddViewProp(lod[1])
setattr(vis, caster[0], caster)
setattr(vis, opacityTransferFunction[0], opacityTransferFunction)
setattr(vis, colorTransferFunction[0], colorTransferFunction)
setattr(vis, gradientTransferFunction[0], gradientTransferFunction)
setattr(vis, volumeProperty[0], volumeProperty)
setattr(vis, volumeMapper[0], volumeMapper)
setattr(vis, compositeFunction[0], compositeFunction)
setattr(vis, outline[0], outline)
setattr(vis, outlineMapper[0], outlineMapper)
setattr(vis, outlineProperty[0], outlineProperty)
setattr(vis, lod[0], lod)
vis.render(ren)
return lod
def render3d(directory, mouse_queue, mouse_move_event):
# Create the renderer, the render window, and the interactor. The renderer
# draws into the render window, the interactor enables mouse- and
# keyboard-based interaction with the scene.
renderer = vtk.vtkRenderer()
render_window = vtk.vtkRenderWindow()
render_window.SetWindowName("Test")
render_window.AddRenderer(renderer)
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(render_window)
# The following reader is used to read a series of 2D slices (images)
# that compose the volume. The slice dimensions are set, and the
# pixel spacing. The data Endianness must also be specified. The reader
# usese the FilePrefix in combination with the slice number to construct
# filenames using the format FilePrefix.%d. (In this case the FilePrefix
# is the root name of the file: quarter.)
reader = vtk.vtkVolume16Reader()
reader.SetDataDimensions(256, 256)
reader.SetImageRange(1, 99)
reader.SetDataByteOrderToLittleEndian()
reader.SetFilePrefix(os.path.join(directory, 'image'))
data_spacing = (1, 1, 2)
reader.SetDataSpacing(data_spacing[0], data_spacing[1], data_spacing[2])
volume_mapper = vtk.vtkSmartVolumeMapper()
volume_mapper.SetInputConnection(reader.GetOutputPort())
volume_mapper.SetBlendModeToComposite()
# Cutting plane
plane = vtk.vtkPlane()
plane.SetOrigin(0, 0, 2)
plane.SetNormal(0, 0, 1)
# create cutter
cutter = vtk.vtkCutter()
cutter.SetCutFunction(plane)
cutter.SetInputConnection(reader.GetOutputPort())
cutter.Update()
cutterMapper = vtk.vtkPolyDataMapper()
cutterMapper.SetInputConnection(cutter.GetOutputPort())
# create plane actor
planeActor = vtk.vtkActor()
planeActor.GetProperty().SetColor(1.0, 1, 0)
planeActor.GetProperty().SetLineWidth(2)
planeActor.SetMapper(cutterMapper)
volume_color = vtk.vtkColorTransferFunction()
volume_color.AddRGBPoint(0, 0.0, 0.0, 0.0)
volume_color.AddRGBPoint(500, 1.0, 0.5, 0.3)
volume_color.AddRGBPoint(1000, 1.0, 0.5, 0.3)
volume_color.AddRGBPoint(1150, 1.0, 1.0, 0.9)
# The opacity transfer function is used to control the opacity
# of different tissue types.
volume_scalar_opacity = vtk.vtkPiecewiseFunction()
volume_scalar_opacity.AddPoint(0, 0.00)
volume_scalar_opacity.AddPoint(500, 0.15)
volume_scalar_opacity.AddPoint(1000, 0.15)
volume_scalar_opacity.AddPoint(1150, 0.85)
# The gradient opacity function is used to decrease the opacity
# in the "flat" regions of the volume while maintaining the opacity
# at the boundaries between tissue types. The gradient is measured
# as the amount by which the intensity changes over unit distance.
# For most medical data, the unit distance is 1mm.
volume_gradient_opacity = vtk.vtkPiecewiseFunction()
volume_gradient_opacity.AddPoint(0, 0.0)
volume_gradient_opacity.AddPoint(90, 0.5)
volume_gradient_opacity.AddPoint(100, 1.0)
# The VolumeProperty attaches the color and opacity functions to the
# volume, and sets other volume properties. The interpolation should
# be set to linear to do a high-quality rendering. The ShadeOn option
# turns on directional lighting, which will usually enhance the
# appearance of the volume and make it look more "3D". However,
# the quality of the shading depends on how accurately the gradient
# of the volume can be calculated, and for noisy data the gradient
# estimation will be very poor. The impact of the shading can be
# decreased by increasing the Ambient coefficient while decreasing
# the Diffuse and Specular coefficient. To increase the impact
# of shading, decrease the Ambient and increase the Diffuse and Specular.
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(volume_color)
volumeProperty.SetScalarOpacity(volume_scalar_opacity)
volumeProperty.SetGradientOpacity(volume_gradient_opacity)
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.ShadeOn()
volumeProperty.SetAmbient(0.4)
volumeProperty.SetDiffuse(0.6)
volumeProperty.SetSpecular(0.2)
# The vtkVolume is a vtkProp3D (like a vtkActor) and controls the position
# and orientation of the volume in world coordinates.
volume = vtk.vtkVolume()
volume.SetMapper(volume_mapper)
volume.SetProperty(volumeProperty)
# Finally, add the volume to the renderer
renderer.AddViewProp(volume)
renderer.AddActor(planeActor)
# Set up an initial view of the volume. The focal point will be the
# center of the volume, and the camera position will be 400mm to the
# patient's left (which is our right).
camera = renderer.GetActiveCamera()
c = volume.GetCenter()
camera.SetFocalPoint(c[0], c[1], c[2])
camera.SetPosition(c[0] + 400, c[1], c[2])
camera.SetViewUp(0, 0, -1)
# Increase the size of the render window
render_window.SetSize(640, 480)
# Interact with the data.
interactor.Initialize()
def test(arg1, arg2):
slice_numbers = []
while not mouse_queue.empty():
slice_numbers += [mouse_queue.get()]
if len(slice_numbers) > 0:
slice = slice_numbers[-1]
plane.SetOrigin(0, 0, data_spacing[2] * slice)
render_window.Render()
interactor.AddObserver(vtk.vtkCommand.TimerEvent, test)
timerId = interactor.CreateRepeatingTimer(1)
render_window.Render()
interactor.Start()
def __init__(self,
dimx=600,
dimy=600,
renWin=None,
iren=None,
ren=None,
debug=False):
'''creates the rendering pipeline'''
# Handle arguments
if renWin is not None:
self.renWin = renWin
else:
self.renWin = vtk.vtkRenderWindow()
if iren is not None:
self.iren = iren
else:
self.iren = vtk.vtkRenderWindowInteractor()
# create a rendering window and renderer
if ren is not None:
self.ren = ren
else:
self.ren = vtk.vtkRenderer()
self.renWin.SetSize(dimx, dimy)
self.renWin.AddRenderer(self.ren)
# img 3D as slice
self.img3D = None
self.slicenos = [0, 0, 0]
self.sliceOrientation = SLICE_ORIENTATION_XY
self.sliceActor = vtk.vtkImageActor()
self.voi = vtk.vtkExtractVOI()
self.wl = vtk.vtkImageMapToWindowLevelColors()
self.ia = vtk.vtkImageHistogramStatistics()
self.sliceActorNo = 0
# Viewer Event manager
self.event = ViewerEventManager()
# create a renderwindowinteractor
self.style = CILInteractorStyle(self)
self.iren.SetInteractorStyle(self.style)
self.iren.SetRenderWindow(self.renWin)
# Render decimation
self.decimate = vtk.vtkDecimatePro()
self.ren.SetBackground(.1, .2, .4)
self.actors = {}
# Help text
self.helpActor = vtk.vtkActor2D()
self.helpActor.GetPositionCoordinate(
).SetCoordinateSystemToNormalizedDisplay()
self.helpActor.GetPositionCoordinate().SetValue(0.1, 0.5)
self.helpActor.VisibilityOff()
self.ren.AddActor(self.helpActor)
# volume render
volumeMapper = vtk.vtkSmartVolumeMapper()
#volumeMapper = vtk.vtkFixedPointVolumeRayCastMapper()
self.volume_mapper = volumeMapper
volumeProperty = vtk.vtkVolumeProperty()
self.volume_property = volumeProperty
# 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)
self.volume = volume
self.volume_render_initialised = False
# axis orientation widget
om = vtk.vtkAxesActor()
ori = vtk.vtkOrientationMarkerWidget()
ori.SetOutlineColor(0.9300, 0.5700, 0.1300)
ori.SetInteractor(self.iren)
ori.SetOrientationMarker(om)
ori.SetViewport(0.0, 0.0, 0.4, 0.4)
ori.SetEnabled(1)
ori.InteractiveOff()
self.orientation_marker = ori
self.iren.Initialize()
def buildPipeline(self):
""" execute() -> None
Dispatch the vtkRenderer to the actual rendering widget
"""
extent = self.input().GetExtent()
rangeBounds = self.getRangeBounds()
self.sliceCenter = [(extent[2 * i + 1] - extent[2 * i]) / 2
for i in range(3)]
spacing = self.input().GetSpacing()
sx, sy, sz = spacing
origin = self.input().GetOrigin()
ox, oy, oz = origin
self._range = [rangeBounds[0], rangeBounds[1], rangeBounds[0], 0]
dataType = self.input().GetScalarTypeAsString()
self.setMaxScalarValue(self.input().GetScalarType())
self.pos = [spacing[i] * extent[2 * i] for i in range(3)]
# if ( (origin[0] + self.pos[0]) < 0.0): self.pos[0] = self.pos[0] + 360.0
bounds = [(origin[i / 2] + spacing[i / 2] * extent[i])
for i in range(6)]
print " @@@VolumeRenderer@@@ Data Type = %s, range = (%f,%f), max_scalar = %s" % (
dataType, rangeBounds[0], rangeBounds[1], self._max_scalar_value)
print "Extent: %s " % str(self.input().GetExtent())
print "Spacing: %s " % str(spacing)
print "Origin: %s " % str(origin)
print "Dimensions: %s " % str(self.input().GetDimensions())
print "Bounds: %s " % str(bounds)
print "Input Bounds: %s " % str(self.input().GetBounds())
print "VolumePosition: %s " % str(self.pos)
# self.inputInfo = self.inputPort.GetInformation()
# translation = inputInfo.Get( ResampleTranslationKey )
# Create transfer mapping scalar value to color
self.colorTransferFunction = vtk.vtkColorTransferFunction()
# Create transfer mapping scalar value to opacity
self.opacityTransferFunction = vtk.vtkPiecewiseFunction()
# The property describes how the data will look
self.volumeProperty = vtk.vtkVolumeProperty()
self.volumeProperty.SetInterpolationType(vtk.VTK_LINEAR_INTERPOLATION)
self.volumeProperty.SetColor(self.colorTransferFunction)
self.volumeProperty.SetScalarOpacity(self.opacityTransferFunction)
# self.volumeProperty.SetGradientOpacity(self.opacityTransferFunction)
# The mapper knows how to render the data
# self.volumeMapperTexture2D = vtk.vtkVolumeTextureMapper2D()
self.volumeMapper = vtk.vtkSmartVolumeMapper()
self.volumeMapper.SetBlendModeToComposite()
self.volumeMapper.CroppingOff()
self.clipper = vtk.vtkBoxWidget()
self.clipper.RotationEnabledOff()
self.clipper.SetPlaceFactor(1.0)
self.clipper.AddObserver('StartInteractionEvent', self.startClip)
self.clipper.AddObserver('EndInteractionEvent', self.endClip)
self.clipper.AddObserver('InteractionEvent', self.executeClip)
# self.clipper.AddObserver( 'AnyEvent', self.clipObserver )
# self.volumeMapper.SetScalarModeToUsePointFieldData()
# self.inputModule.inputToAlgorithm( self.volumeMapper )
# The volume holds the mapper and the property and can be used to
# position/orient the volume
self.volume = vtk.vtkVolume()
self.volume.SetScale(1.0, 1.0, 1.0)
self.volume.SetMapper(self.volumeMapper)
# self.volume.SetScale( spacing[0], spacing[1], spacing[2] )
self.setVolRenderCfg(None, False)
self.volume.SetProperty(self.volumeProperty)
# self.clipper.AddObserver( 'AnyEvent', self.EventWatcher )
# self.input().AddObserver( 'AnyEvent', self.EventWatcher )
self.volume.SetPosition(self.pos)
self.renderer.AddVolume(self.volume)
self.renderer.SetBackground(VTK_BACKGROUND_COLOR[0],
VTK_BACKGROUND_COLOR[1],
VTK_BACKGROUND_COLOR[2])
def __init__(
self,
inputobj=None,
c='RdBu_r',
alpha=(0.0, 0.0, 0.2, 0.4, 0.8, 1.0),
alphaGradient=None,
alphaUnit=1,
mode=0,
shade=False,
spacing=None,
dims=None,
origin=None,
mapper='smart',
):
vtk.vtkVolume.__init__(self)
BaseGrid.__init__(self)
###################
if isinstance(inputobj, str):
if "https://" in inputobj:
from vedo.io import download
inputobj = download(inputobj, verbose=False) # fpath
elif os.path.isfile(inputobj):
pass
else:
inputobj = sorted(glob.glob(inputobj))
###################
if 'gpu' in mapper:
self._mapper = vtk.vtkGPUVolumeRayCastMapper()
elif 'opengl_gpu' in mapper:
self._mapper = vtk.vtkOpenGLGPUVolumeRayCastMapper()
elif 'smart' in mapper:
self._mapper = vtk.vtkSmartVolumeMapper()
elif 'fixed' in mapper:
self._mapper = vtk.vtkFixedPointVolumeRayCastMapper()
elif isinstance(mapper, vtk.vtkMapper):
self._mapper = mapper
else:
print("Error unknown mapper type", [mapper])
raise RuntimeError()
self.SetMapper(self._mapper)
###################
inputtype = str(type(inputobj))
#colors.printc('Volume inputtype', inputtype)
if inputobj is None:
img = vtk.vtkImageData()
elif utils.isSequence(inputobj):
if isinstance(inputobj[0], str): # scan sequence of BMP files
ima = vtk.vtkImageAppend()
ima.SetAppendAxis(2)
pb = utils.ProgressBar(0, len(inputobj))
for i in pb.range():
f = inputobj[i]
picr = vtk.vtkBMPReader()
picr.SetFileName(f)
picr.Update()
mgf = vtk.vtkImageMagnitude()
mgf.SetInputData(picr.GetOutput())
mgf.Update()
ima.AddInputData(mgf.GetOutput())
pb.print('loading...')
ima.Update()
img = ima.GetOutput()
else:
if "ndarray" not in inputtype:
inputobj = np.array(inputobj)
if len(inputobj.shape) == 1:
varr = numpy_to_vtk(inputobj,
deep=True,
array_type=vtk.VTK_FLOAT)
else:
if len(inputobj.shape) > 2:
inputobj = np.transpose(inputobj, axes=[2, 1, 0])
varr = numpy_to_vtk(inputobj.ravel(order='F'),
deep=True,
array_type=vtk.VTK_FLOAT)
varr.SetName('input_scalars')
img = vtk.vtkImageData()
if dims is not None:
img.SetDimensions(dims)
else:
if len(inputobj.shape) == 1:
colors.printc(
"Error: must set dimensions (dims keyword) in Volume.",
c='r')
raise RuntimeError()
img.SetDimensions(inputobj.shape)
img.GetPointData().SetScalars(varr)
#to convert rgb to numpy
# img_scalar = data.GetPointData().GetScalars()
# dims = data.GetDimensions()
# n_comp = img_scalar.GetNumberOfComponents()
# temp = numpy_support.vtk_to_numpy(img_scalar)
# numpy_data = temp.reshape(dims[1],dims[0],n_comp)
# numpy_data = numpy_data.transpose(0,1,2)
# numpy_data = np.flipud(numpy_data)
elif "ImageData" in inputtype:
img = inputobj
elif isinstance(inputobj, Volume):
img = inputobj.inputdata()
elif "UniformGrid" in inputtype:
img = inputobj
elif hasattr(
inputobj,
"GetOutput"): # passing vtk object, try extract imagdedata
if hasattr(inputobj, "Update"):
inputobj.Update()
img = inputobj.GetOutput()
elif isinstance(inputobj, str):
from vedo.io import loadImageData, download
if "https://" in inputobj:
inputobj = download(inputobj, verbose=False)
img = loadImageData(inputobj)
else:
colors.printc("Volume(): cannot understand input type:\n",
inputtype,
c='r')
return
if dims is not None:
img.SetDimensions(dims)
if origin is not None:
img.SetOrigin(origin) ### DIFFERENT from volume.origin()!
if spacing is not None:
img.SetSpacing(spacing)
self._data = img
self._mapper.SetInputData(img)
self.mode(mode).color(c).alpha(alpha).alphaGradient(alphaGradient)
self.GetProperty().SetShade(True)
self.GetProperty().SetInterpolationType(1)
self.GetProperty().SetScalarOpacityUnitDistance(alphaUnit)
# remember stuff:
self._mode = mode
self._color = c
self._alpha = alpha
self._alphaGrad = alphaGradient
self._alphaUnit = alphaUnit
im = alg.GetOutputPort()
#m = vtk.vtkPolyDataMapper()
#m.SetInputConnection(im)
#cf = vtk.vtkContourFilter()
#cf.SetInputConnection(alg.GetOutputPort())
#cf.SetValue(0, 200)
# The volume will be displayed by ray-cast alpha compositing.
# A ray-cast mapper is needed to do the ray-casting, and a
# compositing function is needed to do the compositing along the ray.
#rayCastFunction = vtk.vtkVolumeRayCastCompositeFunction()
#volumeMapper = vtk.vtkVolumeRayCastMapper()
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputConnection( im )
#volumeMapper.SetVolumeRayCastFunction(rayCastFunction)
attr = f['majEigenVal'][:]
min = attr.min()
max = attr.max()
# The color transfer function maps voxel intensities to colors.
# It is modality-specific, and often anatomy-specific as well.
# The goal is to one color for flesh (between 500 and 1000)
# and another color for bone (1150 and over).
volumeColor = vtk.vtkColorTransferFunction()
volumeColor.AddRGBPoint(min, 0.0, 0.0, 0.0)
#volumeColor.AddRGBPoint(500, 1.0, 0.5, 0.3)
#volumeColor.AddRGBPoint(1000, 1.0, 0.5, 0.3)
def BuildView(self):
# ensure python 2-3 compatibility for checking string type (difference with unicode str handeling)
PY3 = sys.version_info[0] == 3
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if (self.ArrayName != ''):
self.Image.GetPointData().SetActiveScalars(self.ArrayName)
if PY3:
string_types = str,
else:
string_types = basestring,
if not isinstance(self.VolumeRenderingMethod, string_types):
self.PrintError('Specified Rendering Method is not of required "string" type')
# create volume mapper and apply requested volume rendering method
volumeMapper = vtk.vtkSmartVolumeMapper()
if self.VolumeRenderingMethod.lower() == 'default':
volumeMapper.SetRequestedRenderModeToDefault()
elif self.VolumeRenderingMethod.lower() == 'gpu':
volumeMapper.SetRequestedRenderModeToGPU()
elif self.VolumeRenderingMethod.lower() == 'ospray':
volumeMapper.SetRequestedRenderModeToOSPRay()
elif self.VolumeRenderingMethod.lower() == 'raycast':
volumeMapper.SetRequestedRenderModeToRayCast()
else:
self.PrintError('Specified Rendering Method: ' + self.VolumeRenderingMethod + ' not supported. Please choose from ["default", "gpu", "ospray", "raycast"]')
volumeMapper.SetInputData(self.Image)
volumeMapper.SetBlendModeToComposite()
# create the volume from the mapper (defining image data and render mode) with the defined properties
# this is the last pipeline step applied. self.Volume just needs to now be added to the Renderer
self.SetPresetVolumeProperty()
self.Volume = vtk.vtkVolume()
self.Volume.SetMapper(volumeMapper)
self.Volume.SetProperty(self.VolumeProperty)
# add the actors to the renderer
self.vmtkRenderer.Renderer.AddVolume(self.Volume)
# This next section is responsible for creating the box outline around the volume's data extent.
if self.BoxOutline:
outline = vtk.vtkOutlineFilter()
outline.SetInputData(self.Image)
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
# The SetInteractor method is how 3D widgets are associated with the
# render window interactor. Internally, SetInteractor sets up a bunch
# of callbacks using the Command/Observer mechanism (AddObserver()).
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
boxWidget.SetPlaceFactor(1.0)
# Place the interactor initially. The output of the reader is used to
# place the box widget.
boxWidget.SetInputData(self.Image)
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
# Add the actors to the renderer
self.vmtkRenderer.Renderer.AddActor(outlineActor)
# add preset callback
self.vmtkRenderer.AddKeyBinding('w','Change volume render property.',self.PresetCallback)
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()