def ipl_open(image_in, open):
ipl_open_settings(open)
extent = image_in.GetExtent()
clip = vtk.vtkImageReslice()
clip.SetInput(image_in)
clip.SetOutputExtent(extent[0] - open - 2, extent[1] + open + 2,
extent[2] - open - 2, extent[3] + open + 2,
extent[4] - open - 2, extent[5] + open + 2)
clip.MirrorOn()
clip.Update()
erode = vtk.vtkImageContinuousErode3D()
erode.SetInputConnection(clip.GetOutputPort())
erode.SetKernelSize(2 * open + 1, 2 * open + 1, 2 * open + 1)
erode.Update()
#Kernel size is twice the dilation distance plus one for the center voxel
dilate = vtk.vtkImageContinuousDilate3D()
dilate.SetInputConnection(erode.GetOutputPort())
dilate.SetKernelSize(2 * open + 1, 2 * open + 1, 2 * open + 1)
dilate.Update()
voi = vtk.vtkExtractVOI()
voi.SetInput(dilate.GetOutput())
voi.SetVOI(extent[0], extent[1], extent[2], extent[3], extent[4],
extent[5])
voi.Update()
image_out = voi.GetOutput()
return image_out
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._imageDilate = vtk.vtkImageContinuousDilate3D()
self._imageErode = vtk.vtkImageContinuousErode3D()
self._imageErode.SetInput(self._imageDilate.GetOutput())
module_utils.setup_vtk_object_progress(self, self._imageDilate,
'Performing greyscale 3D dilation')
module_utils.setup_vtk_object_progress(self, self._imageErode,
'Performing greyscale 3D erosion')
self._config.kernelSize = (3, 3, 3)
configList = [
('Kernel size:', 'kernelSize', 'tuple:int,3', 'text',
'Size of the kernel in x,y,z dimensions.')]
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkImageContinuousDilate3D' : self._imageDilate,
'vtkImageContinuousErode3D' : self._imageErode})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._imageDilate = vtk.vtkImageContinuousDilate3D()
module_utils.setup_vtk_object_progress(self, self._imageDilate,
'Performing greyscale 3D dilation')
self._config.kernelSize = (3, 3, 3)
configList = [
('Kernel size:', 'kernelSize', 'tuple:int,3', 'text',
'Size of the kernel in x,y,z dimensions.')]
ScriptedConfigModuleMixin.__init__(self, configList)
self._viewFrame = self._createWindow(
{'Module (self)' : self,
'vtkImageContinuousDilate3D' : self._imageDilate})
# pass the data down to the underlying logic
self.config_to_logic()
# and all the way up from logic -> config -> view to make sure
self.logic_to_config()
self.config_to_view()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageContinuousDilate3D(), 'Processing.',
('vtkImageData',), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkImageContinuousDilate3D(),
'Processing.', ('vtkImageData', ),
('vtkImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def __init__(self):
"""
Initialization
"""
MorphologicalFilter.__init__(self)
self.vtkfilter = vtk.vtkImageContinuousDilate3D()
self.vtkfilter.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(self.vtkfilter, "ProgressEvent", self.updateProgress)
self.filterDesc = "Replaces each pixel/voxel with maximum value inside kernel\nInput: Grayscale/Binary image\nOutput: Grayscale/Binary image"
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# main morph gradient
self._imageDilate = vtk.vtkImageContinuousDilate3D()
self._imageErode = vtk.vtkImageContinuousErode3D()
self._imageMath = vtk.vtkImageMathematics()
self._imageMath.SetOperationToSubtract()
self._imageMath.SetInput1(self._imageDilate.GetOutput())
self._imageMath.SetInput2(self._imageErode.GetOutput())
# inner gradient
self._innerImageMath = vtk.vtkImageMathematics()
self._innerImageMath.SetOperationToSubtract()
self._innerImageMath.SetInput1(None) # has to take image
self._innerImageMath.SetInput2(self._imageErode.GetOutput())
# outer gradient
self._outerImageMath = vtk.vtkImageMathematics()
self._outerImageMath.SetOperationToSubtract()
self._outerImageMath.SetInput1(self._imageDilate.GetOutput())
self._outerImageMath.SetInput2(None) # has to take image
module_utils.setup_vtk_object_progress(
self, self._imageDilate, 'Performing greyscale 3D dilation')
module_utils.setup_vtk_object_progress(
self, self._imageErode, 'Performing greyscale 3D erosion')
module_utils.setup_vtk_object_progress(
self, self._imageMath, 'Subtracting erosion from '
'dilation')
module_utils.setup_vtk_object_progress(
self, self._innerImageMath, 'Subtracting erosion from '
'image (inner)')
module_utils.setup_vtk_object_progress(
self, self._outerImageMath, 'Subtracting image from '
'dilation (outer)')
self._config.kernelSize = (3, 3, 3)
configList = [('Kernel size:', 'kernelSize', 'tuple:int,3', 'text',
'Size of the kernel in x,y,z dimensions.')]
ScriptedConfigModuleMixin.__init__(
self, configList, {
'Module (self)': self,
'vtkImageContinuousDilate3D': self._imageDilate,
'vtkImageContinuousErode3D': self._imageErode,
'vtkImageMathematics': self._imageMath
})
self.sync_module_logic_with_config()
def __init__(self):
"""
Initialization
"""
MorphologicalFilter.__init__(self)
self.vtkfilter = vtk.vtkImageContinuousDilate3D()
self.vtkfilter.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(self.vtkfilter, "ProgressEvent",
self.updateProgress)
self.filterDesc = "Replaces each pixel/voxel with maximum value inside kernel\nInput: Grayscale/Binary image\nOutput: Grayscale/Binary image"
def dilate(self, neighbours=(2, 2, 2)):
"""Replace a voxel with the maximum over an ellipsoidal neighborhood of voxels.
If `neighbours` of an axis is 1, no processing is done on that axis.
See example script: |erode_dilate.py|_
"""
ver = vtk.vtkImageContinuousDilate3D()
ver.SetInputData(self._data)
ver.SetKernelSize(neighbours[0], neighbours[1], neighbours[2])
ver.Update()
return self._update(ver.GetOutput())
def VTKDilate(x,k=5,l=None,numret=0):
if type(x) == np.ndarray: i = NumToVTKImage(x)
else: i = x
if l is None: l = k
d = vtk.vtkImageContinuousDilate3D()
d.SetKernelSize(k,l,1)
d.SetInputData(i)
o = d.GetOutput()
d.Update()
if numret: return VTKImageToNum(o)
else: return o
def ipl_dilation(image_in, dilate_distance, boundary):
ipl_dilation_settings(dilate_distance, boundary)
extent = image_in.GetExtent()
#Actual distance of pixel dilation
distance = dilate_distance + 1
pad = vtk.vtkImageReslice()
pad.SetInput(image_in)
pad.SetOutputExtent(extent[0] - distance - 1, extent[1] + distance + 1,
extent[2] - distance - 1, extent[3] + distance + 1,
extent[4] - distance - 1, extent[5] + distance + 1)
pad.Update()
#Kernel size is twice the dilation distance plus one for the center voxel
dilate = vtk.vtkImageContinuousDilate3D()
dilate.SetInputConnection(pad.GetOutputPort())
dilate.SetKernelSize(2 * distance + 1, 2 * distance + 1, 2 * distance + 1)
dilate.Update()
ext = dilate.GetOutput().GetExtent()
border = vtk.vtkExtractVOI()
border.SetInput(dilate.GetOutput())
border.SetVOI(ext[0] + boundary[0] * distance,
ext[1] - boundary[0] * distance,
ext[2] + boundary[1] * distance,
ext[3] - boundary[1] * distance,
ext[4] + boundary[2] * distance,
ext[5] - boundary[2] * distance)
border.Update()
clip = vtk.vtkImageReslice()
clip.SetInput(border.GetOutput())
clip.SetOutputExtent(ext[0] + 1, ext[1] - 1, ext[2] + 1, ext[3] - 1,
ext[4] + 1, ext[5] - 1)
clip.MirrorOn()
clip.Update()
image_out = clip.GetOutput()
return image_out
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._imageDilate = vtk.vtkImageContinuousDilate3D()
module_utils.setup_vtk_object_progress(self, self._imageDilate, "Performing greyscale 3D dilation")
self._config.kernelSize = (3, 3, 3)
configList = [("Kernel size:", "kernelSize", "tuple:int,3", "text", "Size of the kernel in x,y,z dimensions.")]
ScriptedConfigModuleMixin.__init__(self, configList)
self._viewFrame = self._createWindow({"Module (self)": self, "vtkImageContinuousDilate3D": self._imageDilate})
# pass the data down to the underlying logic
self.config_to_logic()
# and all the way up from logic -> config -> view to make sure
self.logic_to_config()
self.config_to_view()
def dilate(image,kernel):
dilate = vtk.vtkImageContinuousDilate3D()
dilate.SetInput(image)
dilate.SetKernelSize(kernel[0],kernel[1],kernel[2])
dilate.Update()
return dilate.GetOutput()
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Image pipeline
reader = vtk.vtkImageReader()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExtent(0,63,0,63,1,93)
reader.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
reader.SetDataMask(0x7fff)
dilate = vtk.vtkImageContinuousDilate3D()
dilate.SetInputConnection(reader.GetOutputPort())
dilate.SetKernelSize(11,11,1)
erode = vtk.vtkImageContinuousErode3D()
erode.SetInputConnection(dilate.GetOutputPort())
erode.SetKernelSize(11,11,1)
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(erode.GetOutputPort())
viewer.SetColorWindow(2000)
viewer.SetColorLevel(1000)
viewer.Render()
# --- end of script --
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# main morph gradient
self._imageDilate = vtk.vtkImageContinuousDilate3D()
self._imageErode = vtk.vtkImageContinuousErode3D()
self._imageMath = vtk.vtkImageMathematics()
self._imageMath.SetOperationToSubtract()
self._imageMath.SetInput1(self._imageDilate.GetOutput())
self._imageMath.SetInput2(self._imageErode.GetOutput())
# inner gradient
self._innerImageMath = vtk.vtkImageMathematics()
self._innerImageMath.SetOperationToSubtract()
self._innerImageMath.SetInput1(None) # has to take image
self._innerImageMath.SetInput2(self._imageErode.GetOutput())
# outer gradient
self._outerImageMath = vtk.vtkImageMathematics()
self._outerImageMath.SetOperationToSubtract()
self._outerImageMath.SetInput1(self._imageDilate.GetOutput())
self._outerImageMath.SetInput2(None) # has to take image
module_utils.setup_vtk_object_progress(self, self._imageDilate,
'Performing greyscale 3D dilation')
module_utils.setup_vtk_object_progress(self, self._imageErode,
'Performing greyscale 3D erosion')
module_utils.setup_vtk_object_progress(self, self._imageMath,
'Subtracting erosion from '
'dilation')
module_utils.setup_vtk_object_progress(self, self._innerImageMath,
'Subtracting erosion from '
'image (inner)')
module_utils.setup_vtk_object_progress(self, self._outerImageMath,
'Subtracting image from '
'dilation (outer)')
self._config.kernelSize = (3, 3, 3)
configList = [
('Kernel size:', 'kernelSize', 'tuple:int,3', 'text',
'Size of the kernel in x,y,z dimensions.')]
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkImageContinuousDilate3D' : self._imageDilate,
'vtkImageContinuousErode3D' : self._imageErode,
'vtkImageMathematics' : self._imageMath})
self.sync_module_logic_with_config()
def __init__(self, ren, renWin, iren):
self.ren = ren
self.renWin = renWin
self.iren = iren
# Create a gaussian
gs = vtk.vtkImageGaussianSource()
gs.SetWholeExtent(0, 30, 0, 30, 0, 30)
gs.SetMaximum(255.0)
gs.SetStandardDeviation(5)
gs.SetCenter(15, 15, 15)
# threshold to leave a gap that should show up for
# gradient opacity
t = vtk.vtkImageThreshold()
t.SetInputConnection(gs.GetOutputPort())
t.ReplaceInOn()
t.SetInValue(0)
t.ThresholdBetween(150, 200)
# Use a shift scale to convert to unsigned char
ss = vtk.vtkImageShiftScale()
ss.SetInputConnection(t.GetOutputPort())
ss.SetOutputScalarTypeToUnsignedChar()
# grid will be used for two component dependent
grid0 = vtk.vtkImageGridSource()
grid0.SetDataScalarTypeToUnsignedChar()
grid0.SetGridSpacing(10, 10, 10)
grid0.SetLineValue(200)
grid0.SetFillValue(10)
grid0.SetDataExtent(0, 30, 0, 30, 0, 30)
# use dilation to thicken the grid
d = vtk.vtkImageContinuousDilate3D()
d.SetInputConnection(grid0.GetOutputPort())
d.SetKernelSize(3, 3, 3)
# Now make a two component dependent
iac = vtk.vtkImageAppendComponents()
iac.AddInputConnection(d.GetOutputPort())
iac.AddInputConnection(ss.GetOutputPort())
# Some more gaussians for the four component indepent case
gs1 = vtk.vtkImageGaussianSource()
gs1.SetWholeExtent(0, 30, 0, 30, 0, 30)
gs1.SetMaximum(255.0)
gs1.SetStandardDeviation(4)
gs1.SetCenter(5, 5, 5)
t1 = vtk.vtkImageThreshold()
t1.SetInputConnection(gs1.GetOutputPort())
t1.ReplaceInOn()
t1.SetInValue(0)
t1.ThresholdBetween(150, 256)
gs2 = vtk.vtkImageGaussianSource()
gs2.SetWholeExtent(0, 30, 0, 30, 0, 30)
gs2.SetMaximum(255.0)
gs2.SetStandardDeviation(4)
gs2.SetCenter(12, 12, 12)
gs3 = vtk.vtkImageGaussianSource()
gs3.SetWholeExtent(0, 30, 0, 30, 0, 30)
gs3.SetMaximum(255.0)
gs3.SetStandardDeviation(4)
gs3.SetCenter(19, 19, 19)
t3 = vtk.vtkImageThreshold()
t3.SetInputConnection(gs3.GetOutputPort())
t3.ReplaceInOn()
t3.SetInValue(0)
t3.ThresholdBetween(150, 256)
gs4 = vtk.vtkImageGaussianSource()
gs4.SetWholeExtent(0, 30, 0, 30, 0, 30)
gs4.SetMaximum(255.0)
gs4.SetStandardDeviation(4)
gs4.SetCenter(26, 26, 26)
# we need a few append filters ...
iac1 = vtk.vtkImageAppendComponents()
iac1.AddInputConnection(t1.GetOutputPort())
iac1.AddInputConnection(gs2.GetOutputPort())
iac2 = vtk.vtkImageAppendComponents()
iac2.AddInputConnection(iac1.GetOutputPort())
iac2.AddInputConnection(t3.GetOutputPort())
iac3 = vtk.vtkImageAppendComponents()
iac3.AddInputConnection(iac2.GetOutputPort())
iac3.AddInputConnection(gs4.GetOutputPort())
# create the four component dependend -
# use lines in x, y, z for colors
gridR = vtk.vtkImageGridSource()
gridR.SetDataScalarTypeToUnsignedChar()
gridR.SetGridSpacing(10, 100, 100)
gridR.SetLineValue(250)
gridR.SetFillValue(100)
gridR.SetDataExtent(0, 30, 0, 30, 0, 30)
dR = vtk.vtkImageContinuousDilate3D()
dR.SetInputConnection(gridR.GetOutputPort())
dR.SetKernelSize(2, 2, 2)
gridG = vtk.vtkImageGridSource()
gridG.SetDataScalarTypeToUnsignedChar()
gridG.SetGridSpacing(100, 10, 100)
gridG.SetLineValue(250)
gridG.SetFillValue(100)
gridG.SetDataExtent(0, 30, 0, 30, 0, 30)
dG = vtk.vtkImageContinuousDilate3D()
dG.SetInputConnection(gridG.GetOutputPort())
dG.SetKernelSize(2, 2, 2)
gridB = vtk.vtkImageGridSource()
gridB.SetDataScalarTypeToUnsignedChar()
gridB.SetGridSpacing(100, 100, 10)
gridB.SetLineValue(0)
gridB.SetFillValue(250)
gridB.SetDataExtent(0, 30, 0, 30, 0, 30)
dB = vtk.vtkImageContinuousDilate3D()
dB.SetInputConnection(gridB.GetOutputPort())
dB.SetKernelSize(2, 2, 2)
# need some appending
iacRG = vtk.vtkImageAppendComponents()
iacRG.AddInputConnection(dR.GetOutputPort())
iacRG.AddInputConnection(dG.GetOutputPort())
iacRGB = vtk.vtkImageAppendComponents()
iacRGB.AddInputConnection(iacRG.GetOutputPort())
iacRGB.AddInputConnection(dB.GetOutputPort())
iacRGBA = vtk.vtkImageAppendComponents()
iacRGBA.AddInputConnection(iacRGB.GetOutputPort())
iacRGBA.AddInputConnection(ss.GetOutputPort())
# We need a bunch of opacity functions
# this one is a simple ramp to .2
rampPoint2 = vtk.vtkPiecewiseFunction()
rampPoint2.AddPoint(0, 0.0)
rampPoint2.AddPoint(255, 0.2)
# this one is a simple ramp to 1
ramp1 = vtk.vtkPiecewiseFunction()
ramp1.AddPoint(0, 0.0)
ramp1.AddPoint(255, 1.0)
# this one shows a sharp surface
surface = vtk.vtkPiecewiseFunction()
surface.AddPoint(0, 0.0)
surface.AddPoint(10, 0.0)
surface.AddPoint(50, 1.0)
surface.AddPoint(255, 1.0)
# this one is constant 1
constant1 = vtk.vtkPiecewiseFunction()
constant1.AddPoint(0, 1.0)
constant1.AddPoint(255, 1.0)
# this one is used for gradient opacity
gop = vtk.vtkPiecewiseFunction()
gop.AddPoint(0, 0.0)
gop.AddPoint(20, 0.0)
gop.AddPoint(60, 1.0)
gop.AddPoint(255, 1.0)
# We need a bunch of color functions
# This one is a simple rainbow
rainbow = vtk.vtkColorTransferFunction()
rainbow.SetColorSpaceToHSV()
rainbow.HSVWrapOff()
rainbow.AddHSVPoint(0, 0.1, 1.0, 1.0)
rainbow.AddHSVPoint(255, 0.9, 1.0, 1.0)
# this is constant red
red = vtk.vtkColorTransferFunction()
red.AddRGBPoint(0, 1, 0, 0)
red.AddRGBPoint(255, 1, 0, 0)
# this is constant green
green = vtk.vtkColorTransferFunction()
green.AddRGBPoint(0, 0, 1, 0)
green.AddRGBPoint(255, 0, 1, 0)
# this is constant blue
blue = vtk.vtkColorTransferFunction()
blue.AddRGBPoint(0, 0, 0, 1)
blue.AddRGBPoint(255, 0, 0, 1)
# this is constant yellow
yellow = vtk.vtkColorTransferFunction()
yellow.AddRGBPoint(0, 1, 1, 0)
yellow.AddRGBPoint(255, 1, 1, 0)
#ren = vtk.vtkRenderer()
#renWin = vtk.vtkRenderWindow()
self.renWin.AddRenderer(self.ren)
self.renWin.SetSize(500, 500)
#iren = vtk.vtkRenderWindowInteractor()
self.iren.SetRenderWindow(self.renWin)
self.ren.GetCullers().InitTraversal()
culler = self.ren.GetCullers().GetNextItem()
culler.SetSortingStyleToBackToFront()
# We need 25 mapper / actor pairs which we will render
# in a grid. Going down we will vary the input data
# with the top row unsigned char, then float, then
# two dependent components, then four dependent components
# then four independent components. Going across we
# will vary the rendering method with MIP, Composite,
# Composite Shade, Composite GO, and Composite GO Shade.
# Create the 5 by 5 grids
self.volumeProperty = [[0 for col in range(0, 5)] for row in range(0, 5)]
self.volumeMapper = [[0 for col in range(0, 5)] for row in range(0, 5)]
volume = [[0 for col in range(0, 5)] for row in range(0, 5)]
for i in range(0, 5):
for j in range(0, 5):
self.volumeProperty[i][j] = vtk.vtkVolumeProperty()
self.volumeMapper[i][j] = vtk.vtkFixedPointVolumeRayCastMapper()
self.volumeMapper[i][j].SetSampleDistance(0.25)
volume[i][j] = vtk.vtkVolume()
volume[i][j].SetMapper(self.volumeMapper[i][j])
volume[i][j].SetProperty(self.volumeProperty[i][j])
volume[i][j].AddPosition(i * 30, j * 30, 0)
self.ren.AddVolume(volume[i][j])
for i in range(0, 5):
self.volumeMapper[0][i].SetInputConnection(t.GetOutputPort())
self.volumeMapper[1][i].SetInputConnection(ss.GetOutputPort())
self.volumeMapper[2][i].SetInputConnection(iac.GetOutputPort())
self.volumeMapper[3][i].SetInputConnection(iac3.GetOutputPort())
self.volumeMapper[4][i].SetInputConnection(iacRGBA.GetOutputPort())
self.volumeMapper[i][0].SetBlendModeToMaximumIntensity()
self.volumeMapper[i][1].SetBlendModeToComposite()
self.volumeMapper[i][2].SetBlendModeToComposite()
self.volumeMapper[i][3].SetBlendModeToComposite()
self.volumeMapper[i][4].SetBlendModeToComposite()
self.volumeProperty[0][i].IndependentComponentsOn()
self.volumeProperty[1][i].IndependentComponentsOn()
self.volumeProperty[2][i].IndependentComponentsOff()
self.volumeProperty[3][i].IndependentComponentsOn()
self.volumeProperty[4][i].IndependentComponentsOff()
self.volumeProperty[0][i].SetColor(rainbow)
self.volumeProperty[0][i].SetScalarOpacity(rampPoint2)
self.volumeProperty[0][i].SetGradientOpacity(constant1)
self.volumeProperty[1][i].SetColor(rainbow)
self.volumeProperty[1][i].SetScalarOpacity(rampPoint2)
self.volumeProperty[1][i].SetGradientOpacity(constant1)
self.volumeProperty[2][i].SetColor(rainbow)
self.volumeProperty[2][i].SetScalarOpacity(rampPoint2)
self.volumeProperty[2][i].SetGradientOpacity(constant1)
self.volumeProperty[3][i].SetColor(0, red)
self.volumeProperty[3][i].SetColor(1, green)
self.volumeProperty[3][i].SetColor(2, blue)
self.volumeProperty[3][i].SetColor(3, yellow)
self.volumeProperty[3][i].SetScalarOpacity(0, rampPoint2)
self.volumeProperty[3][i].SetScalarOpacity(1, rampPoint2)
self.volumeProperty[3][i].SetScalarOpacity(2, rampPoint2)
self.volumeProperty[3][i].SetScalarOpacity(3, rampPoint2)
self.volumeProperty[3][i].SetGradientOpacity(0, constant1)
self.volumeProperty[3][i].SetGradientOpacity(1, constant1)
self.volumeProperty[3][i].SetGradientOpacity(2, constant1)
self.volumeProperty[3][i].SetGradientOpacity(3, constant1)
self.volumeProperty[3][i].SetComponentWeight(0, 1)
self.volumeProperty[3][i].SetComponentWeight(1, 1)
self.volumeProperty[3][i].SetComponentWeight(2, 1)
self.volumeProperty[3][i].SetComponentWeight(3, 1)
self.volumeProperty[4][i].SetColor(rainbow)
self.volumeProperty[4][i].SetScalarOpacity(rampPoint2)
self.volumeProperty[4][i].SetGradientOpacity(constant1)
self.volumeProperty[i][2].ShadeOn()
self.volumeProperty[i][4].ShadeOn(0)
self.volumeProperty[i][4].ShadeOn(1)
self.volumeProperty[i][4].ShadeOn(2)
self.volumeProperty[i][4].ShadeOn(3)
self.volumeProperty[0][0].SetScalarOpacity(ramp1)
self.volumeProperty[1][0].SetScalarOpacity(ramp1)
self.volumeProperty[2][0].SetScalarOpacity(ramp1)
self.volumeProperty[3][0].SetScalarOpacity(0, surface)
self.volumeProperty[3][0].SetScalarOpacity(1, surface)
self.volumeProperty[3][0].SetScalarOpacity(2, surface)
self.volumeProperty[3][0].SetScalarOpacity(3, surface)
self.volumeProperty[4][0].SetScalarOpacity(ramp1)
self.volumeProperty[0][2].SetScalarOpacity(surface)
self.volumeProperty[1][2].SetScalarOpacity(surface)
self.volumeProperty[2][2].SetScalarOpacity(surface)
self.volumeProperty[3][2].SetScalarOpacity(0, surface)
self.volumeProperty[3][2].SetScalarOpacity(1, surface)
self.volumeProperty[3][2].SetScalarOpacity(2, surface)
self.volumeProperty[3][2].SetScalarOpacity(3, surface)
self.volumeProperty[4][2].SetScalarOpacity(surface)
self.volumeProperty[0][4].SetScalarOpacity(surface)
self.volumeProperty[1][4].SetScalarOpacity(surface)
self.volumeProperty[2][4].SetScalarOpacity(surface)
self.volumeProperty[3][4].SetScalarOpacity(0, surface)
self.volumeProperty[3][4].SetScalarOpacity(1, surface)
self.volumeProperty[3][4].SetScalarOpacity(2, surface)
self.volumeProperty[3][4].SetScalarOpacity(3, surface)
self.volumeProperty[4][4].SetScalarOpacity(surface)
self.volumeProperty[0][3].SetGradientOpacity(gop)
self.volumeProperty[1][3].SetGradientOpacity(gop)
self.volumeProperty[2][3].SetGradientOpacity(gop)
self.volumeProperty[3][3].SetGradientOpacity(0, gop)
self.volumeProperty[3][3].SetGradientOpacity(2, gop)
self.volumeProperty[4][3].SetGradientOpacity(gop)
self.volumeProperty[3][3].SetScalarOpacity(0, ramp1)
self.volumeProperty[3][3].SetScalarOpacity(2, ramp1)
self.volumeProperty[0][4].SetGradientOpacity(gop)
self.volumeProperty[1][4].SetGradientOpacity(gop)
self.volumeProperty[2][4].SetGradientOpacity(gop)
self.volumeProperty[3][4].SetGradientOpacity(0, gop)
self.volumeProperty[3][4].SetGradientOpacity(2, gop)
self.volumeProperty[4][4].SetGradientOpacity(gop)
self.renWin.Render()
self.ren.GetActiveCamera().Dolly(1.3)
self.ren.GetActiveCamera().Azimuth(15)
self.ren.GetActiveCamera().Elevation(5)
self.ren.ResetCameraClippingRange()
def __init__(self, ren, renWin, iren):
self.ren = ren
self.renWin = renWin
self.iren = iren
# Create a gaussian
gs = vtk.vtkImageGaussianSource()
gs.SetWholeExtent(0, 30, 0, 30, 0, 30)
gs.SetMaximum(255.0)
gs.SetStandardDeviation(5)
gs.SetCenter(15, 15, 15)
# threshold to leave a gap that should show up for
# gradient opacity
t = vtk.vtkImageThreshold()
t.SetInputConnection(gs.GetOutputPort())
t.ReplaceInOn()
t.SetInValue(0)
t.ThresholdBetween(150, 200)
# Use a shift scale to convert to unsigned char
ss = vtk.vtkImageShiftScale()
ss.SetInputConnection(t.GetOutputPort())
ss.SetOutputScalarTypeToUnsignedChar()
# grid will be used for two component dependent
grid0 = vtk.vtkImageGridSource()
grid0.SetDataScalarTypeToUnsignedChar()
grid0.SetGridSpacing(10, 10, 10)
grid0.SetLineValue(200)
grid0.SetFillValue(10)
grid0.SetDataExtent(0, 30, 0, 30, 0, 30)
# use dilation to thicken the grid
d = vtk.vtkImageContinuousDilate3D()
d.SetInputConnection(grid0.GetOutputPort())
d.SetKernelSize(3, 3, 3)
# Now make a two component dependent
iac = vtk.vtkImageAppendComponents()
iac.AddInputConnection(d.GetOutputPort())
iac.AddInputConnection(ss.GetOutputPort())
# Some more gaussians for the four component indepent case
gs1 = vtk.vtkImageGaussianSource()
gs1.SetWholeExtent(0, 30, 0, 30, 0, 30)
gs1.SetMaximum(255.0)
gs1.SetStandardDeviation(4)
gs1.SetCenter(5, 5, 5)
t1 = vtk.vtkImageThreshold()
t1.SetInputConnection(gs1.GetOutputPort())
t1.ReplaceInOn()
t1.SetInValue(0)
t1.ThresholdBetween(150, 256)
gs2 = vtk.vtkImageGaussianSource()
gs2.SetWholeExtent(0, 30, 0, 30, 0, 30)
gs2.SetMaximum(255.0)
gs2.SetStandardDeviation(4)
gs2.SetCenter(12, 12, 12)
gs3 = vtk.vtkImageGaussianSource()
gs3.SetWholeExtent(0, 30, 0, 30, 0, 30)
gs3.SetMaximum(255.0)
gs3.SetStandardDeviation(4)
gs3.SetCenter(19, 19, 19)
t3 = vtk.vtkImageThreshold()
t3.SetInputConnection(gs3.GetOutputPort())
t3.ReplaceInOn()
t3.SetInValue(0)
t3.ThresholdBetween(150, 256)
gs4 = vtk.vtkImageGaussianSource()
gs4.SetWholeExtent(0, 30, 0, 30, 0, 30)
gs4.SetMaximum(255.0)
gs4.SetStandardDeviation(4)
gs4.SetCenter(26, 26, 26)
# we need a few append filters ...
iac1 = vtk.vtkImageAppendComponents()
iac1.AddInputConnection(t1.GetOutputPort())
iac1.AddInputConnection(gs2.GetOutputPort())
iac2 = vtk.vtkImageAppendComponents()
iac2.AddInputConnection(iac1.GetOutputPort())
iac2.AddInputConnection(t3.GetOutputPort())
iac3 = vtk.vtkImageAppendComponents()
iac3.AddInputConnection(iac2.GetOutputPort())
iac3.AddInputConnection(gs4.GetOutputPort())
# create the four component dependent -
# use lines in x, y, z for colors
gridR = vtk.vtkImageGridSource()
gridR.SetDataScalarTypeToUnsignedChar()
gridR.SetGridSpacing(10, 100, 100)
gridR.SetLineValue(250)
gridR.SetFillValue(100)
gridR.SetDataExtent(0, 30, 0, 30, 0, 30)
dR = vtk.vtkImageContinuousDilate3D()
dR.SetInputConnection(gridR.GetOutputPort())
dR.SetKernelSize(2, 2, 2)
gridG = vtk.vtkImageGridSource()
gridG.SetDataScalarTypeToUnsignedChar()
gridG.SetGridSpacing(100, 10, 100)
gridG.SetLineValue(250)
gridG.SetFillValue(100)
gridG.SetDataExtent(0, 30, 0, 30, 0, 30)
dG = vtk.vtkImageContinuousDilate3D()
dG.SetInputConnection(gridG.GetOutputPort())
dG.SetKernelSize(2, 2, 2)
gridB = vtk.vtkImageGridSource()
gridB.SetDataScalarTypeToUnsignedChar()
gridB.SetGridSpacing(100, 100, 10)
gridB.SetLineValue(0)
gridB.SetFillValue(250)
gridB.SetDataExtent(0, 30, 0, 30, 0, 30)
dB = vtk.vtkImageContinuousDilate3D()
dB.SetInputConnection(gridB.GetOutputPort())
dB.SetKernelSize(2, 2, 2)
# need some appending
iacRG = vtk.vtkImageAppendComponents()
iacRG.AddInputConnection(dR.GetOutputPort())
iacRG.AddInputConnection(dG.GetOutputPort())
iacRGB = vtk.vtkImageAppendComponents()
iacRGB.AddInputConnection(iacRG.GetOutputPort())
iacRGB.AddInputConnection(dB.GetOutputPort())
iacRGBA = vtk.vtkImageAppendComponents()
iacRGBA.AddInputConnection(iacRGB.GetOutputPort())
iacRGBA.AddInputConnection(ss.GetOutputPort())
# We need a bunch of opacity functions
# this one is a simple ramp to .2
rampPoint2 = vtk.vtkPiecewiseFunction()
rampPoint2.AddPoint(0, 0.0)
rampPoint2.AddPoint(255, 0.2)
# this one is a simple ramp to 1
ramp1 = vtk.vtkPiecewiseFunction()
ramp1.AddPoint(0, 0.0)
ramp1.AddPoint(255, 1.0)
# this one shows a sharp surface
surface = vtk.vtkPiecewiseFunction()
surface.AddPoint(0, 0.0)
surface.AddPoint(10, 0.0)
surface.AddPoint(50, 1.0)
surface.AddPoint(255, 1.0)
# this one is constant 1
constant1 = vtk.vtkPiecewiseFunction()
constant1.AddPoint(0, 1.0)
constant1.AddPoint(255, 1.0)
# this one is used for gradient opacity
gop = vtk.vtkPiecewiseFunction()
gop.AddPoint(0, 0.0)
gop.AddPoint(20, 0.0)
gop.AddPoint(60, 1.0)
gop.AddPoint(255, 1.0)
# We need a bunch of color functions
# This one is a simple rainbow
rainbow = vtk.vtkColorTransferFunction()
rainbow.SetColorSpaceToHSV()
rainbow.HSVWrapOff()
rainbow.AddHSVPoint(0, 0.1, 1.0, 1.0)
rainbow.AddHSVPoint(255, 0.9, 1.0, 1.0)
# this is constant red
red = vtk.vtkColorTransferFunction()
red.AddRGBPoint(0, 1, 0, 0)
red.AddRGBPoint(255, 1, 0, 0)
# this is constant green
green = vtk.vtkColorTransferFunction()
green.AddRGBPoint(0, 0, 1, 0)
green.AddRGBPoint(255, 0, 1, 0)
# this is constant blue
blue = vtk.vtkColorTransferFunction()
blue.AddRGBPoint(0, 0, 0, 1)
blue.AddRGBPoint(255, 0, 0, 1)
# this is constant yellow
yellow = vtk.vtkColorTransferFunction()
yellow.AddRGBPoint(0, 1, 1, 0)
yellow.AddRGBPoint(255, 1, 1, 0)
#ren = vtk.vtkRenderer()
#renWin = vtk.vtkRenderWindow()
self.renWin.AddRenderer(self.ren)
self.renWin.SetSize(500, 500)
#iren = vtk.vtkRenderWindowInteractor()
self.iren.SetRenderWindow(self.renWin)
self.ren.GetCullers().InitTraversal()
culler = self.ren.GetCullers().GetNextItem()
culler.SetSortingStyleToBackToFront()
# We need 25 mapper / actor pairs which we will render
# in a grid. Going down we will vary the input data
# with the top row unsigned char, then float, then
# two dependent components, then four dependent components
# then four independent components. Going across we
# will vary the rendering method with MIP, Composite,
# Composite Shade, Composite GO, and Composite GO Shade.
# Create the 5 by 5 grids
self.volumeProperty = [[0 for col in range(0, 5)]
for row in range(0, 5)]
self.volumeMapper = [[0 for col in range(0, 5)] for row in range(0, 5)]
volume = [[0 for col in range(0, 5)] for row in range(0, 5)]
for i in range(0, 5):
for j in range(0, 5):
self.volumeProperty[i][j] = vtk.vtkVolumeProperty()
self.volumeMapper[i][j] = vtk.vtkFixedPointVolumeRayCastMapper(
)
self.volumeMapper[i][j].SetSampleDistance(0.25)
self.volumeMapper[i][j].SetNumberOfThreads(1)
volume[i][j] = vtk.vtkVolume()
volume[i][j].SetMapper(self.volumeMapper[i][j])
volume[i][j].SetProperty(self.volumeProperty[i][j])
volume[i][j].AddPosition(i * 30, j * 30, 0)
self.ren.AddVolume(volume[i][j])
for i in range(0, 5):
self.volumeMapper[0][i].SetInputConnection(t.GetOutputPort())
self.volumeMapper[1][i].SetInputConnection(ss.GetOutputPort())
self.volumeMapper[2][i].SetInputConnection(iac.GetOutputPort())
self.volumeMapper[3][i].SetInputConnection(iac3.GetOutputPort())
self.volumeMapper[4][i].SetInputConnection(iacRGBA.GetOutputPort())
self.volumeMapper[i][0].SetBlendModeToMaximumIntensity()
self.volumeMapper[i][1].SetBlendModeToComposite()
self.volumeMapper[i][2].SetBlendModeToComposite()
self.volumeMapper[i][3].SetBlendModeToComposite()
self.volumeMapper[i][4].SetBlendModeToComposite()
self.volumeProperty[0][i].IndependentComponentsOn()
self.volumeProperty[1][i].IndependentComponentsOn()
self.volumeProperty[2][i].IndependentComponentsOff()
self.volumeProperty[3][i].IndependentComponentsOn()
self.volumeProperty[4][i].IndependentComponentsOff()
self.volumeProperty[0][i].SetColor(rainbow)
self.volumeProperty[0][i].SetScalarOpacity(rampPoint2)
self.volumeProperty[0][i].SetGradientOpacity(constant1)
self.volumeProperty[1][i].SetColor(rainbow)
self.volumeProperty[1][i].SetScalarOpacity(rampPoint2)
self.volumeProperty[1][i].SetGradientOpacity(constant1)
self.volumeProperty[2][i].SetColor(rainbow)
self.volumeProperty[2][i].SetScalarOpacity(rampPoint2)
self.volumeProperty[2][i].SetGradientOpacity(constant1)
self.volumeProperty[3][i].SetColor(0, red)
self.volumeProperty[3][i].SetColor(1, green)
self.volumeProperty[3][i].SetColor(2, blue)
self.volumeProperty[3][i].SetColor(3, yellow)
self.volumeProperty[3][i].SetScalarOpacity(0, rampPoint2)
self.volumeProperty[3][i].SetScalarOpacity(1, rampPoint2)
self.volumeProperty[3][i].SetScalarOpacity(2, rampPoint2)
self.volumeProperty[3][i].SetScalarOpacity(3, rampPoint2)
self.volumeProperty[3][i].SetGradientOpacity(0, constant1)
self.volumeProperty[3][i].SetGradientOpacity(1, constant1)
self.volumeProperty[3][i].SetGradientOpacity(2, constant1)
self.volumeProperty[3][i].SetGradientOpacity(3, constant1)
self.volumeProperty[3][i].SetComponentWeight(0, 1)
self.volumeProperty[3][i].SetComponentWeight(1, 1)
self.volumeProperty[3][i].SetComponentWeight(2, 1)
self.volumeProperty[3][i].SetComponentWeight(3, 1)
self.volumeProperty[4][i].SetColor(rainbow)
self.volumeProperty[4][i].SetScalarOpacity(rampPoint2)
self.volumeProperty[4][i].SetGradientOpacity(constant1)
self.volumeProperty[i][2].ShadeOn()
self.volumeProperty[i][4].ShadeOn(0)
self.volumeProperty[i][4].ShadeOn(1)
self.volumeProperty[i][4].ShadeOn(2)
self.volumeProperty[i][4].ShadeOn(3)
self.volumeProperty[0][0].SetScalarOpacity(ramp1)
self.volumeProperty[1][0].SetScalarOpacity(ramp1)
self.volumeProperty[2][0].SetScalarOpacity(ramp1)
self.volumeProperty[3][0].SetScalarOpacity(0, surface)
self.volumeProperty[3][0].SetScalarOpacity(1, surface)
self.volumeProperty[3][0].SetScalarOpacity(2, surface)
self.volumeProperty[3][0].SetScalarOpacity(3, surface)
self.volumeProperty[4][0].SetScalarOpacity(ramp1)
self.volumeProperty[0][2].SetScalarOpacity(surface)
self.volumeProperty[1][2].SetScalarOpacity(surface)
self.volumeProperty[2][2].SetScalarOpacity(surface)
self.volumeProperty[3][2].SetScalarOpacity(0, surface)
self.volumeProperty[3][2].SetScalarOpacity(1, surface)
self.volumeProperty[3][2].SetScalarOpacity(2, surface)
self.volumeProperty[3][2].SetScalarOpacity(3, surface)
self.volumeProperty[4][2].SetScalarOpacity(surface)
self.volumeProperty[0][4].SetScalarOpacity(surface)
self.volumeProperty[1][4].SetScalarOpacity(surface)
self.volumeProperty[2][4].SetScalarOpacity(surface)
self.volumeProperty[3][4].SetScalarOpacity(0, surface)
self.volumeProperty[3][4].SetScalarOpacity(1, surface)
self.volumeProperty[3][4].SetScalarOpacity(2, surface)
self.volumeProperty[3][4].SetScalarOpacity(3, surface)
self.volumeProperty[4][4].SetScalarOpacity(surface)
self.volumeProperty[0][3].SetGradientOpacity(gop)
self.volumeProperty[1][3].SetGradientOpacity(gop)
self.volumeProperty[2][3].SetGradientOpacity(gop)
self.volumeProperty[3][3].SetGradientOpacity(0, gop)
self.volumeProperty[3][3].SetGradientOpacity(2, gop)
self.volumeProperty[4][3].SetGradientOpacity(gop)
self.volumeProperty[3][3].SetScalarOpacity(0, ramp1)
self.volumeProperty[3][3].SetScalarOpacity(2, ramp1)
self.volumeProperty[0][4].SetGradientOpacity(gop)
self.volumeProperty[1][4].SetGradientOpacity(gop)
self.volumeProperty[2][4].SetGradientOpacity(gop)
self.volumeProperty[3][4].SetGradientOpacity(0, gop)
self.volumeProperty[3][4].SetGradientOpacity(2, gop)
self.volumeProperty[4][4].SetGradientOpacity(gop)
self.renWin.Render()
self.ren.GetActiveCamera().Dolly(1.3)
self.ren.GetActiveCamera().Azimuth(15)
self.ren.GetActiveCamera().Elevation(5)
self.ren.ResetCameraClippingRange()
#!/usr/bin/env python
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Image pipeline
reader = vtk.vtkImageReader()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExtent(0, 63, 0, 63, 1, 93)
reader.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
reader.SetDataMask(0x7fff)
dilate = vtk.vtkImageContinuousDilate3D()
dilate.SetInputConnection(reader.GetOutputPort())
dilate.SetKernelSize(11, 11, 1)
erode = vtk.vtkImageContinuousErode3D()
erode.SetInputConnection(dilate.GetOutputPort())
erode.SetKernelSize(11, 11, 1)
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(erode.GetOutputPort())
viewer.SetColorWindow(2000)
viewer.SetColorLevel(1000)
viewer.Render()
# --- end of script --
