def vtkPlotMesh(self, courbure = "MEAN"):
""" Creation du maillage surfacique """
self.meshActor = None
self.vtkMeshCurvature = None
# Creation de l'information des courbures
self.vtkMeshCurvature = vtk.vtkCurvatures()
if courbure == "GAUSS" : self.vtkMeshCurvature.SetCurvatureTypeToGaussian()
if courbure == "MEAN" : self.vtkMeshCurvature.SetCurvatureTypeToMean()
self.vtkMeshCurvature.SetInputConnection(self.outputMesh.GetOutputPort())
self.vtkMeshCurvature.Update()
range_curvature = self.vtkMeshCurvature.GetOutput().GetScalarRange()
# Create color of curvature
Lut = vtk.vtkLookupTable()
Lut.SetNumberOfColors(256)
Lut.SetRange(range_curvature[0], range_curvature[1])
Lut.Build()
# Create the mapper that corresponds the objects of the vtk file
# into graphics elements
self.meshMapper = vtk.vtkPolyDataMapper()
self.meshMapper.SetInputConnection(self.meshNormals.GetOutputPort())
self.meshMapper.SetLookupTable(Lut)
self.meshMapper.SetUseLookupTableScalarRange(1)
# Create the Actor
self.vtkDeleteMesh()
self.meshActor = vtk.vtkActor()
self.meshActor.SetMapper(self.meshMapper)
self.meshActor.GetProperty().SetDiffuseColor(1, 0.2, 0.2)
self.ren.AddActor(self.meshActor)
self.vtkRedraw()
def curvature(actor, method=1, r=1, alpha=1, lut=None, legend=None):
'''
Build a copy of vtkActor that contains the color coded surface
curvature following four different ways to calculate it:
method = 0-gaussian, 1-mean, 2-max, 3-min
[**Example**](https://github.com/marcomusy/vtkplotter/blob/master/examples/tutorial.py)
'''
poly = actor.polydata()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(poly)
curve = vtk.vtkCurvatures()
curve.SetInputConnection(cleaner.GetOutputPort())
curve.SetCurvatureType(method)
curve.InvertMeanCurvatureOn()
curve.Update()
print('CurvatureType set to:', method)
if not lut:
lut = vtk.vtkLookupTable()
lut.SetNumberOfColors(256)
lut.SetHueRange(0.15, 1)
lut.SetSaturationRange(1, 1)
lut.SetValueRange(1, 1)
lut.SetAlphaRange(alpha, 1)
b = poly.GetBounds()
sc = max([b[1]-b[0], b[3]-b[2], b[5]-b[4]])
lut.SetRange(-0.01/sc*r, 0.01/sc*r)
cmapper = vtk.vtkPolyDataMapper()
cmapper.SetInputConnection(curve.GetOutputPort())
cmapper.SetLookupTable(lut)
cmapper.SetUseLookupTableScalarRange(1)
cactor = vtk.vtkActor()
cactor.SetMapper(cmapper)
return cactor
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# we'll be playing around with some vtk objects, this could
# be anything
self._triangleFilter = vtk.vtkTriangleFilter()
self._curvatures = vtk.vtkCurvatures()
self._curvatures.SetCurvatureTypeToMaximum()
self._curvatures.SetInput(self._triangleFilter.GetOutput())
# initialise any mixins we might have
NoConfigModuleMixin.__init__(self,
{'Module (self)' : self,
'vtkTriangleFilter' : self._triangleFilter,
'vtkCurvatures' : self._curvatures})
module_utils.setup_vtk_object_progress(self, self._triangleFilter,
'Triangle filtering...')
module_utils.setup_vtk_object_progress(self, self._curvatures,
'Calculating curvatures...')
self.sync_module_logic_with_config()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkCurvatures(), 'Processing.',
('vtkPolyData',), ('vtkPolyData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def GetCurvature(vtkdata):
curve = vtk.vtkCurvatures()
curve.SetCurvatureTypeToMinimum()
curve.SetInputData(vtkdata)
curve.Update()
vtkdata = curve.GetOutput()
return vtkdata
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# we'll be playing around with some vtk objects, this could
# be anything
self._triangleFilter = vtk.vtkTriangleFilter()
self._curvatures = vtk.vtkCurvatures()
self._curvatures.SetCurvatureTypeToMaximum()
self._curvatures.SetInput(self._triangleFilter.GetOutput())
# initialise any mixins we might have
NoConfigModuleMixin.__init__(
self, {
'Module (self)': self,
'vtkTriangleFilter': self._triangleFilter,
'vtkCurvatures': self._curvatures
})
module_utils.setup_vtk_object_progress(self, self._triangleFilter,
'Triangle filtering...')
module_utils.setup_vtk_object_progress(self, self._curvatures,
'Calculating curvatures...')
self.sync_module_logic_with_config()
def get_curvature_mean(poly_data):
curvatures = vtk.vtkCurvatures()
curvatures.SetInputConnection(poly_data.GetOutputPort())
curvatures.SetCurvatureTypeToMean()
curvatures.Update()
pd = curvatures.GetOutput()
pd.GetPointData().SetActiveScalars('Mean_Curvature')
Mean = vtk_to_numpy(pd.GetPointData().GetArray(1))
return Mean
def get_node_curvatures(vtk_mesh, curvature_type='min'):
curvature = vtk.vtkCurvatures()
if curvature_type == 'min':
curvature.SetCurvatureTypeToMinimum()
elif curvature_type == 'max':
curvature.SetCurvatureTypeToMaximum()
curvature.SetInputData(vtk_mesh)
curvature.Update()
return curvature.GetOutput()
def get_curvature_gaussian(poly_data):
curv = vtk.vtkCurvatures()
curv.SetInputConnection(poly_data.GetOutputPort())
curv.SetCurvatureTypeToGaussian()
curv.Update()
pd = curv.GetOutput()
pd.GetPointData().SetActiveScalars('Gauss_Curvature')
gaussian = vtk_to_numpy(pd.GetPointData().GetArray(1))
return gaussian
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkCurvatures(),
'Processing.', ('vtkPolyData', ),
('vtkPolyData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def compute_curvature(polydata):
curvaturesFilter = vtk.vtkCurvatures()
curvaturesFilter.SetInputData(polydata)
curvaturesFilter.SetCurvatureTypeToMinimum()
curvaturesFilter.SetCurvatureTypeToMaximum()
curvaturesFilter.SetCurvatureTypeToGaussian()
curvaturesFilter.SetCurvatureTypeToMean()
curvaturesFilter.Update()
return curvaturesFilter.GetOutput()
def mean_curvature(s):
curve1 = vtkCurvatures()
s = createPolyData(s.vertices, s.faces)
curve1.SetInput(s)
curve1.SetCurvatureTypeToMean()
curve1.Update()
m = curve1.GetOutput()
m = vtk_to_numpy(m.GetPointData().GetScalars())
return m
def compute_curvatures(self, vertices, faces):
pts, tris = self.arrayToPolydata(vertices, faces)
polys = vtk.vtkPolyData()
polys.SetPoints(pts)
polys.SetPolys(tris)
polys.Update()
# Now we have the sources, lets put them into a list.
sources = list()
sources.append(polys)
sources.append(polys)
curvatures = list()
curvatures.append(vtk.vtkCurvatures())
curvatures.append(vtk.vtkCurvatures())
curvatures[0].SetCurvatureTypeToMaximum()
curvatures[1].SetCurvatureTypeToMinimum()
# Link the pipeline together.
for idx, item in enumerate(sources):
sources[idx].Update()
curvatures[idx].SetInput(sources[idx])
curvatures[idx].Update()
c_min = curvatures[1]
curvMin = c_min.GetOutput().GetPointData().GetScalars()
c_max = curvatures[0]
curvMax = c_max.GetOutput().GetPointData().GetScalars()
min_hist_4 = createHistogram(4, curvMin)
min_hist_8 = createHistogram(8, curvMin)
min_hist_16 = createHistogram(16, curvMin)
max_hist_4 = createHistogram(4, curvMax)
max_hist_8 = createHistogram(8, curvMax)
max_hist_16 = createHistogram(16, curvMax)
#[[MIN_4, MIN_8, MIN_16], [MAX_4, MAX_8, MAX_16]]
return [[min_hist_4, min_hist_8, min_hist_16], [max_hist_4, max_hist_8, max_hist_16]]
def CalculateCurvatures(src):
'''
The source must be triangulated.
:param: src - the source.
:return: vtkPolyData with normal and scalar data representing curvatures.
'''
curvature = vtk.vtkCurvatures()
curvature.SetCurvatureTypeToGaussian()
curvature.SetInputData(src)
curvature.Update()
return curvature.GetOutput()
def CalculateCurvatures(src):
"""
The source must be triangulated.
:param: src - the source.
:return: vtkPolyData with normal and scalar data representing curvatures.
"""
curvature = vtk.vtkCurvatures()
curvature.SetCurvatureTypeToGaussian()
curvature.SetInputData(src)
curvature.Update()
return curvature.GetOutput()
def PlotCurvature(mesh, curvtype):
""" Plots curvature of a mesh """
# Curvatures Filter
curvefilter = vtk.vtkCurvatures()
curvefilter.SetInput(mesh)
if curvtype == 'Mean':
curvefilter.SetCurvatureTypeToMean()
elif curvtype == 'Gaussian':
curvefilter.SetCurvatureTypeToGaussian()
elif curvtype == 'Maximum':
curvefilter.SetCurvatureTypeToMaximum()
else:
curvefilter.SetCurvatureTypeToMinimum()
# Get curves
curvefilter.Update()
# Mapper
mapper = vtk.vtkDataSetMapper()
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
mapper.SetInputData(curvefilter.GetOutput())
else:
mapper.SetInput(curvefilter.GetOutput())
# Actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().LightingOff()
###############################
# Display
###############################
# Render
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Allow user to interact
istyle = vtk.vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(istyle)
ren.AddActor(actor)
iren.Initialize()
renWin.Render()
iren.Start()
def PlotCurvature(mesh, curvtype):
""" Plots curvature of a mesh """
# Curvatures Filter
curvefilter = vtk.vtkCurvatures()
curvefilter.SetInput(mesh)
if curvtype == 'Mean':
curvefilter.SetCurvatureTypeToMean()
elif curvtype == 'Gaussian':
curvefilter.SetCurvatureTypeToGaussian()
elif curvtype == 'Maximum':
curvefilter.SetCurvatureTypeToMaximum()
else:
curvefilter.SetCurvatureTypeToMinimum()
# Get curves
curvefilter.Update()
# Mapper
mapper = vtk.vtkDataSetMapper()
if vtk.vtkVersion().GetVTKMajorVersion() >5:
mapper.SetInputData(curvefilter.GetOutput())
else:
mapper.SetInput(curvefilter.GetOutput())
# Actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().LightingOff()
###############################
# Display
###############################
# Render
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Allow user to interact
istyle = vtk.vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(istyle)
ren.AddActor(actor)
iren.Initialize()
renWin.Render()
iren.Start()
def compute_Curvature(self):
self.curvaturesFilter = vtk.vtkCurvatures()
self.curvaturesFilter.SetInputConnection(self.dmc.GetOutputPort())
self.curvaturesFilter.SetCurvatureTypeToMean()
self.curvaturesFilter.Update()
np.savetxt(
"./result.txt",
np.trim_zeros(
vtk_to_numpy(self.curvaturesFilter.GetOutput().GetPointData().
GetScalars())))
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# initialise any mixins we might have
NoConfigModuleMixin.__init__(self)
mm = self._module_manager
self._cleaner = vtk.vtkCleanPolyData()
self._tf = vtk.vtkTriangleFilter()
self._tf.SetInput(self._cleaner.GetOutput())
self._wspdf = vtk.vtkWindowedSincPolyDataFilter()
#self._wspdf.SetNumberOfIterations(50)
self._wspdf.SetInput(self._tf.GetOutput())
self._wspdf.SetProgressText('smoothing')
self._wspdf.SetProgressMethod(
lambda s=self, mm=mm: mm.vtk_progress_cb(s._wspdf))
self._cleaner2 = vtk.vtkCleanPolyData()
self._cleaner2.SetInput(self._wspdf.GetOutput())
self._curvatures = vtk.vtkCurvatures()
self._curvatures.SetCurvatureTypeToMean()
self._curvatures.SetInput(self._cleaner2.GetOutput())
self._tf.SetProgressText('triangulating')
self._tf.SetProgressMethod(
lambda s=self, mm=mm: mm.vtk_progress_cb(s._tf))
self._curvatures.SetProgressText('calculating curvatures')
self._curvatures.SetProgressMethod(
lambda s=self, mm=mm: mm.vtk_progress_cb(s._curvatures))
self._inputFilter = self._tf
self._inputPoints = None
self._inputPointsOID = None
self._giaGlenoid = None
self._outsidePoints = None
self._outputPolyDataARB = vtk.vtkPolyData()
self._outputPolyDataHM = vtk.vtkPolyData()
self._createViewFrame('Test Module View', {
'vtkTriangleFilter': self._tf,
'vtkCurvatures': self._curvatures
})
self._viewFrame.Show(True)
def Curvature(self, curvature='mean'):
"""
Returns the pointwise curvature of a mesh
Parameters
----------
mesh : vtk.polydata
vtk polydata mesh
curvature string, optional
One of the following strings
Mean
Gaussian
Maximum
Minimum
Returns
-------
curvature : np.ndarray
Curvature values
"""
curvature = curvature.lower()
# Create curve filter and compute curvature
curvefilter = vtk.vtkCurvatures()
curvefilter.SetInputData(self)
if curvature == 'mean':
curvefilter.SetCurvatureTypeToMean()
elif curvature == 'gaussian':
curvefilter.SetCurvatureTypeToGaussian()
elif curvature == 'maximum':
curvefilter.SetCurvatureTypeToMaximum()
elif curvature == 'minimum':
curvefilter.SetCurvatureTypeToMinimum()
else:
raise Exception('Curvature must be either "Mean", ' +
'"Gaussian", "Maximum", or "Minimum"')
curvefilter.Update()
# Compute and return curvature
curves = curvefilter.GetOutput()
return vtk_to_numpy(curves.GetPointData().GetScalars())
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# initialise any mixins we might have
NoConfigModuleMixin.__init__(self)
mm = self._module_manager
self._cleaner = vtk.vtkCleanPolyData()
self._tf = vtk.vtkTriangleFilter()
self._tf.SetInput(self._cleaner.GetOutput())
self._wspdf = vtk.vtkWindowedSincPolyDataFilter()
# self._wspdf.SetNumberOfIterations(50)
self._wspdf.SetInput(self._tf.GetOutput())
self._wspdf.SetProgressText("smoothing")
self._wspdf.SetProgressMethod(lambda s=self, mm=mm: mm.vtk_progress_cb(s._wspdf))
self._cleaner2 = vtk.vtkCleanPolyData()
self._cleaner2.SetInput(self._wspdf.GetOutput())
self._curvatures = vtk.vtkCurvatures()
self._curvatures.SetCurvatureTypeToMean()
self._curvatures.SetInput(self._cleaner2.GetOutput())
self._tf.SetProgressText("triangulating")
self._tf.SetProgressMethod(lambda s=self, mm=mm: mm.vtk_progress_cb(s._tf))
self._curvatures.SetProgressText("calculating curvatures")
self._curvatures.SetProgressMethod(lambda s=self, mm=mm: mm.vtk_progress_cb(s._curvatures))
self._inputFilter = self._tf
self._inputPoints = None
self._inputPointsOID = None
self._giaGlenoid = None
self._outsidePoints = None
self._outputPolyDataARB = vtk.vtkPolyData()
self._outputPolyDataHM = vtk.vtkPolyData()
self._createViewFrame("Test Module View", {"vtkTriangleFilter": self._tf, "vtkCurvatures": self._curvatures})
self._viewFrame.Show(True)
def add_curvature_to_vtk_surface(surface, curvature_type, invert=True):
"""
Adds curvatures (Gaussian, mean, maximum or minimum) calculated by VTK to
each triangle vertex of a vtkPolyData surface.
Args:
surface (vtk.vtkPolyData): a surface of triangles
curvature_type (str): type of curvature to add: 'Gaussian', 'Mean',
'Maximum' or 'Minimum'
invert (boolean, optional): if True (default), VTK will calculate
curvatures as for meshes with opposite pointing normals (their
convention is outwards pointing normals, opposite from ours)
Returns:
the vtkPolyData surface with '<type>_Curvature' property added to each
triangle vertex
"""
if isinstance(surface, vtk.vtkPolyData):
curvature_filter = vtk.vtkCurvatures()
curvature_filter.SetInputData(surface)
if curvature_type == "Gaussian":
curvature_filter.SetCurvatureTypeToGaussian()
elif curvature_type == "Mean":
curvature_filter.SetCurvatureTypeToMean()
elif curvature_type == "Maximum":
curvature_filter.SetCurvatureTypeToMaximum()
elif curvature_type == "Minimum":
curvature_filter.SetCurvatureTypeToMinimum()
else:
raise pexceptions.PySegInputError(
expr='add_curvature_to_vtk_surface',
msg=("One of the following strings required as the second "
"input: 'Gaussian', 'Mean', 'Maximum' or 'Minimum'."))
if invert:
curvature_filter.InvertMeanCurvatureOn() # default Off
curvature_filter.Update()
surface_curvature = curvature_filter.GetOutput()
return surface_curvature
else:
raise pexceptions.PySegInputError(
expr='add_curvature_to_vtk_surface',
msg="A vtkPolyData object required as the first input.")
def get_point_curvatures(self, method='mean'):
curv = vtk.vtkCurvatures()
curv.SetInputData(self.vtkPolyData)
if method == 'mean':
curv.SetCurvatureTypeToMean()
elif method == 'max':
curv.SetCurvatureTypeToMaximum()
elif method == 'min':
curv.SetCurvatureTypeToMinimum()
elif method == 'Gaussian':
curv.SetCurvatureTypeToGaussian()
else:
curv.SetCurvatureTypeToMean()
curv.Update()
n_points = self.vtkPolyData.GetNumberOfPoints()
self.point_attributes['Curvature'] = np.zeros([n_points, 1])
for i in range(n_points):
self.point_attributes['Curvature'][i] = curv.GetOutput(
).GetPointData().GetArray(0).GetValue(i)
def filter_curvature(vtkObject, mode='gaussian'):
"""
Create vtkCurvatures filter on vtkObject.
:param vtkObject: input
:param mode: gaussian or mean
:type vtkObject: :py:class:`vtk.vtkObject`
:type mode: str
>>> image_data = create_image_data_from_array(surf)
>>> cubes = filter_marching_cubes(image_data)
>>> curve = filter_curvature(cubes)
>>> show(curve)
"""
curvature = vtk.vtkCurvatures()
pipe(vtkObject, curvature)
curvature.SetCurvatureTypeToMean()
if mode == 'gaussian':
curvature.SetCurvatureTypeToGaussian()
return curvature
def filter_curvature(vtkObject, mode='gaussian'):
"""
Create vtkCurvatures filter on vtkObject.
:param vtkObject: input
:param mode: gaussian or mean
:type vtkObject: :py:class:`vtk.vtkObject`
:type mode: str
>>> image_data = create_image_data_from_array(surf)
>>> cubes = filter_marching_cubes(image_data)
>>> curve = filter_curvature(cubes)
>>> show(curve)
"""
curvature = vtk.vtkCurvatures()
pipe(vtkObject, curvature)
curvature.SetCurvatureTypeToMean()
if mode == 'gaussian':
curvature.SetCurvatureTypeToGaussian()
return curvature
def compute_curvatures_backup(self, vertices, faces):
pts, tris = self.arrayToPolydata(vertices, faces)
polys = vtk.vtkPolyData()
polys.SetPoints(pts)
polys.SetPolys(tris)
polys.Update()
print "Vertices: " + str(len(vertices))
print "Faces: " + str(tris.GetNumberOfCells())
tri_2 = vtk.vtkTriangleFilter()
tri_2.SetInput(polys)
# The quadric has nasty discontinuities from the way the edges are generated
# so let's pass it though a CleanPolyDataFilter and merge any points which
# are coincident, or very close
cleaner_2 = vtk.vtkCleanPolyData()
cleaner_2.SetInputConnection(tri_2.GetOutputPort())
cleaner_2.SetTolerance(0.005)
# Now we have the sources, lets put them into a list.
sources = list()
sources.append(cleaner_2)
sources.append(cleaner_2)
# sources.append(cleaner_2)
# sources.append(cleaner_2)
curvatures = list()
curvatures.append(vtk.vtkCurvatures())
curvatures.append(vtk.vtkCurvatures())
# curvatures.append(vtk.vtkCurvatures())
# curvatures.append(vtk.vtkCurvatures())
curvatures[0].SetCurvatureTypeToMaximum()
curvatures[1].SetCurvatureTypeToMinimum()
# curvatures[2].SetCurvatureTypeToGaussian()
# curvatures[3].SetCurvatureTypeToMean()
# Link the pipeline together.
for idx, item in enumerate(sources):
sources[idx].Update()
curvatures[idx].SetInputConnection(sources[idx].GetOutputPort())
curvatures[idx].Update()
c_min = curvatures[1]
curvMin = c_min.GetOutput().GetPointData().GetScalars()
c_max = curvatures[0]
curvMax = c_max.GetOutput().GetPointData().GetScalars()
min_hist_4 = createHistogram(4, curvMin)
min_hist_8 = createHistogram(8, curvMin)
min_hist_16 = createHistogram(16, curvMin)
max_hist_4 = createHistogram(4, curvMax)
max_hist_8 = createHistogram(8, curvMax)
max_hist_16 = createHistogram(16, curvMax)
#[[MIN_4, MIN_8, MIN_16], [MAX_4, MAX_8, MAX_16]]
return [[min_hist_4, min_hist_8, min_hist_16], [max_hist_4, max_hist_8, max_hist_16]]
def CurvaturesDemo(self):
# We are going to handle two different sources.
# The first source is a superquadric source.
torus = vtk.vtkSuperquadricSource()
torus.SetCenter(0.0, 0.0, 0.0)
torus.SetScale(1.0, 1.0, 1.0)
torus.SetPhiResolution(64)
torus.SetThetaResolution(64)
torus.SetThetaRoundness(1)
torus.SetThickness(0.5)
torus.SetSize(0.5)
torus.SetToroidal(1)
# Rotate the torus towards the observer (around the x-axis)
torusT = vtk.vtkTransform()
torusT.RotateX(55)
torusTF = vtk.vtkTransformFilter()
torusTF.SetInputConnection(torus.GetOutputPort())
torusTF.SetTransform(torusT)
# The quadric is made of strips, so pass it through a triangle filter as
# the curvature filter only operates on polys
tri = vtk.vtkTriangleFilter()
tri.SetInputConnection(torusTF.GetOutputPort())
# The quadric has nasty discontinuities from the way the edges are generated
# so let's pass it though a CleanPolyDataFilter and merge any points which
# are coincident, or very close
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputConnection(tri.GetOutputPort())
cleaner.SetTolerance(0.005)
# The next source will be a parametric function
rh = vtk.vtkParametricRandomHills()
rhFnSrc = vtk.vtkParametricFunctionSource()
rhFnSrc.SetParametricFunction(rh)
# Now we have the sources, lets put them into a list.
sources = list()
sources.append(cleaner)
sources.append(cleaner)
sources.append(rhFnSrc)
sources.append(rhFnSrc)
# Colour transfer function.
ctf = vtk.vtkColorTransferFunction()
ctf.SetColorSpaceToDiverging()
ctf.AddRGBPoint(0.0, 0.230, 0.299, 0.754)
ctf.AddRGBPoint(1.0, 0.706, 0.016, 0.150)
cc = list()
for i in range(256):
cc.append(ctf.GetColor(float(i) / 255.0))
# Lookup table.
lut = list()
for idx in range(len(sources)):
lut.append(vtk.vtkLookupTable())
lut[idx].SetNumberOfColors(256)
for i, item in enumerate(cc):
lut[idx].SetTableValue(i, item[0], item[1], item[2], 1.0)
if idx == 0:
lut[idx].SetRange(-10, 10)
if idx == 1:
lut[idx].SetRange(0, 4)
if idx == 2:
lut[idx].SetRange(-1, 1)
if idx == 3:
lut[idx].SetRange(-1, 1)
lut[idx].Build()
curvatures = list()
for idx in range(len(sources)):
curvatures.append(vtk.vtkCurvatures())
if idx % 2 == 0:
curvatures[idx].SetCurvatureTypeToGaussian()
else:
curvatures[idx].SetCurvatureTypeToMean()
renderers = list()
mappers = list()
actors = list()
textmappers = list()
textactors = list()
# Create a common text property.
textProperty = vtk.vtkTextProperty()
textProperty.SetFontSize(10)
textProperty.SetJustificationToCentered()
names = [
'Torus - Gaussian Curvature', 'Torus - Mean Curvature',
'Random Hills - Gaussian Curvature',
'Random Hills - Mean Curvature'
]
# Link the pipeline together.
for idx, item in enumerate(sources):
sources[idx].Update()
curvatures[idx].SetInputConnection(sources[idx].GetOutputPort())
mappers.append(vtk.vtkPolyDataMapper())
mappers[idx].SetInputConnection(curvatures[idx].GetOutputPort())
mappers[idx].SetLookupTable(lut[idx])
mappers[idx].SetUseLookupTableScalarRange(1)
actors.append(vtk.vtkActor())
actors[idx].SetMapper(mappers[idx])
textmappers.append(vtk.vtkTextMapper())
textmappers[idx].SetInput(names[idx])
textmappers[idx].SetTextProperty(textProperty)
textactors.append(vtk.vtkActor2D())
textactors[idx].SetMapper(textmappers[idx])
textactors[idx].SetPosition(150, 16)
renderers.append(vtk.vtkRenderer())
gridDimensions = 2
for idx in range(len(sources)):
if idx < gridDimensions * gridDimensions:
renderers.append(vtk.vtkRenderer)
rendererSize = 300
# Create the RenderWindow
#
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(rendererSize * gridDimensions,
rendererSize * gridDimensions)
# Add and position the renders to the render window.
viewport = list()
for row in range(gridDimensions):
for col in range(gridDimensions):
idx = row * gridDimensions + col
viewport[:] = []
viewport.append(
float(col) * rendererSize /
(gridDimensions * rendererSize))
viewport.append(
float(gridDimensions - (row + 1)) * rendererSize /
(gridDimensions * rendererSize))
viewport.append(
float(col + 1) * rendererSize /
(gridDimensions * rendererSize))
viewport.append(
float(gridDimensions - row) * rendererSize /
(gridDimensions * rendererSize))
if idx > (len(sources) - 1):
continue
renderers[idx].SetViewport(viewport)
renderWindow.AddRenderer(renderers[idx])
renderers[idx].AddActor(actors[idx])
renderers[idx].AddActor(textactors[idx])
renderers[idx].SetBackground(0.4, 0.3, 0.2)
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renderWindow)
renderWindow.Render()
interactor.Start()
import vtk_functions
import vtk
import numpy as np
from vtk.util import numpy_support
if __name__ == "__main__":
r = 100
polydata = vtk_functions.read_ply(
"/home/steven/scriptie/inputs/meshes/sphere_r_100_p_20_MLX.ply")
polydata = vtk_functions.normals(polydata)
# Use VTK to get H
mcFilter = vtk.vtkCurvatures()
mcFilter.SetCurvatureTypeToMean()
mcFilter.SetInputData(polydata)
mcFilter.Update()
points = mcFilter.GetOutput().GetPoints()
vals = mcFilter.GetOutput().GetPointData().GetScalars()
mc_errors = []
for i in range(points.GetNumberOfPoints()):
p = points.GetPoint(i)
val = vals.GetComponent(i, 0)
# Compare VTK H with analytic H to derive error
mc_error = abs(val - 1 / r) / (1 / r) * 100
mc_errors.append(mc_error)
def CurvaturesDemo(self, filePath, nominalRadius):
sphere = Sphere(filePath, nominalRadius, False)
errors = np.abs(sphere.fittingError())
print sphere.curvature.max()
print sphere.curvature.argmax()
reader = vtk.vtkOBJReader()
reader.SetFileName(sys.argv[1])
reader.Update()
# Colour transfer function.
ctf = vtk.vtkColorTransferFunction()
ctf.SetColorSpaceToDiverging()
ctf.AddRGBPoint(0.0, 0.230, 0.299, 0.754)
ctf.AddRGBPoint(0.5, 1.0, 1.0, 1.0)
ctf.AddRGBPoint(1.0, 0.706, 0.016, 0.150)
cc = list()
for i in range(256):
cc.append(ctf.GetColor(float(i) / 255.0))
scalars = vtk.vtkFloatArray()
scalars.SetNumberOfComponents(1)
for errorVal in errors:
scalars.InsertNextTuple([errorVal])
mean = np.mean(errors)
std = np.std(errors)
min3 = mean - std
max3 = mean + std
# Now we have the sources, lets put them into a list.
sources = list()
sources.append(reader)
sources.append(reader)
sources.append(sphere.polyData)
sources.append(sphere.polyData)
curvatures = list()
for idx in range(2):
curvatures.append(vtk.vtkCurvatures())
curvatures[idx].SetInputConnection(sources[idx].GetOutputPort())
if idx % 2 == 0:
curvatures[idx].SetCurvatureTypeToGaussian()
curvatures[idx].Update()
npcurv1 = numpy_support.vtk_to_numpy(curvatures[idx].GetOutput().GetPointData().GetScalars())
mean = np.mean(npcurv1)
std = np.std(npcurv1)
min1 = 0.01*(mean - std)
max1 = 0.01*(mean + std)
else:
curvatures[idx].SetCurvatureTypeToMean()
curvatures[idx].Update()
npcurv2 = np.abs(numpy_support.vtk_to_numpy(curvatures[idx].GetOutput().GetPointData().GetScalars()))
mean = np.mean(npcurv2)
std = np.std(npcurv2)
#print 'Curvature (min / max / mean / total): ' + str(np.min(npcurv2)) + ' / ' + str(np.max(npcurv2)) + ' / ' + str(np.mean(npcurv2)) + ' / ' + str(np.sum(npcurv2))
min2 = mean - std
max2 = mean + std
fig = plt.figure()
xa = np.arange(-0.1, 0.1,0.001)
#plt.hist(npcurv1, bins=xa)
plt.hist(npcurv2/npcurv2.max(), bins=xa)
print 'By vtk:'
print npcurv2.max()
print npcurv2.argmax()
plt.gca().set_yscale('log')
plt.show()
# Lookup table.
lut = list()
for idx in range(len(sources)):
lut.append(vtk.vtkLookupTable())
lut[idx].SetNumberOfColors(256)
for i, item in enumerate(cc):
lut[idx].SetTableValue(i, item[0], item[1], item[2], 1.0)
if idx == 0:
lut[idx].SetRange(min1, max1)
if idx == 1:
lut[idx].SetRange(min2, max2)
if idx == 2:
lut[idx].SetRange(min3, max3)
lut[idx].Build()
renderers = list()
mappers = list()
actors = list()
textmappers = list()
textactors = list()
scalarbars = list()
# Create a common text property.
textProperty = vtk.vtkTextProperty()
textProperty.SetFontSize(16)
textProperty.SetJustificationToCentered()
names = ['Sphere - Gaussian Curvature', 'Sphere - Mean Curvature', 'Sphere - Residuals to fitted sphere', 'Sphere - Residuals to fitted sphere']
# Link the pipeline together.
for idx, item in enumerate(sources):
#sources[idx].Update()
mappers.append(vtk.vtkPolyDataMapper())
mappers[idx].SetUseLookupTableScalarRange(1)
if idx < 2:
#print npcurv.min(), npcurv.max()
#print npcurv
mappers[idx].SetInputConnection(curvatures[idx].GetOutputPort())
mappers[idx].SetLookupTable(lut[idx])
else:
#mappers[idx].SetInputConnection(sources[idx].GetOutputPort())
mappers[idx].SetInputData(sources[idx])
mappers[idx].SetColorModeToMapScalars()
#mappers[idx].GetPointData().SetScalars(scalars)
mappers[idx].SetLookupTable(lut[idx])
actors.append(vtk.vtkActor())
actors[idx].SetMapper(mappers[idx])
if idx == 3:
actors[idx].GetProperty().SetEdgeVisibility(1)
actors[idx].GetProperty().SetEdgeColor(0.5, 0.5, 0.5);
actors[idx].GetProperty().SetLineWidth(0.5)
textmappers.append(vtk.vtkTextMapper())
textmappers[idx].SetInput(names[idx])
textmappers[idx].SetTextProperty(textProperty)
textactors.append(vtk.vtkActor2D())
textactors[idx].SetMapper(textmappers[idx])
textactors[idx].SetPosition(150, 16)
scalarbars.append(vtk.vtkScalarBarActor())
scalarbars[idx].SetLookupTable(lut[idx])
renderers.append(vtk.vtkRenderer())
gridDimensions = 2
for idx in range(len(sources)):
if idx < gridDimensions * gridDimensions:
renderers.append(vtk.vtkRenderer)
rendererSize = 300
# Create the RenderWindow
#
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(rendererSize * gridDimensions, 0)
# Add and position the renders to the render window.
viewport = list()
for row in range(gridDimensions):
for col in range(gridDimensions):
idx = row * gridDimensions + col
viewport[:] = []
viewport.append(float(col) * rendererSize / (gridDimensions * rendererSize))
viewport.append(float(gridDimensions - (row+1)) * rendererSize / (gridDimensions * rendererSize))
viewport.append(float(col+1)*rendererSize / (gridDimensions * rendererSize))
viewport.append(float(gridDimensions - row) * rendererSize / (gridDimensions * rendererSize))
if idx > (len(sources) - 1):
continue
renderers[idx].SetViewport(viewport)
renderWindow.AddRenderer(renderers[idx])
renderers[idx].AddActor(actors[idx])
renderers[idx].AddActor(textactors[idx])
renderers[idx].AddActor(scalarbars[idx])
renderers[idx].SetBackground(0.5,0.5,0.5)
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renderWindow)
renderWindow.Render()
interactor.Start()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
curvatureFilter = vtk.vtkCurvatures()
curvatureFilter.SetInput(self.Surface)
if self.CurvatureType == 'mean':
curvatureFilter.SetCurvatureTypeToMean()
elif self.CurvatureType == 'gaussian':
curvatureFilter.SetCurvatureTypeToGaussian()
elif self.CurvatureType == 'maximum':
curvatureFilter.SetCurvatureTypeToMaximum()
elif self.CurvatureType == 'minimum':
curvatureFilter.SetCurvatureTypeToMinimum()
curvatureFilter.Update()
activeScalars = curvatureFilter.GetOutput().GetPointData().GetScalars()
activeScalars.SetName('Curvature')
if self.AbsoluteCurvature:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
activeScalars.SetTuple1(i, abs(value))
neighborhoods = None
if not self.CurvatureOnBoundaries or self.MedianFiltering:
neighborhoods = vtkvmtk.vtkvmtkNeighborhoods()
neighborhoods.SetNeighborhoodTypeToPolyDataManifoldNeighborhood()
neighborhoods.SetDataSet(self.Surface)
neighborhoods.Build()
if not self.CurvatureOnBoundaries:
boundaryExtractor = vtkvmtk.vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInput(self.Surface)
boundaryExtractor.Update()
boundaryIdsArray = vtk.vtkIdTypeArray.SafeDownCast(
boundaryExtractor.GetOutput().GetPointData().GetScalars())
boundaryIds = vtk.vtkIdList()
boundaryIds.SetNumberOfIds(boundaryIdsArray.GetNumberOfTuples())
for i in range(boundaryIdsArray.GetNumberOfTuples()):
boundaryIds.SetId(i, boundaryIdsArray.GetValue(i))
self.Surface.BuildLinks()
for i in range(boundaryIds.GetNumberOfIds()):
pointId = boundaryIds.GetId(i)
neighborhood = neighborhoods.GetNeighborhood(pointId)
values = []
for j in range(neighborhood.GetNumberOfPoints()):
neighborId = neighborhood.GetPointId(j)
if boundaryIds.IsId(neighborId) != -1:
continue
value = activeScalars.GetTuple1(neighborId)
values.append(value)
values.sort()
if not values:
continue
medianValue = values[(len(values) - 1) / 2]
activeScalars.SetTuple1(pointId, medianValue)
if self.MedianFiltering:
for i in range(neighborhoods.GetNumberOfNeighborhoods()):
neighborhood = neighborhoods.GetNeighborhood(i)
values = []
for j in range(neighborhood.GetNumberOfPoints()):
neighborId = neighborhood.GetPointId(j)
value = activeScalars.GetTuple1(neighborId)
values.append(value)
values.sort()
if not values:
continue
medianValue = values[(len(values) - 1) / 2]
activeScalars.SetTuple1(i, medianValue)
if self.BoundedReciprocal:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
reciprocalValue = 1.0 / (self.Epsilon + value)
activeScalars.SetTuple1(i, reciprocalValue)
if self.Offset:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
activeScalars.SetTuple1(i, value + self.Offset)
if self.ReferenceSurface == None:
self.Surface.GetPointData().AddArray(activeScalars)
else:
self.ReferenceSurface.GetPointData().AddArray(activeScalars)
self.Surface = self.ReferenceSurface
smooth.SetFeatureAngle(45)
smooth.SetEdgeAngle(15)
smooth.SetBoundarySmoothing(1)
smooth.SetFeatureEdgeSmoothing(0)
smooth.Update()
'''
# ---- Vertices - smoothed ---------------------
smooth_verts = smooth.GetOutput().GetPoints().GetData()
output_smooth_verts = array(
numpy_support.vtk_to_numpy(smooth_verts).transpose(), 'd')
if debug: print output_smooth_verts
# ---- Curvature ---------------------
curvature = vtk.vtkCurvatures()
curvature.SetInputConnection(smooth.GetOutputPort())
curvature.SetCurvatureTypeToMean()
curvature.Update()
curv = curvature.GetOutput().GetPointData().GetScalars()
output_curvature = array(numpy_support.vtk_to_numpy(curv).transpose(), 'd')
if debug: print min(output_curvature)
if debug: print max(output_curvature)
if debug: print output_curvature
# -------- colours based on curvature ------------
# turn curvature into color
tmp_colors = output_curvature.copy()
def flow(mesh_file, iter_num, show_flow=False):
reader = vtk.vtkPolyDataReader()
reader.SetFileName(mesh_file)
reader.Update()
mesh = reader.GetOutput()
tol = 0.05
q = 1.0
dt = 0.001
orig_mesh = mesh
prev_mesh = mesh
thin_plate_spline_list = []
for i in range(iter_num + 1):
deformed_surface_writer = vtk.vtkPolyDataWriter()
deformed_surface_writer.SetFileName('data/flow/' + str(i) + '.vtk')
deformed_surface_writer.SetInputData(mesh)
deformed_surface_writer.Update()
taubin_smooth = vtk.vtkWindowedSincPolyDataFilter()
taubin_smooth.SetInputData(mesh)
taubin_smooth.SetNumberOfIterations(20)
taubin_smooth.BoundarySmoothingOff()
taubin_smooth.FeatureEdgeSmoothingOff()
taubin_smooth.SetPassBand(0.01)
taubin_smooth.NonManifoldSmoothingOn()
taubin_smooth.NormalizeCoordinatesOn()
taubin_smooth.Update()
mesh = taubin_smooth.GetOutput()
normal_generator = vtk.vtkPolyDataNormals()
normal_generator.SetInputData(mesh)
normal_generator.SplittingOff()
normal_generator.ComputePointNormalsOn()
normal_generator.ComputeCellNormalsOff()
normal_generator.Update()
mesh = normal_generator.GetOutput()
curvatures = vtk.vtkCurvatures()
curvatures.SetCurvatureTypeToMean()
curvatures.SetInputData(mesh)
curvatures.Update()
mean_curvatures = curvatures.GetOutput().GetPointData().GetArray("Mean_Curvature")
normals = normal_generator.GetOutput().GetPointData().GetNormals()
mesh_pts = mesh.GetPoints()
for j in range(mesh.GetNumberOfPoints()):
current_point = mesh.GetPoint(j)
current_normal = np.array(normals.GetTuple3(j))
current_mean_curvature = mean_curvatures.GetValue(j)
pt = np.array(mesh_pts.GetPoint(j))
pt -= dt * current_mean_curvature * current_normal
mesh_pts.SetPoint(j, pt)
mesh_pts.Modified()
mesh.SetPoints(mesh_pts)
mesh.Modified()
# if i % 100 == 0 and show_flow:
# plotter = pyvista.Plotter()
# plotter.add_mesh(mesh)
# plotter.show()
tps_deform = get_thin_plate_spline_deform(prev_mesh, mesh)
prev_mesh = mesh
thin_plate_spline_list.append(tps_deform)
# new_mesh = apply_tps_on_spokes_poly(mesh, thin_plate_spline_list)
# plotter = pyvista.Plotter()
# plotter.add_mesh(new_mesh, color='red', opacity=0.3)
# plotter.add_mesh(orig_mesh, color='blue', opacity=0.3)
# plotter.show()
return mesh, thin_plate_spline_list
# test binary writing and reading for polygons
binaryWriter = vtk.vtkMNIObjectWriter()
binaryWriter.SetInputConnection(stripper.GetOutputPort())
binaryWriter.SetFileName("mni-surface-mesh-binary.obj")
binaryWriter.SetProperty(property0)
binaryWriter.SetFileTypeToBinary()
binaryWriter.Write()
binaryReader = vtk.vtkMNIObjectReader()
binaryReader.SetFileName("mni-surface-mesh-binary.obj")
property2 = binaryReader.GetProperty()
# make a polyline object with color scalars
scalars = vtk.vtkCurvatures()
scalars.SetInputConnection(asciiReader.GetOutputPort())
colors = vtk.vtkLookupTable()
colors.SetRange(-14.5104, 29.0208)
colors.SetAlphaRange(1.0, 1.0)
colors.SetSaturationRange(1.0, 1.0)
colors.SetValueRange(1.0, 1.0)
colors.SetHueRange(0.0, 1.0)
colors.Build()
# this is just to test using the SetMapper option of vtkMNIObjectWriter
mapper = vtk.vtkDataSetMapper()
mapper.SetLookupTable(colors)
mapper.UseLookupTableScalarRangeOn()
edges = vtk.vtkExtractEdges()
# test binary writing and reading for polygons
binaryWriter = vtk.vtkMNIObjectWriter()
binaryWriter.SetInputConnection(stripper.GetOutputPort())
binaryWriter.SetFileName("mni-surface-mesh-binary.obj")
binaryWriter.SetProperty(property0)
binaryWriter.SetFileTypeToBinary()
binaryWriter.Write()
binaryReader = vtk.vtkMNIObjectReader()
binaryReader.SetFileName("mni-surface-mesh-binary.obj")
property2 = binaryReader.GetProperty()
# make a polyline object with color scalars
scalars = vtk.vtkCurvatures()
scalars.SetInputConnection(asciiReader.GetOutputPort())
colors = vtk.vtkLookupTable()
colors.SetRange(-14.5104, 29.0208)
colors.SetAlphaRange(1.0, 1.0)
colors.SetSaturationRange(1.0, 1.0)
colors.SetValueRange(1.0, 1.0)
colors.SetHueRange(0.0, 1.0)
colors.Build()
# this is just to test using the SetMapper option of vtkMNIObjectWriter
mapper = vtk.vtkDataSetMapper()
mapper.SetLookupTable(colors)
mapper.UseLookupTableScalarRangeOn()
edges = vtk.vtkExtractEdges()
def MeanCurvature(self, verbose=False):
self.gauss_mean = False
value_list = []
self.curvaturesFilter_mean = vtk.vtkCurvatures()
self.curvaturesFilter_mean.SetInputConnection(
self.normal_generator_smooth.GetOutputPort())
self.curvaturesFilter_mean.SetCurvatureTypeToMean()
self.curvaturesFilter_mean.Update()
# Use a color series to create a transfer function
scalar_range = [-0.002, 0.001]
#self.curvaturesFilter_gauss.GetOutput().GetScalarRange(scalar_range)
if verbose:
print "scalar_range: ", scalar_range
lut = vtk.vtkColorTransferFunction()
lut.SetColorSpaceToHSV()
num_colors = self.color_series.GetNumberOfColors()
d_color = [0.0, 0.0, 0.0]
for i in range(num_colors):
color = self.color_series.GetColor(i)
d_color[0] = color[0] / 255.0
d_color[1] = color[1] / 255.0
d_color[2] = color[2] / 255.0
t = scalar_range[0] + (scalar_range[1] -
scalar_range[0]) * i / (num_colors - 1)
lut.AddRGBPoint(t, d_color[0], d_color[1], d_color[2])
# print t, " : ",d_color[0], d_color[1], d_color[2]
## make the value list:
poly_data = self.curvaturesFilter_mean.GetOutput()
self.curvature_polydata = poly_data
cell_number = poly_data.GetNumberOfCells()
#poly_data.GetPointData.SetActiveScalars("Mean_Curvature")
point_data = poly_data.GetPointData()
data_array = point_data.GetScalars()
self.total_MC = 0 # total Gaussian curvature
triangle = np.zeros([3, 3], dtype="f") # variable to store triangles
if verbose:
print "first value: ", data_array.GetTuple1(0)
t = float(cell_number)
for i in range(cell_number):
value = data_array.GetTuple1(i)
if verbose:
pdb.update_progress(float(i) / t)
cell = poly_data.GetCell(i)
for j in range(3):
point_id = cell.GetPointId(j)
poly_data.GetPoints().GetPoint(point_id, triangle[j])
if abs(value) < 1.0: # integrate only if ...
self.total_MC = self.total_MC + (CalcArea(triangle) * value)
value_list.append(float(value))
if verbose:
print "\nmax value: ", max(value_list)
print "min value : ", min(value_list)
print "total Gaussian curvature: ", self.total_MC
plt.hist(value_list, bins=100)
plt.suptitle('Mean curvature distribution')
plt.show()
##Create a mapper and actor
mapper = vtk.vtkPolyDataMapper()
mapper.UseLookupTableScalarRangeOn()
mapper.SetInputConnection(
self.curvaturesFilter_mean.GetOutputPort())
mapper.SetLookupTable(lut)
mapper.SetScalarRange(scalar_range)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
##Create a scalar bar actor
scalarBar = vtk.vtkScalarBarActor()
scalarBar.SetLookupTable(mapper.GetLookupTable())
scalarBar.SetNumberOfLabels(5)
##Create text actor
text_actor = vtk.vtkTextActor()
text_actor.SetInput("Mean Curvature")
text_actor.GetTextProperty().SetFontSize(20)
text_actor.GetTextProperty().SetColor(0.5, 0.5, 0.5)
text_actor.SetPosition(100, 16)
self.meancurve_renderer = vtk.vtkRenderer()
self.meancurve_renderer.SetBackground([1., 1., 1.])
self.meancurve_renderer.AddActor(actor)
self.meancurve_renderer.AddActor2D(scalarBar)
self.meancurve_renderer.AddActor2D(text_actor)
return self.total_MC
torus.SetPhiRoundness(1.0) torus.SetThetaRoundness(1.0) torus.SetThickness(0.5) torus.SetSize(0.5) torus.SetToroidal(1) # The quadric is made of strips, so pass it through a triangle filter as # the curvature filter only operates on polys tri = vtk.vtkTriangleFilter() tri.SetInputConnection(torus.GetOutputPort()) # The quadric has nasty discontinuities from the way the edges are generated # so let's pass it though a CleanPolyDataFilter and merge any points which # are coincident, or very close cleaner = vtk.vtkCleanPolyData() cleaner.SetInputConnection(tri.GetOutputPort()) cleaner.SetTolerance(0.005) curve1 = vtk.vtkCurvatures() curve1.SetInputConnection(cleaner.GetOutputPort()) curve1.SetCurvatureTypeToGaussian() curve2 = vtk.vtkCurvatures() curve2.SetInputConnection(cleaner.GetOutputPort()) curve2.SetCurvatureTypeToMean() lut1 = vtk.vtkLookupTable() lut1.SetNumberOfColors(256) lut1.SetHueRange(0.15,1.0) lut1.SetSaturationRange(1.0,1.0) lut1.SetValueRange(1.0,1.0) lut1.SetAlphaRange(1.0,1.0) lut1.SetRange(-20,20) lut2 = vtk.vtkLookupTable() lut2.SetNumberOfColors(256) lut2.SetHueRange(0.15,1.0)
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
curvatureFilter = vtk.vtkCurvatures()
curvatureFilter.SetInputData(self.Surface)
if self.CurvatureType == 'mean':
curvatureFilter.SetCurvatureTypeToMean()
elif self.CurvatureType == 'gaussian':
curvatureFilter.SetCurvatureTypeToGaussian()
elif self.CurvatureType == 'maximum':
curvatureFilter.SetCurvatureTypeToMaximum()
elif self.CurvatureType == 'minimum':
curvatureFilter.SetCurvatureTypeToMinimum()
curvatureFilter.Update()
activeScalars = curvatureFilter.GetOutput().GetPointData().GetScalars()
activeScalars.SetName('Curvature')
if self.AbsoluteCurvature:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
activeScalars.SetTuple1(i,abs(value))
neighborhoods = None
if not self.CurvatureOnBoundaries or self.MedianFiltering:
neighborhoods = vtkvmtk.vtkvmtkNeighborhoods()
neighborhoods.SetNeighborhoodTypeToPolyDataManifoldNeighborhood()
neighborhoods.SetDataSet(self.Surface)
neighborhoods.Build()
if not self.CurvatureOnBoundaries:
boundaryExtractor = vtkvmtk.vtkvmtkPolyDataBoundaryExtractor()
boundaryExtractor.SetInputData(self.Surface)
boundaryExtractor.Update()
boundaryIdsArray = vtk.vtkIdTypeArray.SafeDownCast(boundaryExtractor.GetOutput().GetPointData().GetScalars())
boundaryIds = vtk.vtkIdList()
boundaryIds.SetNumberOfIds(boundaryIdsArray.GetNumberOfTuples())
for i in range(boundaryIdsArray.GetNumberOfTuples()):
boundaryIds.SetId(i,boundaryIdsArray.GetValue(i))
self.Surface.BuildLinks()
for i in range(boundaryIds.GetNumberOfIds()):
pointId = boundaryIds.GetId(i)
neighborhood = neighborhoods.GetNeighborhood(pointId)
values = []
for j in range(neighborhood.GetNumberOfPoints()):
neighborId = neighborhood.GetPointId(j)
if boundaryIds.IsId(neighborId) != -1:
continue
value = activeScalars.GetTuple1(neighborId)
values.append(value)
values.sort()
if not values:
continue
medianValue = values[(len(values) - 1)/2]
activeScalars.SetTuple1(pointId,medianValue)
if self.MedianFiltering:
for i in range(neighborhoods.GetNumberOfNeighborhoods()):
neighborhood = neighborhoods.GetNeighborhood(i)
values = []
for j in range(neighborhood.GetNumberOfPoints()):
neighborId = neighborhood.GetPointId(j)
value = activeScalars.GetTuple1(neighborId)
values.append(value)
values.sort()
if not values:
continue
medianValue = values[(len(values) - 1)/2]
activeScalars.SetTuple1(i,medianValue)
if self.BoundedReciprocal:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
reciprocalValue = 1.0 / (self.Epsilon + value)
activeScalars.SetTuple1(i,reciprocalValue)
if self.Offset:
for i in range(activeScalars.GetNumberOfTuples()):
value = activeScalars.GetTuple1(i)
activeScalars.SetTuple1(i,value + self.Offset)
if self.ReferenceSurface == None:
self.Surface.GetPointData().AddArray(activeScalars)
else:
self.ReferenceSurface.GetPointData().AddArray(activeScalars)
self.Surface = self.ReferenceSurface
def __init__(self, parent = None):
super(VTKFrame, self).__init__(parent)
self.vtkWidget = QVTKRenderWindowInteractor(self)
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
vl = QtGui.QVBoxLayout(self)
vl.addWidget(self.vtkWidget)
vl.setContentsMargins(0, 0, 0, 0)
# Create source
# We are going to handle two different sources.
# The first source is a superquadric source.
torus = vtk.vtkSuperquadricSource();
torus.SetCenter(0.0, 0.0, 0.0)
torus.SetScale(1.0, 1.0, 1.0)
torus.SetPhiResolution (64)
torus.SetThetaResolution(64)
torus.SetThetaRoundness (1)
torus.SetThickness (0.5)
torus.SetSize(0.5)
torus.SetToroidal(1)
# Rotate the torus towards the observer (around the x-axis)
torusT = vtk.vtkTransform()
torusT.RotateX(55)
torusTF = vtk.vtkTransformFilter()
torusTF.SetInputConnection(torus.GetOutputPort())
torusTF.SetTransform(torusT)
# The quadric is made of strips, so pass it through a triangle filter as
# the curvature filter only operates on polys
tri = vtk.vtkTriangleFilter()
tri.SetInputConnection(torusTF.GetOutputPort())
# The quadric has nasty discontinuities from the way the edges are generated
# so let's pass it though a CleanPolyDataFilter and merge any points which
# are coincident, or very close
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputConnection(tri.GetOutputPort())
cleaner.SetTolerance(0.005)
# The next source will be a parametric function
rh = vtk.vtkParametricRandomHills()
rhFnSrc = vtk.vtkParametricFunctionSource()
rhFnSrc.SetParametricFunction(rh)
# Now we have the sources, lets put them into a list.
sources = list()
sources.append(cleaner)
sources.append(cleaner)
sources.append(rhFnSrc)
sources.append(rhFnSrc)
# Colour transfer function.
ctf = vtk.vtkColorTransferFunction()
ctf.SetColorSpaceToDiverging()
ctf.AddRGBPoint(0.0, 0.230, 0.299, 0.754)
ctf.AddRGBPoint(1.0, 0.706, 0.016, 0.150)
cc = list()
for i in range(256):
cc.append(ctf.GetColor(float(i) / 255.0))
# Lookup table.
lut = list()
for idx in range(len(sources)):
lut.append(vtk.vtkLookupTable())
lut[idx].SetNumberOfColors(256)
for i, item in enumerate(cc):
lut[idx].SetTableValue(i, item[0], item[1], item[2], 1.0)
if idx == 0:
lut[idx].SetRange(-10, 10)
if idx == 1:
lut[idx].SetRange(0, 4)
if idx == 2:
lut[idx].SetRange(-1, 1)
if idx == 3:
lut[idx].SetRange(-1, 1)
lut[idx].Build()
curvatures = list()
for idx in range(len(sources)):
curvatures.append(vtk.vtkCurvatures())
if idx % 2 == 0:
curvatures[idx].SetCurvatureTypeToGaussian()
else:
curvatures[idx].SetCurvatureTypeToMean()
renderers = list()
mappers = list()
actors = list()
textmappers = list()
textactors = list()
# Create a common text property.
textProperty = vtk.vtkTextProperty()
textProperty.SetFontSize(10)
textProperty.SetJustificationToCentered()
names = ['Torus - Gaussian Curvature', 'Torus - Mean Curvature', 'Random Hills - Gaussian Curvature', 'Random Hills - Mean Curvature']
# Link the pipeline together.
for idx, item in enumerate(sources):
sources[idx].Update()
curvatures[idx].SetInputConnection(sources[idx].GetOutputPort())
mappers.append(vtk.vtkPolyDataMapper())
mappers[idx].SetInputConnection(curvatures[idx].GetOutputPort())
mappers[idx].SetLookupTable(lut[idx])
mappers[idx].SetUseLookupTableScalarRange(1)
actors.append(vtk.vtkActor())
actors[idx].SetMapper(mappers[idx])
textmappers.append(vtk.vtkTextMapper())
textmappers[idx].SetInput(names[idx])
textmappers[idx].SetTextProperty(textProperty)
textactors.append(vtk.vtkActor2D())
textactors[idx].SetMapper(textmappers[idx])
textactors[idx].SetPosition(150, 16)
renderers.append(vtk.vtkRenderer())
gridDimensions = 2
for idx in range(len(sources)):
if idx < gridDimensions * gridDimensions:
renderers.append(vtk.vtkRenderer)
rendererSize = 300
# Create the RenderWindow
self.vtkWidget.GetRenderWindow().SetSize(rendererSize * gridDimensions, rendererSize * gridDimensions)
# Add and position the renders to the render window.
viewport = list()
for row in range(gridDimensions):
for col in range(gridDimensions):
idx = row * gridDimensions + col
viewport[:] = []
viewport.append(float(col) * rendererSize / (gridDimensions * rendererSize))
viewport.append(float(gridDimensions - (row+1)) * rendererSize / (gridDimensions * rendererSize))
viewport.append(float(col+1)*rendererSize / (gridDimensions * rendererSize))
viewport.append(float(gridDimensions - row) * rendererSize / (gridDimensions * rendererSize))
if idx > (len(sources) - 1):
continue
renderers[idx].SetViewport(viewport)
self.vtkWidget.GetRenderWindow().AddRenderer(renderers[idx])
renderers[idx].AddActor(actors[idx])
renderers[idx].AddActor(textactors[idx])
renderers[idx].SetBackground(0.4,0.3,0.2)
self._initialized = False
torus.SetPhiRoundness(1.0) torus.SetThetaRoundness(1.0) torus.SetThickness(0.5) torus.SetSize(0.5) torus.SetToroidal(1) # The quadric is made of strips, so pass it through a triangle filter as # the curvature filter only operates on polys tri = vtk.vtkTriangleFilter() tri.SetInputConnection(torus.GetOutputPort()) # The quadric has nasty discontinuities from the way the edges are generated # so let's pass it though a CleanPolyDataFilter and merge any points which # are coincident, or very close cleaner = vtk.vtkCleanPolyData() cleaner.SetInputConnection(tri.GetOutputPort()) cleaner.SetTolerance(0.005) curve1 = vtk.vtkCurvatures() curve1.SetInputConnection(cleaner.GetOutputPort()) curve1.SetCurvatureTypeToGaussian() curve2 = vtk.vtkCurvatures() curve2.SetInputConnection(cleaner.GetOutputPort()) curve2.SetCurvatureTypeToMean() lut1 = vtk.vtkLookupTable() lut1.SetNumberOfColors(256) lut1.SetHueRange(0.15, 1.0) lut1.SetSaturationRange(1.0, 1.0) lut1.SetValueRange(1.0, 1.0) lut1.SetAlphaRange(1.0, 1.0) lut1.SetRange(-20, 20) lut2 = vtk.vtkLookupTable() lut2.SetNumberOfColors(256) lut2.SetHueRange(0.15, 1.0)
model_avg_cur_m = np.zeros(1)
model_avg_cur_m_std = np.zeros(1)
for bound in range(1, lith, 1):
#contacts = vtk.vtkDiscreteMarchingCubes()
#contacts.SetInputData(input)
contacts = vtk.vtkMarchingCubes()
contacts.SetInputData(input)
true_bound = bound+0.5
contacts.SetValue(0,true_bound)
contacts.Update()
surface_area = vtk.vtkMassProperties()
surface_area.SetInputConnection(contacts.GetOutputPort())
surface_area.Update()
curvature = vtk.vtkCurvatures()
curvature.SetInputConnection(contacts.GetOutputPort())
curvature.SetCurvatureTypeToMinimum()
#curvature.SetCurvatureTypeToMaximum()
#curvature.SetCurvatureTypeToGaussian()
#curvature.SetCurvatureTypeToMean()
curvature.Update()
gauss = np.frombuffer(curvature.GetOutput().GetPointData().GetArray("Gauss_Curvature"), dtype = float)
mean = np.frombuffer(curvature.GetOutput().GetPointData().GetArray("Mean_Curvature"), dtype = float)
if (true_bound ==1.5):
model_area[0] = surface_area.GetSurfaceArea()
model_sum_cur_g[0] = np.sum(gauss)
model_sum_cur_m[0] = np.sum(mean)
model_sum_cur_g_std[0] = np.std(gauss)
model_sum_cur_m_std[0] = np.std(mean)
model_avg_cur_g[0] = np.mean(gauss)
def main(filename, curvature=0, scalarRange=None, scheme=None):
print("Loading", filename)
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(filename)
curvaturesFilter = vtk.vtkCurvatures()
curvaturesFilter.SetInputConnection(reader.GetOutputPort())
if curvature == 0:
curvaturesFilter.SetCurvatureTypeToMinimum()
elif curvature == 1:
curvaturesFilter.SetCurvatureTypeToMaximum()
elif curvature == 2:
curvaturesFilter.SetCurvatureTypeToGaussian()
else:
curvaturesFilter.SetCurvatureTypeToMean()
curvaturesFilter.Update()
# Get scalar range from command line if present, otherwise use
# range of computed curvature
if scalarRange is None:
scalarRange = curvaturesFilter.GetOutput().GetScalarRange()
# Build a lookup table
if scheme is None:
scheme = 16
colorSeries = vtk.vtkColorSeries()
colorSeries.SetColorScheme(scheme)
print("Using color scheme #:", colorSeries.GetColorScheme(), \
"is", colorSeries.GetColorSchemeName())
lut = vtk.vtkColorTransferFunction()
lut.SetColorSpaceToHSV()
# Use a color series to create a transfer function
numColors = colorSeries.GetNumberOfColors()
for i in range(numColors):
color = colorSeries.GetColor(i)
dColor = [color[0] / 255.0, color[1] / 255.0, color[2] / 255.0]
t = scalarRange[0] + (scalarRange[1] - scalarRange[0]) / (numColors -
1) * i
lut.AddRGBPoint(t, dColor[0], dColor[1], dColor[2])
# Create a mapper and actor
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(curvaturesFilter.GetOutputPort())
mapper.SetLookupTable(lut)
mapper.SetScalarRange(scalarRange)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
# Create a scalar bar
print("Displaying",
curvaturesFilter.GetOutput().GetPointData().GetScalars().GetName())
scalarBarActor = vtk.vtkScalarBarActor()
scalarBarActor.SetLookupTable(mapper.GetLookupTable())
scalarBarActor.SetTitle(
curvaturesFilter.GetOutput().GetPointData().GetScalars().GetName())
scalarBarActor.SetNumberOfLabels(5)
# Create a renderer, render window, and interactor
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
# Add the actors to the scene
renderer.AddActor(actor)
renderer.AddActor2D(scalarBarActor)
renderer.SetBackground(.1, .2, .3) # Background color blue
# Render and interact
renderWindow.Render()
renderWindowInteractor.Start()