def recoSurface(points, bins=256,
c='gold', alpha=1, wire=False, bc='t', legend=None):
'''
Surface reconstruction from sparse points.
[**Example**](https://github.com/marcomusy/vtkplotter/blob/master/examples/advanced/recosurface.py)
'''
if isinstance(points, vtk.vtkActor):
points = points.coordinates()
N = len(points)
if N < 50:
print('recoSurface: Use at least 50 points.')
return None
points = np.array(points)
ptsSource = vtk.vtkPointSource()
ptsSource.SetNumberOfPoints(N)
ptsSource.Update()
vpts = ptsSource.GetOutput().GetPoints()
for i, p in enumerate(points):
vpts.SetPoint(i, p)
polyData = ptsSource.GetOutput()
distance = vtk.vtkSignedDistance()
f = 0.1
x0, x1, y0, y1, z0, z1 = polyData.GetBounds()
distance.SetBounds(x0-(x1-x0)*f, x1+(x1-x0)*f,
y0-(y1-y0)*f, y1+(y1-y0)*f,
z0-(z1-z0)*f, z1+(z1-z0)*f)
if polyData.GetPointData().GetNormals():
distance.SetInputData(polyData)
else:
normals = vtk.vtkPCANormalEstimation()
normals.SetInputData(polyData)
normals.SetSampleSize(int(N/50))
normals.SetNormalOrientationToGraphTraversal()
distance.SetInputConnection(normals.GetOutputPort())
print('Recalculating normals for', N,
'points, sample size=', int(N/50))
b = polyData.GetBounds()
diagsize = np.sqrt((b[1]-b[0])**2 + (b[3]-b[2])**2 + (b[5]-b[4])**2)
radius = diagsize/bins*5
distance.SetRadius(radius)
distance.SetDimensions(bins, bins, bins)
distance.Update()
print('Calculating mesh from points with R =', radius)
surface = vtk.vtkExtractSurface()
surface.SetRadius(radius * .99)
surface.HoleFillingOn()
surface.ComputeNormalsOff()
surface.ComputeGradientsOff()
surface.SetInputConnection(distance.GetOutputPort())
surface.Update()
return Actor(surface.GetOutput(), c, alpha, wire, bc, legend)
def recoSurface(points,
bins=256,
c='gold',
alpha=1,
wire=False,
bc='t',
edges=False,
legend=None):
'''
Surface reconstruction from sparse points.
'''
if isinstance(points, vtk.vtkActor): points = vu.coordinates(points)
N = len(points)
if N < 50:
print('recoSurface: Use at least 50 points.')
return None
points = np.array(points)
ptsSource = vtk.vtkPointSource()
ptsSource.SetNumberOfPoints(N)
ptsSource.Update()
vpts = ptsSource.GetOutput().GetPoints()
for i, p in enumerate(points):
vpts.SetPoint(i, p)
polyData = ptsSource.GetOutput()
distance = vtk.vtkSignedDistance()
f = 0.1
x0, x1, y0, y1, z0, z1 = polyData.GetBounds()
distance.SetBounds(x0 - (x1 - x0) * f, x1 + (x1 - x0) * f,
y0 - (y1 - y0) * f, y1 + (y1 - y0) * f,
z0 - (z1 - z0) * f, z1 + (z1 - z0) * f)
if polyData.GetPointData().GetNormals():
distance.SetInputData(polyData)
vu.setInput(distance, polyData)
else:
normals = vtk.vtkPCANormalEstimation()
vu.setInput(normals, polyData)
normals.SetSampleSize(int(N / 50))
normals.SetNormalOrientationToGraphTraversal()
distance.SetInputConnection(normals.GetOutputPort())
print('Recalculating normals for', N, 'points, sample size=',
int(N / 50))
radius = vu.diagonalSize(polyData) / bins * 5
distance.SetRadius(radius)
distance.SetDimensions(bins, bins, bins)
distance.Update()
print('Calculating mesh from points with R =', radius)
surface = vtk.vtkExtractSurface()
surface.SetRadius(radius * .99)
surface.HoleFillingOn()
surface.ComputeNormalsOff()
surface.ComputeGradientsOff()
surface.SetInputConnection(distance.GetOutputPort())
surface.Update()
return vu.makeActor(surface.GetOutput(), c, alpha, wire, bc, edges, legend)
generate a scalar field by the signed distance from a polydata, save it to stack.tif file, then extract an isosurface from the 3d image. """ from vtkplotter import Plotter, Points, Text, datadir vp = Plotter(verbose=0) act = vp.load(datadir + "290.vtk").normalize().subdivide().computeNormals() # Generate signed distance function and contour it import vtk dist = vtk.vtkSignedDistance() dist.SetInputData(act.polydata()) dist.SetRadius(0.2) # how far out to propagate distance calculation dist.SetBounds(-2, 2, -2, 2, -2, 2) dist.SetDimensions(80, 80, 80) dist.Update() # vp.write(dist.GetOutput(), 'stack.tif') fe = vtk.vtkExtractSurface() fe.SetInputConnection(dist.GetOutputPort()) fe.SetRadius(0.2) # this should match the signed distance radius fe.Update() pts = Points(act.coordinates()) vp.show(fe.GetOutput(), pts, Text(__doc__))
subMapper.SetScaleFactor(0.0)
subActor = vtk.vtkActor()
subActor.SetMapper(subMapper)
# Generate signed distance function and contour it
dist = vtk.vtkSignedDistance()
dist.SetInputConnection(norms.GetOutputPort())
dist.SetRadius(0.1) #how far out to propagate distance calculation
dist.SetBounds(-1,1, -1,1, -1,1)
dist.SetDimensions(50,50,50)
# Extract the surface with modified flying edges
#fe = vtk.vtkFlyingEdges3D()
#fe.SetValue(0,0.0)
fe = vtk.vtkExtractSurface()
fe.SetInputConnection(dist.GetOutputPort())
fe.SetRadius(0.1) # this should match the signed distance radius
# Time the execution
timer = vtk.vtkTimerLog()
timer.StartTimer()
fe.Update()
timer.StopTimer()
time = timer.GetElapsedTime()
print("Points processed: {0}".format(NPts))
print(" Time to generate and extract distance function: {0}".format(time))
print(" Resulting bounds: {}".format(fe.GetOutput().GetBounds()))
feMapper = vtk.vtkPolyDataMapper()
feMapper.SetInputConnection(fe.GetOutputPort())