def booleanOperation(actor1,
actor2,
operation='plus',
c=None,
alpha=1,
wire=False,
bc=None,
edges=False,
legend=None,
texture=None):
'''Volumetric union, intersection and subtraction of surfaces'''
try:
bf = vtk.vtkBooleanOperationPolyDataFilter()
except AttributeError:
vio.printc('Boolean operation only possible for vtk version >= 8', 'r')
return None
poly1 = vu.polydata(actor1, True)
poly2 = vu.polydata(actor2, True)
if operation.lower() == 'plus':
bf.SetOperationToUnion()
elif operation.lower() == 'intersect':
bf.SetOperationToIntersection()
elif operation.lower() == 'minus':
bf.SetOperationToDifference()
bf.ReorientDifferenceCellsOn()
if vu.vtkMV:
bf.SetInputData(0, poly1)
bf.SetInputData(1, poly2)
else:
bf.SetInputConnection(0, poly1.GetProducerPort())
bf.SetInputConnection(1, poly2.GetProducerPort())
bf.Update()
actor = vu.makeActor(bf.GetOutput(), c, alpha, wire, bc, edges, legend,
texture)
return actor
def removeOutliers(points, radius, c='k', alpha=1, legend=None):
'''
Remove outliers from a cloud of points within radius search
'''
isactor = False
if isinstance(points, vtk.vtkActor):
isactor = True
poly = vu.polydata(points)
else:
src = vtk.vtkPointSource()
src.SetNumberOfPoints(len(points))
src.Update()
vpts = src.GetOutput().GetPoints()
for i, p in enumerate(points):
vpts.SetPoint(i, p)
poly = src.GetOutput()
removal = vtk.vtkRadiusOutlierRemoval()
vu.setInput(removal, poly)
removal.SetRadius(radius)
removal.SetNumberOfNeighbors(5)
removal.GenerateOutliersOff()
removal.Update()
rpoly = removal.GetOutput()
print("# of removed outlier points: ", removal.GetNumberOfPointsRemoved(),
'/', poly.GetNumberOfPoints())
outpts = []
for i in range(rpoly.GetNumberOfPoints()):
outpts.append(list(rpoly.GetPoint(i)))
outpts = np.array(outpts)
if not isactor: return outpts
actor = vs.points(outpts, c=c, alpha=alpha, legend=legend)
return actor # return same obj for concatenation
def decimate(actor, fraction=0.5, N=None, verbose=True, boundaries=True):
'''
Downsample the number of vertices in a mesh.
fraction gives the desired target of reduction.
E.g. fraction=0.1
leaves 10% of the original nr of vertices.
'''
poly = vu.polydata(actor, True)
if N: # N = desired number of points
Np = poly.GetNumberOfPoints()
fraction = float(N) / Np
if fraction >= 1: return actor
decimate = vtk.vtkDecimatePro()
vu.setInput(decimate, poly)
decimate.SetTargetReduction(1. - fraction)
decimate.PreserveTopologyOff()
if boundaries: decimate.BoundaryVertexDeletionOn()
else: decimate.BoundaryVertexDeletionOff()
decimate.Update()
if verbose:
print('Input nr. of pts:', poly.GetNumberOfPoints(), end='')
print(' output:', decimate.GetOutput().GetNumberOfPoints())
mapper = actor.GetMapper()
vu.setInput(mapper, decimate.GetOutput())
mapper.Update()
actor.Modified()
if hasattr(actor, 'poly'): actor.poly = decimate.GetOutput()
return actor # return same obj for concatenation
def subdivide(actor, N=1, method=0, legend=None):
'''
Increase the number of points in actor surface
N = number of subdivisions
method = 0, Loop
method = 1, Linear
method = 2, Adaptive
method = 3, Butterfly
'''
triangles = vtk.vtkTriangleFilter()
vu.setInput(triangles, vu.polydata(actor))
triangles.Update()
originalMesh = triangles.GetOutput()
if method == 0: sdf = vtk.vtkLoopSubdivisionFilter()
elif method == 1: sdf = vtk.vtkLinearSubdivisionFilter()
elif method == 2: sdf = vtk.vtkAdaptiveSubdivisionFilter()
elif method == 3: sdf = vtk.vtkButterflySubdivisionFilter()
else:
vio.printc('Error in subdivide: unknown method.', 'r')
exit(1)
if method != 2: sdf.SetNumberOfSubdivisions(N)
vu.setInput(sdf, originalMesh)
sdf.Update()
out = sdf.GetOutput()
if legend is None and hasattr(actor, 'legend'): legend = actor.legend
sactor = vu.makeActor(out, legend=legend)
sactor.GetProperty().SetOpacity(actor.GetProperty().GetOpacity())
sactor.GetProperty().SetColor(actor.GetProperty().GetColor())
sactor.GetProperty().SetRepresentation(
actor.GetProperty().GetRepresentation())
return sactor
def surfaceIntersection(actor1,
actor2,
tol=1e-06,
lw=3,
c=None,
alpha=1,
legend=None):
'''Intersect 2 surfaces and return a line actor'''
try:
bf = vtk.vtkIntersectionPolyDataFilter()
except AttributeError:
vio.printc('surfaceIntersection only possible for vtk version > 6',
'r')
return None
poly1 = vu.polydata(actor1, True)
poly2 = vu.polydata(actor2, True)
bf.SetInputData(0, poly1)
bf.SetInputData(1, poly2)
bf.Update()
if c is None: c = actor1.GetProperty().GetColor()
actor = vu.makeActor(bf.GetOutput(), c, alpha, 0, legend=legend)
actor.GetProperty().SetLineWidth(lw)
return actor
def align(source, target, iters=100, legend=None):
'''
Return a copy of source actor which is aligned to
target actor through vtkIterativeClosestPointTransform() method.
'''
sprop = source.GetProperty()
source = vu.polydata(source)
target = vu.polydata(target)
icp = vtk.vtkIterativeClosestPointTransform()
icp.SetSource(source)
icp.SetTarget(target)
icp.SetMaximumNumberOfIterations(iters)
icp.StartByMatchingCentroidsOn()
icp.Update()
icpTransformFilter = vtk.vtkTransformPolyDataFilter()
vu.setInput(icpTransformFilter, source)
icpTransformFilter.SetTransform(icp)
icpTransformFilter.Update()
poly = icpTransformFilter.GetOutput()
actor = vu.makeActor(poly, legend=legend)
actor.SetProperty(sprop)
setattr(actor, 'transform', icp.GetLandmarkTransform())
return actor
def intersectWithLine(act, p0, p1):
'''Return a list of points between p0 and p1 intersecting the actor'''
if not hasattr(act, 'linelocator'):
linelocator = vtk.vtkOBBTree()
linelocator.SetDataSet(vu.polydata(act, True))
linelocator.BuildLocator()
setattr(act, 'linelocator', linelocator)
intersectPoints = vtk.vtkPoints()
intersection = [0, 0, 0]
act.linelocator.IntersectWithLine(p0, p1, intersectPoints, None)
pts = []
for i in range(intersectPoints.GetNumberOfPoints()):
intersectPoints.GetPoint(i, intersection)
pts.append(list(intersection))
return pts
def cluster(points, radius, legend=None):
'''
Clustering of points in space.
radius, is the radius of local search.
Individual subsets can be accessed through actor.clusters
'''
if isinstance(points, vtk.vtkActor):
poly = vu.polydata(points)
else:
src = vtk.vtkPointSource()
src.SetNumberOfPoints(len(points))
src.Update()
vpts = src.GetOutput().GetPoints()
for i, p in enumerate(points):
vpts.SetPoint(i, p)
poly = src.GetOutput()
cluster = vtk.vtkEuclideanClusterExtraction()
vu.setInput(cluster, poly)
cluster.SetExtractionModeToAllClusters()
cluster.SetRadius(radius)
cluster.ColorClustersOn()
cluster.Update()
idsarr = cluster.GetOutput().GetPointData().GetArray('ClusterId')
Nc = cluster.GetNumberOfExtractedClusters()
sets = [[] for i in range(Nc)]
for i, p in enumerate(points):
sets[idsarr.GetValue(i)].append(p)
acts = []
for i, aset in enumerate(sets):
acts.append(vs.points(aset, c=i))
actor = vu.makeAssembly(acts, legend=legend)
setattr(actor, 'clusters', sets)
print('Nr. of extracted clusters', Nc)
if Nc > 10: print('First ten:')
for i in range(Nc):
if i > 9:
print('...')
break
print('Cluster #' + str(i) + ', N =', len(sets[i]))
print('Access individual clusters through attribute: actor.cluster')
return actor
def cutPlane(actor, origin=(0, 0, 0), normal=(1, 0, 0), showcut=True):
'''
Takes actor and cuts it with the plane defined by a point
and a normal.
showcut = shows the cut away part as thin wireframe
showline = marks with a thick line the cut
'''
plane = vtk.vtkPlane()
plane.SetOrigin(origin)
plane.SetNormal(normal)
poly = vu.polydata(actor)
clipper = vtk.vtkClipPolyData()
vu.setInput(clipper, poly)
clipper.SetClipFunction(plane)
clipper.GenerateClippedOutputOn()
clipper.SetValue(0.)
clipper.Update()
if hasattr(actor, 'GetProperty'):
alpha = actor.GetProperty().GetOpacity()
c = actor.GetProperty().GetColor()
bf = actor.GetBackfaceProperty()
else:
alpha = 1
c = 'gold'
bf = None
leg = None
if hasattr(actor, 'legend'): leg = actor.legend
clipActor = vu.makeActor(clipper.GetOutput(), c=c, alpha=alpha, legend=leg)
clipActor.SetBackfaceProperty(bf)
acts = [clipActor]
if showcut:
cpoly = clipper.GetClippedOutput()
restActor = vu.makeActor(cpoly, c=c, alpha=0.05, wire=1)
acts.append(restActor)
if len(acts) > 1:
asse = vu.makeAssembly(acts)
return asse
else:
return clipActor
def cutterWidget(obj,
outputname='clipped.vtk',
c=(0.2, 0.2, 1),
alpha=1,
bc=(0.7, 0.8, 1),
legend=None):
'''Pop up a box widget to cut parts of actor. Return largest part.'''
apd = vu.polydata(obj)
planes = vtk.vtkPlanes()
planes.SetBounds(apd.GetBounds())
clipper = vtk.vtkClipPolyData()
vu.setInput(clipper, apd)
clipper.SetClipFunction(planes)
clipper.InsideOutOn()
clipper.GenerateClippedOutputOn()
# check if color string contains a float, in this case ignore alpha
al = vc.getAlpha(c)
if al: alpha = al
act0Mapper = vtk.vtkPolyDataMapper() # the part which stays
act0Mapper.SetInputConnection(clipper.GetOutputPort())
act0 = vtk.vtkActor()
act0.SetMapper(act0Mapper)
act0.GetProperty().SetColor(vc.getColor(c))
act0.GetProperty().SetOpacity(alpha)
backProp = vtk.vtkProperty()
backProp.SetDiffuseColor(vc.getColor(bc))
backProp.SetOpacity(alpha)
act0.SetBackfaceProperty(backProp)
#act0 = makeActor(clipper.GetOutputPort())
act0.GetProperty().SetInterpolationToFlat()
vu.assignPhysicsMethods(act0)
vu.assignConvenienceMethods(act0, legend)
act1Mapper = vtk.vtkPolyDataMapper() # the part which is cut away
act1Mapper.SetInputConnection(clipper.GetClippedOutputPort())
act1 = vtk.vtkActor()
act1.SetMapper(act1Mapper)
act1.GetProperty().SetColor(vc.getColor(c))
act1.GetProperty().SetOpacity(alpha / 10.)
act1.GetProperty().SetRepresentationToWireframe()
act1.VisibilityOn()
ren = vtk.vtkRenderer()
ren.SetBackground(1, 1, 1)
ren.AddActor(act0)
ren.AddActor(act1)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(600, 700)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
istyl = vtk.vtkInteractorStyleSwitch()
istyl.SetCurrentStyleToTrackballCamera()
iren.SetInteractorStyle(istyl)
def SelectPolygons(vobj, event):
vobj.GetPlanes(planes)
boxWidget = vtk.vtkBoxWidget()
boxWidget.OutlineCursorWiresOn()
boxWidget.GetSelectedOutlineProperty().SetColor(1, 0, 1)
boxWidget.GetOutlineProperty().SetColor(0.1, 0.1, 0.1)
boxWidget.GetOutlineProperty().SetOpacity(0.8)
boxWidget.SetPlaceFactor(1.05)
boxWidget.SetInteractor(iren)
vu.setInput(boxWidget, apd)
boxWidget.PlaceWidget()
boxWidget.AddObserver("InteractionEvent", SelectPolygons)
boxWidget.On()
vio.printc('\nCutterWidget:\n Move handles to cut parts of the actor', 'm')
vio.printc(' Press q to continue, Escape to exit', 'm')
vio.printc((" Press X to save file to", outputname), 'm')
def cwkeypress(obj, event):
key = obj.GetKeySym()
if key == "q" or key == "space" or key == "Return":
iren.ExitCallback()
elif key == "X":
confilter = vtk.vtkPolyDataConnectivityFilter()
vu.setInput(confilter, clipper.GetOutput())
confilter.SetExtractionModeToLargestRegion()
confilter.Update()
cpd = vtk.vtkCleanPolyData()
vu.setInput(cpd, confilter.GetOutput())
cpd.Update()
vio.write(cpd.GetOutput(), outputname)
elif key == "Escape":
exit(0)
iren.Initialize()
iren.AddObserver("KeyPressEvent", cwkeypress)
iren.Start()
boxWidget.Off()
return act0
def smoothMLS(actor, f=0.2, decimate=1, recursive=0, showNPlanes=0):
'''
Smooth actor or points with a Moving Least Squares variant.
The list actor.variances contain the residue calculated for each point.
Input actor's polydata is modified.
f, smoothing factor - typical range s [0,2]
decimate, decimation factor (an integer number)
recursive, move points while algorithm proceedes
showNPlanes, build an actor showing the fitting plane for N random points
'''
coords = vu.coordinates(actor)
ncoords = len(coords)
Ncp = int(ncoords * f / 100)
nshow = int(ncoords / decimate)
if showNPlanes: ndiv = int(nshow / showNPlanes * decimate)
if Ncp < 5:
vio.printc('Please choose a higher fraction than' + str(f), 1)
Ncp = 5
print('smoothMLS: Searching #neighbours, #pt:', Ncp, ncoords)
poly = vu.polydata(actor, True)
vpts = poly.GetPoints()
locator = vtk.vtkPointLocator()
locator.SetDataSet(poly)
locator.BuildLocator()
vtklist = vtk.vtkIdList()
variances, newsurf, acts = [], [], []
pb = vio.ProgressBar(0, ncoords)
for i, p in enumerate(coords):
pb.print('smoothing...')
if i % decimate: continue
locator.FindClosestNPoints(Ncp, p, vtklist)
points = []
for j in range(vtklist.GetNumberOfIds()):
trgp = [0, 0, 0]
vpts.GetPoint(vtklist.GetId(j), trgp)
points.append(trgp)
if len(points) < 5: continue
points = np.array(points)
pointsmean = points.mean(axis=0) # plane center
uu, dd, vv = np.linalg.svd(points - pointsmean)
a, b, c = np.cross(vv[0], vv[1]) # normal
d, e, f = pointsmean # plane center
x, y, z = p
t = (a * d - a * x + b * e - b * y + c * f - c * z) #/(a*a+b*b+c*c)
newp = [x + t * a, y + t * b, z + t * c]
variances.append(dd[2])
newsurf.append(newp)
if recursive: vpts.SetPoint(i, newp)
if showNPlanes and not i % ndiv:
plane = fitPlane(points, alpha=0.3) # fitting plane
iapts = vs.points(points) # blue points
acts += [plane, iapts]
if decimate == 1 and not recursive:
for i in range(ncoords):
vpts.SetPoint(i, newsurf[i])
setattr(actor, 'variances', np.array(variances))
if showNPlanes:
apts = vs.points(newsurf, c='r 0.6', r=2)
ass = vu.makeAssembly([apts] + acts)
return ass #NB: a demo actor is returned
return actor #NB: original actor is modified
def fxy(z='sin(3*x)*log(x-y)/3',
x=[0, 3],
y=[0, 3],
zlimits=[None, None],
showNan=True,
zlevels=10,
wire=False,
c='b',
bc='aqua',
alpha=1,
legend=True,
texture=None,
res=100):
'''
Build a surface representing the 3D function specified as a string
or as a reference to an external function.
Red points indicate where the function does not exist (showNan).
zlevels will draw the specified number of z-levels contour lines.
Examples:
vp = plotter.vtkPlotter()
vp.fxy('sin(3*x)*log(x-y)/3')
or
def z(x,y): return math.sin(x*y)
vp.fxy(z) # or equivalently:
vp.fxy(lambda x,y: math.sin(x*y))
'''
if isinstance(z, str):
try:
z = z.replace('math.', '').replace('np.', '')
namespace = locals()
code = "from math import*\ndef zfunc(x,y): return " + z
exec(code, namespace)
z = namespace['zfunc']
except:
vio.printc('Syntax Error in fxy()', 1)
return None
ps = vtk.vtkPlaneSource()
ps.SetResolution(res, res)
ps.SetNormal([0, 0, 1])
ps.Update()
poly = ps.GetOutput()
dx = x[1] - x[0]
dy = y[1] - y[0]
todel, nans = [], []
if zlevels:
tf = vtk.vtkTriangleFilter()
vu.setInput(tf, poly)
tf.Update()
poly = tf.GetOutput()
for i in range(poly.GetNumberOfPoints()):
px, py, _ = poly.GetPoint(i)
xv = (px + .5) * dx + x[0]
yv = (py + .5) * dy + y[0]
try:
zv = z(xv, yv)
poly.GetPoints().SetPoint(i, [xv, yv, zv])
except:
todel.append(i)
nans.append([xv, yv, 0])
if len(todel):
cellIds = vtk.vtkIdList()
poly.BuildLinks()
for i in todel:
poly.GetPointCells(i, cellIds)
for j in range(cellIds.GetNumberOfIds()):
poly.DeleteCell(cellIds.GetId(j)) #flag cell
poly.RemoveDeletedCells()
cl = vtk.vtkCleanPolyData()
vu.setInput(cl, poly)
cl.Update()
poly = cl.GetOutput()
if not poly.GetNumberOfPoints():
vio.printc('Function is not real in the domain', 1)
return vtk.vtkActor()
if zlimits[0]:
a = cutPlane(poly, (0, 0, zlimits[0]), (0, 0, 1), False)
poly = vu.polydata(a)
if zlimits[1]:
a = cutPlane(poly, (0, 0, zlimits[1]), (0, 0, -1), False)
poly = vu.polydata(a)
if c is None:
elev = vtk.vtkElevationFilter()
vu.setInput(elev, poly)
elev.Update()
poly = elev.GetOutput()
actor = vu.makeActor(poly,
c=c,
bc=bc,
alpha=alpha,
wire=wire,
legend=legend,
texture=texture)
acts = [actor]
if zlevels:
elevation = vtk.vtkElevationFilter()
vu.setInput(elevation, poly)
bounds = poly.GetBounds()
elevation.SetLowPoint(0, 0, bounds[4])
elevation.SetHighPoint(0, 0, bounds[5])
elevation.Update()
bcf = vtk.vtkBandedPolyDataContourFilter()
vu.setInput(bcf, elevation.GetOutput())
bcf.SetScalarModeToValue()
bcf.GenerateContourEdgesOn()
bcf.GenerateValues(zlevels, elevation.GetScalarRange())
bcf.Update()
zpoly = bcf.GetContourEdgesOutput()
zbandsact = vu.makeActor(zpoly, c='k', alpha=alpha)
zbandsact.GetProperty().SetLineWidth(1.5)
acts.append(zbandsact)
if showNan and len(todel):
bb = actor.GetBounds()
zm = (bb[4] + bb[5]) / 2
nans = np.array(nans) + [0, 0, zm]
nansact = vs.points(nans, c='red', alpha=alpha / 2)
acts.append(nansact)
if len(acts) > 1:
asse = vu.makeAssembly(acts)
return asse
else:
return actor