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 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 pca(points, pvalue=.95, c='c', alpha=0.5, pcaAxes=False, legend=None):
'''
Show the oriented PCA ellipsoid that contains fraction pvalue of points.
axes = True, show the 3 PCA semi axes
Extra info is stored in actor.sphericity, actor.va, actor.vb, actor.vc
(sphericity = 1 for a perfect sphere)
'''
try:
from scipy.stats import f
except:
vio.printc("Error in ellipsoid(): scipy not installed. Skip.", 1)
return None
if len(points) == 0: return None
P = np.array(points, ndmin=2, dtype=float)
cov = np.cov(P, rowvar=0) # covariance matrix
U, s, R = np.linalg.svd(cov) # singular value decomposition
p, n = s.size, P.shape[0]
fppf = f.ppf(pvalue, p, n - p) * (n - 1) * p * (n + 1) / n / (
n - p) # f % point function
ua, ub, uc = np.sqrt(s * fppf) * 2 # semi-axes (largest first)
center = np.mean(P, axis=0) # centroid of the hyperellipsoid
sphericity = (((ua - ub) / (ua + ub))**2 + ((ua - uc) / (ua + uc))**2 +
((ub - uc) / (ub + uc))**2) / 3. * 4.
elliSource = vtk.vtkSphereSource()
elliSource.SetThetaResolution(48)
elliSource.SetPhiResolution(48)
matri = vtk.vtkMatrix4x4()
matri.DeepCopy(
(R[0][0] * ua, R[1][0] * ub, R[2][0] * uc, center[0], R[0][1] * ua,
R[1][1] * ub, R[2][1] * uc, center[1], R[0][2] * ua, R[1][2] * ub,
R[2][2] * uc, center[2], 0, 0, 0, 1))
vtra = vtk.vtkTransform()
vtra.SetMatrix(matri)
ftra = vtk.vtkTransformFilter()
ftra.SetTransform(vtra)
ftra.SetInputConnection(elliSource.GetOutputPort())
ftra.Update()
actor_elli = vu.makeActor(ftra.GetOutput(), c, alpha, legend=legend)
actor_elli.GetProperty().BackfaceCullingOn()
actor_elli.GetProperty().SetInterpolationToPhong()
if pcaAxes:
axs = []
for ax in ([1, 0, 0], [0, 1, 0], [0, 0, 1]):
l = vtk.vtkLineSource()
l.SetPoint1([0, 0, 0])
l.SetPoint2(ax)
l.Update()
t = vtk.vtkTransformFilter()
t.SetTransform(vtra)
vu.setInput(t, l.GetOutput())
t.Update()
axs.append(vu.makeActor(t.GetOutput(), c, alpha))
finact = vu.makeAssembly([actor_elli] + axs, legend=legend)
else:
finact = actor_elli
setattr(finact, 'sphericity', sphericity)
setattr(finact, 'va', ua)
setattr(finact, 'vb', ub)
setattr(finact, 'vc', uc)
return finact
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 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:
print('Recalculating normals for', N, 'points')
normals = vtk.vtkPCANormalEstimation()
vu.setInput(normals, polyData)
normals.SetSampleSize(int(N / 50))
normals.SetNormalOrientationToGraphTraversal()
distance.SetInputConnection(normals.GetOutputPort())
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)
def arrow(startPoint,
endPoint,
c,
s=None,
alpha=1,
legend=None,
texture=None,
res=12,
rwSize=None):
'''Build a 3D arrow from startPoint to endPoint of section size s,
expressed as the fraction of the window size.
If s=None the arrow is scaled proportionally to its length.'''
axis = np.array(endPoint) - np.array(startPoint)
length = np.linalg.norm(axis)
if not length: return None
axis = axis / length
theta = np.arccos(axis[2])
phi = np.arctan2(axis[1], axis[0])
arr = vtk.vtkArrowSource()
arr.SetShaftResolution(res)
arr.SetTipResolution(res)
if s:
sz = 0.02
arr.SetTipRadius(sz)
arr.SetShaftRadius(sz / 1.75)
arr.SetTipLength(sz * 15)
arr.Update()
t = vtk.vtkTransform()
t.RotateZ(phi * 57.3)
t.RotateY(theta * 57.3)
t.RotateY(-90) #put it along Z
if s:
w, h = rwSize
sz = (w + h) / 2 * s
t.Scale(length, sz, sz)
else:
t.Scale(length, length, length)
tf = vtk.vtkTransformPolyDataFilter()
vu.setInput(tf, arr.GetOutput())
tf.SetTransform(t)
tf.Update()
actor = vu.makeActor(tf.GetOutput(),
c,
alpha,
legend=legend,
texture=texture)
actor.GetProperty().SetInterpolationToPhong()
actor.SetPosition(startPoint)
actor.DragableOff()
actor.PickableOff()
setattr(actor, 'base', np.array(startPoint))
setattr(actor, 'top', np.array(endPoint))
return actor
def line(p0,
p1=None,
lw=1,
tube=False,
dotted=False,
c='r',
alpha=1.,
legend=None):
'''Build the line segment between points p0 and p1.
if p0 is a list of points returns the line connecting them.
if tube=True, lines are rendered as tubes of radius lw
'''
#detect if user is passing a list of points:
if vu.isSequence(p0[0]):
ppoints = vtk.vtkPoints() # Generate the polyline
poly = vtk.vtkPolyData()
for i in range(len(p0)):
p = p0[i]
ppoints.InsertPoint(i, p[0], p[1], p[2])
lines = vtk.vtkCellArray() # Create the polyline.
lines.InsertNextCell(len(p0))
for i in range(len(p0)):
lines.InsertCellPoint(i)
poly.SetPoints(ppoints)
poly.SetLines(lines)
else: # or just 2 points to link
lineSource = vtk.vtkLineSource()
lineSource.SetPoint1(p0)
lineSource.SetPoint2(p1)
lineSource.Update()
poly = lineSource.GetOutput()
if tube:
tuf = vtk.vtkTubeFilter()
tuf.SetNumberOfSides(12)
#tuf.CappingOn()
vu.setInput(tuf, poly)
tuf.SetRadius(lw)
tuf.Update()
poly = tuf.GetOutput()
actor = vu.makeActor(poly, c, alpha, legend=legend)
actor.GetProperty().SetInterpolationToPhong()
else:
actor = vu.makeActor(poly, c, alpha, legend=legend)
actor.GetProperty().SetLineWidth(lw)
if dotted:
actor.GetProperty().SetLineStipplePattern(0xf0f0)
actor.GetProperty().SetLineStippleRepeatFactor(1)
setattr(actor, 'base', np.array(p0))
setattr(actor, 'top', np.array(p1))
return actor
def polygon(pos=[0, 0, 0],
normal=[0, 0, 1],
nsides=6,
r=1,
c='coral',
bc='darkgreen',
lw=1,
alpha=1,
legend=None,
texture=None,
followcam=False,
camera=None):
'''Build a 2D polygon of nsides of radius r oriented as normal
If followcam=True the polygon will always reorient itself to current camera.
'''
ps = vtk.vtkRegularPolygonSource()
ps.SetNumberOfSides(nsides)
ps.SetRadius(r)
ps.SetNormal(-np.array(normal))
ps.Update()
tf = vtk.vtkTriangleFilter()
vu.setInput(tf, ps.GetOutputPort())
tf.Update()
mapper = vtk.vtkPolyDataMapper()
vu.setInput(mapper, tf.GetOutputPort())
if followcam: #follow cam
actor = vtk.vtkFollower()
actor.SetCamera(camera)
if not camera:
vu.printc('Warning: vtkCamera does not yet exist for polygon', 5)
else:
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(vc.getColor(c))
# check if color string contains a float, in this case ignore alpha
al = vc.getAlpha(c)
if al: alpha = al
actor.GetProperty().SetOpacity(alpha)
actor.GetProperty().SetLineWidth(lw)
actor.GetProperty().SetInterpolationToFlat()
if bc: # defines a specific color for the backface
backProp = vtk.vtkProperty()
backProp.SetDiffuseColor(vc.getColor(bc))
backProp.SetOpacity(alpha)
actor.SetBackfaceProperty(backProp)
if texture: vu.assignTexture(actor, texture)
vu.assignPhysicsMethods(actor)
vu.assignConvenienceMethods(actor, legend)
actor.SetPosition(pos)
return actor
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)
def hyperboloid(pos=[0, 0, 0],
a2=1,
value=0.5,
height=1,
axis=[0, 0, 1],
c='magenta',
alpha=1,
legend=None,
texture=None,
res=50):
'''
Build a hyperboloid of specified aperture a2 and height, centered at pos.
'''
q = vtk.vtkQuadric()
q.SetCoefficients(2, 2, -1 / a2, 0, 0, 0, 0, 0, 0, 0)
#F(x,y,z) = a0*x^2 + a1*y^2 + a2*z^2
# + a3*x*y + a4*y*z + a5*x*z
# + a6*x + a7*y + a8*z +a9
sample = vtk.vtkSampleFunction()
sample.SetSampleDimensions(res, res, res)
sample.SetImplicitFunction(q)
contours = vtk.vtkContourFilter()
contours.SetInputConnection(sample.GetOutputPort())
contours.GenerateValues(1, value, value)
contours.Update()
axis = np.array(axis) / np.linalg.norm(axis)
theta = np.arccos(axis[2])
phi = np.arctan2(axis[1], axis[0])
t = vtk.vtkTransform()
t.PostMultiply()
t.RotateY(theta * 57.3)
t.RotateZ(phi * 57.3)
t.Scale(1, 1, height)
tf = vtk.vtkTransformPolyDataFilter()
vu.setInput(tf, contours.GetOutput())
tf.SetTransform(t)
tf.Update()
pd = tf.GetOutput()
actor = vu.makeActor(pd, c=c, alpha=alpha, legend=legend, texture=texture)
actor.GetProperty().SetInterpolationToPhong()
actor.GetMapper().ScalarVisibilityOff()
actor.SetPosition(pos)
return actor
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 helix(startPoint=[0, 0, 0],
endPoint=[1, 1, 1],
coils=20,
r=None,
thickness=None,
c='grey',
alpha=1,
legend=None,
texture=None):
'''
Build a spring actor of specified nr of coils between startPoint and endPoint
'''
diff = endPoint - np.array(startPoint)
length = np.linalg.norm(diff)
if not length: return None
if not r: r = length / 20
trange = np.linspace(0, length, num=50 * coils)
om = 6.283 * (coils - .5) / length
pts = [[r * np.cos(om * t), r * np.sin(om * t), t] for t in trange]
pts = [[0, 0, 0]] + pts + [[0, 0, length]]
diff = diff / length
theta = np.arccos(diff[2])
phi = np.arctan2(diff[1], diff[0])
sp = vu.makePolyData(pts)
t = vtk.vtkTransform()
t.RotateZ(phi * 57.3)
t.RotateY(theta * 57.3)
tf = vtk.vtkTransformPolyDataFilter()
vu.setInput(tf, sp)
tf.SetTransform(t)
tf.Update()
tuf = vtk.vtkTubeFilter()
tuf.SetNumberOfSides(12)
tuf.CappingOn()
vu.setInput(tuf, tf.GetOutput())
if not thickness: thickness = r / 10
tuf.SetRadius(thickness)
tuf.Update()
poly = tuf.GetOutput()
actor = vu.makeActor(poly, c, alpha, legend=legend, texture=texture)
actor.GetProperty().SetInterpolationToPhong()
actor.SetPosition(startPoint)
setattr(actor, 'base', np.array(startPoint))
setattr(actor, 'top', np.array(endPoint))
return actor
def ring(pos=[0, 0, 0],
r=1,
thickness=0.1,
axis=[0, 0, 1],
c='khaki',
alpha=1,
wire=False,
legend=None,
texture=None,
res=30):
'''
Build a torus of specified outer radius r internal radius thickness, centered at pos.
'''
rs = vtk.vtkParametricTorus()
rs.SetRingRadius(r)
rs.SetCrossSectionRadius(thickness)
pfs = vtk.vtkParametricFunctionSource()
pfs.SetParametricFunction(rs)
pfs.SetUResolution(res * 3)
pfs.SetVResolution(res)
pfs.Update()
nax = np.linalg.norm(axis)
if nax: axis = np.array(axis) / nax
theta = np.arccos(axis[2])
phi = np.arctan2(axis[1], axis[0])
t = vtk.vtkTransform()
t.PostMultiply()
t.RotateY(theta * 57.3)
t.RotateZ(phi * 57.3)
tf = vtk.vtkTransformPolyDataFilter()
vu.setInput(tf, pfs.GetOutput())
tf.SetTransform(t)
tf.Update()
pd = tf.GetOutput()
actor = vu.makeActor(pd,
c=c,
alpha=alpha,
wire=wire,
legend=legend,
texture=texture)
actor.GetProperty().SetInterpolationToPhong()
actor.SetPosition(pos)
return actor
def ellipsoid(pos=[0, 0, 0],
axis1=[1, 0, 0],
axis2=[0, 2, 0],
axis3=[0, 0, 3],
c='c',
alpha=1,
legend=None,
texture=None,
res=24):
"""
Build a 3D ellipsoid centered at position pos.
Axis1 and axis2 are only used to define sizes and one azimuth angle
"""
elliSource = vtk.vtkSphereSource()
elliSource.SetThetaResolution(res)
elliSource.SetPhiResolution(res)
elliSource.Update()
l1 = np.linalg.norm(axis1)
l2 = np.linalg.norm(axis2)
l3 = np.linalg.norm(axis3)
axis1 = np.array(axis1) / l1
axis2 = np.array(axis2) / l2
axis3 = np.array(axis3) / l3
angle = np.arcsin(np.dot(axis1, axis2))
theta = np.arccos(axis3[2])
phi = np.arctan2(axis3[1], axis3[0])
t = vtk.vtkTransform()
t.PostMultiply()
t.Scale(l1, l2, l3)
t.RotateX(angle * 57.3)
t.RotateY(theta * 57.3)
t.RotateZ(phi * 57.3)
tf = vtk.vtkTransformPolyDataFilter()
vu.setInput(tf, elliSource.GetOutput())
tf.SetTransform(t)
tf.Update()
pd = tf.GetOutput()
actor = vu.makeActor(pd, c=c, alpha=alpha, legend=legend, texture=texture)
actor.GetProperty().BackfaceCullingOn()
actor.GetProperty().SetInterpolationToPhong()
actor.SetPosition(pos)
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 disc(pos=[0, 0, 0],
normal=[0, 0, 1],
r1=0.5,
r2=1,
c='coral',
bc='darkgreen',
lw=1,
alpha=1,
legend=None,
texture=None,
res=12):
'''Build a 2D disc of internal radius r1 and outer radius r2,
oriented perpendicular to normal'''
ps = vtk.vtkDiskSource()
ps.SetInnerRadius(r1)
ps.SetOuterRadius(r2)
ps.SetRadialResolution(res)
ps.SetCircumferentialResolution(res * 4)
ps.Update()
tr = vtk.vtkTriangleFilter()
vu.setInput(tr, ps.GetOutputPort())
tr.Update()
axis = np.array(normal) / np.linalg.norm(normal)
theta = np.arccos(axis[2])
phi = np.arctan2(axis[1], axis[0])
t = vtk.vtkTransform()
t.PostMultiply()
t.RotateY(theta * 57.3)
t.RotateZ(phi * 57.3)
tf = vtk.vtkTransformPolyDataFilter()
vu.setInput(tf, tr.GetOutput())
tf.SetTransform(t)
tf.Update()
pd = tf.GetOutput()
mapper = vtk.vtkPolyDataMapper()
vu.setInput(mapper, pd)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(vc.getColor(c))
# check if color string contains a float, in this case ignore alpha
al = vc.getAlpha(c)
if al: alpha = al
actor.GetProperty().SetOpacity(alpha)
actor.GetProperty().SetLineWidth(lw)
actor.GetProperty().SetInterpolationToFlat()
if bc: # defines a specific color for the backface
backProp = vtk.vtkProperty()
backProp.SetDiffuseColor(vc.getColor(bc))
backProp.SetOpacity(alpha)
actor.SetBackfaceProperty(backProp)
if texture: vu.assignTexture(actor, texture)
vu.assignPhysicsMethods(actor)
vu.assignConvenienceMethods(actor, legend)
actor.SetPosition(pos)
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 _colorPoints(plist, cols, r, alpha, legend):
if len(plist) > len(cols):
vu.printc(("Mismatch in colorPoints()", len(plist), len(cols)), 1)
exit()
if len(plist) != len(cols):
vu.printc(
("Warning: mismatch in colorPoints()", len(plist), len(cols)))
src = vtk.vtkPointSource()
src.SetNumberOfPoints(len(plist))
src.Update()
vertexFilter = vtk.vtkVertexGlyphFilter()
vu.setInput(vertexFilter, src.GetOutput())
vertexFilter.Update()
pd = vertexFilter.GetOutput()
ucols = vtk.vtkUnsignedCharArray()
ucols.SetNumberOfComponents(3)
ucols.SetName("RGB")
for i, p in enumerate(plist):
pd.GetPoints().SetPoint(i, p)
c = np.array(vc.getColor(cols[i])) * 255
if vu.vtkMV:
ucols.InsertNextTuple3(c[0], c[1], c[2])
else:
ucols.InsertNextTupleValue(c)
pd.GetPointData().SetScalars(ucols)
mapper = vtk.vtkPolyDataMapper()
vu.setInput(mapper, pd)
mapper.ScalarVisibilityOn()
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetInterpolationToFlat()
# check if color string contains a float, in this case ignore alpha
al = vc.getAlpha(c)
if al: alpha = al
actor.GetProperty().SetOpacity(alpha)
actor.GetProperty().SetPointSize(r)
return actor
def delaunay2D(plist,
tol=None,
c='gold',
alpha=0.5,
wire=False,
bc=None,
edges=False,
legend=None,
texture=None):
'''
Create a mesh from points in the XY plane.
'''
src = vtk.vtkPointSource()
src.SetNumberOfPoints(len(plist))
src.Update()
pd = src.GetOutput()
for i, p in enumerate(plist):
pd.GetPoints().SetPoint(i, p)
delny = vtk.vtkDelaunay2D()
vu.setInput(delny, pd)
if tol: delny.SetTolerance(tol)
delny.Update()
return vu.makeActor(delny.GetOutput(), c, alpha, wire, bc, edges, legend,
texture)
def box(pos=[0, 0, 0],
length=1,
width=2,
height=3,
normal=(0, 0, 1),
c='g',
alpha=1,
wire=False,
legend=None,
texture=None):
'''Build a box of dimensions x=length, y=width and z=height
oriented along vector normal'''
src = vtk.vtkCubeSource()
src.SetXLength(length)
src.SetYLength(width)
src.SetZLength(height)
src.Update()
poly = src.GetOutput()
axis = np.array(normal) / np.linalg.norm(normal)
theta = np.arccos(axis[2])
phi = np.arctan2(axis[1], axis[0])
t = vtk.vtkTransform()
t.PostMultiply()
t.RotateY(theta * 57.3)
t.RotateZ(phi * 57.3)
tf = vtk.vtkTransformPolyDataFilter()
vu.setInput(tf, poly)
tf.SetTransform(t)
tf.Update()
pd = tf.GetOutput()
actor = vu.makeActor(pd, c, alpha, wire, legend=legend, texture=texture)
actor.SetPosition(pos)
return actor
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
def spheres(centers,
r=1,
c='r',
alpha=1,
wire=False,
legend=None,
texture=None,
res=8):
'''
Build a (possibly large) set of spheres at centers of radius r.
Either c or r can be a list of RGB colors or radii.
'''
cisseq = False
if vu.isSequence(c): cisseq = True
if cisseq:
if len(centers) > len(c):
vu.printc(("Mismatch in spheres() colors", len(centers), len(c)),
1)
exit()
if len(centers) != len(c):
vu.printc(("Warning: mismatch in spheres() colors", len(centers),
len(c)))
risseq = False
if vu.isSequence(r): risseq = True
if risseq:
if len(centers) > len(r):
vu.printc(("Mismatch in spheres() radius", len(centers), len(r)),
1)
exit()
if len(centers) != len(r):
vu.printc(("Warning: mismatch in spheres() radius", len(centers),
len(r)))
if cisseq and risseq:
vu.printc("Limitation: c and r cannot be both sequences.", 1)
exit()
src = vtk.vtkSphereSource()
if not risseq: src.SetRadius(r)
src.SetPhiResolution(res)
src.SetThetaResolution(res)
src.Update()
glyph = vtk.vtkGlyph3D()
glyph.SetSourceConnection(src.GetOutputPort())
psrc = vtk.vtkPointSource()
psrc.SetNumberOfPoints(len(centers))
psrc.Update()
pd = psrc.GetOutput()
vpts = pd.GetPoints()
if cisseq:
glyph.SetColorModeToColorByScalar()
ucols = vtk.vtkUnsignedCharArray()
ucols.SetNumberOfComponents(3)
ucols.SetName("colors")
for i, p in enumerate(centers):
vpts.SetPoint(i, p)
cc = np.array(vc.getColor(c[i])) * 255
if vu.vtkMV:
ucols.InsertNextTuple3(cc[0], cc[1], cc[2])
else:
ucols.InsertNextTupleValue(cc)
pd.GetPointData().SetScalars(ucols)
glyph.ScalingOff()
elif risseq:
glyph.SetScaleModeToScaleByScalar()
urads = vtk.vtkFloatArray()
urads.SetName("scales")
for i, p in enumerate(centers):
vpts.SetPoint(i, p)
urads.InsertNextValue(r[i])
pd.GetPointData().SetScalars(urads)
else:
for i, p in enumerate(centers):
vpts.SetPoint(i, p)
vu.setInput(glyph, pd)
glyph.Update()
mapper = vtk.vtkPolyDataMapper()
vu.setInput(mapper, glyph.GetOutput())
if cisseq: mapper.ScalarVisibilityOn()
else: mapper.ScalarVisibilityOff()
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetInterpolationToPhong()
# check if color string contains a float, in this case ignore alpha
al = vc.getAlpha(c)
if al: alpha = al
actor.GetProperty().SetOpacity(alpha)
if not cisseq:
if texture is not None:
vu.assignTexture(actor, texture)
mapper.ScalarVisibilityOff()
else:
actor.GetProperty().SetColor(vc.getColor(c))
vu.assignConvenienceMethods(actor, legend)
return actor
def cylinder(pos=[0, 0, 0],
r=1,
height=1,
axis=[0, 0, 1],
c='teal',
wire=0,
alpha=1,
edges=False,
legend=None,
texture=None,
res=24):
'''
Build a cylinder of specified height and radius r, centered at pos.
If pos is a list of 2 points, e.g. pos=[v1,v2], build a cylinder with base
centered at v1 and top at v2.
'''
if vu.isSequence(pos[0]): # assume user is passing pos=[base, top]
base = np.array(pos[0])
top = np.array(pos[1])
pos = (base + top) / 2
height = np.linalg.norm(top - base)
axis = top - base
axis = vu.norm(axis)
else:
axis = vu.norm(axis)
base = pos - axis * height / 2
top = pos + axis * height / 2
cyl = vtk.vtkCylinderSource()
cyl.SetResolution(res)
cyl.SetRadius(r)
cyl.SetHeight(height)
cyl.Update()
theta = np.arccos(axis[2])
phi = np.arctan2(axis[1], axis[0])
t = vtk.vtkTransform()
t.PostMultiply()
t.RotateX(90) #put it along Z
t.RotateY(theta * 57.3)
t.RotateZ(phi * 57.3)
tf = vtk.vtkTransformPolyDataFilter()
vu.setInput(tf, cyl.GetOutput())
tf.SetTransform(t)
tf.Update()
pd = tf.GetOutput()
actor = vu.makeActor(pd,
c,
alpha,
wire,
edges=edges,
legend=legend,
texture=texture)
actor.GetProperty().SetInterpolationToPhong()
actor.SetPosition(pos)
setattr(actor, 'base', base)
setattr(actor, 'top', top)
return actor
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
