def simulate(self):
""" Runs the particle simulation. Simulates one time step, dt, of the particle motion.
Calculates the force between each pair of particles and updates particles' motion accordingly
"""
# Main simulation loop
for i in range(self.iterations):
for a in self.particles:
if a.fixed: continue
ftot = vector(0,0,0) # total force acting on particle a
for b in self.particles:
if a.negligible and b.negligible or a==b: continue
ab = a.pos - b.pos
ftot += ((K_COULOMB * a.charge * b.charge) / mag2(ab)) * norm(ab)
a.vel += ftot / a.mass * self.dt # update velocity and position of a
a.pos += a.vel * self.dt
a.vtk_actor.pos(a.pos)
if vp:
vp.render(zoom=1.2)
vp.camera.Azimuth(0.1) # rotate camera
def _func(self, pars):
self.params = pars
d2sum, n = 0.0, self.source.N()
srcpts = self.source.polydata().GetPoints()
mpts = self.msource.polydata().GetPoints()
rng = range(0,n, int(n/self.subsample))
for i in rng:
p1 = srcpts.GetPoint(i)
p2 = self.transform(p1)
tp = self.target.closestPoint(p2)
d2sum += mag2(p2-tp)
mpts.SetPoint(i, p2)
d2sum /= len(rng)
if d2sum<self.chi2:
if d2sum<self.chi2*0.99:
print ( 'Emin ->', d2sum )
self.chi2 = d2sum
return d2sum
scals = np.abs(coords[:, 2]) # let the scalar be the z of point itself
fact = 1. / (bins - 1) # conversion factor btw the 2 ranges
vp = Plotter(verbose=0)
vp.ztitle = 'z == scalar value'
cloud = vp.points(coords)
# fill the vtkImageData object
pb = ProgressBar(0, bins, c=4)
for iz in pb.range():
pb.print()
for iy in range(bins):
for ix in range(bins):
pt = vector(ix, iy, iz) * fact
closestPointsIDs = cloud.closestPoint(pt, N=5, returnIds=True)
num, den = 0, 0
for i in closestPointsIDs: # work out RBF manually on N points
invdist = 1 / (mag2(coords[i] - pt) + 1e-06)
num += scals[i] * invdist
den += invdist
img.SetScalarComponentFromFloat(ix, iy, iz, 0, num / den)
#vp.write(img, 'imgcube.tif') # or .vti
# set colors and transparencies along the scalar range
vol = Volume(img, c=['r', 'g', 'b'], alphas=[0.4, 0.8]) #vtkVolume
act = vp.points(coords / fact)
vp.show([vol, act], viewup='z')
# Align 2 shapes and for each vertex of the first draw
# and arrow to the closest point of the second.
# The source transformation is saved in actor.transform
# rigid=True doesn't allow scaling
#
from vtkplotter import Plotter, printc, mag2
from vtkplotter.analysis import align
vp = Plotter(verbose=0, axes=4)
limb = vp.load('data/270.vtk', alpha=0.3)
rim = vp.load('data/270_rim.vtk')
rim.color('r').lineWidth(4)
arim = align(rim, limb, iters=100, rigid=True)
arim.color('g').lineWidth(4)
vp.actors.append(arim)
d = 0
prim = arim.coordinates()
for p in prim:
cpt = limb.closestPoint(p)
vp.arrow(p, cpt, c='g')
d += mag2(p - cpt) # square of residual distance
printc('ave. squared distance =', d / len(prim), c='g')
vp.show()
