vp.actors = [] # clean up the list of actors
for colony in colonies:
newcells = []
for cell in colony.cells:
if cell.dieAt(t): continue
if cell.divideAt(t):
newc = cell.split() # make daughter cell
vp.add(line(cell.pos, newc.pos, c='k', lw=3, alpha=.5))
newcells.append(newc)
newcells.append(cell)
colony.cells = newcells
pts = [c.pos for c in newcells] # draw all points at once
vp.points(pts, c=colony.color, r= 5, alpha=.80) # nucleus
vp.points(pts, c=colony.color, r=15, alpha=.05) # halo
msg += str(len(colony.cells)) + ','
pb.print(msg+str(int(t)))
vp.show(resetcam=0)
# draw the oriented ellipsoid that contains 50% of the cells
for colony in colonies:
pts = [c.pos for c in colony.cells]
a = pcaEllipsoid(pts, pvalue=0.5, c=colony.color, pcaAxes=0, alpha=.3,
legend='1/rate='+str(colony.cells[0].tdiv)+'h')
vp.add(a)
vp.show(resetcam=0, interactive=1)
'''
Draw the PCA (Principal Component Analysis) ellipsoid that contains
50% of a cloud of Points, then check if points are inside the surface.
Extra info is stored in actor.info['sphericity'], 'va', 'vb', 'vc'.
'''
from vtkplotter import Plotter, pcaEllipsoid, Points, Text
import numpy as np
vp = Plotter(verbose=0, axes=4)
pts = np.random.randn(500, 3) # random gaussian point cloud
act = pcaEllipsoid(pts, pvalue=0.5, pcaAxes=1)
ipts = act.getActor(0).insidePoints(pts) # act is a vtkAssembly
opts = act.getActor(0).insidePoints(pts, invert=True)
vp.add(Points(ipts, c='g'))
vp.add(Points(opts, c='r'))
print('inside points #', len(ipts))
print('outside points #', len(opts))
print('sphericity :', act.info['sphericity'])
vp.add([act, Text(__doc__)])
vp.show()
"""Draw the PCA (Principal Component Analysis) ellipsoid that contains
50% of a cloud of Points, then check if points are inside the surface.
Extra info cab be retrieved with:
mesh.asphericity()
mesh.asphericity_error()
"""
from vtkplotter import Plotter, pcaEllipsoid, Points, Text2D
import numpy as np
vp = Plotter(axes=1)
pts = np.random.randn(500, 3) * [3, 2, 1] # random gaussian point cloud
elli = pcaEllipsoid(pts, pvalue=0.5)
ipts = elli.insidePoints(pts) # elli is a vtkAssembly
opts = elli.insidePoints(pts, invert=True)
vp += Points(ipts, c="g")
vp += Points(opts, c="r")
vp += [elli, Text2D(__doc__)]
print("inside points #", len(ipts))
print("outside points #", len(opts))
print("asphericity:", elli.asphericity(), '+-', elli.asphericity_error())
print("axis 1 size:", elli.va)
print("axis 2 size:", elli.vb)
print("axis 3 size:", elli.vc)
vp.show()