# increase resolution
for p in plant.getOrganRandomParameter(pb.root):
p.dx = 0.2
# Initialize
plant.initialize()
dt = 0.1
N = 400
min_ = np.array([-20, -20, -50])
max_ = np.array([20, 20, 30.])
# test = plant.getOrgans(pb.leaf)
# print("test")
anim = vp.AnimateRoots(plant)
anim.min = min_
anim.max = max_
anim.res = [1, 1, 1]
anim.file = "results/example_plant"
anim.avi_name = "results/example_"
anim.plant = True
anim.start()
for i in range(0, N):
plant.simulate(dt, False)
anim.root_name = "organType"
anim.update()
scale_elongation = pb.EquidistantGrid1D(0, -50, 100)
soil_strength = np.ones((99,))
soil_strength[20:30] = 5 # data, with a very dense layer at -10 to -15 cm
scales = np.exp(-0.4 * soil_strength) # equation (TODO)
scale_elongation.data = scales # set proportionality factors
print("-3 cm ", scale_elongation.getValue(pb.Vector3d(0, 0, -3)))
print("-25 cm", scale_elongation.getValue(pb.Vector3d(0, 0, -25)))
for p in rs.getRootRandomParameter():
p.f_se = scale_elongation # set scale elongation function
rs.initialize()
ana = pb.SegmentAnalyser(rs)
anim = vp.AnimateRoots(ana)
anim.root_name = "creationTime"
anim.file = "example5b"
anim.min = np.array([-10, -10, -50])
anim.max = np.array([10, 10, 0.])
anim.res = np.array([1, 1, 1])
anim.start()
simtime = 60.
dt = 0.1 # small, for animation
for i in range(0, round(simtime / dt)): # Simulation
# update soil model (e.g. soil_strength)
# update scales (e.g. from water content, soil_strength)
scales = np.exp(-0.4 * soil_strength) # (TODO)
rs.readParameters(path + name + ".xml")
""" soil """
min_ = np.array([-5, -5, -15])
max_ = np.array([5, 5, 0.])
res_ = np.array([1, 3, 5])
if not periodic:
sdf = pb.SDF_PlantBox(0.99 * (max_[0] - min_[0]), 0.99 * (max_[1] - min_[1]), 0.99 * (max_[2] - min_[2]))
rs.setGeometry(sdf)
rs.setRectangularGrid(pb.Vector3d(min_), pb.Vector3d(max_), pb.Vector3d(res_), False) # cut and map segments
rs.initialize()
rs.simulate(rs_age, False)
N = round(sim_time / dt)
anim = vp.AnimateRoots(rs)
anim.min = min_
anim.max = max_
anim.res = res_
anim.file = "results/example7a"
anim.start()
for i in range(0, N):
rs.simulate(dt, False)
""" add segment indices """
segs = rs.segments
x = np.zeros(len(segs))
for i, s in enumerate(segs):
try: