rhizotron2 = pb.SDF_PlantContainer(r, r, h, True)
posA = pb.Vector3d(0, r, -h / 2) # origin before rotation
A = pb.Matrix3d.rotX(alpha / 180. * math.pi)
posA = A.times(posA) # origin after rotation
rotatedRhizotron = pb.SDF_RotateTranslate(rhizotron2, alpha, 0, posA.times(-1))
# 2. A split pot experiment
topBox = pb.SDF_PlantBox(22, 20, 5)
sideBox = pb.SDF_PlantBox(10, 20, 35)
left = pb.SDF_RotateTranslate(sideBox, pb.Vector3d(-6, 0, -5))
right = pb.SDF_RotateTranslate(sideBox, pb.Vector3d(6, 0, -5))
box_ = []
box_.append(topBox)
box_.append(left)
box_.append(right)
splitBox = pb.SDF_Union(box_)
# 3. Rhizotubes as obstacles
box = pb.SDF_PlantBox(96, 126, 130) # box
rhizotube = pb.SDF_PlantContainer(6.4, 6.4, 96, False) # a single rhizotube
rhizoX = pb.SDF_RotateTranslate(rhizotube, 90, pb.SDF_Axis.yaxis,
pb.Vector3d(96 / 2, 0, 0))
rhizotubes_ = []
y_ = (-30, -18, -6, 6, 18, 30)
z_ = (-10, -20, -40, -60, -80, -120)
tube = []
for i in range(0, len(y_)):
v = pb.Vector3d(0, y_[i], z_[i])
tube.append(pb.SDF_RotateTranslate(rhizoX, v))
rhizotubes_.append(tube[i])
import sys
sys.path.append("../../..")
import numpy as np
import plantbox as pb
import vtk_plot as vp
rs = pb.RootSystem()
path = "../../../modelparameter/rootsystem/"
name = "Anagallis_femina_Leitner_2010"
rs.readParameters(path + name + ".xml")
# box with a left and a right compartment for analysis
sideBox = pb.SDF_PlantBox(10, 20, 50)
left = pb.SDF_RotateTranslate(sideBox, pb.Vector3d(-4.99, 0, 0))
right = pb.SDF_RotateTranslate(sideBox, pb.Vector3d(4.99, 0, 0))
leftright = pb.SDF_Union(left, right)
rs.setGeometry(leftright)
# left compartment has a minimum of 0.01, 1 elsewhere
maxS = 1. # maximal
minS = 0.1 # minimal
slope = 1. # [cm] linear gradient between min and max
leftC = pb.SDF_Complement(left)
soilprop = pb.SoilLookUpSDF(leftC, maxS, minS, slope)
# Manually set scaling function and tropism parameters
sigma = [0.4, 1., 1., 1., 1.] * 2
for p in rs.getRootRandomParameter():
if p.subType > 2:
p.dx = 0.25 # adjust resolution
p.f_sa = soilprop # Scale insertion angle
print("Analyse time", t)
for j in range(0, len(cores)):
core_analyser = get_result(allRS, t)
core_analyser.crop(cores[i])
core_analyser.pack()
tl = core_analyser.distribution("length", 0, -h, nol,
True) # vertical length distribution
tl = np.array(tl) / (
len(cores) * r * r * math.pi * dz
) # <<< TODO WHY len(cores), its croped to 1 cylinder
result_matrix[i * len(cores) + j, :] = tl
if exportVTP:
vtp_name = name + "_core_cropped" + str(i) + ".vtp"
# export cropped segments for vizualisaten
core_analyser.write(vtp_name)
np.savetxt(name + "_core_matrix.txt", result_matrix, delimiter=', ')
if exportVTP:
g_name = name + "_core.py"
cores_union = pb.SDF_Union(cores)
allRS[0].setGeometry(cores_union) # just for writing
allRS[0].write(g_name)
print("fin.")