rhizotron2 = rb.SDF_PlantContainer(r,r,h,True)
posA = rb.Vector3d(0,r,-h/2) # origin before rotation
A = rb.Matrix3d.rotX(alpha/180.*math.pi)
posA = A.times(posA) # origin after rotation
rotatedRhizotron = rb.SDF_RotateTranslate(rhizotron2,alpha,0,posA.times(-1))
# 2. A split pot experiment
topBox = rb.SDF_PlantBox(22,20,5)
sideBox = rb.SDF_PlantBox(10,20,35)
left = rb.SDF_RotateTranslate(sideBox, rb.Vector3d(-6,0,-5))
right = rb.SDF_RotateTranslate(sideBox, rb.Vector3d(6,0,-5))
box_ = rb.std_vector_SDF_()
box_.append(topBox)
box_.append(left)
box_.append(right)
splitBox = rb.SDF_Union(box_)
# 3. Rhizotubes as obstacles
box = rb.SDF_PlantBox(96,126,130) # box
rhizotube = rb.SDF_PlantContainer(6.4,6.4,96,False) # a single rhizotube
rhizoX = rb.SDF_RotateTranslate(rhizotube, 90, rb.SDF_Axis.yaxis, rb.Vector3d(96/2,0,0))
rhizotubes_ = rb.std_vector_SDF_()
y_ = ( -30, -18, -6, 6, 18, 30 )
z_ = ( -10, -20, -40, -60, -80, -120 )
tube = []
for i in range(0,len(y_)):
v = rb.Vector3d(0,y_[i],z_[i])
tube.append(rb.SDF_RotateTranslate(rhizoX, v))
rhizotubes_.append(tube[i])
name = "Zea_mays_1_Leitner_2010"
rs.openFile(name)
# Pore Geometry
x_ = (-10, -5, 1, 15) # not 0, otherwise we start in crack
y_ = (0, 0, 0, 0)
crack = rb.SDF_PlantBox(0.25, 100, 160) # cm
cracks_ = rb.std_vector_SDF_()
py_cracks = []
for i in range(0, len(y_)):
v = rb.Vector3d(x_[i], y_[i], 0)
py_cracks.append(rb.SDF_RotateTranslate(crack, v))
cracks_.append(py_cracks[-1])
cracks = rb.SDF_Union(cracks_)
rs.setPoreGeometry(cracks)
# Increased elongation within the pores
maxS = 2 # twice the elongation rate within the pore
minS = 1 # normal elongation rate
slope = 0
soil_prop = rb.SoilLookUpSDF(cracks, maxS, minS, slope)
# Adjust Tropism
sigma = [0.4] * 10
for i in range(0, 10):
p = rs.getRootTypeParameter(i + 1)
p.dx = 0.25 # adjust resolution
p.tropismT = rb.TropismType.gravi
p.tropismN = 1 # strength of tropism
import py_rootbox as rb
import math
rs = rb.RootSystem()
name = "Anagallis_femina_Leitner_2010"
rs.openFile(name)
# box with a left and a right compartment for analysis
sideBox = rb.SDF_PlantBox(10, 20, 50)
left = rb.SDF_RotateTranslate(sideBox, rb.Vector3d(-4.99, 0, 0))
right = rb.SDF_RotateTranslate(sideBox, rb.Vector3d(4.99, 0, 0))
leftright = rb.SDF_Union(left, right)
rs.setGeometry(leftright)
# left compartment has a minimum of 0.01, 1 elsewhere
maxS = 1. # maximal
minS = 0.01 # minimal
slope = 1. # [cm] linear gradient between min and max
leftC = rb.SDF_Complement(left)
soilprop = rb.SoilLookUpSDF(leftC, maxS, minS, slope) # for root elongation
soilprop2 = rb.SoilLookUpSDF(left, 1., 0.002, slope) # for branching
# Manually set scaling function and tropism parameters
sigma = [0.4, 1., 1., 1., 1.] * 2
for i in range(0, 10):
p = rs.getRootTypeParameter(i + 1)
p.dx = 0.25 # adjust resolution
p.tropismS = sigma[i]
# 1. Scale elongation
p.se = soilprop
def call(cc):
rs = rb.RootSystem()
#name = "Triticum_aestivum_a_Bingham_2011" # is this the same as your wheat, Shehan?
name = "wheat"
rs.openFile(name)
# Pore Geometry
x_ = (-10, -5, 5, 15) # not 0, otherwise we start in crack
y_ = (0, 0, 0, 0)
#x_=(-10, -5)
#y_=(0,0)
crack = rb.SDF_PlantBox(1.0, 100, 160) # cm
cracks_ = rb.std_vector_SDF_()
py_cracks = []
for i in range(0, len(y_)):
v = rb.Vector3d(x_[i], y_[i], 0)
py_cracks.append(rb.SDF_RotateTranslate(crack, v))
cracks_.append(py_cracks[-1])
cracks = rb.SDF_Union(cracks_)
rs.setPoreGeometry(cracks)
# Increased elongation within the pores
maxS = 2 # twice the elongation rate within the pore
minS = 1 # normal elongation rate
slope = 0
soil_prop = rb.SoilLookUpSDF(cracks, maxS, minS, slope)
# Adjust Tropism
sigma = [0.4] * 10
for i in range(0, 10):
p = rs.getRootTypeParameter(i + 1)
p.dx = 0.25 # adjust resolution
p.tropismT = rb.TropismType.gravi
p.tropismN = 1 # strength of tropism
p.tropismS = sigma[i]
p.se = soil_prop
# Pore Local Axes
v1 = rb.Vector3d(0.67, 0, 0)
v2 = rb.Vector3d(0, 0.67, 0)
v3 = rb.Vector3d(0, 0, 0.67)
rs.setPoreLocalAxes(rb.Matrix3d(v1, v2, v3))
# Pore Conductivity Tensor
t1 = rb.Vector3d(1.33, 0, 0)
t2 = rb.Vector3d(0, 50.33, 0)
t3 = rb.Vector3d(0, 0, 50.33)
rs.setPoreConductivity(rb.Matrix3d(t1, t2, t3))
# Set up depth dependent elongation scaling function
scale_elongation = rb.EquidistantGrid1D(
0, -160, 17) # todo: replace this by reading in data from CSV file
scales = np.zeros(
len(scale_elongation.grid)
) + 0.1 # scales from some equation (scale = function(soil_strength) ), where scale in (0,1)
scale_elongation.data = a2v(scales) # set proportionality factors
# Proportionally scale this function
se2 = rb.ProportionalElongation()
se2.setBaseLookUp(scale_elongation)
# multiply the scale elongation functions
se3 = rb.MultiplySoilLookUps(se2, soil_prop)
# Manually set scaling function
for i in range(0, 10):
p = rs.getRootTypeParameter(i + 1)
p.se = se3
# Initialize
rs.initialize()
# Simulate
simtime = 30 * 8 # e.g. 30 or 60 days
dt = 1 #0.5 * 1./24.
N = round(simtime / dt)
for i in range(0, N):
# time-dependent and depth-dependent scaling function
scales = np.loadtxt('W2.csv', delimiter=';',
usecols=i) # reading in ith column from CSV file
scale_elongation.data = a2v(scales *
1.00) # set the data of scale elongation
rs.simulate(dt)
# Export results (as vtp)
#rs.write("../results/crack.vtp")
# Export cracks
#rs.setGeometry(cracks) # just for vizualisation
#rs.write("../results/crack.py")
z_ = np.linspace(0, -1 * 160, 160)
# Make a root length distribution
ana = rb.SegmentAnalyser(rs)
rl_ = ana.distribution(rb.ScalarType.length, 0, 160, 160, True)
np.set_printoptions(precision=4)
np.savetxt("cw_" + str(cc) + ".txt", rl_, fmt="%.2f")