def analyse(rs, name, simtime, tv0):
top = rb.SDF_PlantBox(1e6, 1e6, 42)
bot = rb.SDF_Complement(top)
ana = rb.SegmentAnalyser(rs)
print()
print(name, ", age", simtime, "days")
print("======================================")
print()
print("Number of ----------------------------")
na = len(rs.getBaseRoots())
print("Axes ", na)
nr = rs.getNumberOfRoots()
print("Roots ", nr)
ns = rs.getNumberOfSegments()
print("Segments ", ns)
print("\nLength (cm) --------------------------")
tl = ana.getSummed("length")
print("L0 ", round(tl))
tl_top = ana.getSummed("length", top)
tl_bot = ana.getSummed("length", bot)
print("Lcomp (top) ", round(tl_top), "(", round(100 * (tl_top / tl)), "%)")
print("Lcomp (bot) ", round(tl_bot), "(", round(100 * (tl_bot / tl)), "%)")
a = rb.SegmentAnalyser(
rs
) # copyFor the record, I had already simulated the RSWMS scenarios with a single root and a large domain (see attached) but I think our parameterization is different as the results loo pretty dissimilar (did you really use 1.8e-5 for kr? Not 1.8e-4? the RS conductance is very small then: 0.0023cm3/hPa/d which explain the stress)
a.filter("order", 0)
l0 = a.getSummed("length")
a = rb.SegmentAnalyser(rs) # copy
a.filter("order", 1)
l1 = a.getSummed("length")
print("Lord (zero) ", round(l0), "(", round(100 * (l0 / tl)), "%)")
print("Lord (first)", round(l1), "(", round(100 * (l1 / tl)), "%)")
print("\nVolume -------------------------------")
tv = ana.getSummed("volume")
print("V0 (cm^3) ", tv)
print("rVol ", tv / tv0)
print()
def analyse(rs, name, simtime, tv0):
top = rb.SDF_PlantBox(1e6, 1e6, 42)
bot = rb.SDF_Complement(top)
ana = rb.SegmentAnalyser(rs)
print()
print(name, ", age", simtime, "days")
print("======================================")
print()
print("Number of ----------------------------")
na = len(rs.getBaseRoots())
print("Axes ", na)
nr = rs.getNumberOfRoots()
print("Roots ", nr)
ns = rs.getNumberOfSegments()
print("Segments ", ns)
print("\nLength (cm) --------------------------")
tl = ana.getSummed(rb.ScalarType.length)
print("L0 ", round(tl))
tl_top = ana.getSummed(rb.ScalarType.length, top)
tl_bot = ana.getSummed(rb.ScalarType.length, bot)
print("Lcomp (top) ", round(tl_top), "(", round(100 * (tl_top / tl)), "%)")
print("Lcomp (bot) ", round(tl_bot), "(", round(100 * (tl_bot / tl)), "%)")
a = rb.SegmentAnalyser(rs) # copy
a.filter(rb.ScalarType.order, 0)
l0 = a.getSummed(rb.ScalarType.length)
a = rb.SegmentAnalyser(rs) # copy
a.filter(rb.ScalarType.order, 1)
l1 = a.getSummed(rb.ScalarType.length)
print("Lord (zero) ", round(l0), "(", round(100 * (l0 / tl)), "%)")
print("Lord (first)", round(l1), "(", round(100 * (l1 / tl)), "%)")
print("\nVolume -------------------------------")
tv = ana.getSummed(rb.ScalarType.volume)
print("V0 (cm^3) ", tv)
print("rVol ", tv / tv0)
print()
rs.openFile(name)
# Manually set tropism to hydrotropism for the first ten root types
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.tropismT = rb.TropismType.hydro
p.tropismN = 2 # strength of tropism
p.tropismS = sigma[i]
# Static soil property
maxS = 0.7 # maximal
minS = 0.1 # minimal
slope = 5 # linear gradient between min and max (cm)
box = rb.SDF_PlantBox(30,30,2) # cm
layer = rb.SDF_RotateTranslate(box, rb.Vector3d(0,0,-16))
soil_prop = rb.SoilPropertySDF(layer, maxS, minS, slope)
# Set the soil properties before calling initialize
rs.setSoil(soil_prop)
# Initialize
rs.initialize()
# Simulate
simtime = 100 # e.g. 30 or 60 days
dt = 1
N = round(simtime/dt)
for _ in range(0,N):
# in a dynamic soil setting you would need to update soil_prop
rs = rb.RootSystem() # Open plant and root parameter from a file name = "Zea_mays_4_Leitner_2014" rs.openFile(name) # 1. Creates a square rhizotron r*r, with height h, rotated around the x-axis r, h, alpha = 20, 4, 45 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_()
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
import py_rootbox as rb
import sys
import numpy as np
import matplotlib.pyplot as plt
rs = rb.RootSystem()
# name = "Triticum_aestivum_a_Bingham_2011" # is this the same as your wheat, Shehan?
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)
for i in range(0,10):
rootsystem.getRootTypeParameter(i+1).dx = 0.25; # they seem to coarse
rootsystem.getRootTypeParameter(i+1).tropismT = rb.TropismType.hydro;
rootsystem.getRootTypeParameter(i+1).tropismN = 3; # N
rootsystem.getRootTypeParameter(i+1).tropismS = sigma[i]; # sigma
# check if it worked
# for i in range(0,10):
# print(rootsystem.getRootTypeParameter(i+1))
print (rootsystem.getRootSystemParameter().seedPos)
#
# Static soil property
#
box = rb.SDF_PlantBox(100,100,2)
layer = rb.SDF_RotateTranslate(box, rb.Vector3d(0,0,-16))
maxS = 0.7 # maximal
minS = 0.1 # minimal
slope = 5 # [cm] linear gradient between min and ma
soilprop = rb.SoilPropertySDF(layer, maxS, minS, slope)
# set the soil properties before calling initialize
rootsystem.setSoil(soilprop);
#
# Initialize
#
rootsystem.initialize(4,5); # it is important to call initialize() after setGeometry()
"""small example in a container"""
import py_rootbox as rb
rootsystem = rb.RootSystem()
# Open plant and root parameter from a file
name = "Anagallis_femina_Leitner_2010"
rootsystem.readParameters("modelparameter/" + name + ".xml")
# Create and set geometry
# 1.creates a cylindrical soil core with top radius 5 cm, bot radius 5 cm, height 50 cm, not square but circular
soilcore = rb.SDF_PlantContainer(5, 5, 40, False)
# 2. creates a square 27*27 cm containter with height 1.4 cm
rhizotron = rb.SDF_PlantBox(1.4, 27, 27)
# Pick 1, or 2
rootsystem.setGeometry(soilcore) # soilcore, or rhizotron
# Initialize
rootsystem.initialize()
# Simulate
rootsystem.simulate(60) # days
# Export final result (as vtp)
rootsystem.write("../results/example_1b.vtp")
# Export container geometry as Paraview Python script
rootsystem.write("../results/example_1b.py")
# Additionally, exports the line segments as .txt file to import into Matlab for postprocessing
#
import py_rootbox as rb
import math
import random
import numpy as np
import matplotlib.pyplot as plt
rootsystem = rb.RootSystem()
name = "Anagallis_femina_Leitner_2010"
nameOutputFile = "RLD_Anagallis_femina_Leitner_2010"
allRS = []
soilcore = rb.SDF_PlantContainer(5, 5, 40, False)
rhizotron = rb.SDF_PlantBox(900, 900, 900)
#
# Creates N root systems
#
N = 100
for i in range(0, N - 1):
rs = rb.RootSystem()
rs.openFile(name)
rs.setGeometry(rhizotron)
allRS.append(rs)
#
# Simulate
#
simtime = 21
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")
from matplotlib import ticker
import matplotlib.colors as colors
rs = rb.RootSystem()
# Open plant and root parameter from a file
name = "Anagallis_femina_Leitner_2010"
rs.openFile(name)
# Create and set geometry
# 1.creates a cylindrical soil core with top radius 5 cm, bot radius 5 cm, height 50 cm, not square but circular
soilcore = rb.SDF_PlantContainer(5, 5, 40, False)
# 2. creates a square 27*27 cm containter with height 1.4 cm
rhizotron = rb.SDF_PlantBox(0.5, 27, 27)
# Pick 1, or 2
rs.setGeometry(rhizotron) # soilcore, or rhizotron
# Initialize
rs.initialize()
# Simulate
rs.simulate(60) # days
# Root system distance function
ana = rb.SegmentAnalyser(rs)
radii = ana.getParameter("radius")
print(radii[10])
import sys
import numpy as np
import matplotlib.pyplot as plt
import csv
rs = rb.RootSystem()
#name = "Triticum_aestivum_a_Bingham_2011" # is this the same as your wheat, Shehan?
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)
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 = 20 # twice the elongation rate within the pore
minS = 1 # normal elongation rate
slope = 0
