import sys
sys.path.append("../../..")
from cmath import pi
import plantbox as pb
import numpy as np
import matplotlib.pyplot as plt
path = "../../modelparameter/rootsystem/"
name = "wheat_zero_std" # "maize_p1_zero_std" #"wheat"
rs = pb.RootSystem()
rs.readParameters(path + name + ".xml")
rs.setSeed(1)
# Manually set scale elongation function
scale_elongation = pb.EquidistantGrid1D(
0, -200, 100) # for root elongation from 0 cm to -100 cm, 100 layers
scales = np.ones((99, )) * 1 # imedance
scale_elongation.data = scales # set proportionality factors
for p in rs.getRootRandomParameter():
p.f_se = scale_elongation
# p.r = 1;
############################################################################
# Soil core analysis
depth, layers = 100., 20
interrow = 1 # inter-row spacing
row = 1 # row spacing
layerVolume = depth / layers * interrow * row
simtime = 200
dt = 0.5
"""Scale root elongation based on EquidistantGrid1D"""
import sys; sys.path.append("../../..")
import plantbox as pb
import numpy as np
import vtk_plot as vp
rs = pb.RootSystem()
path = "../../../modelparameter/rootsystem/"
name = "Anagallis_femina_Leitner_2010"
rs.readParameters(path + name + ".xml")
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])