CRootBox/python/example3d.py at master · Plant-Root-Soil-Interactions-Modelling/CRootBox · GitHub

History

89 lines (71 loc) · 2.13 KB

Raw

"""sensitivity analysis: insertion anlge on root tip distribution"""

import py_rootbox as rb

import math

from multiprocessing import Pool

import numpy as np

import matplotlib.pyplot as plt

# sets all standard deviation to value*s

def set_all_sd(rs, s):

for p in rs.getRootTypeParameter():

p.lbs = p.lb * s

p.las = p.la * s

p.lns = p.ln * s

p.nobs = p.nob * s

p.rs = p.r * s

p.a_s = p.a * s

# Parameters

name = "Triticum_aestivum_a_Bingham_2011"

simtime = 20

N = 50 # resolution of paramter

runs = 10 # iterations

theta0_ = np.linspace(0, math.pi / 2, N)

# One simulation

def simulate(i):

rs = rb.RootSystem()

rs.readParameters("modelparameter/" + name + ".xml")

set_all_sd(rs, 0.) # set all sd to zero

rs.initialize() # copy to tap to basal root parameters

# vary parameter

p1 = rs.getRootTypeParameter(1) # tap root

p4 = rs.getRootTypeParameter(4) # basal roots

p1.theta = theta0_[i]

p4.theta = theta0_[i]

# simulation

rs.initialize() # build again with theta0

rs.simulate(simtime, True)

# target

roots = rs.getPolylines()

depth = 0.

rad_dist = 0.

for r in roots:

depth += r[-1].z

rad_dist += math.hypot(r[-1].x, r[-1].y)

depth /= len(roots)

rad_dist /= len(roots)

return depth, rad_dist

depth_ = np.zeros(N)

rad_dist_ = np.zeros(N)

for r in range(0, runs):

# Parallel execution

param = [] # param is a list of tuples

for i in range(0, N):

param.append((i,))

pool = Pool()

output = pool.starmap(simulate, param)

pool.close()

# Copy results

for i, o in enumerate(output):

depth_[i] += (o[0] / runs)

rad_dist_[i] += (o[1] / runs)

# Figure

fig, axes = plt.subplots(nrows = 1, ncols = 2, figsize = (10, 8))

axes[0].set_xlabel('Insertion angle theta (-)')

axes[1].set_xlabel('Insertion angle theta (-)')

axes[0].set_ylabel('Mean tip depth (cm)')

axes[1].set_ylabel('Mean tip radial distance (cm)')

axes[0].plot(theta0_, depth_)

axes[1].plot(theta0_, rad_dist_)

fig.subplots_adjust()

plt.savefig("../results/example_3d.png")

plt.show()

print("done.")

CRootBox/python/example3d.py at master · Plant-Root-Soil-Interactions-Modelling/CRootBox · GitHub

Uh oh!

Expand file tree

Breadcrumbs

example3d.py

Latest commit

History

Breadcrumbs

example3d.py

File metadata and controls