"""analysis of results using signed distance functions"""
import py_rootbox as rb
import numpy as np
import matplotlib.pyplot as plt
rs = rb.RootSystem()
name = "Brassica_oleracea_Vansteenkiste_2014"
rs.readParameters("modelparameter/" + name + ".xml")
rs.initialize()
rs.simulate(120)
# Soil core analysis
r, depth, layers = 10, 100., 100
soilcolumn = rb.SDF_PlantContainer(r, r, depth, False) # in the center of the root
soilcolumn2 = rb.SDF_RotateTranslate(soilcolumn, 0, 0, rb.Vector3d(10, 0, 0)) # shift 10 cm
# pick one geometry for further analysis
geom = soilcolumn
z_ = np.linspace(0, -1 * depth, layers)
fig, axes = plt.subplots(nrows = 1, ncols = 4, figsize = (16, 8))
for a in axes:
a.set_xlabel('RLD (cm/cm)')
a.set_ylabel('Depth (cm)')
# Make a root length distribution
ana = rb.SegmentAnalyser(rs)
rl_ = ana.distribution("length", 0., depth, layers, True)
axes[0].set_title('All roots (120 days)')
axes[0].plot(rl_, z_)
"""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")
import py_rootbox as rb import math 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
import py_rootbox as rb import math rootsystem = rb.RootSystem() name = "Zea_mays_4_Leitner_2014" # Open plant and root parameter from a file rootsystem.openFile(name) # 1. creates a square rhizotron r*r, with height h, rotated around the x-axis for angle alpha r = 20 h = 4 alpha = 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
