def test_copy():
# Parameter
simtime = 30. # days
dt = 1.
N = round(simtime / dt) # steps
name = "Anagallis_femina_Leitner_2010"
print("\n1 original")
rs = pb.RootSystem()
rs.openFile(name)
rs.setSeed(1) # before initialize to mimic
rs.initialize()
rs2 = pb.RootSystem(rs)
rs.simulate(simtime)
l1 = np.sum(v2a(rs.getParameter("length")))
print("total length", l1)
print("\n2 copy")
rs2.simulate(simtime)
l2 = np.sum(v2a(rs2.getParameter("length")))
print("total length", l2)
print("\n3 rebuild same")
rs3 = pb.RootSystem()
rs3.openFile(name)
rs3.setSeed(1)
rs3.initialize()
rs3.simulate(simtime)
l3 = np.sum(v2a(rs3.getParameter("length")))
print("total length", l3)
return
def test_copy(self):
""" checks if the root system can be copied, and if randomness works """
seed = 110 # random seed
name = "Brassica_oleracea_Vansteenkiste_2014"
rs = pb.RootSystem() # the original
rs.readParameters("../modelparameter/rootsystem/" + name + ".xml")
rs.setSeed(seed)
rs.initialize(False)
rs2 = rs.copy() # copy root system
n1 = rs.rand()
self.assertIsNot(rs2, rs, "copy: not a copy")
self.assertEqual(str(rs), str(rs2),
"copy: the organisms should be equal")
self.assertEqual(rs2.rand(), n1,
"copy: random generator seed was not copied")
rs.simulate(10)
rs2.simulate(10)
n2 = rs.rand()
self.assertEqual(rs2.rand(), n2,
"copy: simulation is not deterministic")
rs3 = pb.RootSystem() # rebuild same
rs3.readParameters("../modelparameter/rootsystem/" + name + ".xml")
rs3.setSeed(seed)
rs3.initialize(False)
self.assertEqual(rs3.rand(), n1,
"copy: random generator seed was not copied")
rs3.simulate(10)
self.assertEqual(rs3.rand(), n2,
"copy: simulation is not deterministic")
def simOnce(name, simtime, lbins, lrange, zbins, zrange, dx, dt):
abins = 100
arange = (-math.pi, math.pi)
hl, hz, ha = None, None, None # histograms
# Simulation
rs = pb.RootSystem()
path = "../../../modelparameter/rootsystem/"
rs.readParameters(path + name + ".xml")
for p in rs.getRootRandomParameter():
p.dx = dx
rs.getRootRandomParameter(
4
).theta = 80. / 180. * math.pi # fix insertion angle of the basal roots
rs.initialize()
N = round(simtime / dt)
for i in range(0, N):
rs.simulate(dt, True)
# Analysis
img = np.zeros((2 * lbins, 2 * lbins))
nodes = rs.getNodes()
tips = rs.getRootTips()
z_ = np.zeros(len(tips))
l_ = np.zeros(len(tips))
alpha_ = np.zeros(len(tips))
c = 0 # counter
mx, my = 0, 0 # mean tip position
for t in tips:
x, y, z = nodes[t].x, nodes[t].y, nodes[t].z
# tip top view
i = math.floor(((x + lrange[1]) / (2. * lrange[1])) * 2. *
float(lbins)) # np.around((x/lrange[1])*lbins+lbins)
j = math.floor(((y + lrange[1]) / (2. * lrange[1])) * 2. *
float(lbins)) # np.around((y/lrange[1])*lbins+lbins)
i = min(i, 2 * lbins - 1)
j = min(j, 2 * lbins - 1)
i = int(max(i, 0))
j = int(max(j, 0))
img[j, i] += 1.
# depth and length distribution
z_[c] = z
l_[c] = math.sqrt(x * x + y * y)
alpha_[c] = math.atan2(x, y)
c += 1
hl, bins = np.histogram(l_, bins=lbins, range=lrange)
hz, bins = np.histogram(z_, bins=zbins, range=zrange)
ha, bins = np.histogram(alpha_, bins=abins, range=arange)
mx += nodes[t].x
my += nodes[t].y
if (len(tips) == 0):
print("No tips?")
return hl, hz, ha, img, mx, my
else:
return hl, hz, ha, img, mx / len(tips), my / len(tips)
def test_dynamics(self):
""" incremental root system growth like needed for coupling"""
name = "Anagallis_femina_Leitner_2010" # "maize_p2" # "Anagallis_femina_Leitner_2010" # "Zea_mays_4_Leitner_2014"
rs = pb.RootSystem()
rs.readParameters("../modelparameter/rootsystem/" + name + ".xml")
rs.initialize(False)
simtime = 60 # days
dt = 1
N = round(simtime / dt)
nodes = np.array((list(map(np.array, rs.getNodes()))))
nodeCTs = np.array(rs.getNodeCTs())
seg = np.array([], dtype=np.int64).reshape(0, 2)
cts = rs.getSegmentCTs()
nonm = 0
for i in range(0, N):
rs.simulate(dt, False)
# MOVE NODES
uni = np.array((list(map(np.array, rs.getUpdatedNodeIndices()))),
dtype=np.int64)
unodes = np.array((list(map(np.array, rs.getUpdatedNodes()))))
ucts = np.array(rs.getUpdatedNodeCTs())
if len(uni) > 0:
nodes[uni] = unodes # do the update
nodeCTs[uni] = ucts
nonm += uni.shape[0]
# NEW NODES
newnodes = np.array((list(map(np.array, rs.getNewNodes()))))
newcts = np.array(rs.getNewNodeCTs())
newsegs = np.array((list(map(np.array, rs.getNewSegments()))),
dtype=np.int64)
if len(newnodes) != 0:
nodes = np.vstack((nodes, newnodes))
nodeCTs = np.append(nodeCTs, newcts)
if len(newsegs) != 0:
seg = np.vstack((seg, newsegs))
nodes_ = np.array((list(map(np.array, rs.getNodes()))))
nodeCTs_ = np.array(rs.getNodeCTs())
seg_ = np.array((list(map(np.array, rs.getSegments()))),
dtype=np.int64)
self.assertEqual(nodes_.shape, nodes.shape,
"incremental growth: node lists are not equal")
self.assertEqual(nodeCTs_.shape, nodeCTs.shape,
"incremental growth: node lists are not equal")
self.assertEqual(seg_.shape, seg.shape,
"incremental growth: node lists are not equal")
uneq = np.sum(nodes_ != nodes) / 3
self.assertEqual(uneq, 0,
"incremental growth: node lists are not equal")
uneq = np.sum(nodeCTs_ != nodeCTs)
self.assertEqual(
uneq, 0,
"incremental growth: node creation time lists are not equal")
seg = np.sort(seg, axis=0) # per default along the last axis
seg_ = np.sort(seg_, axis=0)
uneq = np.sum(seg_ != seg) / 2
self.assertEqual(uneq, 0,
"incremental growth: segment lists are not equal")
def test_rsml(self):
""" checks rsml functionality with Python rsml reader """
name = "Anagallis_femina_Leitner_2010"
rs = pb.RootSystem()
rs.readParameters("../modelparameter/rootsystem/" + name + ".xml")
rs.initialize(False)
simtime = 60
rs.simulate(simtime)
rs.writeRSML(name + ".rsml")
pl, props, funcs = read_rsml(name + ".rsml")
def root_example_rrp2(self):
""" an example used in the tests below, a main root with laterals """
self.plant = pb.RootSystem(
) # store organism (not owned by Organ, or OrganRandomParameter)
p0 = pb.RootRandomParameter(self.plant)
p0.name, p0.subType, p0.la, p0.lb, p0.lmax, p0.ln, p0.lnk, p0.r, p0.dx, p0.dxMin = "taproot", 1, 0.95, 0.8, 10., 1.05, 0.01, 0.8, 0.25, 0.2
p0.successor = [2]
p0.successorP = [1.]
p1 = pb.RootRandomParameter(self.plant)
p1.name, p1.subType, p1.lmax, p1.r, p1.dx = "lateral", 2, 2., 2., 2.
self.plant.setOrganRandomParameter(
p0) # the organism manages the type parameters and takes ownership
self.plant.setOrganRandomParameter(p1)
srp = pb.SeedRandomParameter(self.plant)
self.plant.setOrganRandomParameter(srp)
print("root p0, initial parameters: lmax = ", p0.lmax, ", lb = ",
p0.lb, ", la = ", p0.la, ", ln = ", p0.ln)
param0 = p0.realize() # set up root by hand (without a root system)
print("root p0, realized parameters: lmax = ",
sum((sum(param0.ln), param0.lb, param0.la)), ", lb = ",
param0.lb, ", la = ", param0.la, ", mean ln = ",
np.mean(param0.ln))
if ((param0.lb % p0.dx > 0) and (param0.lb % p0.dx < p0.dxMin * 0.99)):
print("lb value does not fit with dx and dxMin")
print(param0.lb % p0.dx)
if ((param0.la % p0.dx > 0) and (param0.la % p0.dx < p0.dxMin * 0.99)):
print("la value does not fit with dx and dxMin")
print(param0.la % p0.dx)
if (any([(lni % p0.dx > 0 and lni % p0.dx < p0.dxMin * 0.99)
for lni in param0.ln])):
print("ln value does not fit with dx and dxMin")
param0.la, param0.lb = 0, 0 # its important parent has zero length, otherwise creation times are messed up
parentroot = pb.Root(1, param0, True, True, 0., 0.,
pb.Vector3d(0, 0, -1), 0, 0, False,
0) # takes ownership of param0
parentroot.setOrganism(self.plant)
parentroot.addNode(pb.Vector3d(0, 0, -1),
0) # there is no nullptr in Python
self.parentroot = parentroot # store parent (not owned by child Organ)
self.root = pb.Root(self.plant, p0.subType, pb.Vector3d(0, 0, -1), 0,
self.parentroot, 0, 0)
self.root.setOrganism(self.plant)
self.p0 = p0
def test_polylines(self):
"""checks if the polylines have the right tips and bases """
name = "Brassica_napus_a_Leitner_2010"
rs = pb.RootSystem()
rs.readParameters("../modelparameter/rootsystem/" + name + ".xml")
rs.initialize(False)
rs.simulate(7) # days young
polylines = rs.getPolylines() # Use polyline representation of the roots
bases = np.zeros((len(polylines), 3))
tips = np.zeros((len(polylines), 3))
for i, r in enumerate(polylines):
bases[i, :] = [r[0].x, r[0].y, r[0].z]
tips[i, :] = [r[-1].x, r[-1].y, r[-1].z]
nodes = np.array((list(map(np.array, rs.getNodes())))) # Or, use node indices to find tip or base nodes
tipI = rs.getRootTips()
baseI = rs.getRootBases()
uneq = np.sum(nodes[baseI, :] != bases) + np.sum(nodes[tipI, :] != tips)
self.assertEqual(uneq, 0, "polylines: tips or base nodes do not agree")
def initialize_root_systems(N :int, M :int, distN :float, distM :float):
"""
Initializes M*N root systems
@param N number of rows
@param M number of columns
@param distN distance between rows
@param distM distance between columns
@return a list of initialized root systems
"""
allRS = []
for i in range(0, N):
for j in range(0, M):
rs = pb.RootSystem()
rs.readParameters(path + name + ".xml")
rs.getRootSystemParameter().seedPos = pb.Vector3d(distN * i, distM * j, -3.) # cm
rs.initialize(False) # verbose = False
allRS.append(rs)
return allRS
def simulate(i):
rs = pb.RootSystem()
rs.readParameters(path + name + ".xml")
set_all_sd(rs, 0.) # set all sd to zero
p1 = rs.getRootRandomParameter(1) # tap and basal root type
# 1. vary parameter
p1.theta = theta0_[i]
# 2. simulate
rs.initializeLB(1, 1, False)
rs.simulate(simtime, False)
# 3. calculate target
depth = 0. # mean depth
rad_dist = 0. # mean raidal distance
roots = rs.getPolylines()
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
def rs_example_rtp(self):
""" an example used in some of the tests below, 100 basals with laterals """
self.rs = pb.RootSystem()
srp = pb.SeedRandomParameter(self.rs)
srp.subType = 0
srp.seedPos = pb.Vector3d(0., 0., -3.)
srp.maxB = 100
srp.firstB = 10
srp.delayB = 3
self.rs.setRootSystemParameter(srp)
p0 = pb.RootRandomParameter(self.rs)
p0.name, p0.subType, p0.la, p0.lmax, p0.ln, p0.r, p0.dx = "taproot", 1, 10, 101, 89. / 19., 1, 0.5
p0.lb = 2
p0.successor = [2]
p0.successorP = [1.]
p1 = pb.RootRandomParameter(self.rs)
p1.name, p1.subType, p1.la, p1.ln, p1.r, p1.dx = "lateral", 2, 25, 0, 2, 0.1
self.p0, self.p1, self.srp = p0, p1, srp # Python will garbage collect them away, if not stored
self.rs.setOrganRandomParameter(p0) # the organism manages the type parameters
self.rs.setOrganRandomParameter(p1)
"""hydrotropism in a thin layer"""
import sys
sys.path.append("../../..")
sys.path.append("../../../src/python_modules")
import plantbox as pb
import vtk_plot as vp
rs = pb.RootSystem()
path = "../../../modelparameter/rootsystem/"
name = "Anagallis_femina_Leitner_2010"
rs.readParameters(path + name + ".xml")
# Manually set tropism to hydrotropism for the first ten root types
sigma = [0.4, 1., 1., 1., 1.] * 2
for p in rs.getRootRandomParameter():
p.dx = 0.25 # adjust resolution
p.tropismT = pb.TropismType.hydro
p.tropismN = 2 # strength of tropism
p.tropismS = sigma[p.subType - 1]
# Static soil property in a thin layer
maxS = 0.7 # maximal
minS = 0.1 # minimal
slope = 5 # linear gradient between min and max (cm)
box = pb.SDF_PlantBox(30, 30, 2) # cm
layer = pb.SDF_RotateTranslate(box, pb.Vector3d(0, 0, -16))
soil_prop = pb.SoilLookUpSDF(layer, maxS, minS, slope)
# Set the soil properties before calling initialize
rs.setSoil(soil_prop)
import sys
sys.path.append("../../..")
import time
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import ticker
import matplotlib.colors as colors
from pyevtk.hl import gridToVTK
import plantbox as rb
simtime_ = [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
for st in simtime_:
#
# Root system
#
rs = rb.RootSystem()
path = "../../../modelparameter/rootsystem/"
name = "test_root"
rs.readParameters(path + name + ".xml")
#set geometry
width = 4 # cm
depth = 15
soilcore = rb.SDF_PlantContainer(width, width, depth, True)
rs.setGeometry(soilcore)
rs.setSeed(0)
rs.initialize()
for ii in range(0, st):
def simOnce(name, simtime, lbins, lrange, zbins, zrange, dx, dt):
abins = 100
arange = (-math.pi, math.pi)
# Simulation
rs = pb.RootSystem()
rs.openFile(name, "modelparameter/")
for p in rs.getRootRandomParameter():
p.dx = dx
rs.initialize()
rs.getRootRandomParameter(
4
).theta = 80. / 180. * math.pi # fix insertion angle of the basal roots
rs.initialize()
N = round(simtime / dt)
for i in range(0, N):
rs.simulate(dt, True)
# analysis
img = np.zeros((2 * lbins, 2 * lbins))
nodes = rs.getNodes()
tips = rs.getRootTips()
notips = len(tips)
z_ = np.zeros(notips)
l_ = np.zeros(notips)
alpha_ = np.zeros(notips)
c = 0
mx = 0
my = 0
for t in tips:
x = nodes[t].x
y = nodes[t].y
z = nodes[t].z
# tip top view
i = math.floor(((x + lrange[1]) / (2. * lrange[1])) * 2. *
float(lbins)) # np.around((x/lrange[1])*lbins+lbins)
j = math.floor(((y + lrange[1]) / (2. * lrange[1])) * 2. *
float(lbins)) # np.around((y/lrange[1])*lbins+lbins)
i = min(i, 2 * lbins - 1)
j = min(j, 2 * lbins - 1)
i = int(max(i, 0))
j = int(max(j, 0))
img[j, i] += 1.
# depth, and length distribution
z_[c] = z
l_[c] = math.sqrt(x * x + y * y)
alpha_[c] = math.atan2(x, y)
c += 1
hl, bins = np.histogram(l_, bins=lbins, range=lrange)
hz, bins = np.histogram(z_, bins=zbins, range=zrange)
ha, bins = np.histogram(alpha_, bins=abins, range=arange)
mx += nodes[t].x
my += nodes[t].y
return hl, hz, ha, img, mx / len(tips), my / len(tips)
# 1) Opens plant and root parameters from a file
# 2) Simulates root growth
# 3) Outputs a VTP (for vizualisation in ParaView)
#
# Computes analytical solution of moving point/line sources based on Carslaw and Jaeger
#
import sys
sys.path.append("../..")
import numpy as np
import matplotlib.pyplot as plt
from scipy import integrate
import plantbox as rb
rootsystem = rb.RootSystem()
name = "anagallis_straight"
#
# Open plant and root parameter from a file
#
rootsystem.openFile(name)
# rootsystem.writeParameters() # not exposed to python yet
#
# Initialize
#
rootsystem.initialize()
#
# Simulate
def err (fitparams): #parameters to be optimized
lmaxp=fitparams[0]
tropismNp=fitparams[1]
tropismSp=fitparams[2]
rp=fitparams[3]
simtime = 120
M = 4 # number of plants in rows
N = 2 # number of rows
distp = 3 # distance between the root systems along row[cm]
distr =12 # distance between the rows[cm]
interrow=N*distr # inter-row spacing
row=M*distp # row spacing
r, depth, layers = 5, 100., 11 # Soil core analysis
layerVolume = depth / layers * r * r * np.pi
z_ = np.linspace(0, -1 * depth, layers)
times = [120, 60, 30, 10]
soilcolumn = pb.SDF_PlantContainer(r, r, depth, False) # in the center of the root
soilcolumn1 = pb.SDF_RotateTranslate(soilcolumn, 0, 0, pb.Vector3d(-6, 0, 0))
soilcolumn2 = pb.SDF_RotateTranslate(soilcolumn, 0, 0, pb.Vector3d(6, 0, 0))
soilcolumns=[soilcolumn1,soilcolumn, soilcolumn2]
with open('rld.pkl','rb') as f:
measured_RLD = pkl.load(f)
real_RLD=np.reshape(measured_RLD,(measured_RLD.shape[0]*measured_RLD.shape[1]*measured_RLD.shape[2],1))
rld=np.zeros([measured_RLD.shape[0],measured_RLD.shape[1],measured_RLD.shape[2]])
# rld=np.zeros([len(soilcolumns),len(times),layers])
path = "../../modelparameter/rootsystem/"
name = "wheat"
# fig, axes = plt.subplots(nrows = 1, ncols = len(soilcolumns), figsize = (16, 8))
# Make a root length distribution along the soil cores
for k in range(len(soilcolumns)):
# Initializes N*M root systems
allRS = []
for i in range(0, N):
for j in range(0, M):
rs = pb.RootSystem()
rs.readParameters(path + name + ".xml")
p1 = rs.getRootRandomParameter(1) # tap and basal root type
p1.lmax = lmaxp
p1.tropismN=tropismNp
p1.tropismS=tropismSp
p1.r=rp
for p in rs.getRootRandomParameter():
p.lns = 0
p.rs = 0
p.lmaxs = 0
p.thetas = 0
p.las = 0
p.lbs=0
rs.setSeed(1)
rs.getRootSystemParameter().seedPos = pb.Vector3d(distr * i, distp * j, -3.) # cm
rs.initialize()
allRS.append(rs)
# Simulate
for rs in allRS:
rs.simulate(simtime)
# Export results as single vtp files (as polylines)
ana = pb.SegmentAnalyser() # see example 3b
for z, rs in enumerate(allRS):
# vtpname = "results/rlds/plant_" + str(z) + ".vtp"
# rs.write(vtpname)
ana.addSegments(rs) # collect all
# Write all into single file (segments)
# ana.write("results/rlds/all_plants.vtp")
ana.mapPeriodic(interrow, row)
# ana.write("results/rlds/plant_periodic.vtp")
rl_ = []
ana.crop(soilcolumns[k])
ana.pack()
# ana.write("results/rlds/core"+str(k+1)+".vtp")
# axes[k].set_title('Soil core'+' ' +str(k+1))
for j in range(len(times)):
ana.filter("creationTime", 0, times[j])
rl_.append(ana.distribution("length", 0., -depth, layers, True))
# axes[k].plot(np.array(rl_[-1]) / layerVolume, z_)
# axes[k].legend(["120 days", "60 days", "30 days", "15 days"])
rld[k]=np.array(rl_)/layerVolume
# for a in axes:
# a.set_xlabel('RLD $(cm/cm^3)$')
# a.set_ylabel('Depth $(cm)$')
# a.set_xlim(0,np.max(rld))
# fig.subplots_adjust()
# plt.savefig("results/rlds/rld_plot.png")
# plt.show()
RLD=np.reshape(rld,(rld.shape[0]*rld.shape[1]*rld.shape[2],1))
# print(rld)
# with open('results/rlds/rld.pkl','wb') as f:
# pkl.dump(rld, f)
# sys.exit()
err = math.sqrt(sum(((np.subtract(RLD,real_RLD)))**2)/len(RLD)) #NRMSE
return err