def stem_example_rtp(self):
""" an example used in the tests below, a main stem with laterals """
self.plant = pb.Organism(
) # store organism (not owned by Organ, or OrganRandomParameter)
p0 = pb.StemRandomParameter(self.plant)
p0.name, p0.subType, p0.la, p0.lb, p0.lmax, p0.ln, p0.r, p0.dx = "main", 1, 1, 10, 100, (
89. / 19.), 1, 0.5
p0.successor = [3]
p0.successorP = [1.]
p1 = pb.StemRandomParameter(self.plant)
p1.name, p1.subType, p1.la, p1.ln, p1.r, p1.dx = "lateral", 3, 25, 0, 2, 0.1
self.p0, self.p1 = p0, p1 # needed at later point
self.plant.setOrganRandomParameter(
p0) # the organism manages the type parameters and takes ownership
self.plant.setOrganRandomParameter(p1)
# TODO (first node is not set, if seed is used)
self.plant.setOrganRandomParameter(pb.SeedRandomParameter(self.plant))
self.seed = pb.Seed(
self.plant) # store parent (not owned by child Organ)
#
param0 = p0.realize() # set up stem by hand (without a stem system)
param0.la, param0.lb = 0, 0 # its important parent has zero length, otherwise creation times are messed up
parentstem = pb.Stem(1, param0, True, True, 0., 0.,
pb.Vector3d(0, 0, -1), 0, 0, False,
0) # takes ownership of param0
parentstem.setOrganism(self.plant)
parentstem.addNode(pb.Vector3d(0, 0, -3),
0) # there is no nullptr in Python
self.parentstem = parentstem # store parent (not owned by child Organ)
#
self.stem = pb.Stem(self.plant, p0.subType, pb.Vector3d(0, 0, -1), 0,
self.parentstem, 0, 0)
self.stem.setOrganism(self.plant)
def test_parameter(self):
""" tests getParameter() """
plant = pb.Organism()
srp = pb.SeedRandomParameter(plant)
srp.firstB = 0.123
srp.delaySBs = 12
ot = srp.getParameter("organType") # test defaults
st = srp.getParameter("subType")
nz = srp.getParameter("nz")
firstB = srp.getParameter("firstB")
delaySBs = srp.getParameter("delaySB_dev")
firstB2 = srp.getParameter(
"firstB_mean"
) # we can always add "_mean" to avoid naming conflicts
self.assertEqual(ot, 1., "getParameter: value unexpected")
self.assertEqual(st, 0, "getParameter: value unexpected")
self.assertEqual(nz, 1., "getParameter: value unexpected")
self.assertEqual(firstB, 0.123, "getParameter: value unexpected")
self.assertEqual(firstB, firstB2, "getParameter: value unexpected")
self.assertEqual(delaySBs, 12, "getParameter: value unexpected")
srp.firstB = 123 # change values
srp.delaySBs = 456
firstB = srp.getParameter("firstB")
delaySBs = srp.getParameter("delaySB_dev")
self.assertEqual(firstB, 123, "getParameter: value unexpected")
self.assertEqual(delaySBs, 456, "getParameter: value unexpected")
def root_example_rrp(self):
""" an example used in the tests below, a main root with laterals """
self.plant = pb.Organism(
) # 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.r, p0.dx = "taproot", 1, 10., 1., 100., 1., 1.5, 0.5
p0.successor = [2]
p0.successorP = [1.]
p1 = pb.RootRandomParameter(self.plant)
p1.name, p1.subType, p1.lmax, p1.r, p1.dx = "lateral", 2, 25., 2., 0.1
self.p0, self.p1 = p0, p1 # needed at later point
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)
param0 = p0.realize() # set up root by hand (without a root system)
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, -3),
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)
def test_leaf(self):
""" leaf without lateral leafs """
ons = pb.Matrix3d(pb.Vector3d(0., 0., 1.), pb.Vector3d(0., 1., 0.), pb.Vector3d(1., 0., 0.))
plant = pb.Plant() # store organism (not owned by Organ, or OrganRandomParameter)
p0 = pb.LeafRandomParameter(plant)
p0.name, p0.subType, p0.la, p0.lb, p0.lmax, p0.ln, p0.r, p0.dx = "leaf", 1, 3.5, 1., 7.5, 3, 1, 0.1
phi = np.array([-90, -45, 0., 45, 90]) / 180. * np.pi
l = np.array([3, 2.2, 1.7, 2, 3.5])
N = 100 # N is rather high for testing
p0.createLeafRadialGeometry(phi, l, N)
# y = np.array([-3, -3 * 0.7, 0., 3.5 * 0.7, 3.5])
# l = np.array([0., 2.2 * 0.7, 1.7, 1.8 * 0.7, 0.])
# N = 105 # N is rather high for testing
# p0.createLeafGeometry(y, l, N)
plant.setOrganRandomParameter(p0) # the organism manages the type parameters and takes ownership
plant.setOrganRandomParameter(pb.SeedRandomParameter(plant))
# because we cannot pass a nullptr to pb.Leaf(...) L48
param0 = p0.realize() # set up leaf by hand (without a leaf syleaf)
param0.la, param0.lb = 0, 0 # its important parent has zero length, otherwise creation times are messed up
parentleaf = pb.Leaf(1, param0, True, True, 0., 0., ons, 0, False, 0) # takes ownership of param0
parentleaf.setOrganism(plant)
parentleaf.addNode(pb.Vector3d(0, 0, -3), 0) # there is no nullptr in Python
leaf = pb.Leaf(plant, p0.subType, ons, 0, parentleaf , 0)
leaf.setOrganism(plant)
leaf.simulate(7)
vp.plot_leaf(leaf)
def test_toString(self):
""" tests __str__ output """
self.srp = pb.SeedRandomParameter(pb.Organism())
srp = self.srp # rename
srp.name = "the seed"
# print(srp.__str__(False))
# print(srp)
self.assertEqual(srp.__str__(False),
"name: the seed, organType: 1, subType: 0.",
"toString: value unexpected")
def shoot_example(self):
""" example seed parameters used below """
self.plant = pb.Organism()
self.srp = pb.SeedRandomParameter(self.plant)
self.srp.firstB = 10
self.srp.delayB = 7
self.srp.nC = 5
self.srp.firstSB = 21
self.srp.delaySB = 4
self.srp.delayRC = 15
self.srp.nz = 1.
self.srp.subType = 0
def get_srp(self):
self.plant = pb.Organism() # need to store this
srp = pb.SeedRandomParameter(self.plant)
srp.seedPos = pb.Vector3d(0, 0, -2)
srp.firstB = 3 # basal
srp.delayB = 5
srp.maxB = 7
srp.nC = 7
srp.firstSB = 30 # shoot borne
srp.delaySB = 10
srp.delayRC = 70
srp.nz = 0.7
srp.maxTil = 3 # stem
srp.simtime = 10
self.plant.setOrganRandomParameter(srp)
return srp
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_constructors(self):
""" tests constructor and copy """
plant = pb.Organism()
srp = pb.SeedRandomParameter(plant)
srp.firstB = 123
srp.firstBs = 456
srp.nz = 789
srp2 = srp.copy(plant)
self.assertIsNot(srp, srp2,
"copy: organ type parameter set is not copied")
self.assertEqual(srp2.name, srp.name, "copy: value unexpected")
self.assertEqual(srp2.organType, srp.organType,
"copy: value unexpected")
self.assertEqual(srp2.subType, srp.subType, "copy: value unexpected")
self.assertEqual(srp2.firstB, srp.firstB, "copy: value unexpected")
self.assertEqual(srp2.firstBs, srp.firstBs, "copy: value unexpected")
self.assertEqual(srp2.nz, srp.nz, "copy: value unexpected")
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)
def test_xml(self):
""" write the organ as xml, and rereads it """
self.shoot_example()
otp = self.srp # rename
otp.name = "best_seed"
otp.subType = 0
otp.writeXML("seed.xml")
otp2 = pb.SeedRandomParameter(self.plant)
otp2.readXML("seed.xml")
self.assertEqual(otp2.name, otp.name, "xml: value unexpected")
self.assertEqual(otp2.organType, otp.organType,
"xml: value unexpected")
self.assertEqual(otp2.subType, otp.subType, "xml: value unexpected")
self.assertEqual(otp2.firstB, otp.firstB,
"xml: value unexpected") # value
self.assertEqual(otp2.delayRC, otp.delayRC,
"xml: value unexpected") # value
self.assertEqual(otp2.firstBs, otp.firstBs,
"xml: value unexpected") # dev
self.assertEqual(otp2.delayRCs, otp.delayRCs,
"xml: value unexpected") # dev
def stem_example_rtp(self, phytomereGrowth = "sequential"):
""" an example used in the tests below, a main stem with laterals """
self.plant = pb.Plant() # store organism (not owned by Organ, or OrganRandomParameter)
p0 = pb.StemRandomParameter(self.plant)
p0.name, p0.subType, p0.la, p0.lb, p0.lmax, p0.ln, p0.r, p0.dx, p0.dxMin = "main", 1, 10., 10., 100., 1., 1.5, 1, 0.5
p0.delayLat = 1.
p0.delayNG = 2.
p0.successor = [5]
p0.successorP = [1.]
if phytomereGrowth == "sequential":
p0.nodalGrowth = 0
if phytomereGrowth == "equal":
p0.nodalGrowth = 1
p1 = pb.StemRandomParameter(self.plant)
p1.name, p1.subType, p1.lmax, p1.r, p1.dx, p1.dxMin = "lateral", 5, 5., 2., 1, 0.5
self.p0, self.p1 = p0, p1 # needed at later point
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)
# creates seed organ (otherwise throws error in plant::simulate())
# test == True => no need to give root parameter
self.plant.initialize(verbose = False, test = True)
param0 = p0.realize() # set up stem by hand (without a stem system)
param0.la, param0.lb = 0, 0 # its important parent has zero length, otherwise creation times are messed up
self.ons = pb.Matrix3d(pb.Vector3d(0., 0., 1.), pb.Vector3d(0., 1., 0.), pb.Vector3d(1., 0., 0.))
parentstem = pb.Stem(1, param0, True, True, 0., 0., self.ons, 0, False, 0) # takes ownership of param0
parentstem.setOrganism(self.plant)
parentstem.addNode(pb.Vector3d(0, 0, -3), 0) # there is no nullptr in Python
self.parentstem = parentstem # store parent (not owned by child Organ)
self.stem = pb.Stem(self.plant, p0.subType, self.ons, 0, self.parentstem , 0)
self.stem.setOrganism(self.plant)
p2.dx = 0.25 # [cm] axial resolution
p2.a, p2.a_s = 0.0501, 0.0069 # [cm] radius TODO
p2.theta = (180. - 98.45) / 180. * np.pi # [rad]
# p2.lmax, p2.lmaxs = 3.339, 0.2 * 3.339 # fit k and r
# p2.r, p2.rs = 3.745, 0.1 * 3.745 # fit k and r
p2.lmax, p2.lmaxs = 5, 0.5 # fit r
p2.r, p2.rs = 0.483, 0.1 * 0.483 # fit r
p2.r, p2.rs = 0.823, 0.1 * 0.823 # fit r (last measurement removed)
# by visual comparison
p2.tropismT, p2.tropismN, p2.tropismS = pb.TropismType.gravi, 1, 0.2
rs.setOrganRandomParameter(p0)
rs.setOrganRandomParameter(p1)
rs.setOrganRandomParameter(p2)
""" seed """
srp = pb.SeedRandomParameter(rs) # with default values
srp.seedPos = pb.Vector3d(0., 0., -0.6) # [cm] seed position TODO ?
srp.maxB = 0 # [-] number of basal roots (neglecting basal roots and shoot borne)
rs.setRootSystemParameter(srp)
""" container geometry """
length = 7.425 # cm
height = 14.31 # cm
rhizotron = pb.SDF_PlantBox(length, length, height)
rs.setGeometry(rhizotron) # soilcore, or rhizotron
# elongation impedance at boundaries
layer = 0.5 # cm
smaller_rhizotron = pb.SDF_PlantBox(length - 2 * layer, length - 2 * layer,
height - layer)
scale_elongation = Boundary_Elongation_Impedance(
smaller_rhizotron, 0.1) # 1 instead of 0.1 would disable the impedance
def create_basil(): plant = pb.Plant() p0 = pb.RootRandomParameter(plant) # with default values, p1 = pb.RootRandomParameter(plant) # all standard deviations are 0 s2 = pb.StemRandomParameter(plant) s3 = pb.StemRandomParameter(plant) l1 = pb.LeafRandomParameter(plant) p0.name = "taproot" p0.a = 0.2 # [cm] radius p0.subType = 1 # [-] index starts at 1 p0.lb = 5 # [cm] basal zone p0.la = 10 # [cm] apical zone p0.lmax = 30 # [cm] maximal root length, number of lateral branching nodes = round((lmax-lb-la)/ln) + 1 p0.ln = 1. # [cm] inter-lateral distance (16 branching nodes) p0.theta = 0. # [rad] p0.r = 1 # [cm/day] initial growth rate p0.dx = 10 # [cm] axial resolution p0.successor = [2] # add successors p0.successorP = [1] # probability that successor emerges p0.tropismT = pb.TropismType.gravi # p0.tropismN = 1.8 # [-] strength of tropism p0.tropismS = 0.2 # [rad/cm] maximal bending p1.name = "lateral" p1.a = 0.1 # [cm] radius p1.subType = 2 # [1] index starts at 1 p1.lmax = 15 # # [cm] apical zone p1.lmaxs = 0.15 # [cm] standard deviation of the apical zone p1.theta = 90. / 180. * np.pi # [rad] p1.r = 2 # initial growth rate p1.dx = 1 # [cm] axial resolution p1.tropismT = pb.TropismType.gravi # exo p1.tropismN = 2 # [-] strength of tropism p1.tropismS = 0.1 # [rad/cm] maximal bending s2.name = "mainstem" s2.subType = 1 s2.lmax = 25 # s2.lmaxs = 1 s2.lb = 3 s2.la = 0 s2.ln = 3 # This value is normally the Inter-lateral distance [cm], but with decussate plant, this value is # multiplied by 2 s2.lnf = 5 # This value means "successors in a decussate position" s2.RotBeta = 1 s2.BetaDev = 0 s2.InitBeta = 0 s2.gf = 1 s2.successor = [2] s2.successorP = [1] s2.tropismT = 4 # s2.theta = 1/6 s2.theta = 0 s2.tropismN = 18 s2.tropismS = 0.01 s3.name = "invisible" # The invisible stem representing the bud of the leaf s3.subType = 2 s3.la = 0 s3.ln = 0 s3.lmax = 5 s3.RotBeta = 1 s3.BetaDev = 0 s3.InitBeta = 0.5 s3.tropismS = 0 s3.lnf = 5 l1.name = 'basil' l1.subType = 2 l1.lb = 2 l1.la = 0.2 l1.lmax = 5 l1.r = 0.5 l1.RotBeta = 0.5 l1.BetaDev = 0 l1.InitBeta = 0.5 l1.tropismT = 1 l1.tropismN = 5 l1.tropismS = 0.1 l1.theta = 0.35 l1.thetas = 0.05 l1.gf = 1 l1.lnf = 5 # If not precised, it will not be possible to do the opposite decussate arrangement plant.setOrganRandomParameter(p0) plant.setOrganRandomParameter(p1) plant.setOrganRandomParameter(s2) plant.setOrganRandomParameter(s3) plant.setOrganRandomParameter(l1) srp = pb.SeedRandomParameter(plant) # with default values # srp.seedPos = pb.Vector3d(10, 10, -3.) # [cm] seed position srp.seedPos = pb.Vector3d(0, 0, -3.) # [cm] seed position srp.maxB = 0 # [-] number of basal roots (neglecting basal roots and shoot borne) srp.firstB = 10. # [day] first emergence of a basal root srp.delayB = 3. # [day] delay between the emergence of basal roots plant.setOrganRandomParameter(srp) return plant
def create_arabidopsis(): plant = pb.Plant() p0 = pb.RootRandomParameter(plant) # with default values, p1 = pb.RootRandomParameter(plant) # all standard deviations are 0 s1 = pb.StemRandomParameter(plant) s2 = pb.StemRandomParameter(plant) s3 = pb.StemRandomParameter(plant) s4 = pb.StemRandomParameter(plant) l1 = pb.LeafRandomParameter(plant) p0.name = "taproot" p0.a = 0.2 # [cm] radius p0.subType = 1 # [-] index starts at 1 p0.lb = 5 # [cm] basal zone p0.la = 10 # [cm] apical zone p0.lmax = 30 # [cm] maximal root length, number of lateral branching nodes = round((lmax-lb-la)/ln) + 1 p0.ln = 1. # [cm] inter-lateral distance (16 branching nodes) p0.theta = 0. # [rad] p0.r = 1 # [cm/day] initial growth rate p0.dx = 10 # [cm] axial resolution p0.successor = [2] # add successors p0.successorP = [1] # probability that successor emerges p0.tropismT = pb.TropismType.gravi # p0.tropismN = 1.8 # [-] strength of tropism p0.tropismS = 0.2 # [rad/cm] maximal bending p1.name = "lateral" p1.a = 0.1 # [cm] radius p1.subType = 2 # [1] index starts at 1 p1.lmax = 15 # # [cm] apical zone p1.lmaxs = 0.15 # [cm] standard deviation of the apical zone p1.theta = 90. / 180. * np.pi # [rad] p1.r = 2 # initial growth rate p1.dx = 1 # [cm] axial resolution p1.tropismT = pb.TropismType.gravi # exo p1.tropismN = 2 # [-] strength of tropism p1.tropismS = 0.1 # [rad/cm] maximal bending s1.name = "mainstem" s1.subType = 1 s1.lmax = 25 s1.lmaxs = 1 s1.lb = 0 s1.lbs = 0.1 s1.la = 3 s1.las = 0.1 s1.ln = 3 s1.lns = 0.2 s1.lnf = 0 # 1 peut être cool s1.RotBeta = 0 s1.BetaDev = 0 s1.InitBeta = 0 s1.gf = 1 s1.successor = [3, 2] s1.successorP = [0.3, 0.7] # s1.successor = [3] # s1.successorP = [1] s1.tropismT = 1 s1.theta = 0. s1.thetas = 0.05 s1.tropismN = 2 s1.tropismS = 0.005 s1.r = 1 s1.rs = 0.05 s2.name = "secondary_stem" s2.subType = 3 s2.lmax = 7 s2.lmaxs = 0.2 s2.lb = 0 s2.la = 2 s2.ln = 2 s2.lns = 0.1 s2.lnf = 0 s2.RotBeta = 2 / 3 s2.BetaDev = 0.1 s2.InitBeta = 0 s2.gf = 1 s2.successor = [2] s2.successorP = [1] s2.tropismT = 4 s2.theta = 0.3 s2.thetas = 0.02 s2.tropismN = 18 s2.tropismS = 0.01 s2.r = 0.5 s2.rs = 0.02 s3.name = "invisible stem" s3.subType = 2 s3.lmax = 5 s3.la = 0 s3.ln = 0 s3.RotBeta = 2/3 s3.BetaDev = 0 s3.InitBeta = 0. s3.lb = 0 s3.la = 0 s3.ln = 0 s3.lnf = 0 s3.RotBeta = 2 / 3 s3.BetaDev = 0 s3.InitBeta = 0 s3.gf = 1 s3.tropismT = 1 s3.theta = 0.3 s3.tropismN = 18 s3.tropismS = 0.01 s3.r = 1 l1.name = 'leaf_under_second_stem' l1.subType = 2 l1.lb = 2 l1.la = 0.2 l1.lmax = 5 l1.lmaxs = 0.1 l1.r = 0.5 l1.rs = 0.02 l1.RotBeta = 0.5 l1.BetaDev = 0 l1.InitBeta = 0. l1.tropismT = 1 l1.tropismN = 5 l1.tropismS = 0.15 l1.theta = 0.35 l1.gf = 1 s4.name = "rosette" # Cannot be a leaf organ because we can only create 1 leaf organ subType s4.subType = 4 s4.lmax = 10 s4.lmaxs = 0.2 s4.lb = 1 s4.la = 0 s4.ln = 2 s4.lnf = 0 s4.RotBeta = 3 / 5 s4.BetaDev = 0.02 s4.InitBeta = 0 s4.gf = 1 s4.tropismT = 1 s4.theta = 0.3 s4.thetas = 0.02 s4.tropismN = 18 s4.tropismS = 0.01 s4.r = 0.5 s4.rs = 0.02 plant.setOrganRandomParameter(p0) plant.setOrganRandomParameter(p1) plant.setOrganRandomParameter(s1) plant.setOrganRandomParameter(s2) plant.setOrganRandomParameter(s3) plant.setOrganRandomParameter(s4) plant.setOrganRandomParameter(l1) srp = pb.SeedRandomParameter(plant) # with default values srp.seedPos = pb.Vector3d(0., 0., -3.) # [cm] seed position srp.maxB = 0 # [-] number of basal roots (neglecting basal roots and shoot borne) srp.firstB = 10. # [day] first emergence of a basal root srp.delayB = 3. # [day] delay between the emergence of basal roots srp.maxTil = 10 plant.setOrganRandomParameter(srp) return plant
""" shows inter lateral spacing (ln) and how a linear slope (lnk) can modify them """
import sys
sys.path.append("../../..")
sys.path.append("../../../src/python_modules")
import plantbox as pb
import matplotlib.pyplot as plt
import numpy as np
fig, axes = plt.subplots(2, 3, figsize=(15, 7))
rs = pb.RootSystem()
srp = pb.SeedRandomParameter(rs)
srp.firstB, srp.delayB, srp.maxB = 1., 1., 0
rs.setRootSystemParameter(srp)
dx0, dx1 = 100, 1 # very large resolution for taproot
theta = 70 / 180 * np.pi
p0 = pb.RootRandomParameter(rs)
p0.name, p0.subType, p0.lmax, p0.r, p0.dx, p0.theta = "taproot", 1, 50., 2., dx0, 0. # parameters as before
p0.tropismT, p0.tropismN, p0.tropismS = pb.TropismType.gravi, 2, 0.1
p0.successor, p0.successorP = [2], [1.] # set up successors
p0.lns = 0. # test with other values...
p0.lb, p0.la = 0., 0.
rs.setOrganRandomParameter(p0)
p1 = pb.RootRandomParameter(rs)
p1.name, p1.subType, p1.lmax, p1.r, p1.dx, p1.theta = "lateral", 2, 30., 1., dx1, theta
p1.tropismT, p1.tropismN, p1.tropismS = pb.TropismType.exo, 2, 0.2
rs.setOrganRandomParameter(p1)
import sys; sys.path.append(".."); sys.path.append("../../src/python_modules"); sys.path.append("../../")
import numpy as np
import matplotlib.pyplot as plt
import plantbox as pb
import vtk_plot as vp
plant = pb.Plant()
seed_rp = pb.SeedRandomParameter(plant)
seed_rp.subType = 0
plant.setOrganRandomParameter(seed_rp)
root_rp = pb.RootRandomParameter(plant)
root_rp.subType = 1
root_rp.lmax = 1
root_rp.r = 0.1
root_rp.theta = 0
plant.setOrganRandomParameter(root_rp)
stem_rp = pb.StemRandomParameter(plant)
stem_rp.subType = 1
stem_rp.la = 1.
stem_rp.lb = 5
stem_rp.lmax = 7.5
stem_rp.ln = 1
stem_rp.theta = 0
stem_rp.successor = [2]
stem_rp.successorP = [1]
plant.setOrganRandomParameter(stem_rp)
