def timer_callback_(obj, ev):
""" animation call back function (called every 0.1 second) """
global rootActor
global c
c += 1
print("hello", c)
rs.simulate(1)
ana = pb.SegmentAnalyser(rs)
pd = vp.segs_to_polydata(ana, 1., ["radius", "subType", "creationTime"])
newRootActor, rootCBar = vp.plot_roots(pd, "creationTime", False)
renWin = iren.GetRenderWindow()
ren = renWin.GetRenderers().GetFirstRenderer()
ren.RemoveActor(rootActor)
newRootActor.RotateX(-90)
ren.AddActor(newRootActor)
ren.ResetCamera()
rootActor = newRootActor
iren.Render()
if c >= max_age:
c = 0
rs.initialize()
def vector_3d(a):
return pb.Vector3d(a[0], a[1], a[2])
""" root problem """
r = XylemFluxPython("RootSystem.rsml") # returns a MappedSegments object
segs = r.rs.segments
nodes = r.rs.nodes
for i in range(0, len(nodes)):
nodes[i] = vector_3d(np.array(nodes[i]) / 100.)
r.rs.nodes = nodes
""" Mixed plot """
ana = pb.SegmentAnalyser(r.rs)
pd = vp.segs_to_polydata(ana, 1.e-2, ["radius", "subType", "creationTime"])
print("Root system bounds", pd.GetBounds())
rootActor, rootCBar = vp.plot_roots(pd, "creationTime", False)
ug = vp.read_vtu("benchmark3d_2-00001.vtu")
print("Mesh bounds", ug.GetBounds())
meshActor, meshCBar = vp.plot_mesh(
ug, "water content", "",
False) # "pressure head" # e.g. "S_liq" "water content"
vp.render_window([rootActor, meshActor], "mixed fun", meshCBar).Start()
# # Plot, using vtk
# rootActor, cBar = vp.plot_roots(rs, "creationTime", False)
# rootActor.RotateX(90) # to look at it from top
# vp.render_window(rootActor,"top view", cBar).Start()
# try:
# x[c] = rs.seg2cell[s.y - 1]
# except:
# x[c] = -1
y = np.zeros(x.shape[0])
for i in range(0, x.shape[0]):
y[i] = i % 2 if x[i] >= 0 else i % 2 - 2 #
for i in range(0, x.shape[0]):
x[i] = x[i] if x[i] >= 0 else -1
ana = pb.SegmentAnalyser(r.rs)
ana.addData("linear_index", x) # node data are converted to segment data
ana.addData("zebra", y)
pd = vp.segs_to_polydata(ana, 1., ["radius", "subType", "creationTime", "linear_index", "zebra"])
rootActor, rootCBar = vp.plot_roots(pd, "zebra", False)
""" Mesh """
width_ = max_ - min_
ind_ = res_ / width_
print("min ", min_)
print("max ", max_)
print("width ", width_)
print("cuboids", 1 / ind_)
grid = vp.uniform_grid(min_, max_, res_)
meshActor, meshCBar = vp.plot_mesh(grid, "", "", False)
vp.render_window([meshActor, rootActor], "Test mapping", rootCBar).Start()
import rsml_reader as rsml
import estimate_root_params as es
from xylem_flux import XylemFluxPython
import vtk_plot as vp
import plantbox as pb
time = range(1, 3) # measurement times (not in the rsml)
name = ["RSML/m1/dicot/lupin/lupin_d{:g}.rsml".format(a) for a in range(1, 10)]
# time = range(1, 3) # measurement times (not in the rsml)
# name = ["RSML/m1/monocot/maize/PL0{:g}_DAS0{:g}.rsml".format(1, a) for a in range(1, 8)]
# time = [75] # measurement times (not in the rsml)
# name = ["RSML/Maize_Kutschera.rsml"]
rs = XylemFluxPython(
name[0]) # parses rsml, XylemFluxPython.rs is of type MappedRootSegments
ana = pb.SegmentAnalyser(
rs.rs) # convert MappedRootSegments to a SegmentAnalyser
# radii = ana.data["radius"] # DOES NOT WORK (why?)
# for i in range(0, len(radii)):
# radii[i] /= 116.93
# ana.data["radius"] = radii
pd = vp.segs_to_polydata(
ana, 1. /
116.93) # makes a vtkPolydata (to save as .vtp, or visualize with vtk)
vp.plot_roots(pd, "radius") # plots vtkPolydata into an interactive window
p_s = np.linspace(-14000, -10000, 3001)
p_s[0:10] = -300
# 3 meter down, resolution in mm, dry with moist top
soil_index = lambda x, y, z: int(-10 * z)
r.rs.setSoilGrid(soil_index)
""" Numerical solution"""
rx = r.solve_neumann(
simtime, -0., p_s,
True) # True: matric potential given per cell (not per segment)
print("Transpiration", r.collar_flux(0., rx, [p_s]), "cm3/day")
eswp = 0.
n = len(r.rs.segments)
seg2cell = r.rs.seg2cell
for i in range(0, n):
eswp += suf[i] * p_s[seg2cell[i]]
print()
print("Equivalent soil water potential", eswp)
z = r.rs.nodes[1].z
print("Root collar potential ", rx[1], "node z", z, "psi",
p_s[soil_index(0, 0, z)])
print()
""" Additional vtk plot """
ana = pb.SegmentAnalyser(r.rs)
ana.addData("rx", rx) # node data are converted to segment data
pd = vp.segs_to_polydata(
ana, 1., ["radius", "subType", "creationTime", "length", "rx", "suf"])
vp.plot_roots(pd, "rx")