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()
True) # cut and map segments
""" add segment indices """
segs = rs.segments
x = np.zeros(len(segs))
for i, s in enumerate(segs):
try:
x[i] = rs.seg2cell[i]
except: # in case the segment is not within the domain
x[i] = -1
""" infos on a specific cell"""
ci = rs.soil_index(0, 0, -7)
print("Cell at [0,0,-7] has index", ci)
try:
print(len(rs.cell2seg[ci]), "segments in this cell:")
print(rs.cell2seg[ci])
except:
print("There are no segments in this cell")
""" vizualise roots """
# ana = pb.SegmentAnalyser(rs) # <---- wrong!
ana = pb.SegmentAnalyser(rs.mappedSegments())
ana.addData("linear_index", x)
pd = vp.segs_to_polydata(ana, 1.,
["radius", "subType", "creationTime", "linear_index"])
rootActor, rootCBar = vp.plot_roots(pd, "linear_index", "segment index plot",
False)
""" vizualise soil """
grid = vp.uniform_grid(min_, max_, res_) # for visualization
meshActor, meshCBar = vp.plot_mesh(grid, "", "", False)
vp.render_window([meshActor, rootActor], "Test mapping", rootCBar,
grid.GetBounds()).Start()
rs.getNumberOfSegments()) # shoot segments are mapped
ana = pb.SegmentAnalyser(
rs.mappedSegments()
) # rs is MappedSegments and RootSystem. So passing rs it is not unique which constructor is called.
print("Number of segments", len(ana.segments), "x", len(x), "and", len(y))
ana.addData("linear_index", x) # node data are converted to segment data
ana.addData("zebra", y)
ana.mapPeriodic(max_[0] - min_[0], max_[1] - min_[1]) # data are also split
pd = vp.segs_to_polydata(
ana, 1., ["radius", "subType", "creationTime", "linear_index", "zebra"])
rootActor, rootCBar = vp.plot_roots(pd, "linear_index", 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()
grid = vp.uniform_grid(min_, max_, res_)
actors = vp.plot_mesh_cuts(pd, "linear_index")
print(actors)
print(len(actors))
# actors.extend([rootActor])
vp.render_window(actors, "Test mapping", rootCBar).Start()
import numpy as np
import matplotlib.pyplot as plt
""" root problem """
rs = pb.RootSystem()
path = "../../../../modelparameter/rootsystem/"
name = "Anagallis_femina_Leitner_2010"
rs.readParameters(path + name + ".xml")
for p in rs.getRootRandomParameter(): # Modify axial resolution
p.dx = 5 # [cm] adjust resolution
rs.initialize()
""" initial growth """
rs.simulate(1)
ana = pb.SegmentAnalyser(rs)
pd = vp.segs_to_polydata(ana, 1., ["radius", "subType", "creationTime"])
rootActor, rootCBar = vp.plot_roots(pd, "creationTime", False)
iren = vp.render_window(rootActor, "Animation", rootCBar)
c = 0
max_age = 60
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"])