def test_coord(self):
pl = pb.MappedPlant()
path = "../modelparameter/plant/"
name = "test_relcoord"
pl.readParameters(path + name + ".xml")
#stochastic = False => thus rand() always give 0.5 for Tropism. => result only change according to sigma
pl.initialize(stochastic=False)
dt = 1
steps = 100
for step in range(steps):
pl.simulate(1, False)
pl.write("test_relcoord.vtp")
params = pl.organParam
seedPosx = params[1][0].seedPos.x
seedPosy = params[1][0].seedPos.y
seedPosz = params[1][0].seedPos.z
#print(params[1][0].seedPos)
roots = pl.getOrgans(2)
leaves = pl.getOrgans(4)
#stems = pl.getOrgans(3)
rootSubtypes = [o.param().subType for o in roots]
#stemSubtypes = [ o.param().subType for o in stems]
#roots1 = np.array(roots)[np.where([st == 1 for st in rootSubtypes])[0]]
#roots2 = np.array(roots)[np.where([st == 2 for st in rootSubtypes])[0]]
roots3 = np.array(roots)[np.where([st == 3 for st in rootSubtypes])[0]]
#stems1 = np.array(roots)[np.where([st == 1 for st in stemSubtypes])[0]]
#stems3 = np.array(roots)[np.where([st == 3 for st in stemSubtypes])[0]]
rootTipsX = [
np.array(r.getNode(r.getNumberOfNodes() - 1))[0] for r in roots3
]
rootTipsY = [
np.array(r.getNode(r.getNumberOfNodes() - 1))[1] for r in roots3
]
rootTipsZ = [
np.array(r.getNode(r.getNumberOfNodes() - 1))[2] for r in roots3
]
leafTipsX = [
np.array(r.getNode(r.getNumberOfNodes() - 1))[0] for r in leaves
]
leafTipsY = [
np.array(r.getNode(r.getNumberOfNodes() - 1))[1] for r in leaves
]
leafTipsZ = [
np.array(r.getNode(r.getNumberOfNodes() - 1))[2] for r in leaves
]
for i in range(0, len(rootTipsX)):
#print(rootTipsX[i], leafTipsX[i])
self.assertAlmostEqual(
rootTipsX[i] - seedPosx, -(leafTipsX[i] - seedPosx), 10,
"tip of 3rd lat root and leaf n°" + str(i) + " not symetric")
for i in range(0, len(rootTipsY)):
#print(rootTipsY[i]*10**16, leafTipsY[i]*10**16)
self.assertAlmostEqual(
rootTipsY[i] * 10**16, leafTipsY[i] * 10**16, 10,
"tip of 3rd lat root and leaf n°" + str(i) + " not symetric")
for i in range(0, len(rootTipsZ)):
#print(rootTipsZ[i]-seedPosz, leafTipsZ[i]-seedPosz, seedPosz)
self.assertAlmostEqual(
rootTipsZ[i] - seedPosz, -(leafTipsZ[i] - seedPosz), 10,
"tip of 3rd lat root and leaf n°" + str(i) + " not symetric")
#p_g = -2000 # water potential of the guard cell
RH = 0.5 # relative humidity
TairC = 20
p_a = -1000 #default outer water potential
simtime = 14.0 # [day] for task b
k_soil = []
Q = 900e-6 # mol quanta m-2 s-1 light, example from leuning1995
cs = 350e-6 #co2 paartial pressure at leaf surface (mol mol-1)
TairK = TairC + 273.15
es = 0.61078 * math.exp(17.27 * TairC / (TairC + 237.3))
ea = es * RH
VPD = es - ea
# root system
pl = pb.MappedPlant() #pb.MappedRootSystem() #pb.MappedPlant()
path = "../../../modelparameter/plant/" #"../../../modelparameter/rootsystem/"
name = "manyleaves" #"Anagallis_femina_Leitner_2010" # Zea_mays_1_Leitner_2010
pl.readParameters(path + name + ".xml")
""" soil """
min_ = np.array([-5, -5, -15])
max_ = np.array([9, 4, 0])
res_ = np.array([5, 5, 5])
pl.setRectangularGrid(pb.Vector3d(min_), pb.Vector3d(max_), pb.Vector3d(res_),
True) # cut and map segments
pl.initialize()
pl.simulate(simtime, False)
#rs.simulate(simtime, False) #test to see if works in case of several simulate
r = Leuning(pl)
dir_name = "/results"
dir_name2 = home_dir + dir_name
test = os.listdir(dir_name2)
for item in test:
if item.endswith("10.txt"):
os.remove(os.path.join(dir_name2, item))
if item.endswith("10.vtk"):
os.remove(os.path.join(dir_name2, item))
if item.endswith("10.vtp"):
os.remove(os.path.join(dir_name2, item))
######################
#
# plant
#
#######################
pl = pb.MappedPlant(seednum=1) #set seed
path = "../../../modelparameter/plant/" #"../../../modelparameter/rootsystem/"
name = "4testrel"
pl.readParameters(path + name + ".xml")
dt = 1
steps = 35
pl.initialize(verbose=True)
for step in range(steps):
print("\n\n\nstep n°", step)
pl.simulate(dt, True)
ana = pb.SegmentAnalyser(pl)
ana.write("results/example_10_%s.vtp" % (step))