def test_hydraulic_prop_attributes_the_right_properties_to_the_different_organs(
):
simple_shoot = potted_syrah()
simple_shoot.node(simple_shoot.root).vid_base = architecture.mtg_base(
simple_shoot, vtx_label='inT')
vid_base = simple_shoot.node(simple_shoot.root).vid_base
for vtx_id in traversal.post_order2(simple_shoot, vid_base):
n = simple_shoot.node(vtx_id)
if n.label.startswith('LI'):
n.E = 0.
n.An = 0.
hydraulic.hydraulic_prop(simple_shoot,
mass_conv=18.01528,
length_conv=1.e-2,
a=2.6,
b=2.0,
min_kmax=0.)
for vtx_id in traversal.post_order2(simple_shoot, vid_base):
n = simple_shoot.node(vtx_id)
assert hasattr(n, 'Flux')
assert hasattr(n, 'FluxC')
if n.label.startswith(('in', 'cx', 'Pet')):
assert hasattr(n, 'Kmax')
def hydraulic_prop(g, mass_conv=18.01528, length_conv=1.e-2, a=2.6, b=2.0, min_kmax=0.):
"""Computes water flux `Flux` and maximum hydraulic conductivity `Kmax` of each hydraulic segment. Both properties
are then attached to the corresponding mtg nodes.
Args:
g (openalea.mtg.MTG): a multiscale tree graph object
mass_conv (float): [gr mol-1] molar mass of H2O
length_conv (float): conversion coefficient from the length unit of the mtg to that of [1 m]
a (float): [kg s-1 MPa-1] slope of the Kh(D) relationship, see :func:`conductivity_max` for details
b (float): [-] exponent of the Kh(D) relationship, see :func:`conductivity_max` for details
min_kmax (float): [kg s-1 m MPa-1] minimum value for the maximum conductivity, see :func:`conductivity_max`
for details
Returns:
(openalea.mtg.MTG): the multiscale tree graph object
Notes:
The units of **Flux** and **Kmax** properties are related:
- if `Flux` is given as water flux [kg s-1], then `Kmax` is in [kg m s-1 Pa-1] (or [kg m s-1 MPa-1])
- else if `Flux` is given as water flux density [kg m-2 s-1], then `Kmax` is in [kg m-1 s-1 Pa-1]
(or [kg m-1 s-1 MPa-1])
Transpiration flux density per leaf surface area `E` (propery of the :arg:`mtg`) must be in [mol m-2 s-1],
otherwise, the :arg:`mass_conv` value must be re-adapted
The resulting water potential, calculated in :func:`transient_xylem_water_potential` is then given in [MPa]
"""
vid_base = g.node(g.root).vid_base
for vtx_id in traversal.post_order2(g, vid_base):
n = g.node(vtx_id)
if n.label.startswith('LI'):
try:
leaf_area = n.leaf_area * 1.
except (AttributeError, TypeError):
leaf_area = surf(n.geometry) * length_conv ** 2 # [m2]
# Note: The surface of the leaf mesh is overestimated compared to allometry results
# leaf_area = (0.0175*(n.Length*10.)**1.9057)*LengthConv**2 #[m2]
n.leaf_area = leaf_area
n.Flux = (n.E * mass_conv * 1.e-3) * leaf_area
# n.FluxC = ((n.An)*44.0095*1.e-9)*leaf_area # [kgCO2 s-1]
n.FluxC = n.An * leaf_area # [umol s-1]
elif n.label.startswith(('in', 'cx', 'Pet')):
n.Flux = sum([vtx.Flux for vtx in n.children()])
diam = 0.5 * (n.TopDiameter + n.BotDiameter) * length_conv
n.Kmax = conductivity_max(diam, a, b, min_kmax)
n.FluxC = sum([vtx.FluxC for vtx in n.children()])
elif n.label.startswith('rhyzo'):
n.Flux = sum([vtx.Flux for vtx in n.children()])
n.FluxC = sum([vtx.FluxC for vtx in n.children()])
n.Kmax = None
return g
def hydraulic_prop(mtg, vtx_label='inT', MassConv=18.01528, LengthConv=1.e-2,
a=2.6, b=2.0, min_kmax=0.):
"""
Returns water flux, `F` [kg s-1] and maximum stem conductivity [kg m s-1 Pa-1] of each internode.
:Attention:
1. The units of **F** and **K** are related:
- if `F` is given as water flux [kg s-1], then `K` must be given as [kg m s-1 Pa-1] (or [kg m s-1 MPa-1])
- else if `F` is given as water flux density [kg m-2 s-1], then `K` must be given as [kg m-1 s-1 Pa-1] (or [kg m-1 s-1 MPa-1]).
2. Transpiration flux density per leaf surface area `E` must be in [mol m-2 s-1], otherwise, the `MassConv` value must be readapted.
The resulting water portential, calculated in :func:`transient_xylem_water_potential` is then given in [MPa].
:Parameters:
- **mtg**: an MTG object
- **vtx_label**: string, the label prefix of the basal vertex at highest scale
- **MassConv**: molar mass of H2O [gr mol-1]
- **LengthConv**: conversion coefficient from the length unit of the mtg to that of 1 m
- **a** and **b**: respectively the slope and power parameters for the Kh(D) relationship
- **min_kmax**: float, minimum value for the maximum conductivity [kg s-1 m MPa-1]
"""
# Getting the basal vertex of the highest scale vertices
vid_base = mtg.node(mtg.root).vid_base
for vtx_id in traversal.post_order2(mtg,vid_base):
n = mtg.node(vtx_id)
if n.label.startswith('LI'):
try:
leaf_area = n.leaf_area*1.
except:
leaf_area = surf(n.geometry)*LengthConv**2 #[m2]
# leaf_area = (0.0175*(n.Length*10.)**1.9057)*LengthConv**2 #[m2]
n.leaf_area = leaf_area
# Note: The surface of the leaf mesh is overestimated compared to allometry results
n.Flux = ((n.E)*MassConv*1.e-3)*leaf_area
# n.FluxC = ((n.An)*44.0095*1.e-9)*leaf_area # [kgCO2 s-1]
n.FluxC = (n.An)*leaf_area # [umol s-1]
elif n.label.startswith(('in','cx','Pet')):
n.Flux = sum([vtx.Flux for vtx in n.children()])
Diam = 0.5*(n.TopDiameter + n.BotDiameter)*LengthConv
n.Kmax = k_max(Diam,a,b,min_kmax)
n.FluxC = sum([vtx.FluxC for vtx in n.children()])
elif n.label.startswith('rhyzo'):
n.Flux = sum([vtx.Flux for vtx in n.children()])
n.FluxC = sum([vtx.FluxC for vtx in n.children()])
n.Kmax = None
return mtg
def pipemodel(mtg, rootradius, leafradius, root=None):
from math import log
from openalea.mtg.traversal import post_order2
if root is None:
roots = mtg.roots(scale=mtg.max_scale())
assert len(roots) == 1
root = roots[0]
vertices = list(post_order2(mtg, root))
leaves = [vid for vid in vertices if len(mtg.children(vid)) == 0]
# pipeexponent = log(len(leaves)) / (log(rootradius) - log(leafradius))
# print pipeexponent
# invpipeexponent = 1./ pipeexponent
radiusprop = dict()
for vid in leaves:
radiusprop[vid] = leafradius
nbelems = dict()
for vid in leaves:
nbelems[vid] = 1
for vid in vertices:
if not vid in nbelems:
nbelems[vid] = sum([nbelems[child]
for child in mtg.children(vid)]) + 1
print(root, nbelems[root])
# pipeexponent = log(nbelems[root]) / (log(rootradius) - log(leafradius))
pipeexponent = (log(rootradius) - log(leafradius)) / log(nbelems[root])
print(pipeexponent)
invpipeexponent = 1. / pipeexponent
for vid in vertices:
if not vid in radiusprop:
radiusprop[vid] = leafradius * (nbelems[vid]**pipeexponent)
# for vid in post_order2(mtg, root):
# if not vid in radiusprop:
# rad = pow(sum([pow(radiusprop[child], pipeexponent) for child in mtg.children(vid)]), invpipeexponent)
# radiusprop[vid] = rad
return radiusprop
def pipemodel(mtg, rootradius, leafradius, root = None):
from math import log
from openalea.mtg.traversal import post_order2
if root is None:
roots = mtg.roots(scale=mtg.max_scale())
assert len(roots) == 1
root = roots[0]
vertices = list(post_order2(mtg, root))
leaves = [vid for vid in vertices if len(mtg.children(vid)) == 0]
#pipeexponent = log(len(leaves)) / (log(rootradius) - log(leafradius))
#print pipeexponent
#invpipeexponent = 1./ pipeexponent
radiusprop = dict()
for vid in leaves: radiusprop[vid] = leafradius
nbelems = dict()
for vid in leaves: nbelems[vid] = 1
for vid in vertices:
if not vid in nbelems:
nbelems[vid] = sum([nbelems[child] for child in mtg.children(vid)]) + 1
print root, nbelems[root]
#pipeexponent = log(nbelems[root]) / (log(rootradius) - log(leafradius))
pipeexponent = (log(rootradius) - log(leafradius))/log(nbelems[root])
print pipeexponent
invpipeexponent = 1./ pipeexponent
for vid in vertices:
if not vid in radiusprop:
radiusprop[vid] = leafradius*(nbelems[vid]**pipeexponent)
#for vid in post_order2(mtg, root):
# if not vid in radiusprop:
# rad = pow(sum([pow(radiusprop[child], pipeexponent) for child in mtg.children(vid)]), invpipeexponent)
# radiusprop[vid] = rad
return radiusprop
