Parameters class#
example from the documentation
The main model parameters are grouped in the python class parameters, see openalea.hydroroot.init_parameter.Parameters. The parameters may be passed to the class by reading a yaml file, see openalea.hydroroot.init_parameter.Parameters.read_file.
There are two solvers in HydroRoot project. The first, used for the paper Boursiac et al. 2022, is a purely water transport model. The second is a solute and water transport model see Bauget et al. 2023. Therefore, the solute category in the yaml file has meaning only for the second solver.
click to see an example of parameter.yml file
archi:
#if read_architecture is true then architecture will be constructed from the file(s) given by input_dir and input_file
#otherwise the architecture will be generated according to the parameters
read_architecture: True
#Input architecture from scanned image (distance_from_base_(mm) \t lateral_root_length_(mm) \t order)
#folder name
input_dir: data/
#File name:
#may be a list of names, eg. [file1, file2, file3] wildcar may be used
input_file: [Exp03_P2.txt]
#seed used to generate an MTG, for a same seed we got the same MTG, if no seed is given a seed is generated randomly
#integer, list of integer or nothing
seed:
#file names with length laws relative path
#file format: "LR_length_mm" ; "relative_distance_to_tip"
#laws used to generate lateral roots of the 1st order (1_order_law), and lateral roots of order above 1 (2_order_law)
length_file:
- data/length_LR_order1_Exp33_20-10-09.csv
- data/length_LR_order1_Exp33_20-10-09.csv
#length of the primary root
#float or list of float
#unit: m
primary_length: 0.3
#branching delay
#float or list of float
#unit: m
branching_delay: 1.07e-3
#branching variability
#float between [0 ; 1], 0.25 means 25%
branching_variability: 0.25
#maximum roots order
order_max: 1
#vertices length
#unit: m
segment_length: 1.0e-3
#part of roots without any lateral root, distance from tip
#float or list of float
#unit: m
nude_length: 0.021
#reference radius of the primary root
#float
#unit: m
ref_radius: 0.525e-3
#radius decrease factor applied when increasing order
#float
#radius lateral order n: r = order_decrease_factor^n * ref_radius
order_decrease_factor: 0.36
hydro:
#radial conductivity
#float
#unit: microL/(s.MPa.m2)
k0: 174.7
#axial_conductance_data
# - [x1, ......, xn]
# - [K1, ....., Kn]
#list of float
#unit: microL.m/(s.Mpa)
axial_conductance_data:
- [0, 0.06, 0.13, 0.18, 0.23, 0.29, 0.43]
- [2.301E-04, 2.266E-04, 2.230E-02, 2.196E-02, 2.172E-02, 2.577E-02, 1.954E-01]
solute:
#J_s: active pumping rate
#float
#unit: mol/(m2.s)
J_s: 1.714E-07
#P_s: permeability coefficient
#float
#unit: m/s
P_s: 6.438E-10
#Cse: concentration of permeating solutes
#float
#unit: mol/m3 or mM
Cse: 13.96 #13.96 -> pi CTR = -0.034 MPa
#Ce: concentration of non-permeating solutes
#float
#unit: mol/m3 or mM
Ce: 0.
#sigma: reflexion coefficient
#float
#dimensionless
Sigma: 0.85 #
experimental:
#water flux at the root base
#float
#unit: microL/s
Jv: 0.0
#hydric potential outside the roots (pressure chamber)
#float
#unit: MPa
psi_e: 0.101325
#hydric potential at the root base (e.g. atmospheric pressure for decapitated plant)
#float
#unit: MPa
psi_base: .101325
output:
#distance from the base for intercepts calculation
# float or list of float
#unit: m
intercepts: []
#factor to explore a k0 range
# float or list of float
radfold: 1.0
#like radfold but apply to axial_conductance_data
axfold: 1.0
#number of run with the same set of parameters i.e. number of different seeds
#integer
#enable only if read_architecture is false
run_nb: 1
Few parameters may be set to lists allowing to run successive simulations. For list of number there are two syntax: [x1, …, xn] or range(start, end, step). For example, range(0.02, 0.09, 0.02) or [0.02, 0.04, 0.06, 0.08] will give the same results. The parameter will take successively the values 0.02, 0.04, 0.06 and 0.08. The parameter run_nb would be useful with read_architecture = False and no given seed to generate different architectures.
Note: Parameter is just a python class. It can not be used directly with Hydroroot functions, intermediary script should be used. We will give you some examples using scripts that be found at openalea/hydroroot in example or doc/examples directories.
[1]:
from openalea.hydroroot.main import hydroroot_flow, root_builder
from openalea.hydroroot.init_parameter import Parameters
from openalea.hydroroot.read_file import read_archi_data
from openalea.widgets.plantgl import PlantGL # notebook viewer 3D
from openalea.plantgl.algo.view import view # 2D view
from openalea.hydroroot.display import mtg_scene
Read the yaml file and set the Parameters variables#
assuming that the code is run from the example folder
[2]:
parameter = Parameters()
parameter.read_file('parameters_plant_01.yml')
Read the architecture file and build the MTG#
[3]:
fname = parameter.archi['input_dir'] + parameter.archi['input_file'][0]
df = read_archi_data(fname)
g, primary_length, total_length, surface, seed = root_builder( primary_length = parameter.archi['primary_length'],
delta = parameter.archi['branching_delay'],
nude_length = parameter.archi['nude_length'],
df = df,
segment_length = parameter.archi['segment_length'],
length_data = parameter.archi['length_data'],
order_max = parameter.archi['order_max'],
order_decrease_factor = parameter.archi['order_decrease_factor'],
ref_radius = parameter.archi['ref_radius'])
Calculation of the equivalent conductance and the sap flux#
[4]:
g, Keq, Jv = hydroroot_flow(g, segment_length = parameter.archi['segment_length'],
psi_e = parameter.exp['psi_e'],
psi_base = parameter.exp['psi_base'],
axial_conductivity_data = parameter.hydro['axial_conductance_data'],
radial_conductivity_data = parameter.hydro['k0'])
[5]:
result=f"""
primary length (m): {primary_length}
surface (m2): {surface}
total length (m): {total_length}
flux (microL/s): {Jv}
"""
print(result)
primary length (m): 0.10300000000000001
surface (m2): 0.0004625701757655344
total length (m): 1.6260000000000001
flux (microL/s): 0.0028789143185531108
Display the local water uptake heatmap#
to reduce notebook size we use here a 2D view but you can use the openalea.widgets PlantGL(s) to display an interactive 3D view
[6]:
s = mtg_scene(g, prop_cmap = 'j') # create a scene from the mtg with the property j is the radial flux in ul/s
view(s) # use PlantGL(s) to display in 3D
