init_parameter#

Created on Tue Dec 3 10:45:01 2019

@author: F. Bauget

Parameters class:
init:

set the default values

Methods:

  • read_file: read the Yaml configuration file containing the model parameters into a Class.

  • init_calculation: perform some initialization

  • parameters_to_list: convert some parameters to list if they are not

class openalea.hydroroot.init_parameter.Parameters[source]#

Bases: object

Init Parameters class. Set setting default values and structure

Parameters contains 5 dictionaries grouping inputs in 5 gategories:
  • archi: all inputs related to the architecture generation or reconstruction

    • read_architecture: Bool, True = read the architecture from a data (i.e. reconstructed MTG)

    • input_dir: string, input directory of the architecture file

    • input_file: list of string, architecture files

    • seed: integer or list of integer, seed for the Markov generator, if none seed is generated

    • length_file: list of strings, files name (included relative path) containing data used to calculate

      length laws for the laterals generation

    • length_data: float data containing in the files above

    • primary_length: float or list of float, length of the primary root

    • branching_delay: float or list of float, average distance between to branching

    • branching_variability: float, add variability in the delay

    • order_max: integer, maximum laterals order

    • segment_length: float, length of the vertices

    • nude_length: float or list of float, length from the tip without any branching

    • ref_radius: float, radius of the primary root

    • order_decrease_factor: float, decrease factor apply to the radius to account for its decrease

      with lateral order

  • hydro: inputs related to the hydrodynamics

    • k0: float, the radial conductivity

    • axial_conductance_data: list of 2 list of float, the axial conductance vs distance from the tip

  • solute: inputs related to solutes transport eather permating or not

    • J_s: float, active pumping rate

    • P_s: float, permeability coefficient

    • Cse: float, concentration of permeating solutes

    • Ce: float, concentration of non-permeating solutes

    • sigma: float, reflextion coefficient

  • exp: inputs related to the experimental conditions and measurements

    • jv: float, measured flux at the base

    • psi_e: float, water potential surrounding the root

    • psi_base: float, water potential at the base

  • output: inputs related to the simulations and its output

    • radfold: float or list of float, in factor to k0

    • axfold: float or list of float, in factor to axial_conductance_data

    • intercepts: list of float, distance from base to calculate the number of intercepts

    • run_nb: int, number of simulation with the same set of input

init_calculation()[source]#

Set archi[‘length_data’] by reading the two files archi[‘length_file’]

Set the seed to None if seed is not an integer nor a list of integer

Returns:

itself

parameters_to_list(parameter)[source]#
transform parameter to a list

  • in the yaml file it is possible to use the following syntaxe “range(start, end, step)” then a test checks this syntax and the corresponding list is calculated

  • if it is a float or integer, then it is transformed to a list of one single element

Parameters:

parameter – the parameter to transform to a list

Returns:

  • parameter

read_file(filename=None)[source]#

Read the input yaml file, set the class variables and perform some initialization see init_calculation()

Parameters:

filename – (string) - the input yaml file (Default value = None)

Download the source file ../../src/openalea/hydroroot/init_parameter.py.