main#

openalea.hydroroot.main.hydroroot(primary_length=0.15, delta=0.002, beta=0.25, order_max=5, segment_length=0.0001, nude_length=0.02, seed=2, ref_radius=0.0001, order_decrease_factor=0.7, k0=300, Jv=0.1, psi_e=0.4, psi_base=0.1, length_data=None, axial_conductivity_data=None, radial_conductivity_data=None, n=None)[source]#

Simulate a root system and compute global conductance and flux. see hydroroot_mtg() and hydroroot_flow() deprecated :param primary_length: (Default value = 0.15) :param delta: (Default value = 2.e-3) :param beta: (Default value = 0.25) :param order_max: (Default value = 5) :param segment_length: (Default value = 1e-4) :param nude_length: (Default value = 0.02) :param seed: (Default value = 2) :param ref_radius: (Default value = 1e-4) :param order_decrease_factor: (Default value = 0.7) :param k0: (Default value = 300) :param Jv: (Default value = 0.1) :param psi_e: (Default value = 0.4) :param psi_base: (Default value = 0.1) :param length_data: (Default value = None) :param axial_conductivity_data: (Default value = None) :param radial_conductivity_data: (Default value = None) :param n: (Default value = None)

openalea.hydroroot.main.hydroroot_flow(g, segment_length=0.0001, k0=300, Jv=0.1, psi_e=0.4, psi_base=0.1, axial_conductivity_data=None, radial_conductivity_data=None)[source]#

Flux and equivalent conductance calculation

Parameters:

  • g – MTG

  • segment_length – (float) - not used vertices length in hydroroot in m (Default value = 1.0e-4) #TODO not used delete it

  • k0 – (float) - not used radial conductivity in \(10^{-9}\ m.s^{-1}.MPa^{-1}\) (Default value = 300) #TODO not used delete it

  • Jv – (Float) not used because invert_model=True in Flux.Flux (Default value = 0.1) #TODO delete it or add invert_model in arguments

  • psi_e – (Float) external hydrostatic potential in MPa (Default value = 0.4)

  • psi_base – (Float) root base hydrostatic potential in MPa (Default value = 0.1)

  • axial_conductivity_data – (2 list of Float) axial conductance (\(10^{-9}\ m^4.MPa^{-1}.s^{-1}\)) versus distance to tip (m) (Default value = None)

  • radial_conductivity_data – (2 list of Float) radial conductivity (\(10^{-9}\ m.MPa^{-1}.s^{-1}\)) versus distance to tip (m) (Default value = None)

Returns:

  • g (MTG): the MTG with the following properties filled: K (axial conductance), k (radial donductivity),

    j (radial flux), J_out (axial flux), psi_in and psi_out (hydrostatic pressure into the root at the input and output of a MTG node

  • Keq (float): the equivalent conductance of the whole root

  • Jv_global (float): the outgoing flux at the root base

openalea.hydroroot.main.hydroroot_from_data(primary_length=0.15, delta=0.002, beta=0.25, order_max=5, segment_length=0.0001, nude_length=0.02, seed=2, ref_radius=0.0001, order_decrease_factor=0.7, k0=300, Jv=0.1, psi_e=0.4, psi_base=0.1, length_data=None, axial_conductivity_data=None, radial_conductivity_data=None, primary_length_data=None, lateral_length_data=None)[source]#

Reconstruct a root system and compute global conductance and flux. deprecated :param primary_length_data: list Float (Default value = None) :param lateral_length_data: list Float (Default value = None) :param return: :param g: MTG :param surface: float :param volume: float :param Keq: float :param Jv_global: float :param see: func :param primary_length: (Default value = 0.15) :param delta: (Default value = 2.e-3) :param beta: (Default value = 0.25) :param order_max: (Default value = 5) :param segment_length: (Default value = 1e-4) :param nude_length: (Default value = 0.02) :param seed: (Default value = 2) :param ref_radius: (Default value = 1e-4) :param order_decrease_factor: (Default value = 0.7) :param k0: (Default value = 300) :param Jv: (Default value = 0.1) :param psi_e: (Default value = 0.4) :param psi_base: (Default value = 0.1) :param length_data: (Default value = None) :param axial_conductivity_data: (Default value = None) :param radial_conductivity_data: (Default value = None)

openalea.hydroroot.main.hydroroot_mtg(primary_length=0.15, delta=0.002, beta=0.25, order_max=5, segment_length=0.0001, nude_length=0.02, seed=2, ref_radius=0.0001, order_decrease_factor=0.7, length_data=None, n=None, **kwds)[source]#

Simulate and generate a root system.

Parameters:

  • primary_length – Float (Default value = 0.15)

  • delta – Float (Default value = 2.e-3)

  • beta – Float (Default value = 0.25)

  • order_max – int (Default value = 5)

  • segment_length – Float (Default value = 1e-4)

  • nude_length – Float (Default value = 0.02)

  • seed – int (Default value = 2)

  • ref_radius – Float (Default value = 1e-4)

  • order_decrease_factor – Float (Default value = 0.7)

  • length_data – pandas dataframe (Default value = None)

  • n – int (Default value = None)

Returns:

  • g (MTG)

  • surface (float)

  • volume (float)

openalea.hydroroot.main.hydroroot_solute_flow(g, psi_e=0.4, psi_base=0.1, k0=None, axial_conductivity_data=None, radial_conductivity_data=None, J_s=1e-07, Ps=1e-09, Cse=1.396e-08, Ce=0.0, sigma=1.0, Temp=298, C_base=None, eps=1e-09)[source]#

Water and solute fluxes and equivalent conductance calculation on an MTG

Parameters:

  • g – MTG

  • psi_e – (Float) external hydrostatic potential in MPa (Default value = 0.4)

  • psi_base – (Float) root base hydrostatic potential in MPa (Default value = 0.1)

  • k0 – (float) - uniform radial conductivity in \(10^{-9}\ m.s^{-1}.MPa^{-1}\) (Default value = None)

  • axial_conductivity_data – (2 list of Float) axial conductance profile (\(10^{-9}\ m^4.MPa^{-1}.s^{-1}\)) versus distance to tip (m) (Default value = None)

  • radial_conductivity_data – (2 list of Float) radial conductivity profile (\(10^{-9}\ m.MPa^{-1}.s^{-1}\)) versus distance to tip (m) (Default value = None)

  • J_s – (float) active pumping rate in mol/(m2.s) (Default value = 1e-7)

  • Ps – (float) permeability coefficient in m/s (Default value = 1e-9)

  • Cse – (float) initial permeating solute concentration inside the root in mol/microL (Default value = 13.96e-9)

  • Ce – (float) initial non-permeating solute concentration outside the root in mol/microL (Default value = 0.)

  • sigma – (float) - the reflexion coefficient between 0 and 1 (Default value = 1.0)

  • Temp – (float) - temperature in Kelvin (Default value = 298)

  • C_base – (float) solute concentration at the root base in mol/microL (Default value = None)

  • eps – (float) convergence criterium (Default value = 1e-9)

Returns:

  • g (MTG): the MTG with the following properties filled: K (axial conductance), k (radial donductivity),

    j (radial flux), J_out (axial flux), psi_in and psi_out (hydrostatic pressure into the root at the input and output of a MTG node)

  • Jv_global (float): the outgoing flux at the root base

openalea.hydroroot.main.root_builder(primary_length=0.13, seed=None, delta=0.002, nude_length=0.02, df=None, segment_length=0.0001, length_data=None, branching_variability=0.25, order_max=4.0, order_decrease_factor=0.7, ref_radius=7e-05, Flag_radius=False)[source]#

wrapper function: build a MTG with properties that are set like : radius, vertex length, position (distance to tip) and mylength (distance to base). The MTG is either generated or built from a DataFrame. The unit length in hydroroot should be in m.

Parameters:

  • primary_length – (float) - primary root length for generated mtg (Default value = 0.13)

  • seed – (int) - seed for generated mtg (Default value = None)

  • delta – (float) - branching delay for generated mtg in hydroroot should be in m (Default value = 2.0e-3)

  • nude_length – (float) - length from tip without lateral for generated mtg (Default value = 2.0e-2)

  • df – (DataFrame) - DataFrame with the architecture data to be reconstructed if not None (Default value = None)

  • segment_length – (float) - vertices length in hydroroot should be in m (Default value = 1.0e-4)

  • length_data – (string list) - the file name with the length data laws (Default value = None)

  • branching_variability – (float) (Default value = 0.25)

  • order_max – (float) (Default value = 4.0)

  • order_decrease_factor – (float) (Default value = 0.7)

  • ref_radius – (float) - radius in hydroroot should be in m (Default value = 7.0e-5)

  • Flag_radius – (boolean) - True if radius exist in df (Default value = False)

Returns:

  • g: MTG with the different properties set or computed (see comments above),

  • primary_length: primary root length (output for generated mtg)

  • total_length: total root length

  • surface: total root surface

  • _seed: the seed used in the generator

see also generator.measured_root.mtg_from_aqua_data() for details about df

openalea.hydroroot.main.soil_1D(g, soil_data=None)[source]#

add a soil as heterogeneous water potential along

This is $Psi_e$ versus depth with $depth>0$.

Parameters:

  • g – MTG

  • soil_data – tuple of 2 lists, (z,psi_e) z=depth (m), psi_e=water potential (MPa)

Returns:

g

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