Reference guide

This manual details, for each module of openalea.cnwgrass.growth, the functions and objects included in openalea.cnwgrass.growth, describing what they are and what they do.

openalea.cnwgrass.growth package

growth

The model Growth.

Mechanistic model of wheat growth. See:

• growth.simulation for the front-end of the model,

• growth.model for the equations of the model,

• growth.parameters for the parameters of the model.

openalea.cnwgrass.growth.model module

class openalea.cnwgrass.growth.model.GrowthModel

Bases: object

calculate_delta_Nstruct(delta_mstruct)

delta Nstruct of hidden zone and emerged tissue (lamina and sheath).

Parameters:

delta_mstruct (float) – delta of mstruct (g)

Returns:

delta Nstruct (g)

Return type:

float

static calculate_delta_emerged_tissue_mstruct(SW, previous_mstruct, metric)

delta mstruct of emerged tissue (lamina, sheath and internode). Calculated from tissue area.

Parameters:

• SW (float) – For Lamina : Structural Specific Weight (g m-2); For sheath and internode : Lineic Structural Weight (g m-1)

• previous_mstruct (float) – mstruct at the previous time step i.e. not yet updated (g)

• metric (float) – For Lamina : Area at the current time step, as updated by the geometrical model (m2); For sheath and internode : Length at the current time step (m)

Returns:

delta mstruct (g)

Return type:

float

calculate_delta_internode_enclosed_mstruct(internode_L, delta_internode_L, ratio_mstruct_DM)

Relation between length and mstruct for the internode segment located in the hidden zone. Same relationship than for enclosed leaf corrected by RATIO_ENCLOSED_LEAF_INTERNODE. Parameters alpha_mass_growth and beta_mass_growth estimated from Williams (1975) and expressed in g of dry mass. The actual ratio_mstruct_DM is then used to convert in g of structural dry mass.

Parameters:

• internode_L (float) – Enclosed internode length (m)

• delta_internode_L (float) – delta of enclosed internode length (m)

• ratio_mstruct_DM (float) – Ratio mstruct/dry matter (dimensionless)

Returns:

delta_enclosed_internode_mstruct (g)

Return type:

float

calculate_delta_internode_enclosed_mstruct_postL(delta_internode_pseudo_age, internode_pseudo_age, internode_L, internode_pseudostem_L, internode_Lmax, LSIW, enclosed_mstruct)

mstruct of the enclosed internode from the ligulation of the leaf to the end of elongation. Final mstruct of the enclosed internode matches internode mstruct calculation when it is mature.

Parameters:

• delta_internode_pseudo_age (float) – Delta of Pseudo age of the internode since beginning of automate elongation (s)

• internode_pseudo_age (float) – Pseudo age of the internode since beginning of automate elongation (s)

• internode_L (float) – Current length of the internode (m)

• internode_pseudostem_L (float) – Pseudostem length of the internode (m)

• internode_Lmax (float) – Final length of the internode (m)

• LSIW (float) – Lineic Structural Internode Weight (g m-1)

• enclosed_mstruct (float) – mstruct of the enclosed leaf (g)

Returns:

delta_internode_enclosed_mstruct (g)

Return type:

float

calculate_delta_leaf_enclosed_mstruct(leaf_L, delta_leaf_L, ratio_mstruct_DM, init_leaf_L=None, leaf_pseudo_age=None)

Relation between length and mstruct for the leaf segment located in the hidden zone during the exponential-like growth phase. Parameters alpha_mass_growth and beta_mass_growth estimated from Williams (1960) and expressed in g of dry mass The actual ratio_mstruct_DM is then used to convert in g of structural dry mass.

Parameters:

• leaf_L (float) – Total leaf length (m)

• delta_leaf_L (float) – delta of leaf length (m)

• ratio_mstruct_DM (float) – Ratio mstruct/dry matter (dimensionless)

• init_leaf_L (float) – Total leaf length before update in Hydraulics sub-model (m). Not used in this instance of the model

• leaf_pseudo_age (float) – Pseudo age of the leaf since beginning of automate elongation (s). Not used in this instance of the model

Returns:

delta_leaf_enclosed_mstruct (g)

Return type:

float

calculate_delta_leaf_enclosed_mstruct_postE(delta_leaf_pseudo_age, leaf_pseudo_age, leaf_pseudostem_L, enclosed_mstruct, LSSW, sucrose, mstruct)

mstruct of the enclosed leaf from the emergence of the leaf to the end of elongation. Final mstruct of the enclosed leaf matches sheath mstruct calculation when it is mature. #TODO : Hiddenzone mstruct calculation is not correct for sheath shorten than previous one. :param float delta_leaf_pseudo_age: Delta of Pseudo age of the leaf since beginning of automate elongation (s) :param float leaf_pseudo_age: Pseudo age of the leaf since beginning of automate elongation (s) :param float leaf_pseudostem_L: Pseudostem length (m) :param float enclosed_mstruct: mstruct of the enclosed leaf (g) :param float LSSW: Lineic Structural Sheath Weight (g m-1) :param float sucrose: Sucrose amount (µmol C) :param float mstruct: Structural mass (g)

Returns:

delta_leaf_enclosed_mstruct (g)

Return type:

float

static calculate_export(delta_mstruct, metabolite, hiddenzone_mstruct)

Export of metabolite from the hidden zone towards the emerged part of the leaf integrated over delta_t.

Parameters:

• delta_mstruct (float) – Delta of structural dry mass of the emerged part of the leaf (g)

• metabolite (float) – Metabolite amount in the hidden zone (µmol C or N)

• hiddenzone_mstruct (float) – Structural mass of the hidden zone (g)

Returns:

metabolite export (µmol N)

Return type:

float

calculate_init_cytokinins_emerged_tissue(delta_mstruct)

Initial amount of cytokinins allocated in the mstruct of a newly emerged tissue.

Parameters:

delta_mstruct (float) – Delta of structural dry mass of the emerged part of the leaf (g)

Returns:

cytokinins addition (AU)

Return type:

float

calculate_mineral_plant(mstruct, senesced_mstruct)

Mineral mass.

Parameters:

• mstruct (float) – structural mass of the plant (g)

• senesced_mstruct (float) – senesced structural mass of the plant (g)

Returns:

Mineral mass of the plant (g)

Return type:

float

static calculate_ratio_mstruct_DM(mstruct, sucrose, fructans, amino_acids, proteins)

Ratio mstruct/dry matter (dimensionless)

Parameters:

• mstruct (float) – Structural mass (g)

• sucrose (float) – Sucrose amount (µmol C)

• fructans (float) – Fructans amount (µmol C)

• amino_acids (float) – Amino acids amount (µmol N)

• proteins (float) – proteins amount (µmol N)

Returns:

Ratio mstruct/dry matter (dimensionless)

Return type:

float

calculate_roots_mstruct_growth(sucrose, amino_acids, mstruct, delta_teq, postflowering_stages, nb_leaves, xylem_water_potential=None)

Root structural dry mass growth integrated over delta_t

Parameters:

• sucrose (float) – Amount of sucrose in roots (µmol C)

• amino_acids (float) – Amount of amino acids in roots (µmol N)

• mstruct (float) – Root structural mass (g)

• delta_teq (float) – Time compensated for the effect of temperature - Time equivalent at Tref (s)

• postflowering_stages (bool) – Option : True to run a simulation with postflo parameter

• nb_leaves (int) – Current number of leaves on the axis

• xylem_water_potential (float) – Water potential of xylem (Mpa)

Returns:

mstruct_C_growth (µmol C), mstruct_growth (g), Nstruct_growth (g), Nstruct_N_growth (µmol N)

Return type:

(float, float, float, float)

calculate_roots_s_mstruct_sucrose(delta_roots_mstruct, s_Nstruct_amino_acids_N)

Consumption of sucrose for the calculated mstruct growth (µmol C consumed by mstruct growth)

Parameters:

• delta_roots_mstruct (float) – mstruct growth of the roots (g)

• s_Nstruct_amino_acids_N (float) – Total amino acid consumption (µmol N) due to Nstruct (µmol N)

Returns:

Sucrose consumption (µmol C)

Return type:

float

static calculate_s_Nstruct_amino_acids(delta_hiddenzone_Nstruct, delta_lamina_Nstruct, delta_sheath_Nstruct, delta_internode_Nstruct)

Consumption of amino acids for the calculated mstruct growth (µmol N consumed by mstruct growth)

Parameters:

• delta_hiddenzone_Nstruct (float) – Nstruct growth of the hidden zone (g)

• delta_lamina_Nstruct (float) – Nstruct growth of the lamina (g)

• delta_sheath_Nstruct (float) – Nstruct growth of the sheath (g)

• delta_internode_Nstruct (float) – Nstruct growth of the internode (g)

Returns:

Amino acid consumption (µmol N)

Return type:

float

calculate_s_mstruct_sucrose(delta_hiddenzone_mstruct, delta_lamina_mstruct, delta_sheath_mstruct, s_Nstruct_amino_acids_N)

Consumption of sucrose for the calculated mstruct growth (µmol C consumed by mstruct growth)

Parameters:

• delta_hiddenzone_mstruct (float) – mstruct growth of the hidden zone (g)

• delta_lamina_mstruct (float) – mstruct growth of the lamina (g)

• delta_sheath_mstruct (float) – mstruct growth of the sheath (g)

• s_Nstruct_amino_acids_N (float) – Total amino acid consumption (µmol N) due to Nstruct (µmol N)

Returns:

Sucrose consumption (µmol C)

Return type:

float

static calculate_sheath_mstruct(sheath_L, LSSW)

mstruct of the sheath. Final mstruct of the enclosed leaf matches sheath mstruct calculation when it is mature.

Parameters:

• sheath_L (float) – Sheath length (m)

• LSSW (float) – Lineic Structural Sheath Weight (g m-1).

Returns:

Structural mass of the sheath (g)

Return type:

float

hiddenzone_outputs

the outputs computed by Growth

class openalea.cnwgrass.growth.model.GrowthModelHydraulics

Bases: GrowthModel

calculate_delta_leaf_enclosed_mstruct(leaf_L, delta_leaf_L, ratio_mstruct_DM, init_leaf_L=0, leaf_pseudo_age=0)

Relation between length and mstruct for the leaf segment located in the hidden zone during the exponential-like growth phase. Parameters alpha_mass_growth and beta_mass_growth estimated from Williams (1960) and expressed in g of dry mass The actual ratio_mstruct_DM is then used to convert in g of structural dry mass.

Parameters:

• leaf_L (float) – Total leaf length after update in Hydraulics sub-model (m)

• delta_leaf_L (float) – delta of leaf length (m)

• ratio_mstruct_DM (float) – Ratio mstruct/dry matter (dimensionless)

• init_leaf_L (float) – Total leaf length before update in Hydraulics sub-model (m)

• leaf_pseudo_age (float) – Pseudo age of the leaf since beginning of automate elongation (s)

Returns:

delta_leaf_enclosed_mstruct (g)

Return type:

float

calculate_roots_mstruct_growth(sucrose, amino_acids, mstruct, delta_teq, postflowering_stages, nb_leaves=None, xylem_water_potential=0)

Root structural dry mass growth integrated over delta_t

Parameters:

• sucrose (float) – Amount of sucrose in roots (µmol C)

• amino_acids (float) – Amount of amino acids in roots (µmol N)

• mstruct (float) – Root structural mass (g)

• delta_teq (float) – Time compensated for the effect of temperature - Time equivalent at Tref (s)

• postflowering_stages (bool) – Option : True to run a simulation with postflo parameter

• nb_leaves (int) – Current number of leaves on the axis

• xylem_water_potential (float) – Water potential of xylem (Mpa)

Returns:

mstruct_C_growth (µmol C), mstruct_growth (g), Nstruct_growth (g), Nstruct_N_growth (µmol N)

Return type:

(float, float, float, float)

openalea.cnwgrass.growth.simulation module

class openalea.cnwgrass.growth.simulation.Simulation(delta_t=1, hydraulics=False, update_parameters=None)

Bases: object

The Simulation class permits to initialize and run a simulation.

axis_inputs

The inputs and outputs of Growth at each scale.

delta_t

the delta t of the simulation (in seconds)

hydraulics

Checks whether the Hydraulic version should be used

initialize(inputs)

Initialize inputs from inputs.

Parameters:

inputs (dict) – must be a dictionary with the same structure as inputs.

inputs

inputs is a dictionary of dictionaries: {‘hiddenzone’: {(plant_index, axis_label, metamer_index): {hiddenzone_input_name: hiddenzone_input_value, …}, …},

‘elements’: {(plant_index, axis_label, metamer_index, organ_label, element_label): {organ_input_name: organ_input_value, …}, …}, ‘roots’: {(plant_index, axis_label): {root_input_name: root_input_value, …}, …}}

outputs

outputs is a dictionary of dictionaries: {‘hiddenzone’: {(plant_index, axis_label, metamer_index): {hiddenzone_input_name: hiddenzone_input_value, …}, …},

‘elements’: {(plant_index, axis_label, metamer_index, organ_label, element_label): {organ_input_name: organ_input_value, …}, …} ‘roots’: {(plant_index, axis_label): {root_input_name: root_input_value, …}, …}}

run(postflowering_stages=False)

Run the simulation.

Parameters:

postflowering_stages (bool) – if True the model will calculate root growth with the parameters calibrated for post flowering stages

exception openalea.cnwgrass.growth.simulation.SimulationError

Bases: Exception

exception openalea.cnwgrass.growth.simulation.SimulationRunError

Bases: SimulationError

openalea.cnwgrass.growth.converter module

openalea.cnwgrass.growth.converter.HIDDENZONE_TOPOLOGY_COLUMNS = ['plant', 'axis', 'metamer']

the columns which define the topology in the input/output dataframe

openalea.cnwgrass.growth.converter.from_dataframes(hiddenzone_inputs, element_inputs, root_inputs, axis_inputs)

Convert inputs/outputs from Pandas dataframe to Growth format.

Parameters:

• hiddenzone_inputs (pandas.DataFrame) – Hidden zone inputs dataframe to convert, with one line by hidden zone.

• element_inputs (pandas.DataFrame) – Element inputs dataframe to convert, with one line by element.

• root_inputs (pandas.DataFrame) – Root inputs dataframe to convert, with one line by root.

• axis_inputs (pandas.DataFrame) – axis inputs dataframe to convert, with one line by axis.

Returns:

The inputs in a dictionary.

Return type:

dict [str, dict]

see also:: see simulation.Simulation.inputs for the structure of Growth inputs.

openalea.cnwgrass.growth.converter.to_dataframes(data_dict, axis_outputs, hiddenzone_outputs, element_outputs, root_outputs)

Convert outputs from Growth format to Pandas dataframe.

Parameters:

• data_dict (dict) – The outputs in Morphogenesis format.

• axis_outputs (list) – The list of output names for axes

• hiddenzone_outputs (list) – The list of output names for hiddenzones

• element_outputs (list) – The list of output names for elements

• root_outputs (list) – The list of output names for roots

Returns:

Four dataframes : for hiddenzone outputs, element outputs, roots outputs and axes outputs

Return type:

pandas.DataFrame

openalea.cnwgrass.growth.parameters module

openalea.cnwgrass.growth.parameters.AMINO_ACIDS_MOLAR_MASS_N_RATIO = 0.135

Mean contribution of N in amino acids mass of the major amino acids of plants (Glu, Gln, Ser, Asp, Ala, Gly)

openalea.cnwgrass.growth.parameters.CONVERSION_FACTOR_20_TO_12 = 0.45

modified_Arrhenius_equation(12)/modified_Arrhenius_equation(20)

openalea.cnwgrass.growth.parameters.C_MOLAR_MASS = 12

Carbon molar mass (g mol-1)

openalea.cnwgrass.growth.parameters.HEXOSE_MOLAR_MASS_C_RATIO = 0.42

Contribution of C in hexose mass

openalea.cnwgrass.growth.parameters.MINERAL_LIVING_TISSUE = 0.05

Mineral content of the structural mass (g g-1 mstruct) (Thornley and Cannell, 2000)

openalea.cnwgrass.growth.parameters.MINERAL_SENESCED_TISSUE = 0.025

Mineral content of the structural mass of a senescent tissue (g g-1 mstruct) (Thornley and Cannell, 2000)

openalea.cnwgrass.growth.parameters.N_MOLAR_MASS = 14

Nitrogen molar mass (g mol-1)

class openalea.cnwgrass.growth.parameters.OrganInit

Bases: object

Initial values for organs

Nresidual

g

Nstruct

g

amino_acids

µmol N

conc_cytokinins

AU / g mstruct # Not used

cytokinins

g

fructan

µmol C

green_area

m2

mstruct

g

nitrates

µmol N

proteins

µmol N

senesced_length_element

m

senesced_mstruct

g

sucrose

µmol C

openalea.cnwgrass.growth.parameters.PROTEINS_MOLAR_MASS_N_RATIO = 0.151

Mean contribution of N in protein mass (Penning De Vries 1989)

class openalea.cnwgrass.growth.parameters.Parameters

Bases: object

AMINO_ACIDS_C_RATIO

Mean number of mol of C in 1 mol of the major amino acids of plants (Glu, Gln, Ser, Asp, Ala, Gly) from (Penning de Vries, Witlage and Kremer, 1978)

AMINO_ACIDS_N_RATIO

Mean number of mol of N in 1 mol of the major amino acids of plants (Glu, Gln, Ser, Asp, Ala, Gly) from (Penning de Vries, Witlage and Kremer, 1978)

BETA

Parameter of the relation between leaf mass and leaf length (dimensionless)

FITTED_L0

Fitted value of leaf length at t=0 after rescaling the beta function with L0 (m); Fournier 2005 sur courbe corrigee

FITTED_L0_IN

Scaling factor of the internode in automate growth (dimensionless), fitted from Malvoisin 1984 II

INIT_CYTOKININS_EMERGED_TISSUE

Initial concentration of cytokinins allocated in the mstruct of a newly emerged tissue (AU g-1)

K_ROOTS_GROWTH_POSTFLO

Affinity coefficient of root structural dry matter growth (µmol C g-1 MS) post flo

K_ROOTS_GROWTH_PREFLO

Affinity coefficient of root structural dry matter growth (µmol C g-1 MS) pre flo

RATIO_AMINO_ACIDS_MSTRUCT

Mass of N (under amino acid/protein form, g) in 1 g of mstruct (Penning de Vries, Witlage and Kremer, 1978)

RATIO_ENCLOSED_LEAF_INTERNODE

lamina of the specific structural dry masses (from data of J. Bertheloot, 2004)

Type:

We use ratio sheath

RATIO_MSTRUCT_DM

Ratio mstruct/dry matter (dimensionless)

RATIO_SUCROSE_MSTRUCT

0.384 from (Penning de Vries, Witlage and Kremer, 1978), 0.444 for cellulose (about 45% C in

Type:

Mass of C (under carbohydrate form, g) in 1 g of mstruct

VMAX_ROOTS_GROWTH_POSTFLO

Maximal rate of root structural dry matter growth (µmol C s-1 g-1 MS) post flo at 12°C

VMAX_ROOTS_GROWTH_PREFLO

Maximal rate of root structural dry matter growth (µmol C s-1 g-1 MS) pre flo at 12°C

VMAX_ROOTS_GROWTH_SEMINALS

Maximal rate of root structural dry matter growth used during seed emergence (µmol C s-1 g-1 MS). Deals with the transition from seminal to nodal roots.

Vmax_roots_growth(nb_leaves)

conc_sucrose_offset

sucrose concentration under which no root growth occurs (µmol of C g-1 mstruct) - same for leaf and internode growth, see morphogenesis

te

end of leaf elongation in automate growth (s at 12°c); fitted from adapted data from Fournier 2005

te_IN

end of internode elongation in automate growth (s at 12°c) ; fitted from Malvoisin 1984 II

class openalea.cnwgrass.growth.parameters.ParametersHydraulics

Bases: Parameters

K_ROOTS_GROWTH

Affinity coefficient of root structural dry matter growth (µmol C g-1 MS) post flo

n

Shape parameter of hydraulic regulation of root growth (-)

te_IN

end of internode elongation in automate growth; Ljutovac 2002, 250pl.m-2

water_potential_crit

Critical xylem water potential at which root growth is reduced by 50% (Sharp et al., 2004)

openalea.cnwgrass.growth.parameters.RATIO_C_MSTRUCT_ROOTS = 0.444

same as shoot

Type:

Mean contribution of carbon to root structural dry mass (g C g-1 Mstruct)

openalea.cnwgrass.growth.parameters.RATIO_N_MSTRUCT_ROOTS = 0.005

same as shoot

Type:

Mean contribution of nitrogen to root structural dry mass (g N g-1 Mstruct)

openalea.cnwgrass.growth.parameters.parameters_factory(hydraulics=False)

Factory for parameter instantiation according to the version of the model used

Parameters:

hydraulics (bool) – if True the model will assume the coupling to the turgor-driven growth model

Returns:

Instance of Parameters oo ParametersHydraulics