Reference guide

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

openalea.farquharwheat package

farquharwheat

The model Farquhar-Wheat

openalea.farquharwheat.model module

openalea.farquharwheat.model.calculate_photosynthesis(PAR, surfacic_nitrogen, NSC_Retroinhibition, surfacic_NSC, Ts, Ci)

Computes photosynthesis rate following Farquhar’s model with regulation by organ temperature and nitrogen content. In this version, most of the parameters are derived from Braune et al. (2009) on barley and Evers et al. (2010) for N dependencies.

Parameters:

• PAR (float) – PAR absorbed (µmol m-2 s-1)

• surfacic_nitrogen (float) – surfacic nitrogen content(g m-2) including or not structural nitrogen depending on parameter.MODEL_VERSION

• NSC_Retroinhibition (bool) – if True, Ag is inhibited by surfacic NSC (Non-Structural Carbohydrates).

• surfacic_NSC (float) – surfacic content of NSC (Non-Structural Carbohydrates) (µmol C m-2).

• Ts (float) – organ temperature (degree C)

• Ci (float) – internal CO2 (µmol mol-1), Ci = 0.7*CO2air for the first iteration

Returns:

Ag (µmol m-2 s-1), An (µmol m-2 s-1), Rd (µmol m-2 s-1)

Return type:

(float, float, float)

openalea.farquharwheat.model.calculate_surfacic_WSC(sucrose, starch, fructan, green_area)

Surfacic content of water soluble carbohydrates # TODO: rename by non structural carbohydrates because starch is not water-soluble.

Parameters:

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

• starch (float) – amount of starch (µmol C)

• fructan (float) – amount of fructan (µmol C)

• green_area (float) – green area (m-2)

Returns:

Surfacic content of water soluble carbohydrates (µmol C m-2)

Return type:

float

openalea.farquharwheat.model.calculate_surfacic_nitrogen(nitrates, amino_acids, proteins, Nstruct, green_area)

Surfacic content of nitrogen

Parameters:

• nitrates (float) – amount of nitrates (µmol N)

• amino_acids (float) – amount of amino_acids (µmol N)

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

• Nstruct (float) – structural N (g)

• green_area (float) – green area (m-2)

Returns:

Surfacic nitrogen (g m-2)

Return type:

float

openalea.farquharwheat.model.calculate_surfacic_nonstructural_nitrogen(nitrates, amino_acids, proteins, green_area)

Surfacic content of non-structural nitrogen

Parameters:

• nitrates (float) – amount of nitrates (µmol N)

• amino_acids (float) – amount of amino_acids (µmol N)

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

• green_area (float) – green area (m-2)

Returns:

Surfacic non-structural nitrogen (g m-2)

Return type:

float

openalea.farquharwheat.model.calculate_surfacic_nonstructural_nitrogen_Farquhar(surfacic_photosynthetic_proteins)

Estimate of non structural SLN used in Farquhar

Parameters:

surfacic_photosynthetic_proteins (float) – surfacic proteins content (µmol N m-2)

Returns:

Surfacic non-structural nitrogen (g m-2)

Return type:

float

openalea.farquharwheat.model.calculate_surfacic_photosynthetic_proteins(proteins, green_area)

Surfacic content of photosynthetic proteins

Parameters:

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

• green_area (float) – green area (m-2)

Returns:

Surfacic non-structural nitrogen (g m-2)

Return type:

float

openalea.farquharwheat.model.run(surfacic_nitrogen, NSC_Retroinhibition, surfacic_NSC, width, height, PAR, Ta, ambient_CO2, RH, Ur, organ_name, height_canopy)

Computes the photosynthesis of a photosynthetic element. The photosynthesis is computed by using the biochemical FCB model (Farquhar et al., 1980) coupled to the semiempirical BWB model of stomatal conductance (Ball, 1987).

Parameters:

• surfacic_nitrogen (float) – surfacic nitrogen content of organs (g m-2), could include total N or proteic N only depending on parameter.SurfacicProteins Properly speaking, photosynthesis should be related to proteins (RubisCO), but parameters of most Farquhar models are calibrated on total N measurements (DUMAS method). We use only non-structural nitrogen to overcome issues in the case of extrem scenarios (high SLN for thick leaves under low nitrogen conditions). If None, surfacic_nitrogen = NA_0

• NSC_Retroinhibition (bool) – if True, Ag is inhibited by surfacic NSC (Non-Structural Carbohydrates).

• surfacic_NSC (float) – surfacic content of NSC (Non-Structural Carbohydrates) (µmol C m-2).

• width (float) – width of the organ (or diameter for stem organ) (m), characteristic dimension to be considered for heat transfer through forced convection (by wind).

• height (float) – height of the organ from soil (m)

• PAR (float) – absorbed PAR (µmol m-2 s-1)

• Ta (float) – air temperature (°C)

• ambient_CO2 (float) – air CO2 (µmol mol-1)

• RH (float) – relative humidity (decimal fraction)

• Ur (float) – wind at the reference height (zr) (m s-1), e.g. top of the canopy + 2m (in the case of wheat, Ur can be approximated as the wind speed at 2m from soil)

• organ_name (str) – name of the organ to which belongs the element (used to distinguish lamina from cylindric organs)

• height_canopy (float) – total canopy height (m)

Returns:

Ag (µmol m-2 s-1), An (µmol m-2 s-1), Rd (µmol m-2 s-1), Tr (mmol m-2 s-1), Ts (°C) and gsw (mol m-2 s-1)

Return type:

(float, float, float, float, float, float)

openalea.farquharwheat.simulation module

class openalea.farquharwheat.simulation.Simulation(update_parameters=None)

Bases: object

The Simulation class permits to initialize and run a simulation.

initialize(inputs)

Initialize inputs from inputs.

Parameters:

inputs (dict) –

Dictionary of two dictionaries :

• elements : The inputs by element.

• axes : The inputs by axis.

inputs must be a dictionary with the same structure as inputs.

See Model.run

for more information about the inputs.

inputs

The inputs of Farquhar-Wheat.

inputs is a dictionary of dictionaries:

{(plant_index, axis_label, metamer_index, organ_label, element_label): {element_input_name: element_input_value, …}, …}

See Model.run for more information about the inputs.

outputs

The outputs of Farquhar-Wheat.

outputs is a dictionary of dictionaries:

{(plant_index, axis_label, metamer_index, organ_label, element_label): {element_output_name: element_output_value, …}, …}

See Model.run for more information about the outputs.

run(Ta, ambient_CO2, RH, Ur)

Compute Farquhar variables for each element in inputs and put the results in outputs.

Parameters:

• Ta (float) – air temperature at t (degree Celsius)

• ambient_CO2 (float) – air CO2 at t (µmol mol-1)

• RH (float) – relative humidity at t (decimal fraction)

• Ur (float) – wind speed at the top of the canopy at t (m s-1)

exception openalea.farquharwheat.simulation.SimulationError

Bases: Exception

exception openalea.farquharwheat.simulation.SimulationInputsError

Bases: SimulationError

openalea.farquharwheat.converter module

openalea.farquharwheat.converter.AXIS_TOPOLOGY_COLUMNS = ['plant', 'axis']

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

openalea.farquharwheat.converter.ELEMENT_TOPOLOGY_COLUMNS = ['plant', 'axis', 'metamer', 'organ', 'element']

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

openalea.farquharwheat.converter.FARQUHARWHEAT_AXES_INPUTS = ['SAM_temperature', 'height_canopy']

the inputs needed by FarquharWheat at axis scale

openalea.farquharwheat.converter.FARQUHARWHEAT_ELEMENTS_INPUTS = ['width', 'height', 'PARa', 'nitrates', 'amino_acids', 'proteins', 'Nstruct', 'green_area', 'sucrose', 'starch', 'fructan', 'PARa_prim', 'area_prim']

the inputs needed by FarquharWheat at element scale

openalea.farquharwheat.converter.FARQUHARWHEAT_ELEMENTS_INPUTS_OUTPUTS = {'Ag', 'An', 'Nstruct', 'PARa', 'PARa_prim', 'Rd', 'Tr', 'Ts', 'amino_acids', 'area_prim', 'fructan', 'green_area', 'gs', 'height', 'nitrates', 'proteins', 'starch', 'sucrose', 'width'}

the inputs and outputs of FarquharWheat.

openalea.farquharwheat.converter.FARQUHARWHEAT_ELEMENTS_OUTPUTS = ['Ag', 'An', 'Rd', 'Tr', 'Ts', 'gs', 'width', 'height']

the outputs computed by FarquharWheat

openalea.farquharwheat.converter.from_dataframe(element_inputs, axes_inputs)

Convert inputs/outputs from Pandas dataframe to Farquhar-Wheat format.

Parameters:

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

• axes_inputs (pandas.DataFrame) – axes inputs dataframe to convert, with one line per axis (Shoot Apical Meristem)

Returns:

The inputs/outputs in a dictionary.

Return type:

dict [dict]

seealso:: see simulation.Simulation.inputs and simulation.Simulation.outputs

for the structure of Farquhar-Wheat inputs/outputs.

openalea.farquharwheat.converter.to_dataframe(data_dict)

Convert inputs/outputs from Farquhar-Wheat format to Pandas dataframe.

Parameters:

data_dict (dict) – The inputs/outputs in Farquhar-Wheat format.

Returns:

one dataframe for element outputs

Return type:

pandas.DataFrame

seealso:: see simulation.Simulation.inputs and simulation.Simulation.outputs

for the structure of Farquhar-Wheat inputs/outputs.

openalea.farquharwheat.parameters module

farquharwheat.paramters

The module farquharwheat.parameters defines the constant parameters.

class openalea.farquharwheat.parameters.AxisDefaultProperties

Bases: object

Properties by default for the axis. Used in FarquharWheat facade.

openalea.farquharwheat.parameters.DELTA_CONVERGENCE = 0.01

The relative delta for Ci and Ts convergence.

class openalea.farquharwheat.parameters.ElementDefaultProperties

Bases: object

Properties by default for the elements. Used in FarquharWheat facade.

PARa_prim

For calculations at primitive scale

area_prim

For calculations at primitive scale

openalea.farquharwheat.parameters.KELVIN_DEGREE = 273.15

Conversion factor from degree C to Kelvin

openalea.farquharwheat.parameters.NSC_Retroinhibition = True

If True, NSC (Non-Structural Carbohydrates) downregulate photosynthesis

openalea.farquharwheat.parameters.Psurf_to_SLNnonstruct = 1.06

Conversion factor from surfacic protein content to non-structural SLN (estimation from NEMA and Ljutovac simulations)

openalea.farquharwheat.parameters.SurfacicProteins = True

If True, surfacic proteins used to regulate photosynthesis ; if not total N

openalea.farquharwheat.parameters.prim_scale = False

If True, photosynthesis calculated at primitive scale, if not at organ scale