Reference guide

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

openalea.senescwheat package

senescwheat

The model Senesc-Wheat

openalea.senescwheat.model module

class openalea.senescwheat.model.SenescenceModel

Bases: object

classmethod calculate_N_content_total(proteins, amino_acids, nitrates, Nstruct, max_mstruct, Nresidual)

N content in the whole element (both green and senesced tissues).

Parameters:

• proteins (float) – protein concentration (µmol N proteins g-1 mstruct)

• amino_acids (float) – amino acids concentration (µmol N amino acids g-1 mstruct)

• nitrates (float) – nitrates concentration (µmol N nitrates g-1 mstruct)

• Nstruct (float) – structural N mass (g). Should be constant during leaf life.

• max_mstruct (float) – structural mass maximal of the element i.e. structural mass of the whole element before senescence (g)

• Nresidual (float) – residual mass of N in the senescent tissu (g)

Returns:

N_content_total (between 0 and 1)

Return type:

float

classmethod calculate_delta_mstruct_root(rate_mstruct_death, rate_Nstruct_death, delta_teq)

delta of structural mass due to senescence of roots

Parameters:

• rate_mstruct_death (float) – relative delta of root structural mass over delta_t (g s-1)

• rate_Nstruct_death (float) – relative delta of root N structural mass over delta_t (g s-1)

• delta_teq (float) – Temperature-consensated time = time duration at a reference temperature (s)

Returns:

delta_mstruct (g), delta_Nstruct (g)

Return type:

tuple [float, float]

classmethod calculate_delta_mstruct_shoot(relative_delta_green_area, prev_mstruct, prev_Nstruct)

delta of structural mass due to senescence of photosynthetic elements

Parameters:

• relative_delta_green_area (float) – relative variation of a photosynthetic element green area (dimensionless)

• prev_mstruct (float) – previous value of an organ structural mass (g)

• prev_Nstruct (float) – previous value of an organ structural N (g)

Returns:

delta_mstruct (g), delta_Nstruct (g)

Return type:

tuple [float, float]

classmethod calculate_forced_relative_delta_green_area(green_area_df, group_id, prev_green_area)

relative green_area variation due to senescence

Parameters:

• green_area_df (pandas.DataFrame) – a pandas DataFrame containing the green area values for each photosynthetic element at each time

• group_id (tuple) – the group id to be used to select data in the DataFrame

• prev_green_area (float) – previous value of an organ green area (m-2)

Returns:

new_green_area (m-2), relative_delta_green_area (dimensionless)

Return type:

tuple [float, float]

classmethod calculate_if_element_is_over(green_area, is_growing, mstruct)

Define is an element is fully senescent

Parameters:

• green_area (float) – Green area of the element (m2)

• is_growing (bool) – flag is the element is still growing

• mstruct (float) – Strucural mass of the element (g)

Returns:

is_over which indicates if the element is fully senescent

Return type:

bool

classmethod calculate_relative_delta_green_area(organ_name, prev_green_area, proteins, max_proteins, delta_t, update_max_protein)

relative green_area variation due to senescence

Parameters:

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

• prev_green_area (float) – previous value of an organ green area (m-2)

• proteins (float) – protein concentration (µmol N proteins g-1 mstruct)

• max_proteins (float) – maximal protein concentrations experienced by the organ (µmol N proteins g-1 mstruct)

• delta_t (float) – value of the timestep (s)

• update_max_protein (bool) – whether to update the max proteins or not.

Returns:

new_green_area (m-2), relative_delta_green_area (dimensionless)

Return type:

tuple [float, float]

classmethod calculate_relative_delta_mstruct_roots(rate_mstruct_death, root_mstruct, delta_teq)

Relative delta of root structural dry matter (g) over delta_t

Parameters:

• rate_mstruct_death (float) – Rate of mstruct loss by root senescence (g mstruct s-1)

• root_mstruct (float) – actual mstruct of roots (g)

• delta_teq (float) – Temperature-consensated time = time duration at a reference temperature (s)

Returns:

relative_delta_mstruct (dimensionless)

Return type:

float

classmethod calculate_relative_delta_senesced_length(organ_name, prev_senesced_length, length, proteins, max_proteins, delta_t, update_max_protein)

relative senesced length variation

Parameters:

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

• prev_senesced_length (float) – previous senesced length of an organ (m-2)

• length (float) – organ length (m)

• proteins (float) – protein concentration (µmol N proteins g-1 mstruct)

• max_proteins (float) – maximal protein concentrations experienced by the organ (µmol N proteins g-1 mstruct)

• delta_t (float) – value of the timestep (s)

• update_max_protein (bool) – whether to update the max proteins or not.

Returns:

new_senesced_length (m), relative_delta_senesced_length (dimensionless), max_proteins (µmol N proteins g-1 mstruct)

Return type:

tuple [float, float, float]

classmethod calculate_remobilisation(metabolite, relative_delta_structure)

Metabolite remobilisation due to senescence over DELTA_T (µmol).

Parameters:

• metabolite (float) – amount of any metabolite to be remobilised (µmol)

• relative_delta_structure (float) – could be relative variation of a photosynthetic element green area or relative variation of mstruct

Returns:

metabolite remobilisation (µmol)

Return type:

float

classmethod calculate_remobilisation_proteins(organ, element_index, proteins, relative_delta_green_area, ratio_N_mstruct_max, full_remob)

Protein remobilisation due to senescence over DELTA_T. Part is remobilised as amino_acids (µmol N), the rest is increasing Nresidual (g).

Parameters:

• organ (str) – name of the organ

• element_index (int) – phytomer rank

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

• relative_delta_green_area (float) – relative variation of a photosynthetic element green area

• ratio_N_mstruct_max (float) – N content in the whole element (both green and senesced tissues).

• full_remob (bool) – whether all proteins should be remobilised

Returns:

Quantity of proteins remobilised either in amino acids, either in residual N (µmol), Quantity of proteins converted into amino_acids (µmol N), Increment of Nresidual (g)

Return type:

tuple [float, float, float]

classmethod calculate_roots_senescence(mstruct, Nstruct, postflowering_stages)

Root senescence :param float mstruct: structural mass (g) :param float Nstruct: structural N (g) :param bool postflowering_stages: if True the model will calculate root growth with the parameters calibrated for post flowering stages

Returns:

Rate of mstruct loss by root senescence (g mstruct s-1), rate of Nstruct loss by root senescence (g Nstruct s-1)

Return type:

tuple [float, float]

openalea.senescwheat.simulation module

class openalea.senescwheat.simulation.Simulation(delta_t=1, update_parameters=None)

Bases: object

The Simulation class permits to initialize and run a simulation.

delta_t

the delta t of the simulation (in seconds)

initialize(inputs)

Initialize inputs from inputs.

Parameters:

inputs (dict) – The inputs by roots and element. inputs must be a dictionary with the same structure as inputs.

inputs

The inputs of Senesc-Wheat.

inputs is a dictionary of dictionaries:

{‘roots’: {(plant_index, axis_label): {roots_input_name: roots_input_value, …}, …},

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

outputs

The outputs of Senesc-Wheat.

outputs is a dictionary of dictionaries:

{‘roots’: {(plant_index, axis_label): {roots_output_name: roots_output_value, …}, …},

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

run(forced_max_protein_elements=None, opt_full_remob=False, postflowering_stages=False)

Compute Senesc-Wheat outputs from inputs, and update outputs.

Parameters:

• forced_max_protein_elements (set) – The elements ids with fixed max proteins.

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

• opt_full_remob (bool) – whether all proteins should be remobilised

openalea.senescwheat.converter module

openalea.senescwheat.converter.AXES_TOPOLOGY_COLUMNS = ['plant', 'axis']

the columns which define the topology of a roots in the input/output dataframe

openalea.senescwheat.converter.ELEMENTS_TOPOLOGY_COLUMNS = ['plant', 'axis', 'metamer', 'organ', 'element']

the columns which define the topology of an element in the input/output dataframe

openalea.senescwheat.converter.ROOTS_TOPOLOGY_COLUMNS = ['plant', 'axis']

the columns which define the topology of a roots in the input/output dataframe

openalea.senescwheat.converter.SENESCWHEAT_AXES_INPUTS = ['delta_teq', 'delta_teq_roots', 'sum_TT']

the inputs needed by SenescWheat at axis scale

openalea.senescwheat.converter.SENESCWHEAT_AXES_INPUTS_OUTPUTS = ['delta_teq', 'delta_teq_roots', 'sum_TT']

the inputs and outputs of SenescWheat at axis scale

openalea.senescwheat.converter.SENESCWHEAT_AXES_OUTPUTS = []

the outputs computed by SenescWheat at axis scale

openalea.senescwheat.converter.SENESCWHEAT_ELEMENTS_INPUTS = ['green_area', 'senesced_length_element', 'length', 'proteins', 'mstruct', 'senesced_mstruct', 'max_proteins', 'Nstruct', 'nitrates', 'amino_acids', 'starch', 'fructan', 'cytokinins', 'sucrose', 'is_growing', 'max_mstruct', 'Nresidual', 'age']

the inputs needed by SenescWheat at element scale

openalea.senescwheat.converter.SENESCWHEAT_ELEMENTS_INPUTS_OUTPUTS = ['N_content_total', 'Nresidual', 'Nstruct', 'age', 'amino_acids', 'cytokinins', 'fructan', 'green_area', 'is_growing', 'is_over', 'length', 'max_mstruct', 'max_proteins', 'mstruct', 'nitrates', 'proteins', 'senesced_length_element', 'senesced_mstruct', 'starch', 'sucrose']

the inputs and outputs of SenescWheat at elements scale

openalea.senescwheat.converter.SENESCWHEAT_ELEMENTS_OUTPUTS = ['senesced_length_element', 'green_area', 'mstruct', 'senesced_mstruct', 'Nstruct', 'starch', 'sucrose', 'fructan', 'proteins', 'amino_acids', 'cytokinins', 'nitrates', 'N_content_total', 'Nresidual', 'is_over']

the outputs computed by SenescWheat at elements scale

openalea.senescwheat.converter.SENESCWHEAT_ROOTS_INPUTS = ['sucrose', 'amino_acids', 'mstruct', 'senesced_mstruct', 'Nstruct', 'cytokinins']

the inputs needed by SenescWheat at roots scale

openalea.senescwheat.converter.SENESCWHEAT_ROOTS_INPUTS_OUTPUTS = ['Nstruct', 'amino_acids', 'cytokinins', 'mstruct', 'rate_mstruct_death', 'senesced_mstruct', 'sucrose']

the inputs and outputs of SenescWheat at roots scale

openalea.senescwheat.converter.SENESCWHEAT_ROOTS_OUTPUTS = ['rate_mstruct_death', 'mstruct', 'senesced_mstruct', 'Nstruct', 'cytokinins']

the outputs computed by SenescWheat at roots scale

openalea.senescwheat.converter.from_dataframes(roots_inputs, axes_inputs, elements_inputs)

Convert inputs/outputs from Pandas dataframes to Senesc-Wheat format.

Parameters:

• roots_inputs (pandas.DataFrame) – Roots inputs dataframe to convert, with one line by roots.

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

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

Returns:

The inputs/outputs in a dictionary.

Return type:

dict [str, dict]

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

for the structure of Senesc-Wheat inputs/outputs.

openalea.senescwheat.converter.to_dataframes(data_dict)

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

Parameters:

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

Returns:

One dataframe for roots inputs/outputs, one dataframe for axes inputs/outputs, one dataframe for elements inputs/outputs.

Return type:

(pandas.DataFrame, pandas.DataFrame, pandas.DataFrame)

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

for the structure of Senesc-Wheat inputs/outputs.

openalea.senescwheat.parameters module

senescwheat.parameters

Parameters used in the model of senescence.

openalea.senescwheat.parameters.AGE_EFFECT_SENESCENCE = 450

Age-induced senescence (degree-day since leaf emergence calculated from elong-wheat as equivalent at 12°C)

openalea.senescwheat.parameters.DEFAULT_RATIO_N_MSTRUCT = 0.005

default N content in total organ mass (senesced + green) if phytomer rank not found above

openalea.senescwheat.parameters.MIN_GREEN_AREA = 5e-09

Minimal green area of an element (m2). Below this area, set green_area to 0.0.

openalea.senescwheat.parameters.N_MOLAR_MASS = 14

Molar mass of nitrogen (g mol-1)

openalea.senescwheat.parameters.SENESCENCE_ROOTS_POSTFLOWERING = 1.575e-07

Rate of root turnover at 12°C (s-1). Value at 20°C coming from Johnson and Thornley (1985), see also Asseng et al. (1997).