# -*- coding: latin-1 -*-
from __future__ import division # use '//' to do integer division
from openalea.senescwheat import parameters
"""
senescwheat.model
~~~~~~~~~~~~~~~~~~~
Model of senescence.
"""
[docs]
class SenescenceModel(object):
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@classmethod
def calculate_N_content_total(cls, proteins, amino_acids, nitrates, Nstruct, max_mstruct, Nresidual):
""" N content in the whole element (both green and senesced tissues).
:param float proteins: protein concentration (µmol N proteins g-1 mstruct)
:param float amino_acids: amino acids concentration (µmol N amino acids g-1 mstruct)
:param float nitrates: nitrates concentration (µmol N nitrates g-1 mstruct)
:param float Nstruct: structural N mass (g). Should be constant during leaf life.
:param float max_mstruct: structural mass maximal of the element i.e. structural mass of the whole element before senescence (g)
:param float Nresidual: residual mass of N in the senescent tissu (g)
:return: N_content_total (between 0 and 1)
:rtype: float
"""
return ((proteins + amino_acids + nitrates) * 1E-6 * parameters.N_MOLAR_MASS + Nresidual + Nstruct) / max_mstruct
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@classmethod
def calculate_forced_relative_delta_green_area(cls, green_area_df, group_id, prev_green_area):
"""relative green_area variation due to senescence
:param pandas.DataFrame green_area_df: a pandas DataFrame containing the green area values for each photosynthetic element at each time
:param tuple group_id: the group id to be used to select data in the DataFrame
:param float prev_green_area: previous value of an organ green area (m-2)
:return: new_green_area (m-2), relative_delta_green_area (dimensionless)
:rtype: tuple [float, float]
"""
new_green_area = green_area_df.get_group(group_id).green_area.values[0]
relative_delta_green_area = (prev_green_area - new_green_area) / prev_green_area
return new_green_area, relative_delta_green_area
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@classmethod
def calculate_relative_delta_green_area(cls, organ_name, prev_green_area, proteins, max_proteins, delta_t, update_max_protein):
"""relative green_area variation due to senescence
:param str organ_name: name of the organ to which belongs the element (used to distinguish lamina from stem organs)
:param float prev_green_area: previous value of an organ green area (m-2)
:param float proteins: protein concentration (µmol N proteins g-1 mstruct)
:param float max_proteins: maximal protein concentrations experienced by the organ (µmol N proteins g-1 mstruct)
:param float delta_t: value of the timestep (s)
:param bool update_max_protein: whether to update the max proteins or not.
:return: new_green_area (m-2), relative_delta_green_area (dimensionless)
:rtype: tuple [float, float]
.. todo:: remove update_max_protein
"""
if organ_name == 'blade':
fraction_N_max = parameters.FRACTION_N_MAX['blade']
else:
fraction_N_max = parameters.FRACTION_N_MAX['stem']
# Overwrite max proteins
if max_proteins < proteins and update_max_protein:
max_proteins = proteins
new_green_area = prev_green_area
relative_delta_green_area = 0
# Senescence if (actual proteins/max_proteins) < fraction_N_max
elif max_proteins == 0 or (proteins / max_proteins) < fraction_N_max:
senesced_area = min(prev_green_area, parameters.SENESCENCE_MAX_RATE * delta_t)
new_green_area = max(0., prev_green_area - senesced_area)
relative_delta_green_area = senesced_area / prev_green_area
else:
new_green_area = prev_green_area
relative_delta_green_area = 0
return new_green_area, relative_delta_green_area, max_proteins
# Temporaire
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@classmethod
def calculate_relative_delta_senesced_length(cls, organ_name, prev_senesced_length, length, proteins, max_proteins, delta_t, update_max_protein):
"""relative senesced length variation
:param str organ_name: name of the organ to which belongs the element (used to distinguish lamina from stem organs)
:param float prev_senesced_length: previous senesced length of an organ (m-2)
:param float length: organ length (m)
:param float proteins: protein concentration (µmol N proteins g-1 mstruct)
:param float max_proteins: maximal protein concentrations experienced by the organ (µmol N proteins g-1 mstruct)
:param float delta_t: value of the timestep (s)
:param bool update_max_protein: whether to update the max proteins or not.
:return: new_senesced_length (m), relative_delta_senesced_length (dimensionless), max_proteins (µmol N proteins g-1 mstruct)
:rtype: tuple [float, float, float]
.. todo:: remove update_max_protein
"""
if organ_name == 'blade':
fraction_N_max = parameters.FRACTION_N_MAX['blade']
else:
fraction_N_max = parameters.FRACTION_N_MAX['stem']
# Overwrite max proteins
if max_proteins < proteins and update_max_protein:
max_proteins = proteins
new_senesced_length = prev_senesced_length
relative_delta_senesced_length = 0
# Senescence if (actual proteins/max_proteins) < fraction_N_max
elif max_proteins == 0 or (proteins / max_proteins) < fraction_N_max:
senesced_length = parameters.SENESCENCE_LENGTH_MAX_RATE * delta_t
new_senesced_length = min(length, prev_senesced_length + senesced_length)
if length == new_senesced_length:
relative_delta_senesced_length = 1
else:
relative_delta_senesced_length = 1 - (length - new_senesced_length) / (length - prev_senesced_length)
else:
new_senesced_length = prev_senesced_length
relative_delta_senesced_length = 0
return new_senesced_length, relative_delta_senesced_length, max_proteins
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@classmethod
def calculate_delta_mstruct_shoot(cls, relative_delta_green_area, prev_mstruct, prev_Nstruct):
"""delta of structural mass due to senescence of photosynthetic elements
:param float relative_delta_green_area: relative variation of a photosynthetic element green area (dimensionless)
:param float prev_mstruct: previous value of an organ structural mass (g)
:param float prev_Nstruct: previous value of an organ structural N (g)
:return: delta_mstruct (g), delta_Nstruct (g)
:rtype: tuple [float, float]
"""
delta_mstruct = prev_mstruct * relative_delta_green_area
delta_Nstruct = prev_Nstruct * relative_delta_green_area
return delta_mstruct, delta_Nstruct
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@classmethod
def calculate_remobilisation(cls, metabolite, relative_delta_structure):
"""Metabolite remobilisation due to senescence over DELTA_T (µmol).
:param float metabolite: amount of any metabolite to be remobilised (µmol)
:param float relative_delta_structure: could be relative variation of a photosynthetic element green area or relative variation of mstruct
:return: metabolite remobilisation (µmol)
:rtype: float
"""
return metabolite * relative_delta_structure
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@classmethod
def calculate_if_element_is_over(cls, green_area, is_growing, mstruct):
"""Define is an element is fully senescent
:param float green_area: Green area of the element (m2)
:param bool is_growing: flag is the element is still growing
:param float mstruct: Strucural mass of the element (g)
:return: is_over which indicates if the element is fully senescent
:rtype: bool
"""
is_over = False
if (green_area < parameters.MIN_GREEN_AREA or mstruct == 0) and not is_growing:
is_over = True
return is_over
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@classmethod
def calculate_remobilisation_proteins(cls, 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).
:param str organ: name of the organ
:param int element_index: phytomer rank
:param float proteins: amount of proteins (µmol N)
:param float relative_delta_green_area: relative variation of a photosynthetic element green area
:param float ratio_N_mstruct_max: N content in the whole element (both green and senesced tissues).
:param bool full_remob: whether all proteins should be remobilised
:return: 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)
:rtype: tuple [float, float, float]
"""
if full_remob or organ != 'blade':
remob_proteins = delta_amino_acids = proteins * relative_delta_green_area
delta_Nresidual = 0
else:
if ratio_N_mstruct_max <= parameters.RATIO_N_MSTRUCT.get(element_index, parameters.DEFAULT_RATIO_N_MSTRUCT): # all the proteins are converted into Nresidual
remob_proteins = proteins
delta_Nresidual = remob_proteins * 1E-6 * parameters.N_MOLAR_MASS
delta_amino_acids = 0
else: # part of the proteins are converted into amino_acids
remob_proteins = proteins * relative_delta_green_area
delta_amino_acids = remob_proteins
delta_Nresidual = 0
return remob_proteins, delta_amino_acids, delta_Nresidual
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@classmethod
def calculate_roots_senescence(cls, 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
:return: Rate of mstruct loss by root senescence (g mstruct s-1), rate of Nstruct loss by root senescence (g Nstruct s-1)
:rtype: tuple [float, float]
"""
if postflowering_stages:
rate_senescence = parameters.SENESCENCE_ROOTS_POSTFLOWERING
else:
rate_senescence = parameters.SENESCENCE_ROOTS_PREFLOWERING
return mstruct * rate_senescence, Nstruct * rate_senescence
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@classmethod
def calculate_relative_delta_mstruct_roots(cls, rate_mstruct_death, root_mstruct, delta_teq):
"""Relative delta of root structural dry matter (g) over delta_t
:param float rate_mstruct_death: Rate of mstruct loss by root senescence (g mstruct s-1)
:param float root_mstruct: actual mstruct of roots (g)
:param float delta_teq: Temperature-consensated time = time duration at a reference temperature (s)
:return: relative_delta_mstruct (dimensionless)
:rtype: float
"""
return (rate_mstruct_death * delta_teq) / root_mstruct
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@classmethod
def calculate_delta_mstruct_root(cls, rate_mstruct_death, rate_Nstruct_death, delta_teq):
"""delta of structural mass due to senescence of roots
:param float rate_mstruct_death: relative delta of root structural mass over delta_t (g s-1)
:param float rate_Nstruct_death: relative delta of root N structural mass over delta_t (g s-1)
:param float delta_teq: Temperature-consensated time = time duration at a reference temperature (s)
:return: delta_mstruct (g), delta_Nstruct (g)
:rtype: tuple [float, float]
"""
delta_mstruct = rate_mstruct_death * delta_teq
delta_Nstruct = rate_Nstruct_death * delta_teq
return delta_mstruct, delta_Nstruct
