"""

This module, with only one function "initialized_data(), initializes data related to

substrate, monomer, enzyme, and microbe, as well as their distribution on the spatial grid,

preceding the actual decompostion-related computations.

"""

import pandas as pd

import numpy as np

from substrate import Substrate

from monomer import Monomer

from enzyme import Enzyme

from microbe import Microbe

from utility import expand

def initialize_data(runtime_parameters, site):

"""

Initialize all data required.

Parameters:

runtime_parameters: user-specified parameters setting up the system;

all other paras loaded by reading the parameters.csv

site: where the inputs reside

Return:

Data_Dictionary: a dictionary of all variables that feeds the grid.py module

"""

# Load all input files

parameters = pd.read_csv(site+'/'+'parameters.csv', header=None, index_col=0).astype('float32') # parameters

substrates_init = pd.read_csv(site+'/'+'initial_substrates.csv', header=0, index_col=0).astype('float32') # initial substrates

sub_mon_input = pd.read_csv(site+'/'+'sub_mon_inputs.csv', header=0, index_col=0).astype('float32') # inputs of substrates and monomers

Ea_input = pd.read_csv(site+'/'+"enzyme_ea.csv", header=0, index_col=0).astype('float32') # enzyme activation energy

# climate forcings

climate = pd.read_csv(site+'/'+'climate.csv', header=0, index_col=0)

# daily temperature and water potential

daily_temp = climate['Temp'].to_numpy(dtype='float32') # temperaure series

daily_psi = climate['Psi'].to_numpy(dtype='float32') # water potential series

#...an instance of Substrate class

Substrates = Substrate(runtime_parameters,parameters,substrates_init)

#...substrate initial pool size

substrates_initial_pool = Substrates.Substrates_start

#...substrate input rate

substrates_input_rate = Substrates.substrate_input(sub_mon_input)

#...substrates-produced monomers

substrates_produced_monomers = Substrates.substrate_produced_monomer()

#...substrates degradation required enzymes

substrates_req_enzyme = Substrates.substrate_degradation_enzyme()

#...an instance of Monomer class

Monomers = Monomer(runtime_parameters,parameters)

#...monomers initial pool size

monomers_initial_pool = Monomers.monomer_initialization(substrates_initial_pool)

#...initial monomer ratios

monomer_ratio_inital = Monomers.monomer_ratios(monomers_initial_pool)

#...monomers input rate

monomers_input_rate = Monomers.monomer_input_rate(sub_mon_input)

#...monomers uptake required enzymes

monomers_uptake_reqenzyme = Monomers.monomer_uptake_reqenzyme()

#...an instance of Enzyme class

Enzymes = Enzyme(runtime_parameters,parameters,substrates_initial_pool.index)

#...enzyme initial pool size:0

enzymes_initial_pool = Enzymes.enzyme_pool_initialization()

#...enzyme attributes

enzymes_attributes = Enzymes.enzyme_attributes()

#...enzymes of substrate degradation Ea

enzymes_Ea = Enzymes.enzyme_Ea(Ea_input)

#...monomers uptake enzyme Ea

enzymes_uptake_Ea = Enzymes.enzyme_uptake_Ea()

#...enzymes of substrate degradation Vmax

enzymes_Vmax,enzymes_Vmax_T = Enzymes.enzyme_Vmax(substrates_req_enzyme)

#...monomers uptake enzyme Vmax

enzymes_uptake_Vmax= Enzymes.enzyme_uptake_Vmax(monomers_uptake_reqenzyme)

#...enzymes of substrate degradation Km

enzymes_Km = Enzymes.enzyme_Km(enzymes_Vmax)

#...monomers uptake enzyme Km

enzymes_uptake_Km = Enzymes.enzyme_uptake_Km(enzymes_uptake_Vmax)

#...an instance of Microbe class

Microbes = Microbe(runtime_parameters,parameters)

#...Microbial pool initialization

microbial_pool = Microbes.microbial_pool_initialization()

#...Microbial community initialization

microbial_community = Microbes.microbial_community_initialization(microbial_pool[0],microbial_pool[1])

#...Microbial minimum ratios

microbial_min_ratios = Microbes.minimum_cell_quota()

#...Microbial enzyme genes

microbial_enzyme_gene = Microbes.microbe_enzyme_gene()

#...Microbial osmolyte genes

microbial_osmolyte_gene = Microbes.microbe_osmolyte_gene()

#...Microbial uptake genes

microbial_uptake_gene = Microbes.microbe_uptake_gene(substrates_req_enzyme,microbial_enzyme_gene,substrates_produced_monomers)

#...Microbial uptake cost

microbial_uptake_cost = Microbes.microbe_uptake_cost(microbial_uptake_gene)

#...Microbial enzyme production rate

microbial_enzyme_prod_rate = Microbes.microbe_enzproduction_rate(microbial_enzyme_gene,enzymes_attributes)

#...Microbial osmolyte productoin rate

microbial_osmolyte_prod_rate = Microbes.microbe_osmoproduction_rate(microbial_osmolyte_gene)

#...Microbial drought tolerance

microbial_drought_tol = Microbes.microbe_drought_tol(microbial_osmolyte_prod_rate[2],microbial_osmolyte_prod_rate[3])

#...Microbial mortality

microbial_mortality = Microbes.microbe_mortality(microbial_pool[1])

#...Dump all initialized data into a dictionary; NOTE: variables with expand() put on the spatial grid

gridsize = int(runtime_parameters.loc['gridsize',1])

Data_Dictionary = {

"Substrates": expand(substrates_initial_pool,gridsize),

"SubInput": expand(substrates_input_rate,gridsize),

"ReqEnz": substrates_req_enzyme,

"MonomersProduced": substrates_produced_monomers,

"Monomers": expand(monomers_initial_pool,gridsize),

"Monomer_ratio":expand(monomer_ratio_inital,gridsize),

"MonInput": expand(monomers_input_rate,gridsize),

"Uptake_ReqEnz":expand(monomers_uptake_reqenzyme,gridsize),

"Enzymes": expand(enzymes_initial_pool,gridsize),

"Km0": expand(enzymes_Km,gridsize), # enzyme half-saturation constant

"Uptake_Km0": expand(enzymes_uptake_Km,gridsize), # transporter half-saturation constant

"Uptake_Ea": expand(enzymes_uptake_Ea,gridsize), # transporter acitivation energy

"Uptake_Vmax0": expand(enzymes_uptake_Vmax,gridsize), # transporter reaction rate

"Ea": expand(enzymes_Ea,gridsize), # enzyme activation energy

"Vmax0": expand(enzymes_Vmax_T,gridsize), # enzyme reaction rate

"EnzAttrib": enzymes_attributes, # enzyme stoichiometry and energy cost

"Microbes_pp": microbial_pool[0], # tuple[0]: microbes preceding placement

"fb": microbial_pool[1], # tuple[1]: fungi index

"Microbes": microbial_community[0], # tuple[0]: initialized spatial microbes

"Bac_density": microbial_community[1], # tuple[1]: initialized bacterial density

"Fun_density": microbial_community[2], # tuple[2]: initialized fungal density

"MinRatios": expand(microbial_min_ratios,gridsize), # microbial cell min. ratios

"UptakeGenes": expand(microbial_uptake_gene,gridsize), # transporter gene distribution across taxa

"OsmoGenes": expand(microbial_osmolyte_gene,gridsize),# osmolyte gene distribution across taxa

"EnzGenes": expand(microbial_enzyme_gene,gridsize), # enzyme gene distribution across taxa

"UptakeGenes_trait": expand(microbial_uptake_cost[0],gridsize), # single gene cost of transporter

"OsmoProdConsti_trait":expand(microbial_osmolyte_prod_rate[0],gridsize), # single gene cost of constitutive osmolyte

"OsmoProdInduci_trait":expand(microbial_osmolyte_prod_rate[1],gridsize), # single gene cost of inducible osmolyte

"EnzProdConsti_trait": expand(microbial_enzyme_prod_rate[0],gridsize), # single gene cost of constitutive enzyme

"EnzProdInduci_trait": expand(microbial_enzyme_prod_rate[1],gridsize), # single gene cost of inducible enzyme

"UptakeGenesCost": expand(microbial_uptake_cost[1],gridsize), # distribution of transporter gene cost across taxa

"OsmoProdConsti": expand(microbial_osmolyte_prod_rate[2],gridsize), # distribution of consti. osmolyte gene cost across taxa

"OsmoProdInduci": expand(microbial_osmolyte_prod_rate[3],gridsize), # distribution of induci. osmolyte gene cost across taxa

"EnzProdConstit": expand(microbial_enzyme_prod_rate[2],gridsize), # distribution of consti. enzyme gene cost across taxa

"EnzProdInduce": expand(microbial_enzyme_prod_rate[3],gridsize), # distribution of induci. enzyme gene cost across taxa

"TaxDroughtTol": expand(microbial_drought_tol,gridsize), # distribution of taxon-specific drought tol.

'basal_death_prob': microbial_mortality[0], # basal death probability

'death_rate': microbial_mortality[1], # change rate of death prob. agaist mositure

"AE_ref": parameters.loc["CUE_ref",1], # Reference assimilation efficiency: 0.5

"AE_temp": parameters.loc["CUE_temp",1], # AE temperature sensitivity; default: -0.016

'Uptake_Maint_cost': parameters.loc['Uptake_Maint_cost',1], # constant of transporter maintenence cost

'C_min': parameters.loc['C_min',1], # C threshold of cell lysis

'N_min': parameters.loc['N_min',1], # N threshold of cell lysis

'P_min': parameters.loc['P_min',1], # P threshold of cell lysis

'max_size_b': parameters.loc['max_size_b',1], # C quota threshold for bacterial cell division

'max_size_f': parameters.loc['max_size_f',1], # C quota threshold for fungal cell division

'wp_fc': parameters.loc['wp_fc',1], # threshold below which microbes start to respond to drought

'wp_th': parameters.loc['wp_th',1], # threshold below which microbes in full swing to respond to drought

'alpha': parameters.loc['alpha',1], # factor delineating curve concavity of microbial response to drought

'Temp': daily_temp, # temperature

'Psi': daily_psi # water potential

}

return Data_Dictionary