Merge branch '99-feature-crop-model-config-file' into 'develop'

[feature] Crop model config file

See merge request !14

INPUTS/CROPS/GRASSIM/management/management_frequency_example.yml

+cutType:
+    Value: graze
+    Type: string
+    Limit: ['None', 'graze', 'mow']
+    Description: Determines how biomass is removed
+cutDecisionType:
+    Value: frequency
+    Type: string
+    Limit: ['None', 'dates', 'sward_height', 'frequency']
+    Description: Specifies when cutting takes place
+biomassRemovalType:
+    Value: max_BM
+    Type: string
+    Limit: ['None', 'max_BM', 'cut_height']
+    Description: Defines the extent of biomass removal
+rotationType:
+    Value: None
+    Type: string
+    Limit: ['None', 'dates', 'sward_height', 'frequency']
+    Description: Specifies when rotation occurs
+fertilizationType:
+    Value: None
+    Type: string
+    Limit: ['None', 'dates', 'days_after_cut']
+    Description: Specifies when fertilization occurs
+
+
+number_of_cutting_periods:
+    Value: 1
+    Type: integer
+    Limit: [1,100]
+    Description: Number of cutting periods
+cutting_start_1:
+    Value: '15-04'
+    Type: string
+    Description: start date of cutting period 1 
+cutting_end_1: 
+    Value: '15-07'
+    Type: string
+    Description: end date of cutting period 1 
+cutting_frequency_1:
+    Value: 1
+    Type: integer
+    Limit: [1,365]
+    Unit: day
+    Description: cutting frequency of period 1
+
+max_BM:
+    Value: 300
+    Type: float
+    Limit: [0,50000]
+    Unit: kg/ha/day
+    Description: Maximum daily sry biomass consumption
+min_available_height:
+    Value: 0.03
+    Type: float
+    Limit: [0,1]
+    Unit: meter
+    Description: minimum grazing height
+priority_order:
+    Value: ['GV', 'GR', 'DV', 'DR']
+    Type: list
+    Description : priority order of biomass consumption

INPUTS/CROPS/GRASSIM/variables_to_save.yml

@@ -6,9 +6,13 @@ soil_variables:
 - Vp
 
 crop_variables:
+- BM
 - N_uptake
 - QNGV
 - FNH
 - GRO
 - GROGV
 - SENGV
+
+management_variables:
+- exported_BM

INPUTS/CROPS/config/grassim_example.yml

+crop_model: grassim
+crop_init: crop_init_example.yml
+soil_init: soil_init_example.yml
+PFT_composition: PFT_composition.yml
+PFT_values: Parameters_values_PFT.csv
+Kc_values: Kc_values.yml
+management: management_frequency_example.yml
+variables_to_save: variables_to_save.yml
\ No newline at end of file

INPUTS/CROPS/config/simple_example.yml

+crop_model: simple
+crop_init: crop_init.yaml
+soil_init: soil_init.yaml
+crop_parameters: crops_parameters.csv

INPUTS/CROPS/config/stics_example.yml

+crop_model: stics
+simu_init: simu_init.yaml

MODULES/CROPS/GRASSIM/run_grassim.py

@@ -13,15 +13,16 @@ from MODULES.CROPS.GRASSIM.management.management import Management
 from MODULES.DATA_MANAGEMENT.yaml_inputs_provider import YAML_Inputs_provider
 from MODULES.CROPS.evapotranspiration_FAO56_PM import get_ET0
 
-def run_grassim(WD, daily_irr, lat, alt):
+def run_grassim(config, WD, daily_irr, lat, alt):
+
+    soil_init = YAML_Inputs_provider(file=f"CROPS/GRASSIM/soil/{config['soil_init']}").inputs
+    crop_init = YAML_Inputs_provider(file=f"CROPS/GRASSIM/crop/{config['crop_init']}").inputs
+    kc_values = YAML_Inputs_provider(file=f"CROPS/GRASSIM/crop/{config['Kc_values']}").inputs
+    pft_composition = YAML_Inputs_provider(file=f"CROPS/GRASSIM/{config['PFT_composition']}").inputs
+    pft_values = pd.read_csv(f"INPUTS/CROPS/GRASSIM/{config['PFT_values']}",header=0, sep=";", decimal='.')
+    management = YAML_Inputs_provider(file=f"CROPS/GRASSIM/management/{config['management']}").inputs
     
-    crop_init = YAML_Inputs_provider(file='CROPS/GRASSIM/crop/crop_init_example.yml').inputs
-    kc_values = YAML_Inputs_provider(file='CROPS/GRASSIM/crop/Kc_values.yml').inputs
-    pft_composition = YAML_Inputs_provider(file='CROPS/GRASSIM/PFT_composition.yml').inputs
-    pft_values = pd.read_csv('INPUTS/CROPS/GRASSIM/Parameters_values_PFT.csv',header=0, sep=";", decimal='.')
-    management = YAML_Inputs_provider(file='CROPS/GRASSIM/management/management_dates_example.yml').inputs
-    soil_init = YAML_Inputs_provider(file='CROPS/GRASSIM/soil/soil_init_example.yml').inputs
-    with open("INPUTS/CROPS/GRASSIM/variables_to_save.yml", "r") as file:
+    with open(f"INPUTS/CROPS/GRASSIM/{config['variables_to_save']}", "r") as file:
         variables_to_save = yaml.safe_load(file)
 
     simulation_dates = get_sim_dates(WD)

MODULES/CROPS/SIMPLE/run_simple.py

@@ -13,14 +13,14 @@ from MODULES.DATA_MANAGEMENT.yaml_inputs_provider import YAML_Inputs_provider
 from MODULES.CROPS.evapotranspiration_FAO56_PM import get_ET0
 
 
-def run_independant_years_of_crop(option_2D, WD, daily_irr, lat, alt):
+def run_independant_years_of_crop(config, option_2D, WD, daily_irr, lat, alt):
     
-    Crop_init = YAML_Inputs_provider(file = 'CROPS/SIMPLE/crop_init.yaml').inputs
+    Crop_init = YAML_Inputs_provider(file = f"CROPS/SIMPLE/{config['crop_init']}").inputs
     list_rows_to_skip = list(np.arange(1, int(Crop_init['CropID']), 1))
-    Crop_param = pd.read_csv('INPUTS/CROPS/SIMPLE/crops_parameters.csv', 
+    Crop_param = pd.read_csv(f"INPUTS/CROPS/SIMPLE/{config['crop_parameters']}", 
                              skiprows=lambda x: x in list_rows_to_skip, 
                              nrows=1).to_dict('records')[0]
-    Soil_param = YAML_Inputs_provider(file = 'CROPS/SIMPLE/soil_init.yaml').inputs
+    Soil_param = YAML_Inputs_provider(file = f"CROPS/SIMPLE/{config['soil_init']}").inputs
     
     Soil_plot = water_balance.Soil(Soil_param)
     Crop_plot = simple.Crop(Crop_param, 

MODULES/CROPS/STICS/JAVA/run_java_stics.py

@@ -16,9 +16,9 @@ import pandas as pd
 import numpy as np
 
 
-def run_independant_usms(WD, daily_irr, scenario_P):
+def run_independant_usms(config, WD, daily_irr, scenario_P):
     
-    Simu_init = YAML_Inputs_provider('CROPS/STICS/simu_init.yaml').inputs
+    Simu_init = YAML_Inputs_provider(f"CROPS/STICS/{config['simu_init']}").inputs
     
     WD_files_dict = generate_weather_data_file(WD, daily_irr,
                                                scenario_P['LocationName'])

MODULES/CROPS/run_crop_simulations.py

@@ -11,21 +11,21 @@ from MODULES.CROPS.GRASSIM.run_grassim import run_grassim
 
 
 
-def run_crop_simu(crop_model, option_2D, WD, daily_irr, scenario_P):
+def run_crop_simu(config, option_2D, WD, daily_irr, scenario_P):
         
-    if crop_model == 1:
+    if config['crop_model'] == 'simple':
         
-        Soil_plot, Crop_plot = run_independant_years_of_crop(option_2D, WD, daily_irr, 
+        Soil_plot, Crop_plot = run_independant_years_of_crop(config, option_2D, WD, daily_irr, 
                                                              scenario_P['Latitude'],
                                                              scenario_P['Altitude'])
         
-    if crop_model == 2:
+    if config['crop_model'] == 'stics':
 
-        Soil_plot, Crop_plot = run_independant_usms(WD, daily_irr, scenario_P)        
+        Soil_plot, Crop_plot = run_independant_usms(config, WD, daily_irr, scenario_P)        
         
-    if crop_model == 3:
+    if config['crop_model'] == 'grassim':
         
-        Soil_plot, Crop_plot = run_grassim(WD, daily_irr, scenario_P['Latitude'], scenario_P['Altitude'])
+        Soil_plot, Crop_plot = run_grassim(config, WD, daily_irr, scenario_P['Latitude'], scenario_P['Altitude'])
         
     
     return Soil_plot, Crop_plot

main.py

@@ -8,6 +8,7 @@
 import numpy as np
 import os
 import pickle
+import yaml
 from MODULES.user_support_tools import PASE_Logger
 from MODULES.DATA_MANAGEMENT.yaml_inputs_provider import YAML_Inputs_provider, Inputs_aggregator
 from MODULES.DATA_MANAGEMENT.weather_data_provider import Weather_data
@@ -97,7 +98,6 @@ L.get_daily_irradiation_map(Sun_positions_samp.SP,
 #DiffuseGround = L.Get_diffuse_map_byFlag(Flags=["wheat","corn"])
 #DirectGround = L.Get_direct_map_byFlag(Flags=["crop"])
 
-
 # Examples of visualisation for the direct light map, diffuse light map (sky view factor)
 # and daily irradiation map. Those lines are for PV system with no rotation axis. 
 j = 5 #day definition
@@ -190,16 +190,18 @@ PV_central = PV_Production(PV_params_dict)
 PV_central.get_several_years_of_electricity_production(Sun_positions_complete, Light_instance.data, WD.nyears_data)
 
 
-
 ### CROP MODEL
-#Temporary lines, those 2 parameters (crop_model and option_2D) should be in SCENARIOS input files (general parameters)
-crop_model = 1 # 1 pour SIMPLE, 2 pour STICS JAVA et 3 pour GRASSIM
+#Temporary line, this parameters (option_2D) should be in SCENARIOS input files (general parameters)
 option_2D = 1 # 0 pour pas de spatialisation et 1 pour une spatialisation du modèle de culture
-Soil_plot, Crop_plot = run_crop_simu(crop_model, option_2D, WD.nyears_daily_data, 
+
+with open('INPUTS/CROPS/config/grassim_example.yml', 'r') as file:
+    config_1 = yaml.safe_load(file)
+    
+Soil_plot, Crop_plot = run_crop_simu(config_1, option_2D, WD.nyears_daily_data, 
                                      L.daily_irr_spat,
                                      Loc_1)
 
 show_light_map2(L.sourcepoints[:,:-1], 
-                Crop_plot.nyears_data['2008']['Dry_yield']['2008-10-10 00:00:00']/100, 
+                Crop_plot[0].nyears_data['2008']['BM']['2008-10-10 00:00:00']/100, 
                 PV_1_3Dconfig.PV_central_PD,
-                "Dry yield SIMPLE 2008 [t/ha]")
+                "Biomass Gras-Sim 2008 [t/ha]")