Flowering

example/MORPHOFLOR/inputs/plan_simulation.csv

@@ -1,4 +1,29 @@
-temp_vern_min,temp_vern_inter,temp_vern_max,daily_vern_rate,basic_vern_rate,photoperiod_min,photoperiod_max,max_photo_ind_rate,coeff_primordia_emission_vegetative,coeff_primordia_emission_reproductive,derivationLength,option_tallage,option_senescence,option_floraison,meteo_filename,sowing_date,site,value_C,Premiecroiss,PS_compensation_point,leaf_primary_induction_coeff,leaf_secondary_induction_coeff,increase_growth_Premiecroiss,increase_growth_C,name,Scenario
-0,6,13,0.00135,0.01,10,16,1,1,2,4400,False,False,False,environnement_morphoflor.csv,2018_01_16,treatment_4_bloc_1,2.4,81.92163517,14.1,1,1,1,1,simulation_sans_vern,0
-0,6,13,0.00135,0.01,10,16,0.1,1,3,4800,False,False,True,environnement_morphoflor.csv,2018_11_13,treatment_2_bloc_1,1.8,93,14.1,1,0.1,0.5,1.17,simulation_nouvelle,1
-0,6,13,0.00135,0.01,10,16,0.1,1,3,4800,False,False,True,environnement_morphoflor.csv,2018_11_13,treatment_2_bloc_1,1.8,93,14.1,1,0.1,0.5,1.17,simulation_ancienne,1000
+temp_vern_min,temp_vern_inter,temp_vern_max,daily_vern_rate,basic_vern_rate,photoperiod_min,photoperiod_max,max_photo_ind_rate,coeff_primordia_emission_vegetative,coeff_primordia_emission_reproductive,derivationLength,option_tallage,option_senescence,option_floraison,meteo_filename,sowing_date,site,value_C,Premiecroiss,PS_compensation_point,leaf_primary_induction_coeff,leaf_secondary_induction_coeff,increase_growth_Premiecroiss,increase_growth_C,Scenario,name
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,5.5,60,14.1,1,1,1,1,160,simulation_160
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,5.5,65,14.1,1,1,1,1,161,simulation_161
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,5.5,70,14.1,1,1,1,1,162,simulation_162
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,5.5,75,14.1,1,1,1,1,163,simulation_163
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,5.75,60,14.1,1,1,1,1,164,simulation_164
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,5.75,65,14.1,1,1,1,1,165,simulation_165
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,5.75,70,14.1,1,1,1,1,166,simulation_166
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,5.75,75,14.1,1,1,1,1,167,simulation_167
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.0,60,14.1,1,1,1,1,168,simulation_168
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.0,65,14.1,1,1,1,1,169,simulation_169
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.0,70,14.1,1,1,1,1,170,simulation_170
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.0,75,14.1,1,1,1,1,171,simulation_171
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.25,60,14.1,1,1,1,1,172,simulation_172
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.25,65,14.1,1,1,1,1,173,simulation_173
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.25,70,14.1,1,1,1,1,174,simulation_174
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.25,75,14.1,1,1,1,1,175,simulation_175
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.5,60,14.1,1,1,1,1,176,simulation_176
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.5,65,14.1,1,1,1,1,177,simulation_177
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.5,70,14.1,1,1,1,1,178,simulation_178
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.5,75,14.1,1,1,1,1,179,simulation_179
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.75,60,14.1,1,1,1,1,180,simulation_180
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.75,65,14.1,1,1,1,1,181,simulation_181
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.75,70,14.1,1,1,1,1,182,simulation_182
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,6.75,75,14.1,1,1,1,1,183,simulation_183
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,7.0,60,14.1,1,1,1,1,184,simulation_184
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,7.0,65,14.1,1,1,1,1,185,simulation_185
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,7.0,70,14.1,1,1,1,1,186,simulation_186
+0,6,13,0.00135,0,10,16,1,1,2,4400,False,False,True,environnement_morphoflor.csv,2019_01_16,treatment_4_all_blocks,7.0,75,14.1,1,1,1,1,187,simulation_187

example/MORPHOFLOR/run_lgrass.py

@@ -18,7 +18,7 @@ def run_lgrass(scenario_id=1, inputs_dir_path='inputs', outputs_dir_path='output
     """
 
     # Scenario to be run
-    scenarii_df = pd.read_csv(os.path.join('inputs', 'plan_simulation.csv'), index_col='Scenario')
+    scenarii_df = pd.read_csv(os.path.join('inputs', 'plan_simulation_repro.csv'), index_col='Scenario')
     scenario = scenarii_df.loc[scenario_id].to_dict()
     scenario_name = scenario['name']
 
@@ -38,6 +38,8 @@ def run_lgrass(scenario_id=1, inputs_dir_path='inputs', outputs_dir_path='output
     lsystem.option_tallage = scenario['option_tallage']
     lsystem.option_senescence = scenario['option_senescence']
     lsystem.option_floraison = scenario['option_floraison']
+    lsystem.cutting_height = scenario['cutting_height']
+    lsystem.cutting_end = scenario['cutting_end']
     lsystem.meteo_path = os.path.join(inputs_dir_path, scenario['meteo_filename'])
     lsystem.sowing_date = scenario['sowing_date']
     lsystem.site = scenario['site']
@@ -60,7 +62,7 @@ def run_lgrass(scenario_id=1, inputs_dir_path='inputs', outputs_dir_path='output
 if __name__ == '__main__':
     inputs = 'inputs'
     outputs = 'outputs'
-    scenario = 1000
+    scenario = 11101
 
     try:
         opts, args = getopt.getopt(sys.argv[1:], "i:o:s:d", ["inputs=", "outputs=", "scenario="])

example/MORPHOFLOR/simulation_plan_generator.py

@@ -8,28 +8,27 @@
 temp_vern_inter_list = [6]
 temp_vern_max_list = [13]
 daily_vern_rate_list = [0.00135]
-basic_vern_rate_list = [0.01]
+basic_vern_rate_list = [0]
 photoperiod_min_list = [10]
 photoperiod_max_list = [16]
 max_photo_ind_rate_list = [1]
 coeff_primordia_emission_vegetative_list = [1]
 coeff_primordia_emission_reproductive_list = [2]
-derivationLength_list = [3000]
+derivationLength_list = [4400]
 option_tallage_list = ["False"]
 option_senescence_list = ["False"]
-option_floraison_list = ["False"]
+option_floraison_list = ["True"]
 meteo_filename_list = ["environnement_morphoflor.csv"]
 sowing_date_list = ["2019_01_16"]
-treatment_bloc = list(itertools.product([4], [1, 2, 3, 4, 5, 6, 7, 8, 9]))
-site_list = ["treatment_" + str(n[0]) + "_bloc_" + str(n[1]) for n in treatment_bloc]
-cutting_dates_list = [np.nan]
-value_C_list = np.round(np.arange(3.4, 6.1, 0.1), decimals=2)
-Premiecroiss_list = np.round(np.arange(100, 105, 5), decimals=2)
+site_list = ["treatment_" + "4" + "_all_blocks"]
+value_C_list = np.round(np.arange(7.25, 8, 0.25), decimals=2)
+Premiecroiss_list = np.round(np.arange(45, 75, 5), decimals=2)
 PS_compensation_point_list = [14.1]
 leaf_primary_induction_coeff_list = [1]
 leaf_secondary_induction_coeff_list = [1]
 increase_growth_Premiecroiss_list = [1]
 increase_growth_C_list = [1]
+HCOUP_list = [50]
 
 
 simulation_plan = pd.DataFrame(columns=["temp_vern_min",
@@ -49,14 +48,14 @@
                            "meteo_filename",
                            "sowing_date",
                            "site",
-                           "cutting_dates",
                            "value_C",
                            "Premiecroiss",
                            "PS_compensation_point",
                            "leaf_primary_induction_coeff",
                            "leaf_secondary_induction_coeff",
                            "increase_growth_Premiecroiss",
-                           "increase_growth_C"])
+                           "increase_growth_C",
+                           "HCOUP"])
 
 for i in itertools.product(temp_vern_min_list,
                            temp_vern_inter_list,
@@ -75,14 +74,14 @@
                            meteo_filename_list,
                            sowing_date_list,
                            site_list,
-                           cutting_dates_list,
                            value_C_list,
                            Premiecroiss_list,
                            PS_compensation_point_list,
                            leaf_primary_induction_coeff_list,
                            leaf_secondary_induction_coeff_list,
                            increase_growth_Premiecroiss_list,
-                           increase_growth_C_list):
+                           increase_growth_C_list,
+                           HCOUP_list):
     simulation_plan = simulation_plan.append(pd.DataFrame([i], columns=["temp_vern_min",
                            "temp_vern_inter",
                            "temp_vern_max",
@@ -100,17 +99,18 @@
                            "meteo_filename",
                            "sowing_date",
                            "site",
-                           "cutting_dates",
                            "value_C",
                            "Premiecroiss",
                            "PS_compensation_point",
                            "leaf_primary_induction_coeff",
                            "leaf_secondary_induction_coeff",
                            "increase_growth_Premiecroiss",
-                           "increase_growth_C"]))
+                           "increase_growth_C",
+                           "HCOUP"]))
 
 
-simulation_plan['Scenario'] = [i for i in range(4351, simulation_plan.shape[0] + 4351)]
+id_first_simulation = 314
+simulation_plan['Scenario'] = [i for i in range(id_first_simulation, simulation_plan.shape[0] + id_first_simulation)]
 simulation_plan['name'] = 'simulation_' + simulation_plan['Scenario'].astype(str)
 
-simulation_plan.to_csv(os.path.join('inputs', 'plan_simulation.csv'), index=False)
+simulation_plan.to_csv(os.path.join('inputs', 'plan_simulation_veg.csv'), index=False)

example/calibration_GEVES_2021/calcul_photoperiode_meteo_GEVES.py

@@ -0,0 +1,17 @@
+import pandas as pd
+from lgrass import meteo_ephem
+
+meteo_data = pd.read_csv('D:/Simon/Python/lgrass/example/GEVES/Meteo_GEVES_sans_photoperiode.csv', sep=',')
+meteo_data.date = pd.to_datetime(meteo_data.date, format='%Y_%m_%d')
+
+new_meteo_data = pd.DataFrame()
+
+for site in meteo_data.site.unique():
+    meteo_site = meteo_data.loc[meteo_data['site'] == site]
+    a = meteo_ephem.daylength_series(meteo_site)
+    new_meteo_data = new_meteo_data.append(a)
+
+new_meteo_data.date = new_meteo_data.date.astype('string')
+new_meteo_data['date'] = new_meteo_data['date'].str.replace('-', '_')
+
+new_meteo_data.to_csv('D:/Simon/Python/lgrass/example/GEVES/Meteo_GEVES.csv', index=False)

example/calibration_GEVES_2021/graphs/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore