Skip to content

Commit

Permalink
Merge pull request #17 from SimonRouet/flowering
Browse files Browse the repository at this point in the history 
Flowering
  • Loading branch information
@rbarillot
rbarillot committed Jun 14, 2021
2 parents 80e9c7c + 16bf5fc commit 1436d65
Show file tree
Hide file tree
Showing 18 changed files with 53,880 additions and 8,576 deletions.
Binary file modified example/MORPHOFLOR/inputs/Parametre_plante_Lgrass.xls
View file
Binary file not shown.
17,976 changes: 9,461 additions & 8,515 deletions example/MORPHOFLOR/inputs/environnement_morphoflor.csv
View file

Large diffs are not rendered by default.

33 changes: 29 additions & 4 deletions example/MORPHOFLOR/inputs/plan_simulation.csv
View file
Original file line number Diff line number Diff line change
@@ -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
6 changes: 4 additions & 2 deletions example/MORPHOFLOR/run_lgrass.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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']

Expand All @@ -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']
Expand All @@ -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="])
Expand Down
32 changes: 16 additions & 16 deletions example/MORPHOFLOR/simulation_plan_generator.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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,
Expand All @@ -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",
Expand All @@ -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)
17 changes: 17 additions & 0 deletions example/calibration_GEVES_2021/calcul_photoperiode_meteo_GEVES.py
View file
Original file line number Diff line number Diff line change
@@ -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)
4 changes: 4 additions & 0 deletions example/calibration_GEVES_2021/graphs/.gitignore
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
# Ignore everything in this directory
*
# Except this file
!.gitignore
Loading

0 comments on commit 1436d65

Please sign in to comment.