def generate_bgeom(step=None):
from openalea.lpy import Lsystem
import os
print('Scene generator launched')
l = Lsystem(
lsysfile, {
'RESOLUTION': 2,
'daystep': 1,
'TIMEBAR': False,
'LEAFY': True,
'WITH_INFLO': True,
'EXPORT_TO_MTG': False
})
if step is None:
firststep = 0
nbsteps = l.derivationLength
else:
firststep = step
nbsteps = step + 1
open(stepfile, 'w').write(str(nbsteps))
if not os.path.exists(workingrep): os.makedirs(workingrep)
for step in range(firststep, nbsteps):
if step == firststep: lstring = l.derive(firststep + 1)
else: lstring = l.derive(lstring, step, 1)
lscene = l.sceneInterpretation(lstring)
fname = join(workingrep, bgeomfile.format(str(step).zfill(4)))
lscene.save(tempbgeomfile)
os.rename(tempbgeomfile, fname)
print("Scene", step, "generated ...")
def run_lgrass(scenario_id=1,
inputs_dir_path='inputs',
outputs_dir_path='outputs'):
""" Run lgrass.lpy file from external script
:param str inputs_dir_path: the path to the input files (meteo, list of simulations...)
:param str outputs_dir_path: the path to the outputs files
:param int scenario_id: the index of the scenario to be run from the list of simulations CSV file
"""
# Scenario to be run
scenarii_df = pd.read_csv(os.path.join('inputs', 'plan_simulation.csv'),
index_col='Scenario')
scenario = scenarii_df.loc[scenario_id].to_dict()
scenario_name = scenario['name']
# Update parameters of flowering model
flowering_model = lgrass.flowering_functions.FloweringFunctions()
flowering_model.param.__dict__.update(
(k, scenario[k])
for k in set(scenario).intersection(flowering_model.param.__dict__))
# Load lsystem
lpy_filename = os.path.join(lgrass.__path__[0], "lgrass.lpy")
lsystem = Lsystem(lpy_filename)
# Update parameters
lsystem.option_profile = "plateau"
lsystem.flowering_model = flowering_model
lsystem.derivationLength = int(scenario['derivationLength'])
lsystem.option_tallage = scenario['option_tallage']
lsystem.option_senescence = scenario['option_senescence']
lsystem.option_floraison = scenario['option_floraison']
lsystem.meteo_path = os.path.join(inputs_dir_path,
scenario['meteo_filename'])
lsystem.sowing_date = scenario['sowing_date']
lsystem.site = scenario['site']
lsystem.output_induction_file_name = '{}_induction'.format(scenario_name)
lsystem.output_organ_lengths_file_name = '{}_organ_lengths'.format(
scenario_name)
lsystem.cutting_dates = [] if pd.isna(scenario['cutting_dates']) \
else [scenario['cutting_dates']] if isinstance(scenario['cutting_dates'], int) \
else [int(i) for i in scenario['cutting_dates'].split("_")]
lsystem.ParamP[0]['C'] = scenario['value_C']
lsystem.ParamP[0]['Premiecroiss'] = scenario['Premiecroiss']
lsystem.ParamP[0]['PS_compensation_point'] = scenario[
'PS_compensation_point']
if outputs_dir_path:
lsystem.OUTPUTS_DIRPATH = outputs_dir_path
# Run the lsystem
try:
lsystem.derive(
) # permet le declenchement de la fonction "End" du script lpy
lsystem.clear()
except Exception as e:
print(e)
def test_run(overwrite_desired_data=False):
lpy_filename = os.path.join(lgrass.__path__[0], "lgrass.lpy")
lsys = Lsystem(lpy_filename)
axiom = lsys.axiom
lsys.meteo_path = os.path.join(INPUTS_DIRPATH, 'meteo_file.csv')
lsys.INPUTS_DIRPATH = INPUTS_DIRPATH
lsys.OUTPUTS_DIRPATH = OUTPUTS_DIRPATH
lsys.GRAPHS_DIRPATH = GRAPHS_DIRPATH
lsys.derivationLength = NSTEP
lsys.DureeExp = NSTEP
lsys.option_tallage = True
lsys.option_senescence = True
lsys.option_floraison = True
lsys.option_caribu = 'Off'
lsys.option_tiller_regression = False
lsys.option_mophogenetic_regulation_by_carbone = False
lsys.derive(axiom, NSTEP)
# convert the outputs to Pandas dataframe
surface_biomass = pd.read_csv(lsys.chemin_fichier1.name)
evol = pd.read_csv(lsys.chemin_fichier2.name)
output_induction_file_path = os.path.join(OUTPUTS_DIRPATH,
'output_induction.csv')
output_induction = pd.read_csv(output_induction_file_path)
output_organ_lengths_file_path = os.path.join(OUTPUTS_DIRPATH,
'output_organ_lengths.csv')
output_organ_lengths = pd.read_csv(output_organ_lengths_file_path)
# # compare outputs
compare_actual_to_desired(OUTPUTS_DIRPATH, surface_biomass,
DESIRED_SORTIE_SURFACE_BIOMASS_FILENAME,
lsys.chemin_fichier1.name,
overwrite_desired_data)
compare_actual_to_desired(OUTPUTS_DIRPATH, evol,
DESIRED_SERIE_FOLIAIRE_FILENAME,
lsys.chemin_fichier2.name,
overwrite_desired_data)
compare_actual_to_desired(OUTPUTS_DIRPATH, output_induction,
DESIRED_OUTPUT_INDUCTION_FILENAME,
output_induction_file_path,
overwrite_desired_data)
compare_actual_to_desired(OUTPUTS_DIRPATH, output_organ_lengths,
DESIRED_OUTPUT_ORGAN_LENGTHS_FILENAME,
output_organ_lengths_file_path,
overwrite_desired_data)
if overwrite_desired_data:
print("New desired files written")
else:
print("Test passed successfully")
def generate_bgeom(step=None, endstep=None):
from openalea.lpy import Lsystem
import os
print('Scene generator launched')
l = Lsystem(
lsysfile, {
'SEED': 0,
'TREE': 0,
'RESOLUTION': 2,
'TIMESTEP': 1,
'TIMEBAR': False,
'LEAFY': True,
'WITH_INFLO': True,
'TEXTURE': True,
'GENERALIZEDCYLINDER': True,
'WITH_GLM': True,
'FRUIT_MODEL': False,
'GLM_RESTRICTION': None,
'_GLM_TYPE': 3,
'EXPORT_TO_MTG': False
})
if step is None:
firststep = 0
endstep = l.derivationLength
else:
firststep = step
if endstep is None:
endstep = l.derivationLength
else:
assert endstep < l.derivationLength
open(stepfile, 'w').write(str(endstep))
if not os.path.exists(workingrep): os.makedirs(workingrep)
for step in range(firststep, endstep):
if step == firststep: lstring = l.derive(firststep + 1)
else: lstring = l.derive(lstring, step, 1)
lscene = l.sceneInterpretation(lstring)
fname = join(workingrep, bgeomfile.format(str(step).zfill(4)))
lscene.save(tempbgeomfile)
os.rename(tempbgeomfile, fname)
print("Scene", step, "generated ...")
def generate(seed = 0, tree = 0, fdist = 4, regenerate = False):
from openalea.lpy import Lsystem
import os
rep = glob.glob(pattern.format(tree, seed, '*' , fdist))
if len(rep) == 2 and not regenerate:
print('Do not regenerate', seed, tree, fdist)
return True
l = Lsystem(lsysfile,{'RESOLUTION' : 1, 'daystep' : 30, 'TIMEBAR' : False, 'LEAFY' : True, 'WITH_INFLO' : True, 'EXPORT_TO_MTG' : False, 'TREE' : tree, 'SEED' : seed, 'FRUITBRANCHSIZE' : fdist})
if l.tree_load:
print('Generate', seed, tree, fdist)
try:
lstring = l.derive()
return True
except:
return False
else :
print('Not loaded tree', tree)
return False
