def run_lsystem(lsystem='simple_maize_nolight.lpy', parameters=None):
if parameters:
lsys = Lsystem(lsystem, {'parameters': parameters})
else:
lsys = Lsystem(lsystem)
lstring = lsys.iterate()
lscene = lsys.sceneInterpretation(lstring)
return lsys, lstring, lscene
def test_mtglpy_topvine():
fn = path('vinemtg_n.lpy')
if not fn.exists():
return
l = Lsystem(str(fn))
parameters = {}
parameters['carto_file'] = 'geom_n.dat'
parameters['picle_file'] = 'vine_n.dat'
parameters['TTfin'] = None
#l.context().updateNamespace(parameters)
c_iter = l.getLastIterationNb()
nbstep = l.derivationLength - c_iter
tree = l.iterate(l.axiom, c_iter, nbstep)
scene = l.sceneInterpretation(tree)
mtg = lpy2mtg(tree, l, scene)
print(len(mtg))
axial_tree = AxialTree()
axial_tree = mtg2lpy(mtg, l, axial_tree)
g = lpy2mtg(axial_tree, l, scene)
assert len(g) == len(mtg)
#axial_tree = mtg2axialtree(mtg, scale, parameters, axial_tree)
# Check
assert True
return mtg, tree, axial_tree
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 update_itable(self):
path = str(self.dirname / 'index-table.json')
self.write_itable(self.itable, path)
# update combi_parameters.csv
path = str(self.dirname / 'combi_params.csv')
parameters = self.itable.values()
allkeys = set().union(*parameters)
def _missing(d):
return len(allkeys - set(d.keys()))
if any([_missing(p) for p in parameters]):
self.activate()
new = []
for p in parameters:
lsys = Lsystem(self.walter, {'params': p})
newp = {
k: lsys.context().locals().get(k, 'undef')
for k in allkeys
}
new.append(newp)
parameters = new
combi = []
for k, v in zip(self.itable, parameters):
d = {'ID': k}
d.update(v)
combi.append(d)
df = pd.DataFrame(combi)
df.to_csv(path, index=False, sep='\t')
def run_lsys(**kwds):
params = {k: v for k, v in _lsys_params.iteritems()}
params.update(kwds)
l = Lsystem('sensitivityanalysis.lpy', params)
lstring = l.iterate()
lscene = l.sceneInterpretation(lstring)
return lstring, lscene
def force_cut(lstring):
fake_rule = """
Fake:
produce Fake"""
fake_lsys = Lsystem()
fake_lsys.addRule(fake_rule)
fake_lsys.axiom = lstring
return fake_lsys.iterate()
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 str2mtg(s):
#s = s.replace('N', 'F')
tree = AxialTree(s)
l = Lsystem()
l.addInterpretationRule('N --> F', 0)
geom_tree = l.homomorphism(tree)
scene = l.sceneInterpretation(geom_tree)
scale = dict(list(zip(('P', 'A', 'N', 'L', 'F'), (1, 2, 3, 3, 3))))
mtg = axialtree2mtg(tree, scale, scene)
return tree, mtg, scene
def test_cut_bug():
lsystem_file = pj(data_access.get_data_dir(), 'check_cut_module.lpy')
lsys = Lsystem(lsystem_file)
lstring = lsys.iterate()
# cut branches
new_lstring = force_cut(lstring)
lscene = lsys.sceneInterpretation(lstring)
for sid in lscene.todict():
assert sid in range(len(lstring))
# suucceed if correction is needed (old lpy version)
# assert new_lstring[sid].name == 'Internode'
# succeed on more recent lpy version
assert lstring[sid].name == 'Internode'
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 lsystem(file_name, axiom='', derivationlength=-1, parameters={}):
""" Build a lsystem object from file_name """
l = Lsystem(file_name, parameters)
if len(axiom):
l.makeCurrent()
if type(axiom) != AxialTree:
axiom = AxialTree(axiom)
l.axiom = axiom
#l.done()
if derivationlength >= 0:
l.derivationLength = derivationlength
return l
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
def run(self, sim_id=None, dry_run=False, **kwds):
"""Run WALTer in project dir
Parameters
----------
sim_id:
simulation identifier
dry_run: (bool)
prevent running the simulation (do only side effects).
**kwds:
walter parameters values (as named arguments)
Examples
--------
p = Project()
p.run(nb_plt_utiles=1,
dist_border_x=0,
dist_border_y=0,
nbj=30,
beginning_CARIBU=290)
Returns
-------
the lsystem and lstring generated by the run
"""
self.activate()
already_known_id = self.itable.keys()
if sim_id is None:
sim_id = self.get_id(kwds)
if sim_id not in already_known_id:
self.update_itable()
lsys, lstring = None, None
if not dry_run:
lsys = Lsystem(self.walter, {'params': kwds, 'ID': sim_id})
time_start = time.time()
lstring = lsys.iterate()
time_stop = time.time()
with open(
self.output_path(sim_id=sim_id) / "Simulation_time.txt",
'w') as time_file:
time_file.write(str(time_stop - time_start))
return lsys, lstring
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 test_mtglpy():
fn = path('ex_luz4.lpy')
if not fn.exists():
return
l = Lsystem('ex_luz4.lpy')
tree = l.iterate()
scene = l.sceneInterpretation(tree)
mtg = lpy2mtg(tree, l, scene)
print(len(mtg))
axial_tree = AxialTree()
axial_tree = mtg2lpy(mtg, l, axial_tree)
print(len(axial_tree))
#axial_tree = mtg2axialtree(mtg, scale, parameters, axial_tree)
# Check
assert True
return mtg, tree
def lpy_plot(self, line):
from math import ceil, sqrt, floor
try:
ip = get_ipython()
except NameError:
ip = None
args = parse_argstring(self.lpy_plot, line)
file = args.file
sizes = [int(i.strip()) for i in args.size.split(',')]
cell = args.cell
size_display = (int(sizes[0]),
int(sizes[1])) if len(sizes) > 1 else (int(sizes[0]),
int(sizes[0]))
ls = Lsystem(file)
rows = cols = ceil(sqrt(ls.derivationLength + 1))
size = rows * cell
start = -size / 2 + cell / 2
sw = SceneWidget(size_display=size_display, size_world=size)
sw.add(ls.sceneInterpretation(ls.axiom), position=(start, start, 0))
def plot():
tree = ls.axiom
for i in range(1, ls.derivationLength):
row = floor(i / rows)
col = (i - row * cols)
x = row * cell + start
y = col * cell + start
tree = ls.derive(tree, i, 1)
sw.add(ls.sceneInterpretation(tree), (x, y, 0))
ip.events.unregister('post_run_cell', plot)
if ip:
ip.events.register('post_run_cell', plot)
return sw
def parse_extern_modules(lpyfile):
""" Parse an lpyfile to retrieve its modules and expected extern parameters """
lines = list(open(lpyfile).readlines())
externs = set()
def f(**kwd):
nonlocal externs
externs = externs.union(set(kwd.keys()))
code = ''.join([l for l in lines if l.startswith('extern')])
n = {'extern' : f, 'externs' : externs}
exec(code, n, n)
code2 = ''.join([l for l in lines if l.startswith('module')])
from openalea.lpy import Lsystem
l = Lsystem()
l.setCode(code2)
l.makeCurrent()
modules = {}
for m in l.execContext().declaredModules():
modules[m.name] = m.parameterNames
l.done()
return externs, modules
def generate_mtg(trees=list(range(3)), params=dict()):
from openalea.lpy import Lsystem
from openalea.mtg import MTG
from openalea.mtg.algo import union
g = None
for tree in trees:
print('Generate tree', tree)
nparams = params.copy()
nparams.update({
'TREE': tree,
'TIMESTEP': 180 if not params['FRUIT_MODEL'] else 90,
'EXPORT_TO_MTG': True,
'PARALLELFRUITMODEL': False
})
nparams.setdefault('WITH_GLM', True)
l = Lsystem(basename(lsysfile), nparams)
lstring = l.iterate()
resmtg = l.resultmtg
assert type(resmtg) == MTG
if g is None:
g = resmtg
else:
g = union(g, resmtg)
return g
flowering_param.param.temp_vern_min = x[0]
flowering_param.param.temp_vern_inter = x[1]
flowering_param.param.temp_vern_max = x[2]
flowering_param.param.daily_vern_rate = x[3]
flowering_param.param.basic_vern_rate = x[4]
flowering_param.param.photoperiod_min = x[5]
flowering_param.param.photoperiod_max = x[6]
flowering_param.param.max_photo_ind_rate = x[7]
flowering_param.param.coeff_primordia_emission_vegetative = x[8]
flowering_param.param.coeff_primordia_emission_reproductive = x[9]
name = str(x[10][0]) + "_" + str(x[10][1])
print(name)
names.append(name)
lpy_filename = os.path.join('lgrass.lpy')
testsim[name] = Lsystem(lpy_filename)
testsim[name].derivationLength = 200
testsim[name].meteo_path = 'D:/Simon/Comites_de_these/Comite_de_these_2/Modelisation/Meteo_sites_GEVES_daylength.csv'
testsim[name].sowing_date = x[10][1]
testsim[name].site = x[10][0]
testsim[name].flowering_model = flowering_param
testsim[name].output_induction_file_name = 'induction_' + name
testsim[name].output_organ_lengths_file_name = 'organ_lengths_' + name
# function to run an L-system from the 'testsim' dictionnary
def runlsystem(n):
testsim[names[n]].derive() # permet le declenchement de la fonction "End" du script lpy
# print(testsim[names[n]].output_dict)
# with open(os.path.join(OUTPUTS_DIRPATH, 'sortie_test_path', str(n) + '.csv'), 'wb') as sortie_test_path:
def shoot_grow(g, demand_only=True):
lsys = Lsystem(str(os.path.join(lsysdir, 'morphogenesis.lpy')), {'demand_only': demand_only})
lsys.axiom = mtg2lpy(g, lsys, AxialTree())
axt = lsys.iterate()
scene = lsys.sceneInterpretation(axt)
return lpy2mtg(axt, lsys, scene)
def shoot_init(carbon_seed_stock=0.1):
lsys = Lsystem(str(os.path.join(lsysdir, 'morphogenesis.lpy')), {'carbon_seed_stock': carbon_seed_stock})
axialtree = lsys.axiom
scene = lsys.sceneInterpretation(axialtree)
return lpy2mtg(axialtree, lsys, scene)
# -*- coding: utf-8 -*-
"""Simple converter of lpy files to ply format."""
import os
import sys
from openalea.lpy import Lsystem
from openalea.plantgl.all import Tesselator
usage = """Convert lpy file to ply format
usage: {} FILE"""
if len(sys.argv) != 2:
print(usage.format(__name__))
lpy_file = sys.argv[1]
lsys = Lsystem(lpy_file)
ply_file = os.path.splitext(
os.path.basename(os.path.expanduser(lpy_file)))[0]
ply_file = ply_file + '.ply'
n = lsys.derivationLength
tree = lsys.axiom
for i in range(n):
# Apply rewritting rules on the tree -> One step of simulation
tree = lsys.iterate(tree, 1)
scene = lsys.sceneInterpretation(tree)
d = Tesselator()
nind = 0
nvert = 0
vert_part = ''
if len(sys.argv) == 2:
out_meth = 'ply'
else:
out_meth = sys.argv[2]
# Connect to I/O channels
in1 = CisInput('LPy_time')
if out_meth == 'ply':
out = CisPlyOutput('LPy_mesh')
elif out_meth == 'obj':
out = CisObjOutput('LPy_mesh')
else:
out = CisAsciiArrayOutput('LPy_mesh', '%f\t%f\t%f\t%f\t%f\t%f\t%f\t%f\t%f\n')
# Create lsystem & discretizer
lsys = Lsystem(fname)
d = Tesselator()
# Continue looping until no more input times
# TODO: Automated unit conversion
mm_to_cm = 0.1
flag = True
while (flag):
# Receive next step
flag, result = in1.recv()
if not flag:
print("LPy: End of input.")
break
niter = result[0]
print("LPy: Received request for step %d" % niter)
def runmodel(fname):
from openalea.lpy import Lsystem
l = Lsystem(fname)
lstring = l.iterate()
l.plot(lstring)
def animatemodel(fname):
from openalea.lpy import Lsystem
l = Lsystem(fname)
l.animate()
# :param lsystem: lsystem that can be used to create the 3d representation of axialtree
# :return: adapted axialtree
# """
#
# def repr_geom(self):
# return __scene
#
# scene = lsystem.sceneInterpretation(axialtree)
# axialtree.__scene = scene
# axialtree._repr_geom_ = types.MethodType(repr_geom, axialtree)
#
# return axialtree
context = {}
lsystem = Lsystem()
axialtree = AxialTree()
# axialtree = adapt_axialtree(axialtree, lsystem)
code = '''
"""
input = lstring="_(0.01)-(90)F(1)"
output = lstring
"""
N = 2
derivation length: N
production:
def createtree(path):
lsys = Lsystem(path)
lstring = lsys.iterate()
lscene = lsys.sceneInterpretation(lstring)
return lscene
def import_lpy_controls(filepath):
if not path(filepath).isfile():
return
control = dict()
f = open(filepath, 'r')
script = f.read()
f.close()
if script is None: script = ""
beginTag = LpyParsing.InitialisationBeginTag
if not beginTag in script:
return str(script), control
else:
txts = str(script).split(beginTag)
new_script = txts[0]
context_to_translate = txts[1]
context = Lsystem().context()
context.initialiseFrom(beginTag + context_to_translate)
managers = get_managers()
visualparameters = []
scalars = []
functions = []
curves = []
geoms = []
lpy_code_version = 1.0
if context.has_key('__lpy_code_version__'):
lpy_code_version = context['__lpy_code_version__']
if context.has_key('__scalars__'):
scalars_ = context['__scalars__']
scalars = [ProduceScalar(v) for v in scalars_]
if context.has_key('__functions__') and lpy_code_version <= 1.0:
functions = context['__functions__']
for n, c in functions:
c.name = n
functions = [c for n, c in functions]
funcmanager = managers['Function']
geoms += [(funcmanager, func) for func in functions]
if context.has_key('__curves__') and lpy_code_version <= 1.0:
curves = context['__curves__']
for n, c in curves:
c.name = n
curves = [c for n, c in curves]
curvemanager = managers['Curve2D']
geoms += [(curvemanager, curve) for curve in curves]
if context.has_key('__parameterset__'):
for panelinfo, objects in context['__parameterset__']:
for typename, obj in objects:
visualparameters.append((managers[typename], obj))
for scalar in scalars:
control[unicode(scalar.name)] = scalar.value
for (manager, geom) in geoms:
if geom != list():
control[geom.getName()] = geom
for (manager, geom) in visualparameters:
if geom != list():
control[geom.getName()] = geom
new_controls = []
for name, value in control.items():
interfaces = guess_interface(value)
if interfaces:
new_controls.append(Control(name, interfaces[0], value))
try:
control["color map"] = to_color(context.turtle.getColorList())
except AttributeError:
pass
else:
new_controls.append(
Control("color map", 'IColorList', control["color map"]))
for control in new_controls:
register_control(control)