def duplicate(g, n=1):
if g.nb_vertices(scale=1) == n:
return g
g1 = g.sub_mtg(g.root)
for i in range(n-1):
g1 = union(g1,g)
return g1
def import_mtgfile(filename):
"""
parameters:
-----------
filename : names of mtg
return:
-------
a function which import mtg corresponding to the mtg names
"""
def name(f):
"return base name without extension"
return f.basename().splitext()[0]
filenames = filename
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
mtgfile = dict((k, f) for k, f in mtg_path.items() if k in filenames)
if len(filenames) == 1:
g = MTG(mtgfile[filenames[0]])
return g
else:
metaMTG = MTG()
for i in mtgfile:
metaMTG = algo.union(metaMTG, MTG(mtgfile[i]))
return metaMTG
def duplicate(g, replicates=1, grem=None):
"""construct a mtg replicating g n times and adding grem"""
g_rep = replicate(g, replicates)
if grem is not None:
g = grem
g = union(g, g_rep)
else:
g = g_rep
return g
def replicate(g, target=1):
""" replicate the plants in g up to obtain target new plants"""
current = g.nb_vertices(scale=1)
if target <= current:
return g
assert target % current == 0
# otherwise use nrem + union
nduplication = int(numpy.log2(1. * target / current))
missing = target - current * numpy.power(2, nduplication)
cards = numpy.power(2, range(nduplication))
add_g = [False] * len(cards)
for i in reversed(range(len(cards))):
if cards[i] <= missing:
add_g[i] = True
missing -= cards[i]
assert missing == 0
g_add = None
g_dup = g.sub_mtg(g.root)
for i in range(nduplication):
g1 = g_dup.sub_mtg(g_dup.root)
g_dup = union(g_dup, g1)
if add_g[i]:
g1 = g.sub_mtg(g.root)
if g_add is None:
g_add = g1
else:
g_add = union(g_add, g1)
if g_add is not None:
g_dup = union(g_dup, g_add)
return g_dup
def replicate(g, target=1):
current = g.nb_vertices(scale=1)
if target <= current:
return g
assert target % current == 0
#otherwise use nrem + union
nduplication = int(numpy.log2(1. * target / current))
missing = target - current * numpy.power(2,nduplication)
cards = numpy.power(2, range(nduplication))
add_g = [False] * len(cards)
for i in reversed(range(len(cards))):
if cards[i] <= missing:
add_g[i] = True
missing -= cards[i]
assert missing == 0
g_add = None
g_dup = g.sub_mtg(g.root)
for i in range(nduplication):
g1 = g_dup.sub_mtg(g_dup.root)
g_dup = union(g_dup, g1)
if add_g[i]:
g1 = g.sub_mtg(g.root)
if g_add is None:
g_add = g1
else:
g_add = union(g_add, g1)
if g_add is not None:
g_dup = union(g_dup,g_add)
return g_dup
def setup_canopy(self, age = 10):
self.canopy_age = age
# produce plants positionned at origin
if self.nrem > 0:
canopy = RunAdel(age, self.pars_rem, adelpars=self.run_adel_pars)
grem = mtg_factory(canopy, adel_metamer, leaf_sectors=self.nsect, leaves=self.leaves, stand=None, split=self.split, aborting_tiller_reduction=self.aborting_tiller_reduction)
grem = mtg_interpreter(grem, self.leaves, face_up = self.face_up, classic= self.classic)
if self.nquot > 0:
canopy = RunAdel(age, self.pars_quot, adelpars=self.run_adel_pars)
gquot = mtg_factory(canopy, adel_metamer, leaf_sectors=self.nsect, leaves=self.leaves, stand=None, split=self.split, aborting_tiller_reduction=self.aborting_tiller_reduction)
gquot = mtg_interpreter(gquot, self.leaves, face_up = self.face_up, classic= self.classic)
gquot = replicate(gquot, self.nquot * self.duplicate)
if self.nrem > 0:
g = grem
if self.nquot > 0:
g = union(g, gquot)
else:
g = gquot
#update positions and domain if smart stand is used
if self.stand.density_curve is not None:
new_nplants, self.domain, self.positions, self.domain_area = self.stand.smart_stand(self.nplants, at=age)
assert new_nplants == self.nplants
# dispose plants and renumber them
pos = g.property('position ')
az = g.property('azimuth')
lab = g.property('label')
geom = g.property('geometry')
for i,vid in enumerate(g.vertices(1)):
lab[vid] = 'plant' + str(i + 1)
pos[vid] = self.positions[i]
az[vid] = self.plant_azimuths[i]
for gid in g.components_at_scale(vid, g.max_scale()):
if gid in geom:
geom[gid] = transform_geom(geom[gid], self.positions[i], self.plant_azimuths[i])
return g
def on_change_get_files(widget, event, data):
# load mtgs
misc.all_mtg = MTG()
for file in data:
g = read_mtg_file(file_paths[file])
misc.all_mtg = union(misc.all_mtg, g)
# update table
if misc.all_mtg:
df = get_table_mtg(misc.all_mtg)
# TODO:
update_grid(df, tableMTG)
else:
update_grid(pd.DataFrame(), tableMTG)
# update genotype selections
update_selection_items()
# update file description
print_files_description()
def reader_uploaded():
if files_upload.get_files():
upfile = files_upload.get_files()
for f in upfile:
# if a mtg file with the same name already exists - nothing is done
if not os.path.isfile(data_directory + '/' + f['name']):
# ADD the file to the mtg database
# TODO: Add the possibility to not add it
content = f['file_obj'].read()
tmp = open(data_directory + '/' + f['name'], 'w')
tmp.write(content.decode('utf-8'))
tmp.close()
# then add it to the all_mtg
g = read_mtg(content.decode('utf-8'))
misc.all_mtg = union(misc.all_mtg, g)
global files, file_paths
files, file_paths = get_files()
files_selection.items = files
update_selection_items()
def import_mtgfile(filename):
"""Import a MTG file from genotype name, in sharedata repo
:param filename: genotype = name of the file
:type filename: string
:return: a MTG loaded from the file
:rtype: MTG
"""
filenames = filename
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
mtgfile = dict((k, f) for k, f in mtg_path.items() if k in filenames)
if len(filenames) == 1:
g = MTG(mtgfile[filenames[0]])
return g
else:
metaMTG = MTG()
for i in mtgfile:
metaMTG = algo.union(metaMTG, MTG(mtgfile[i]))
return metaMTG
def test_extract_at_plant_scale():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
mtg = MTG()
for k, genotype in enumerate(mtg_path):
if (genotype=="Sicile") or (genotype=="Nils") or (genotype=='origine_stolon_gariguetteDV_6novembre2018') \
or (genotype=='friendlyfruit_varieties'):
pass
else:
mtg = union(mtg, read_mtg_file(mtg_path[genotype]))
genotypes = mtg.property('Genotype')
for geno in set(genotypes.values()):
vids = [
vid for vid in mtg.vertices(scale=1) if genotypes.get(vid) == geno
]
df = extract_at_plant_scale(mtg, vids)
assert not df.empty
assert set(df['Genotype']) == {geno}
def mtg_turtle(g, symbols):
''' Compute the geometry on each node of the MTG using Turtle geometry. '''
from openalea.mtg import turtle
plants = g.component_roots_at_scale_iter(g.root, scale=1)
nplants = g.nb_vertices(scale=1)
gt = MTG()
def adel_visitor(g, v, turtle):
# 1. retriev the node
n = g.node(v)
angle = float(n.Laz) if n.Laz else 0.
turtle.rollL(angle)
if g.edge_type(v) == '+':
if not n.label.startswith('L'):
angle = n.Ginc or n.Einc
angle = float(angle) if angle is not None else 0.
turtle.up(angle)
# 2. Compute the geometric symbol
mesh, can_label = compute_element(n, symbols)
if mesh:
n.geometry = transform(turtle, mesh)
n.can_label = can_label
# 3. Update the turtle
turtle.setId(v)
if n.label.startswith('S'):
turtle.f(n.length)
# Get the azimuth angle
for plant in plants:
gplant = g.sub_mtg(plant)
scene = turtle.TurtleFrame(gplant,visitor=adel_visitor)
gt = union(gplant,gt)
return gt
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
def test1():
g = aml.MTG('data/test7.mtg')
g1 = g.sub_mtg(g.root)
assert len(g1) == len(g)
g2 = union(g, g1)
assert len(g2) == 2 * len(g) - 1