def initialize_mtg(root, nodelabel = 'N'):
from openalea.mtg import MTG
mtg = MTG()
plantroot = mtg.root
branchroot = mtg.add_component(plantroot,label='P')
noderoot = mtg.add_component(branchroot,label=nodelabel)
mtg.property('position')[noderoot] = root
mtg.property('radius')[noderoot] = None
assert len(mtg.property('position')) == 1
return mtg
def initialize_mtg(root, nodelabel='N'):
from openalea.mtg import MTG
mtg = MTG()
plantroot = mtg.root
branchroot = mtg.add_component(plantroot, label='P')
noderoot = mtg.add_component(branchroot, label=nodelabel)
mtg.property('position')[noderoot] = root
mtg.property('radius')[noderoot] = None
assert len(mtg.property('position')) == 1
return mtg
def test_insert_elements():
g = MTG()
labels = g.property('label')
add_plant(g)
elts = [{'label': 'elt1'}, {'label': 'elt2'}]
collar = find_label('collar', g)[0]
insert_elements(g, collar, elts)
elt1 = find_label('elt1', g)[0]
assert labels[g.parent(elt1)] == 'baseElement'
assert labels[g.children(elt1)[0]] == 'elt2'
def test_add_axe():
g = MTG()
labels = g.property('label')
p1 = add_plant(g)
p2 = add_plant(g)
vid_axe = add_axe(g, 'T0')
assert g.complex(vid_axe) == p1
assert labels[g.parent(vid_axe)] == 'MS'
vid_axe = add_axe(g, 'T1.3', plant_number=2)
assert g.complex(vid_axe) == p2
assert labels[g.parent(vid_axe)] == 'T1'
vid_metamer0 = g.component_roots_at_scale(vid_axe, 3)[0]
assert labels[g.parent(vid_metamer0)] == "metamer3"
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 read_lsystem_string( string,
symbol_at_scale,
functional_symbol={},
mtg=None ):
"""Read a string generated by a lsystem.
:Parameters:
- `string`: The lsystem string representing the axial tree.
- `symbol_at_scale`: A dict containing the scale for each symbol name.
:Optional parameters:
- `functional_symbol`: A dict containing a function for specific symbols.
The args of the function have to be coherent with those in the string.
The return type of the functions have to be a dictionary of properties: dict(name, value)
:Return:
MTG object
"""
import openalea.plantgl.all as pgl
s = string
def transform(turtle, mesh):
x = turtle.getUp()
z = turtle.getHeading()
bo = pgl.BaseOrientation(x, z^x)
matrix = pgl.Transform4(bo.getMatrix())
matrix.translate(turtle.getPosition())
mesh = mesh.transform(matrix)
return mesh
# 1. Create the mtg structure.
if mtg is None:
mtg = MTG()
# 2. add some properties to the MTG
mtg.add_property('index')
mtg.add_property('can_label')
mtg.add_property('geometry')
mtg.add_property('tissue_type')
vid = mtg.root # vid of the support tree, i.e. at the finest scale
current_vertex = mtg.root
branching_stack = []
pending_edge = '' # edge type for the next edge to be created
scale = 0
lsys_symbols = ['[', ']', '/', '+', '^', 'f']
modules = symbol_at_scale.keys()
symbols = lsys_symbols + modules
index = dict(zip(symbol_at_scale.keys(), [0]*len(symbol_at_scale)))
is_ramif = False
# 2. Create a PlantGL Turtle...
turtle = pgl.Turtle()
max_scale = max(symbol_at_scale.values())
for edge_type in symbols:
if edge_type != 'f':
s = s.replace(edge_type, '\n%s'%edge_type)
else:
s = s.replace('f(', '\nf(')
l = s.split()
try:
plant_name = [s for s in symbol_at_scale.keys() if 'plant' in s.lower()][0]
except:
ValueError("""Incorrect plant name (should be plant)""")
for node in l:
# Check if node is a module
tag = node[0]
if tag == '[':
branching_stack.append(vid)
turtle.push()
is_ramif = True
elif tag == ']':
vid = branching_stack.pop()
current_vertex = vid
scale = mtg.scale(vid)
turtle.pop()
is_ramif = False
elif tag == '/':
args = get_args(node[1:])
if args:
angle = get_float(args[1:-1])
turtle.rollR(angle)
else:
turtle.rollR()
elif tag == '+':
args = get_args(node[1:])
if args:
angle = get_float(args[1:-1])
turtle.left(angle)
else:
turtle.left()
elif tag == '^':
args = get_args(node[1:])
if args:
angle = get_float(args[1:-1])
turtle.up(angle)
else:
turtle.up()
elif tag == 'f' and node[1] == '(':
args = get_args(node[1:])
if args:
length = get_float(args[1:-1])
if length > 0:
turtle.f(length)
else:
turtle.f()
else:
# add new modules to the mtg (i.e. add nodes)
name = get_name(node)
if name not in modules:
print 'Unknow element %s'% name
continue
module_scale = symbol_at_scale[name]
if is_ramif:
edge_type = '+'
else:
edge_type = '<'
log(node, module_scale, edge_type )
if module_scale == scale:
if mtg.scale(vid) == scale:
vid = mtg.add_child(vid, edge_type=edge_type, label=name)
current_vertex = vid
pending_edge = ''
log('','Cas 1.1', scale,
'mtg.scale(vid)', mtg.scale(vid),
'generated vertex', vid)
assert mtg.scale(vid) == module_scale
else:
# add the edge to the current vertex
current_vertex = mtg.add_child(current_vertex,
edge_type=edge_type,
label=name)
log('', 'Cas 1.2', scale,
'mtg.scale(vid)', mtg.scale(vid),
'generated vertex', current_vertex)
assert mtg.scale(current_vertex) == module_scale
is_ramif = False
elif module_scale > scale:
log('', 'Cas 2', scale, 'mtg.scale(vid)', mtg.scale(vid))
old_current_vertex = current_vertex
while module_scale > scale:
if mtg.scale(vid) == scale:
assert vid == current_vertex
vid = mtg.add_component(vid)
current_vertex = vid
log('', '', 'Cas 2.1', scale, 'generate new component', current_vertex)
scale += 1
if module_scale == scale:
assert mtg.scale(current_vertex) == module_scale
mtg.property('label')[current_vertex] = name
break
else:
scale += 1
current_vertex = mtg.add_component(current_vertex)
else:
log(node, 'add_child(%d, child=%d)'%(old_current_vertex, current_vertex))
mtg.property('label')[current_vertex] = name
if mtg.scale(vid) == scale:
vid = mtg.add_child(vid, child=current_vertex, edge_type=edge_type)
is_ramif = False
else:
assert module_scale < scale
while module_scale < scale:
scale -= 1
current_vertex = mtg.complex(current_vertex)
else:
current_vertex = mtg.add_child(current_vertex, edge_type=edge_type, label=name)
assert mtg.scale(current_vertex) == module_scale
# MANAGE the properties, the geometry and the indices!!!
index[name] += 1
if name == plant_name:
for k in index.keys():
if k != name:
index[k] = 0
mtg.property('index')[current_vertex] = index[name]
if name in functional_symbol:
features = eval(node, functional_symbol)
geom = features.get('geometry')
canlabel = features.get('label')
ttype = features.get('tissue_type')
if geom:
# get the transformation from the turtle
geom = transform(turtle, geom)
mtg.property('geometry')[current_vertex] = geom
if name == 'StemElement':
# parse args to know how the turtle has to move .
args = get_args(node)[1:-1]
list_args= args.split(',')
length = float(list_args[1]) # 2nd arg
if length > 0:
turtle.f(length)
if canlabel:
canlabel.elt_id = index[name]
plant_id = mtg.complex_at_scale(current_vertex, scale=1)
canlabel.plant_id = mtg.property('index')[plant_id]
mtg.property('can_label')[current_vertex] = canlabel
if ttype:
mtg.property('tissue_type')[current_vertex] = ttype
mtg = fat_mtg(mtg)
return mtg
def new_mtg_factory(parameters, metamer_factory=adel_metamer, leaf_sectors=1,
leaves=None, stand=None, axis_dynamics=None,
add_elongation=False,
topology=('plant', 'axe_id', 'numphy'), split=False,
aborting_tiller_reduction=1.0, leaf_db=None):
"""A 'clone' of mtg_factory that uses mtg_edition functions
"""
if leaf_db is not None:
raise AdelDeprecationError(
'leaf_db argument is deprecated, use leaves argument instead')
if leaves is None:
dynamic_leaf_db = {0: False}
leaves = {0: None}
else:
dynamic_leaf_db = {k: leaves[k].dynamic for k in leaves}
g = MTG()
# buffers
# for detection of newplant/newaxe
prev_plant = 0
prev_axe = -1
dp = parameters
nrow = len(dp['plant'])
species = 0
for i in range(nrow):
plant, num_metamer = [int(convert(dp.get(x)[i], undef=None)) for x in
[topology[e] for e in [0, 2]]]
axe = dp.get(topology[1])[i]
args = properties_from_dict(dp, i, exclude=topology)
# Add plant if new
if plant != prev_plant:
if axe != 'MS':
raise ValueError('Main stem is expected first when a new plant '
'is declared')
position, azimuth = (0, 0, 0), 0
if stand and len(stand) >= plant:
position, azimuth = stand[plant - 1]
plant_properties = {'position': position, 'azimuth': azimuth,
'refplant_id': args.get('refplant_id'),
'species': species}
timetable = None
if axis_dynamics:
timetable = axis_dynamics[str(plant)][str(axe)]
mainstem_properties = dict(timetable=timetable,
HS_final=args.get('HS_final'),
nff=args.get('nff'),
hasEar=args.get('hasEar'),
azimuth=args.get('az_insertion'))
add_plant(g, plant_number=plant, plant_properties=plant_properties,
axis_properties=mainstem_properties)
prev_plant = plant
# Add axis
if axe != prev_axe and axe != 'MS':
timetable = None
if axis_dynamics:
timetable = axis_dynamics[str(plant)][str(axe)]
axe_properties = dict(timetable=timetable,
HS_final=args.get('HS_final'),
nff=args.get('nff'),
hasEar=args.get('hasEar'),
azimuth=args.get('az_insertion'))
add_axe(g, axe, plant, axis_properties=axe_properties)
prev_axe = axe
# Add metamer
assert num_metamer > 0
# args are added to metamers only if metamer_factory is none,
# otherwise compute metamer components
components = []
if metamer_factory:
xysr_key = None
if leaves[species] is not None and 'LcType' in args and 'LcIndex' in args:
lctype = int(args['LcType'])
lcindex = int(args['LcIndex'])
if lctype != -999 and lcindex != -999:
age = None
if dynamic_leaf_db[species]:
age = float(args[
'rph']) - 0.3 # age_db = HS - rank + 1 = ph - 1.3 - rank +1 = rph - .3
if age != 'NA':
age = max(0, int(float(age)))
xysr_key = leaves[species].get_leaf_key(lctype, lcindex, age)
elongation = None
if add_elongation:
startleaf = -.4
endleaf = 1.6
stemleaf = 1.2
startE = endleaf
endE = startE + (endleaf - startleaf) / stemleaf
endBlade = endleaf
if args['Gl'] > 0:
endBlade = args['Ll'] / args['Gl'] * (endleaf - startleaf)
elongation = {'startleaf': startleaf, 'endBlade': endBlade,
'endleaf': endleaf, 'endE': endE}
if not 'ntop' in args:
args.update({'ntop': None})
if not 'Gd' in args:
args.update({'Gd': 0.19})
args.update({'split': split})
if args.get('HS_final') < args.get('nff'):
for what in (
'Ll', 'Lv', 'Lr', 'Lsen', 'L_shape', 'Lw_shape', 'Gl',
'Gv', 'Gsen', 'Gd', 'El', 'Ev', 'Esen', 'Ed'):
args.update(
{what: args.get(what) * aborting_tiller_reduction})
components = metamer_factory(Lsect=leaf_sectors, shape_key=xysr_key,
elongation=elongation, leaves=leaves[species],
**args)
args = {'L_shape': args.get('L_shape')}
#
metamer_properties = args
internode, sheath, blade = None, None, None
elts = {k: [] for k in ('internode', 'sheath', 'blade')}
if len(components) > 0:
internode, sheath, blade = components
internode.pop('label')
sheath.pop('label')
blade.pop('label')
elts['internode'] = internode.pop('elements')
elts['sheath'] = sheath.pop('elements')
elts['blade'] = blade.pop('elements')
vid_metamer = add_vegetative_metamer(g, plant, axe,
metamer_properties=metamer_properties,
internode_properties=internode,
sheath_properties=sheath,
blade_properties=blade)
for organ in g.components(vid_metamer):
label = g.property('label')[organ]
if label in elts and len(elts[label]) > 0:
insert_elements(g, organ, elts[label])
return fat_mtg(g)
