def tpg2mtg(graph, properties=['index'], root_ids=None, mtg = None, binary_sorter = None):
"""
:Parameters:
- `graph`(TPG) - a tempora property graph,
- `properties`(list) - list of properties to export in MTG
- `root_ids`(list) - list of root ids (@t0) to build the MTG
"""
if root_ids is None:
root_ids = [i for i in graph.vertices() if len(graph.parents(i)) == 0 and len(graph.children(i)) > 0]
from openalea.mtg import MTG
if mtg is None:
mtg = MTG()
mtg.add_property('tpg_cid')
for p in properties:
mtg.add_property(p)
meristem_id = mtg.add_component(mtg.root, label='M')
def translate_property(mtg, graph, mcid, tcid):
mtg.property('tpg_cid')[mcid] = tcid
for p in properties:
try:
mtg.property(p)[mcid] = graph.vertex_property(p)[tcid]
except:
continue
def iterable(obj):
try :
iter(obj)
return True
except TypeError,te:
return False
def convertToMyMTG(g):
from openalea.mtg import MTG
def addProperties(mtg, vid, px, py, pz, radius):
mtg.property('position')[vid] = Vector3(px, py, pz)
mtg.property('radius')[vid] = radius
mtg = MTG()
mtg.add_property('position')
mtg.add_property('radius')
plantroot = mtg.root
branchroot = mtg.add_component(plantroot, label='B')
noderoot = mtg.add_component(branchroot, label='N')
rdic = g.property('radius')
for k, r in rdic.iteritems():
parentid = g.parent(k)
px = g.property('XX')[k]
py = g.property('YY')[k]
pz = g.property('ZZ')[k]
if parentid == None:
addProperties(mtg, k, px, py, pz, r)
else:
label = g.label(k)
if label == 'N':
vid = mtg.add_child(parentid, edge_type='<', label='N')
else:
vid = mtg.add_child(parentid, edge_type='+', label='B')
addProperties(mtg, vid, px, py, pz, r)
return mtg
def tpg2mtg(graph,
properties=['index'],
root_ids=None,
mtg=None,
binary_sorter=None):
"""
Args:
graph:(TPG) - a tempora property graph,
properties:(list) - list of properties to export in MTG
root_ids:(list) - list of root ids (@t0) to build the MTG
"""
if root_ids is None:
root_ids = [
i for i in graph.vertices()
if len(graph.parents(i)) == 0 and len(graph.children(i)) > 0
]
from openalea.mtg import MTG
if mtg is None:
mtg = MTG()
mtg.add_property('tpg_cid')
for p in properties:
mtg.add_property(p)
meristem_id = mtg.add_component(mtg.root, label='M')
def translate_property(mtg, graph, mcid, tcid):
mtg.property('tpg_cid')[mcid] = tcid
for p in properties:
try:
mtg.property(p)[mcid] = graph.vertex_property(p)[tcid]
except:
continue
def iterable(obj):
try:
iter(obj)
return True
except TypeError, te:
return False
def convertToMyMTG(g):
from openalea.mtg import MTG
def addProperties(mtg, vid, px, py, pz, radius):
mtg.property('position')[vid] = Vector3(px,py,pz)
mtg.property('radius')[vid] = radius
mtg = MTG()
mtg.add_property('position')
mtg.add_property('radius')
plantroot = mtg.root
branchroot = mtg.add_component(plantroot,label='B')
noderoot = mtg.add_component(branchroot,label='N')
rdic = g.property('radius')
for k,r in rdic.iteritems():
parentid = g.parent(k)
px = g.property('XX')[k]
py = g.property('YY')[k]
pz = g.property('ZZ')[k]
if parentid == None:
addProperties(mtg, k, px, py, pz, r)
else:
label = g.label(k)
if label == 'N':
vid = mtg.add_child(parentid,edge_type='<',label='N')
else:
vid = mtg.add_child(parentid,edge_type='+',label='B')
addProperties(mtg, vid, px, py, pz, r)
return mtg
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
