def topological_table_to_mtg(csv_file, epsilon=1e-6):
f = open(csv_file)
l=f.readline()
sniffer = csv.Sniffer()
dialect = sniffer.sniff(l)
# Go from start of file
f.seek(0)
reader = csv.DictReader(f, dialect=dialect)
# Build the MTG
g = MTG()
topology = ['plant', 'axe', 'numphy']
# buffers
prev_plant = 0
prev_axe = -1
prev_metamer = -1
vid_plant = -1
vid_axe = -1
vid_metamer = -1
vid_node = -1
# store the metamer vids of the axis 0
metamers = []
nodes = []
edge_type = '<'
for d in reader:
plant, axe, num_metamer = [int(convert(d.get(x),undef=None)) for x in topology]
#print 'adding vertices for plant: %d, axe:%d, metamer: %d'%(plant, axe, num_metamer)
# Add new plant
if plant != prev_plant:
label = 'plant'+str(plant)
vid_plant = g.add_component(g.root, edge_type='/',label=label)
vid_axe = -1
vid_metamer = -1
vid_node = -1
prev_axe = -1
#??
if num_metamer < prev_metamer:
prev_axe = -1
prev_metamer = -1
# Add an axis
if axe != prev_axe:
label = 'axe'+str(axe)
if axe == 0:
vid_axe = g.add_component(vid_plant,edge_type='/',label=label)
vid_node = -1
else:
#args['edge_type'] = '+'
edge_type = '+'
vid_axe = g.add_child(vid_axe, edge_type=edge_type, label=label)
#vid, vid_axe = g.add_child_and_complex(metamers[axe], complex=vid_axe, **args)
# Add metamers
args = properties(d, exclude=topology)
assert num_metamer > 0
label = 'metamer'+str(num_metamer)
new_axe = True
if axe==0 and num_metamer==1:
metamers=[]
edge_type = '/'
vid_metamer = g.add_component(vid_axe, edge_type='/', label = label, **args)
elif num_metamer == 1:
# Add the first element connected to previous metamer on the previous axis
edge_type = '+'
vid_metamer, vid_axe = g.add_child_and_complex(metamers[axe-1], complex=vid_axe, edge_type='+',label=label, **args)
vid_node = nodes[axe-1]
else:
edge_type = '<'
vid_metamer = g.add_child(vid_metamer, label=label, edge_type='<',**args)
new_axe = False
if axe == 0:
metamers.append(vid_metamer)
# Add internode, sheath, and lamina
nb_internodes = 0
nb_sheath = 0
nb_leaf = 0
# Internode
if args['Ev'] > 0.:
if args['Esen'] > args['Ev']:
if vid_node == -1:
vid_node= g.add_component(vid_metamer, label='Esen', edge_type='/',length=args['Ev'],po=args['Epos'], diam=args['Ed'] )
assert edge_type == '/'
else:
vid_node, vid_metamer= g.add_child_and_complex(vid_node, complex=vid_metamer, label='Esen', edge_type=edge_type,length=args['Ev'],po=args['Epos'], diam=args['Ed'] )
else:
if vid_node == -1:
vid_node= g.add_component(vid_metamer, label='Egreen', edge_type='/',length=args['Ev']-args['Esen'],po=args['Epo'], diam=args['Ed'] )
assert edge_type == '/'
else:
vid_node, vid_metamer= g.add_child_and_complex(vid_node, complex=vid_metamer, label='Egreen', edge_type=edge_type,length=args['Ev']-args['Esen'],po=args['Epo'], diam=args['Ed'] )
vid_node = g.add_child(vid_node, label='Esen', edge_type='<',length=args['Esen'],po=args['Epos'], diam=args['Ed'])
else:
if new_axe and args['Gv'] == 0.:
if vid_node == -1:
vid_node= g.add_component(vid_metamer, label='Egreen', edge_type='/',length=0.,po=args['Epo'], diam=args['Ed'] )
else:
vid_node, vid_metamer= g.add_child_and_complex(vid_node, complex=vid_metamer, label='Egreen', edge_type=edge_type,length=0.,po=args['Epo'], diam=args['Ed'] )
# Sheath
if args['Gv'] > 0.:
if args['Gsen'] > args['Gv']:
vid_node= g.add_child(vid_node, label='Gsen', edge_type='<',length=args['Gv'],po=args['Gpos'], diam=args['Gd'] )
else:
vid_node = g.add_child(vid_node, label='Ggreen', edge_type='<',length=args['Gv']-args['Gsen'],po=args['Gpo'], diam=args['Gd'] )
vid_node = g.add_child(vid_node, label='Gsen', edge_type='<',length=args['Gsen'],po=args['Gpos'], diam=args['Gd'])
if axe == 0:
nodes.append(vid_node)
# Laminae
if args['Lv'] > 0.:
if args['Lsen'] > args['Lv']:
l_node= g.add_child(vid_node, label='Lsen', edge_type='+',length=args['Lv'],po=args['Lpos'],
Ll=args['Ll'], Lw= args['Lw'], LcType=args['LcType'], LcIndex=args['LcIndex'], Linc=args['Linc'], Laz=args['Laz'],
srb=0, srt=1)
else:
l_node = g.add_child(vid_node, label='Lgreen', edge_type='+',length=args['Lv']-args['Lsen'],po=args['Lpo'],
Ll=args['Ll'], Lw= args['Lw'], LcType=args['LcType'], LcIndex=args['LcIndex'], Linc=args['Linc'], Laz=args['Laz'],
srb=0, srt=1-(args['Lsen']/args['Lv']))
l_node = g.add_child(l_node, label='Lsen', edge_type='<',length=args['Lsen'],po=args['Lpos'],
Ll=args['Ll'], Lw= args['Lw'], LcType=args['LcType'], LcIndex=args['LcIndex'], Linc=args['Linc'], Laz=args['Laz'],
srt=1, srb=1-(args['Lsen']/args['Lv']))
prev_plant = plant
prev_axe = axe
prev_metamer = num_metamer
f.close()
return fat_mtg(g)
