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_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 mtg_factory(params, sectors = 1):
""" Construct a MTG from a dictionary.
The dictionary contains the parameters and a list of elements. Sector is an integer giving the number of LeafElements per Leaf
The keys of params are:
- plant: indx of plant
- axe:
- numphy
- Lv
- L_shape
- Lsen
- Lw_shape
- LcType
- LcIndex
- Linc
- Laz
- Lpo
- Lpos
- Gl
- Gv
- Gsen
- Gpo
- Gpos
- Gd
- Ginc
- El
- Ev
- Esen
- Ed
- Einc
- Epo
- Epos
:TODO:
* add length and final_length (DONE)
* fix naming convention for Linc: relative inclination (DONE)
* Add a scale to define the tissue types (ear, sheath, laminae, gain)
* diam and final_diam (resp. width)
* function reset length
* function phenology(g, table) -> dynamic parameters (start_thermaltime, end_thermaltime)
* function growthThermaltime(g, tt, dtt): tt=thermaltime du couvert
* function growthThermaltime(g, tt, dtt, stress factor)
* stress factor: offre/demande
- demand = :math:`D=\int_{tt}^{tt+dtt}{S(x)dx}*\rho_s+\int_{tt}^{tt+dtt}{V(x)dx}*\rho_v`
- offre : :math:`sum{E_abs}*\eps_b`
=> ds = ds_predit* stress_factor
* give the area to the leaf model
* update properties
"""
if not _check_adel_parameters(params):
raise ValueError('Adel parameters are invalid')
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 = '<'
dp = params
nrow = len(params['plant'])
for i in range(nrow):
#plant, axe, num_metamer = [int(convert(d.get(x),undef=None)) for x in topology]
plant = int(dp['plant'][i])
try:
axe = int(dp['axe'][i])
except:
axe = int(dp['ms_insertion'][i])
num_metamer = int(dp['numphy'][i])
#plant, axe, num_metamer = [int(convert(d.get(x),undef=None)) for x in topology]
#print 'plant: %d, axe:%d, nb_metamers: %d'%(plant, axe, num_metamer)
# Add new plant
if plant != prev_plant:
label = 'plant'+str(plant)
vid_plant = g.add_component(g.root, label=label, edge_type='/')
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 = '+'
assert g.parent(vid_plant) is None
new_axe = g.add_child(vid_axe,edge_type=edge_type,label=label)
print vid_axe, new_axe, vid_plant
assert g.parent(vid_plant) is None
#vid, vid_axe = g.add_child_and_complex(metamers[axe], complex=vid_axe, **args)
# Add metamers
args = properties_from_dict(dp,i,exclude=topology)
assert num_metamer > 0
label = 'metamer'+str(num_metamer)
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 = g.add_component(vid_axe, label=label, **args)
vid_metamer = g.add_child(metamers[axe-1], child=vid_metamer, edge_type='+')
vid_node = nodes[axe-1]
else:
edge_type = '<'
vid_metamer = g.add_child(vid_metamer, label=label, edge_type='<',**args)
if axe == 0:
metamers.append(vid_metamer)
# Add internode, sheath, and lamina
# Visible Internode
#if args['Ev'] > 0.:
tissue = 'internode'
# Several cases:
Egreen = args['Ev']-args['Esen'] if args['Ev']-args['Esen'] >0. else 0.
Esen = args['Ev'] if Egreen == 0. else args['Esen']
# - Green element and perhaps a senescent one
if vid_node == -1:
# first metamer on the axis
vid_node= g.add_component(vid_metamer, label='StemElement', edge_type='/',
length=Egreen,final_length=args['El'],po=args['Epo'], diam=args['Ed'], tissue=tissue, inclination=args['Einc'] )
assert edge_type == '/'
else:
# first element on the metamer which has a parent metamer on the axis
new_node = g.add_component(vid_metamer)
vid_node= g.add_child(vid_node,child=new_node,
label='StemElement', edge_type=edge_type,
length=Egreen,final_length=args['El'],po=args['Epo'], diam=args['Ed'], tissue=tissue, inclination=args['Einc'] )
# Add a senescent element
#if args['Esen'] > 0.:
vid_node = g.add_child(vid_node, label='StemElement', edge_type='<',
length=Esen,final_length=args['El'],po=args['Epos'], diam=args['Ed'], tissue=tissue, sen=True, inclination=0.)
# Sheath
# Same logic that described previously.
Ggreen = args['Gv']-args['Gsen'] if args['Gv']-args['Gsen'] >0. else 0.
Gsen = args['Gv'] if Ggreen == 0. else args['Gsen']
vid_node= g.add_child(vid_node, label='StemElement', edge_type='<',
length=Ggreen,final_length=args['Gl'],po=args['Gpo'], diam=args['Gd'], tissue=tissue, inclination=args['Ginc'] )
#if args['Gsen'] > 0.:
vid_node= g.add_child(vid_node, label='StemElement', edge_type='<',
length=Gsen,final_length=args['Gl'],po=args['Gpos'], diam=args['Gd'], sen=True, tissue=tissue, inclination=0.)
if axe == 0:
nodes.append(vid_node)
# Lamina
#if args['Lv'] > 0.:
l_node = vid_node
tissue='lamina'
ds = 1. / sectors
srlim = 1.-(args['Lsen']/args['Lv'])
st = ds
edge_type = '+'
Laz = args['Laz']
Lgreen = args['Lv']-args['Lsen'] if args['Lv']-args['Lsen'] >0. else 0.
Lsen = args['Lv'] if Lgreen == 0. else args['Lsen']
for isect in range(sectors):
# create one green and/or one senescent sector
srb_green = st-ds
srt_green = min(st, max(srb_green,srlim))
srb_sen = srt_green
srt_sen= st
l_node = g.add_child(l_node, label='LeafElement', edge_type=edge_type,
length=args['Lv'],final_length=args['L_shape'],po=args['Lpo'],
Ll=args['Ll'], Lw= args['Lw_shape'], LcType=args['LcType'],
LcIndex=args['LcIndex'], Laz=Laz,Linc=args['Linc'],
srb=srb_green, srt=srt_green, tissue=tissue)
l_node = g.add_child(l_node, label='LeafElement', edge_type='<',
length=args['Lv'],final_length=args['L_shape'],po=args['Lpos'],
Ll=args['Ll'], Lw= args['Lw_shape'], LcType=args['LcType'],
LcIndex=args['LcIndex'], Laz=Laz,Linc=args['Linc'],
srb=srb_sen, srt=srt_sen, sen=True, tissue=tissue)
st += ds
edge_type = '<'
prev_plant = plant
prev_axe = axe
prev_metamer = num_metamer
return fat_mtg(g)
