def load_and_update():
# read adelwheat inputs
adel2 = AdelWheatDyn(seed=1, scene_unit='m',leaves=echap_leaves(xy_model='Soissons_byleafclass'))
adel2.pars = adel2.read_pars(dir='adel_issue4')
g2 = adel2.load(dir='adel_issue4')
adel2.update_geometry(g2)
def create_init_MTG_with_tillers(nplants=1,
sowing_density=250.,
plant_density=250.,
inter_row=0.15,
nff=12,
nsect=1,
seed=1,
leaves=None):
stand = AgronomicStand(sowing_density=sowing_density,
plant_density=plant_density,
inter_row=inter_row,
noise=0.04,
density_curve_data=None)
em = TillerEmission(primary_tiller_probabilities={
'T1': 1.,
'T2': 0.5,
'T3': 0.5,
'T4': 0.3
})
reg = TillerRegression(ears_per_plant=3)
axp = AxePop(MS_leaves_number_probabilities={str(nff): 1},
Emission=em,
Regression=reg)
plants = axp.plant_list(nplants=nplants)
hs = HaunStage(mean_nff=nff)
pgen = PlantGen(HSfit=hs)
axeT, dimT, phenT = pgen.adelT(plants)
axeT = axeT.sort_values(['id_plt', 'id_cohort', 'N_phytomer'])
devT = devCsv(axeT, dimT, phenT)
adel = AdelWheatDyn(nplants=nplants,
nsect=nsect,
devT=devT,
stand=stand,
seed=seed,
sample='sequence',
leaves=leaves,
scene_unit='m')
age = hs.TT(
reg.hs_debreg(nff=nff)
) # date a laquelle debut des regression. Problemes : 1) toutes les feuilles pas encore visibles, 2) il y a des feuilles senescentes
g = adel.setup_canopy(
age
) # MG : je ne crois pas que id_cohort soit renvoyee par la fonction R runAdel
return adel, g
def create_init_MTG_with_tillers(nplants=1, sowing_density=250., plant_density=250.,
inter_row=0.15, nff=12, nsect=1, seed=1):
stand = AgronomicStand(sowing_density=sowing_density,
plant_density=plant_density, inter_row=inter_row,
noise=0.04, density_curve_data=None)
em = TillerEmission()
reg = TillerRegression(ears_per_plant=3)
axp = AxePop(MS_leaves_number_probabilities={str(nff): 1}, Emission=em, Regression=reg)
plants = axp.plant_list(nplants=nplants)
hs = HaunStage(mean_nff=nff)
pgen = PlantGen(HSfit=hs)
axeT, dimT, phenT = pgen.adelT(plants)
axeT = axeT.sort_values(['id_plt', 'id_cohort', 'N_phytomer'])
devT = devCsv(axeT, dimT, phenT)
adel = AdelWheatDyn(nplants=nplants, nsect=nsect, devT=devT, stand=stand,
seed=seed, sample='sequence', scene_unit='m')
age = hs.TT(12)
g = adel.setup_canopy(age)
return adel, g
def test_add_metamer():
# create a plant with 3 metamers
adel = AdelWheatDyn(seed=1234)
g = adel.setup_canopy()
labels = g.property('label')
metamers = [vid for vid in labels if labels[vid].startswith('metamer')]
assert len(metamers) == 3
# add empty new metamer
vid = adel.add_metamer(g, 1, 'MS')
new_metamer = g.node(vid)
metamers = [vid for vid in labels if labels[vid].startswith('metamer')]
assert len(metamers) == 4
internode, sheath, blade = new_metamer.components()
assert blade.length == 0
elts = [c.label for c in blade.components()]
assert elts == ['baseElement', 'topElement']
# grow leaf and check components
blade.length = 6
blade.visible_length = 3
adel.update_geometry(g)
assert blade.area > 0
elts = [c.label for c in blade.components()]
assert len(elts) > 2
def old_load_and_update():
# But working for old inputs
adel3 = AdelWheatDyn(seed=1234, scene_unit='m')
g3 = adel3.load(dir='adel_saved')
adel3.update_geometry(g3)
for vid_elt in g.components_at_scale(vid_org,5):
g.property('senesced_length')[vid_elt] = 0.
g.property('senesced_area')[vid_elt] = 0.
if g.property('label')[vid_org] == 'blade' :
g.property('width')[vid_org] = width_dict[org_id]
g.property('shape_max_width')[vid_org] = width_dict[org_id]
g.property('visible_length')[vid_org] = elt_dict[ tuple(list(org_id) + ['LeafElement1']) ]['length']
g.property('age')[vid_org] = age_dict[org_id]
elif g.property('label')[vid_org] == 'sheath' :
g.property('diameter')[vid_org] = width_dict[org_id]
g.property('visible_length')[vid_org] = elt_dict[tuple(list(org_id) + ['StemElement'])]['length']
adel.update_geometry(g)
adel.plot(g)
# Save mtg
adel.save(g)
# save adel pars
adel.save_pars()
adel2 = AdelWheatDyn(seed=1, scene_unit='m',leaves=echap_leaves(xy_model='Soissons_byleafclass'))
adel2.pars = adel2.read_pars()
g2 = adel2.load()
adel2.update_geometry(g2)
adel2.plot(g2)