def update_plot(g):
# Compute severity by leaf
severity_by_leaf = compute_severity_by_leaf(g, label='LeafElement')
set_property_on_each_id(g,
'severity',
severity_by_leaf,
label='LeafElement')
# Visualization
g = alep_colormap(g,
'severity',
cmap=green_yellow_red(levels=100),
lognorm=False,
zero_to_one=False,
vmax=100)
leaves = get_leaves(g, label='LeafElement')
pos_sen = g.property('position_senescence')
for leaf in leaves:
if pos_sen[leaf] == 0.:
g.node(leaf).color = (157, 72, 7)
scene = plot3d(g)
Viewer.display(scene)
return scene
def test_transport_rain_two_metamers(interleaf=10.,
density = 350.,
layer_thickness=0.01,
leaf_sectors = 7,
density_emitted=1e5,
by_sector = False,
display_scene = False):
g, domain_area, domain, convunit = adel_two_metamers_stand(leaf_sectors=leaf_sectors,
density=density,
interleaf=interleaf,
leaf_length=20,
leaf_width=1,
Einc=0)
if display_scene:
scene = plot3d(g)
Viewer.display(scene)
weather = sample_weather_with_rain()
leaves = get_leaf_ids(g)
DU = emission_source(g, leaves,
domain_area=domain_area,
density_emitted=density_emitted)
transporter = PopDropsTransport(domain=domain, domain_area=domain_area,
dh=layer_thickness, convUnit=convunit,
group_dus=True)
if sum(DU.values())>0:
deposits = transporter.disperse(g, DU, weather)
return count_du_source_target(deposits, leaves, by_sector=False)
def testdyn(nplants=1,start = 100,step = 50, nstep=30,dec=10,az=0):
from time import sleep
pars, d = adelR(nplants,start)
pos = [(i*dec,0,0) for i in range(nplants)]
g=mtg_factory(d,adel_metamer, leaf_sectors=1,leaf_db=leafdb, stand = [(pos[i],az) for i in range(nplants)])
g=mtg_interpreter(g)
time = start
oldcanopy = RunAdel(time,pars)
for i in range(nstep):
s = plot3d(g)
Viewer.display(s)
#sleep(2)
time = start + (i + 1) * step
canopy = RunAdel(time,pars)
mtg_update_from_table(g, canopy, oldcanopy)
g=mtg_interpreter(g)
oldcanopy = canopy
return g,d
# TO DO : senescence leaf shrink
# tester secteurs > 1
#df=DataFrame(d)
#df.Lv
#df.ix[1:7,6:9]
#df[['Gl','Gv','Ll','Lv','Lr','L_shape']]
# import numpy as np
# from alinea.popdrops.Rain import get_area_and_normal
# a1,_=get_area_and_normal(g1.property('geometry'))
# a1 = dict(((k,np.sum(v)) for k,v in a1.iteritems()))
def update_plot(g):
from alinea.alep.architecture import set_property_on_each_id
from alinea.alep.disease_outputs import compute_severity_by_leaf
from alinea.adel.mtg_interpreter import plot3d
from openalea.plantgl.all import Viewer
# Compute severity by leaf
severity_by_leaf = compute_severity_by_leaf(g, label='LeafElement')
set_property_on_each_id(g,
'severity',
severity_by_leaf,
label='LeafElement')
# Visualization
g = alep_colormap(g,
'severity',
cmap=green_yellow_red(levels=100),
lognorm=False,
zero_to_one=False,
vmax=100)
leaves = get_leaves(g, label='LeafElement')
pos_sen = g.property('position_senescence')
for leaf in leaves:
if pos_sen[leaf] == 0.:
g.node(leaf).color = (157, 72, 7)
scene = plot3d(g)
Viewer.display(scene)
return scene
def newmtg(canopy,dec=10,az=0):
from alinea.adel.newmtg import mtg_factory, adel_metamer
from alinea.adel.mtg_interpreter import mtg_interpreter, plot3d
g=mtg_factory(canopy,adel_metamer, leaf_sectors=1,leaf_db=leafdb, stand = [((dec,0,0),az)])
g=mtg_interpreter(g)
s = plot3d(g)
return g,s
def newmtg(canopy, dec=10, az=0):
from alinea.adel.newmtg import mtg_factory, adel_metamer
from alinea.adel.mtg_interpreter import mtg_interpreter, plot3d
g = mtg_factory(canopy,
adel_metamer,
leaf_sectors=1,
leaf_db=leafdb,
stand=[((dec, 0, 0), az)])
g = mtg_interpreter(g)
s = plot3d(g)
return g, s
def scene(g, property=None):
if property:
g = colormap(g, property, cmap='jet', lognorm=True)
colored = g.property('color')
colors = {
vid: colored.get(vid, colored.get(g.complex(vid), [0, 0, 0]))
for vid in g.vertices(scale=g.max_scale())
}
else:
colors = None
s = plot3d(g, colors=colors
) # use the one of openalea.plantframe.color instead ?
return s
def ground_cover(g, domain, camera = {'type':'perspective', 'distance':200., 'fov':50., 'azimuth':0, 'zenith':0.}, image_width = 4288, image_height = 2848, getImages=False, replicate=None):
"""
compute ground cover based on is_green/not_green property of g
"""
from alinea.adel.mtg_interpreter import plot3d
colors_def = {'green':[0, 255, 0], 'senescent' : [255, 0, 0]}
greeness = g.property('is_green')
colors = {k:colors_def['green'] if greeness[k] else colors_def['senescent'] for k in greeness}
scene = plot3d(g, colors=colors)
gc, im, box = color_ground_cover(scene, domain, colors_def = colors_def, camera = camera, image_width = image_width, image_height = image_height, getImages=getImages, replicate=replicate)
return gc, im, box
def update_plot(g):
# Compute severity by leaf
severity_by_leaf = compute_severity_by_leaf(g, label = 'LeafElement')
set_property_on_each_id(g, 'severity', severity_by_leaf, label = 'LeafElement')
# Visualization
g = alep_colormap(g, 'severity', cmap=green_yellow_red(levels=100),
lognorm=False, zero_to_one=False, vmax=100)
leaves = get_leaves(g, label='LeafElement')
pos_sen = g.property('position_senescence')
for leaf in leaves:
if pos_sen[leaf]==0.:
g.node(leaf).color = (157, 72, 7)
scene = plot3d(g)
Viewer.display(scene)
return scene
def testdyn(nplants=1, start=100, step=50, nstep=30, dec=10, az=0):
from time import sleep
pars, d = adelR(nplants, start)
pos = [(i * dec, 0, 0) for i in range(nplants)]
g = mtg_factory(d,
adel_metamer,
leaf_sectors=1,
leaf_db=leafdb,
stand=[(pos[i], az) for i in range(nplants)])
g = mtg_interpreter(g)
time = start
oldcanopy = RunAdel(time, pars)
for i in range(nstep):
s = plot3d(g)
Viewer.display(s)
#sleep(2)
time = start + (i + 1) * step
canopy = RunAdel(time, pars)
mtg_update_from_table(g, canopy, oldcanopy)
g = mtg_interpreter(g)
oldcanopy = canopy
return g, d
# TO DO : senescence leaf shrink
# tester secteurs > 1
#df=DataFrame(d)
#df.Lv
#df.ix[1:7,6:9]
#df[['Gl','Gv','Ll','Lv','Lr','L_shape']]
# import numpy as np
# from alinea.popdrops.Rain import get_area_and_normal
# a1,_=get_area_and_normal(g1.property('geometry'))
# a1 = dict(((k,np.sum(v)) for k,v in a1.iteritems()))
def update_plot(g):
from alinea.alep.architecture import set_property_on_each_id
from alinea.alep.disease_outputs import compute_severity_by_leaf
from alinea.adel.mtg_interpreter import plot3d
from openalea.plantgl.all import Viewer
# Compute severity by leaf
severity_by_leaf = compute_severity_by_leaf(g, label = 'lf')
set_property_on_each_id(g, 'severity', severity_by_leaf, label = 'lf')
# Visualization
g = alep_colormap(g, 'severity', cmap=green_yellow_red(levels=100),
lognorm=False, zero_to_one=False, vmax=100)
brown = (100,70,30)
trunk_ids = [n for n in g if g.label(n).startswith('tronc')]
for id in trunk_ids:
trunk = g.node(id)
trunk.color = brown
scene = plot3d(g)
Viewer.display(scene)
return scene
def ground_cover(
g,
domain,
camera={
'type': 'perspective',
'distance': 200.,
'fov': 50.,
'azimuth': 0,
'zenith': 0.
},
image_width=4288,
image_height=2848,
getImages=False,
replicate=None):
"""
compute ground cover based on is_green/not_green property of g
"""
from alinea.adel.mtg_interpreter import plot3d
colors_def = {'green': [0, 255, 0], 'senescent': [255, 0, 0]}
greeness = g.property('is_green')
colors = {
k: colors_def['green'] if greeness[k] else colors_def['senescent']
for k in greeness
}
scene = plot3d(g, colors=colors)
gc, im, box = color_ground_cover(scene,
domain,
colors_def=colors_def,
camera=camera,
image_width=image_width,
image_height=image_height,
getImages=getImages,
replicate=replicate)
return gc, im, box
def update_plot(g):
from alinea.alep.architecture import set_property_on_each_id
from alinea.alep.disease_outputs import compute_severity_by_leaf
from alinea.adel.mtg_interpreter import plot3d
from openalea.plantgl.all import Viewer
# Compute severity by leaf
severity_by_leaf = compute_severity_by_leaf(g, label = 'LeafElement')
set_property_on_each_id(g, 'severity', severity_by_leaf, label = 'LeafElement')
# Visualization
g = alep_colormap(g, 'severity', cmap=green_yellow_red(levels=100),
lognorm=False, zero_to_one=False, vmax=100)
leaves = get_leaves(g, label='LeafElement')
pos_sen = g.property('position_senescence')
for leaf in leaves:
if pos_sen[leaf]==0.:
g.node(leaf).color = (157, 72, 7)
scene = plot3d(g)
Viewer.display(scene)
return scene
# extract_leaves
from alinea.adel.wheat import extract_wheat
db = extract_wheat.extract_leaf_info(pj(DATA_IN_DIR, 'laminaCurv.RData'),
pj(DATA_IN_DIR, 'lamina2D.RData'))
# fit leaves
from alinea.adel.fit import fit
db, discard = fit.fit_leaves(db, NUMBER_OF_LONGITUDINAL_DIVISIONS)
# set the rotation angle of the plant on itself. Permits to randomize the orientation of each leaf.
stand = zip(positions, [0 for i in range(len(positions))])
g = mtg_factory(metamers_parameters.to_dict('list'), adel_metamer, leaf_db = db, stand = stand)
#add geometry
g = mtg_interpreter(g)
## plot (uncomment the next 2 lines to plot the 3D model)
scene = plot3d(g)
Viewer.display(scene)
# call caribu
from alinea.caribu.caribu_star import caribu_star
geom = g.property('geometry')
star, exposed_area = caribu_star(geom, directions = NUMBER_OF_DIRECTIONS, domain = domain, convUnit = convUnit)#cf caribu_star doc for output interpretation
caribu_out = pandas.DataFrame([(adel_label(g,vid), star[vid], exposed_area[vid]) for vid in star],
columns=['adel_label', 'star', 'exposed_area'])
caribu_out_filepath = pj(DATA_OUT_DIR, 'caribu_out' + str(angle_of_incidence) + '.csv')
print 'Save caribu output to', caribu_out_filepath
caribu_out.to_csv(caribu_out_filepath, na_rep='NA', index=False)
# Calculate the star for each class of metamers (metamer1, metamer2, metamer3, etc).
# Star is "ratio viewed area / area". It takes into consideration the angles of
pj(DATA_IN_DIR, 'lamina2D.RData'))
# fit leaves
from alinea.adel.fit import fit
db, discard = fit.fit_leaves(db, NUMBER_OF_LONGITUDINAL_DIVISIONS)
# set the rotation angle of the plant on itself. Permits to randomize the orientation of each leaf.
stand = zip(positions, [0 for i in range(len(positions))])
g = mtg_factory(metamers_parameters.to_dict('list'),
adel_metamer,
leaf_db=db,
stand=stand)
#add geometry
g = mtg_interpreter(g)
## plot (uncomment the next 2 lines to plot the 3D model)
scene = plot3d(g)
Viewer.display(scene)
# call caribu
from alinea.caribu.caribu_star import caribu_star
geom = g.property('geometry')
star, exposed_area = caribu_star(
geom,
directions=NUMBER_OF_DIRECTIONS,
domain=domain,
convUnit=convUnit) #cf caribu_star doc for output interpretation
caribu_out = pandas.DataFrame(
[(adel_label(g, vid), star[vid], exposed_area[vid]) for vid in star],
columns=['adel_label', 'star', 'exposed_area'])
caribu_out_filepath = pj(DATA_OUT_DIR,
def adel_scene_node(g):
return plot3d(g)
