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 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 view_distri_layers(self, g, nb_dispersal_units = 1e5, vmax = None,
position_source = 3./5, return_df=False):
from alinea.alep.architecture import set_property_on_each_id
from alinea.alep.alep_color import alep_colormap, green_yellow_red
from alinea.alep.disease_outputs import plot3d_transparency
from openalea.plantgl.all import Viewer
import matplotlib.pyplot as plt
import pandas as pd
# Compute severity by leaf
self.leaves_in_grid(g)
layers = self.layers.keys()
layers.sort()
layer = layers[int(position_source*len(layers))]
if len(self.layers[layer])>0:
leaf = self.layers[layer][0]
else:
non_empty = {k:v for k,v in self.layers.iteritems() if len(v)>0}
leaf = self.layers[min(non_empty.keys(), key=lambda k:abs(k-layer))][0]
deposits = {k:sum([du.nb_dispersal_units for du in v]) for k,v in
self.disperse(g, dispersal_units = {leaf : nb_dispersal_units}).iteritems()}
set_property_on_each_id(g, 'nb_dispersal_units', deposits)
# Visualization
if vmax is None:
vmax = 2*max(deposits.values())/3
g = alep_colormap(g, 'nb_dispersal_units', cmap=green_yellow_red(),
lognorm=False, zero_to_one=False,
vmax = vmax)
d = [np.arange(vmax)]
fig, ax = plt.subplots()
ax.imshow(d, cmap = green_yellow_red())
transp = {vid:0. for k,v in self.layers.iteritems() for vid in v}
set_property_on_each_id(g, 'transparency', transp)
for id in g:
if not id in deposits:
g.node(id).color = (0,0,0)
g.node(id).transparency = 0.7
elif deposits[id]==0.:
g.node(id).color = (0,0,0)
g.node(id).transparency = 0.7
else:
g.node(id).transparency = 0.
scene = plot3d_transparency(g)
Viewer.display(scene)
if return_df==True:
depo_layer = {k:sum([deposits[vid] for vid in v if vid in deposits])
for k,v in self.layers.iteritems()}
df = pd.DataFrame([[k,v] for k, v in depo_layer.iteritems()])
df = df.sort(0)
df[2] = df[1]/df[1].sum()
fig, ax = plt.subplots()
ax.plot(df[2], df[0], 'k')
ax.set_ylabel('Height', fontsize = 16)
ax.set_xlabel('Proportion of deposits', fontsize = 16)
return df
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 view_distri_layers(self, g, density_dispersal_units=1000., vmax=None):
from alinea.alep.architecture import set_property_on_each_id
from alinea.alep.alep_color import alep_colormap, green_yellow_red
from alinea.alep.disease_outputs import plot3d_transparency
from openalea.plantgl.all import Viewer
import matplotlib.pyplot as plt
# Compute severity by leaf
nb_dus = density_dispersal_units * self.domain_area
deposits = {
k: sum([du.nb_dispersal_units for du in v])
for k, v in self.contaminate(g, nb_dus).iteritems()
}
set_property_on_each_id(g, 'nb_dispersal_units', deposits)
# Visualization
if vmax is None:
vmax = 2 * max(deposits.values()) / 3
g = alep_colormap(g,
'nb_dispersal_units',
cmap=green_yellow_red(),
lognorm=False,
zero_to_one=False)
d = [np.arange(vmax)]
fig, ax = plt.subplots()
ax.imshow(d, cmap=green_yellow_red())
geometries = g.property('geometry')
leaves = get_leaves(g, label='LeafElement')
leaves = [l for l in leaves if l in geometries]
transp = {vid: 0. for k, v in self.layers.iteritems() for vid in v}
set_property_on_each_id(g, 'transparency', transp)
for id in g:
if not id in deposits:
g.node(id).color = (1, 1, 1)
g.node(id).transparency = 0.7
elif deposits[id] == 0.:
g.node(id).color = (1, 1, 1)
g.node(id).transparency = 0.7
else:
g.node(id).transparency = 0.
scene = plot3d_transparency(g)
Viewer.display(scene)
def plot_layers(self, g):
from alinea.alep.architecture import set_property_on_each_id
from alinea.alep.alep_color import alep_colormap
from alinea.alep.disease_outputs import plot3d_transparency
from openalea.plantgl.all import Viewer
# Compute severity by leaf
self.leaves_in_grid(g)
layers = self.layers
layer_by_leaf = {vid:k for k,v in layers.iteritems() for vid in v}
set_property_on_each_id(g, 'height', layer_by_leaf)
# Visualization
g = alep_colormap(g, 'height', cmap='prism',
lognorm=False, zero_to_one=False)
geometries = g.property('geometry')
leaves = get_leaves(g, label='LeafElement')
leaves = [l for l in leaves if l in geometries]
transp = {vid:0. for k,v in layers.iteritems() for vid in v}
set_property_on_each_id(g, 'transparency', transp)
scene = plot3d_transparency(g)
Viewer.display(scene)
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 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 update_plot(g, leaf_source):
# Compute severity by leaf
nb_dus_by_leaf = count_dispersal_units_by_leaf(g, label = 'LeafElement')
set_property_on_each_id(g, 'nb_dus', nb_dus_by_leaf, label = 'LeafElement')
# Visualization
g = alep_colormap(g, 'nb_dus', cmap=green_yellow_red(levels=1000),
lognorm=False, zero_to_one=False, vmax=25)
# pos_sen = g.property('position_senescence')
for id in g:
if not id in nb_dus_by_leaf:
# g.node(id).color = (255,255,255)
# g.node(id).color = (113,113,113)
# g.node(id).transparency = 0.9
g.node(id).transparency = 0.
else:
g.node(id).transparency = 0.
g.node(leaf_source).color = (230, 62, 218)
g.node(leaf_source).transparency = 0.
scene = plot3d(g)
Viewer.display(scene)
return scene
""" Gather different strategies for modeling dispersal of fungus propagules.
def plot_severity_rust_by_leaf(g, senescence=True,
transparency=None,
label='LeafElement'):
""" Display the MTG with colored leaves according to disease severity
Parameters
----------
g: MTG
MTG representing the canopy
senescence: bool
True if senescence must be displayed, False otherwise
transparency: float[0:1]
Transparency of the part of the MTG without lesion
label: str
Label of the part of the MTG concerned by the calculation
Returns
-------
scene:
Scene containing the MTG attacked by the disease
"""
from alinea.alep.architecture import set_property_on_each_id, get_leaves
from alinea.alep.alep_color import alep_colormap, green_yellow_red
from alinea.adel.mtg_interpreter import plot3d
from alinea.alep.disease_outputs import plot3d_transparency
from openalea.plantgl.all import Viewer
# Visualization
lesions = g.property('lesions')
leaves = get_leaves(g, label=label)
severity_by_leaf = {}
for lf in leaves:
if lf in lesions:
leaf = g.node(lf)
severity_by_leaf[lf] = sum([l.surface for l in leaf.lesions])*100./leaf.area if leaf.area>0 else 0.
else:
severity_by_leaf[lf] = 0.
set_property_on_each_id(g, 'severity', severity_by_leaf, label=label)
g = alep_colormap(g, 'severity', cmap=green_yellow_red(levels=100),
lognorm=False, zero_to_one=False, vmax=100)
if senescence==True:
leaves = get_leaves(g, label=label)
sen_lengths = g.property('senesced_length')
green_lengths = g.property('green_length')
for leaf in leaves:
if sen_lengths[leaf]>0. and round(green_lengths[leaf],15)==0.:
g.node(leaf).color = (157, 72, 7)
if transparency!=None:
for id in g:
if not id in severity_by_leaf:
g.node(id).color = (255,255,255)
g.node(id).transparency = 0.9
elif severity_by_leaf[id]==0.:
g.node(id).color = (255,255,255)
g.node(id).transparency = transparency
else:
g.node(id).transparency = 0.
scene = plot3d_transparency(g)
else:
scene = plot3d_transparency(g)
Viewer.display(scene)
return scene
""" Gather different strategies for modeling dispersal of fungus propagules.
def plot_severity_rust_by_leaf(g,
senescence=True,
transparency=None,
label='LeafElement'):
""" Display the MTG with colored leaves according to disease severity
Parameters
----------
g: MTG
MTG representing the canopy
senescence: bool
True if senescence must be displayed, False otherwise
transparency: float[0:1]
Transparency of the part of the MTG without lesion
label: str
Label of the part of the MTG concerned by the calculation
Returns
-------
scene:
Scene containing the MTG attacked by the disease
"""
from alinea.alep.architecture import set_property_on_each_id, get_leaves
from alinea.alep.alep_color import alep_colormap, green_yellow_red
from alinea.adel.mtg_interpreter import plot3d
from alinea.alep.disease_outputs import plot3d_transparency
from openalea.plantgl.all import Viewer
# Visualization
lesions = g.property('lesions')
leaves = get_leaves(g, label=label)
severity_by_leaf = {}
for lf in leaves:
if lf in lesions:
leaf = g.node(lf)
severity_by_leaf[lf] = sum([
l.surface for l in leaf.lesions
]) * 100. / leaf.area if leaf.area > 0 else 0.
else:
severity_by_leaf[lf] = 0.
set_property_on_each_id(g, 'severity', severity_by_leaf, label=label)
g = alep_colormap(g,
'severity',
cmap=green_yellow_red(levels=100),
lognorm=False,
zero_to_one=False,
vmax=100)
if senescence == True:
leaves = get_leaves(g, label=label)
sen_lengths = g.property('senesced_length')
green_lengths = g.property('green_length')
for leaf in leaves:
if sen_lengths[leaf] > 0. and round(green_lengths[leaf], 15) == 0.:
g.node(leaf).color = (157, 72, 7)
if transparency != None:
for id in g:
if not id in severity_by_leaf:
g.node(id).color = (255, 255, 255)
g.node(id).transparency = 0.9
elif severity_by_leaf[id] == 0.:
g.node(id).color = (255, 255, 255)
g.node(id).transparency = transparency
else:
g.node(id).transparency = 0.
scene = plot3d_transparency(g)
else:
scene = plot3d_transparency(g)
Viewer.display(scene)
return scene
