def display(self, color=[190, 205, 205], add=False, transparency=0):
from openalea.plantgl.all import Scene, Shape, Material, FaceSet, Viewer
from random import randint
s = Scene()
for facedart in self.elements(2):
lastdart = facedart
positions = []
for dart in self.orderedorbit(facedart, [0, 1]):
if self.alpha(0, dart) != lastdart:
positions.append(self.get_position(dart))
lastdart = dart
if color is None:
mat = Material(
(randint(0, 255), randint(0, 255), randint(0, 255)),
transparency=transparency)
else:
mat = Material(tuple(color),
diffuse=0.25,
transparency=transparency)
s.add(
Shape(FaceSet(positions, [range(len(positions))]), mat,
facedart))
if add:
Viewer.add(s)
else:
Viewer.display(s)
def display(self, degree = None, add = False, randomcolor = True):
from openalea.plantgl.all import Scene, Shape, Material, FaceSet, Polyline, PointSet, Viewer
from random import randint
s = Scene()
m = Material()
if degree is None: degree = self.degree
if degree >= 2:
try:
ccw = self.orientation()
except ValueError:
ccw = set()
for fid in self.iterate_over_each_i_cell(2):
if fid in ccw: ofid = self.alpha(0,fid)
else: ofid = fid
positions = []
for dart, deg in self.orderedorbit_iter(ofid,[0,1]):
if deg != 1:
positions.append(self.get_position(dart))
s.add(Shape(FaceSet(positions, [range(len(positions))]) , Material((randint(0,255),randint(0,255),randint(0,255))) if randomcolor else m))
elif degree == 1:
for eid in self.iterate_over_each_i_cell(1):
s.add(Shape(Polyline([self.get_position(eid),self.get_position(self.alpha(0,eid))]) ,Material((randint(0,255),randint(0,255),randint(0,255))) ))
elif degree == 0:
s.add(Shape(PointSet([self.get_position(pid) for pid in self.iterate_over_each_i_cell(0)]) ,Material((randint(0,255),randint(0,255),randint(0,255))) ))
if add : Viewer.add(s)
else : Viewer.display(s)
def display(self, color=(190, 205, 205), add=False):
"""
Display the 2-cells of a 2-G-Map using the ordered orbit of its darts in PlantGL.
For each face element, retrieve the position of its ordered face darts and add a FaceSet PlantGL object to the scene.
Example : s += pgl.Shape(pgl.FaceSet( [[0,0,0],[1,0,0],[1,1,0],[0,1,0]], [[0,1,2,3]]) , pgl.Material((0,100,0))) # for a green square
"""
from openalea.plantgl.all import Scene, Shape, Material, FaceSet, Viewer
from random import randint
s = Scene()
for facedart in self.elements(2):
lastfart = facedart
positions = []
for dart in self.oderedorbit(facedart, [0, 1]):
if self.alpha(0, dart) != lastfart:
positions.append(self.get_position(dart))
lastfart = dart
if color is None:
mat = Material(
(randint(0, 255), randint(0, 255), randint(0, 255)))
else:
mat = Material(tuple(color), diffuse=0.25)
s.add(
Shape(FaceSet(positions, [range(len(positions))]), mat,
facedart))
if add:
Viewer.add(s)
else:
Viewer.display(s)
def color_MTG_Nitrogen(g, df, t, SCREENSHOT_DIRPATH):
def color_map(N):
if 0 <= N <= 0.5: # TODO: organe senescent (prendre prop)
vid_colors = [150, 100, 0]
elif 0.5 < N < 5: # Fvertes
vid_colors = [int(255 - N * 51), int(255 - N * 20), 50]
else:
vid_colors = [0, 155, 0]
return vid_colors
def calculate_Total_Organic_Nitrogen(amino_acids, proteins, Nstruct):
"""Total amount of organic N (amino acids + proteins + Nstruct).
:param float amino_acids: Amount of amino acids (µmol N)
:param float proteins: Amount of proteins (µmol N)
:param float Nstruct: Structural N mass (g)
:return: Total amount of organic N (mg)
:rtype: float
"""
return (amino_acids + proteins) * 14E-3 + Nstruct * 1E3
colors = {}
groups_df = df.groupby(['plant', 'axis', 'metamer', 'organ', 'element'])
for vid in g.components_at_scale(g.root, scale=5):
pid = int(g.index(g.complex_at_scale(vid, scale=1)))
axid = g.property('label')[g.complex_at_scale(vid, scale=2)]
mid = int(g.index(g.complex_at_scale(vid, scale=3)))
org = g.property('label')[g.complex_at_scale(vid, scale=4)]
elid = g.property('label')[vid]
id_map = (pid, axid, mid, org, elid)
if id_map in groups_df.groups.keys():
N = (g.property('proteins')[vid] *
14E-3) / groups_df.get_group(id_map)['mstruct'].iloc[0]
# N = (calculate_Total_Organic_Nitrogen(g.property('amino_acids')[vid], g.property('proteins')[vid], g.property('Nstruct')[vid])) / g.property('mstruct')[vid]
colors[vid] = color_map(N)
else:
g.property('geometry')[vid] = None
# plantgl
s = to_plantgl(g, colors=colors)[0]
Viewer.add(s)
Viewer.camera.setPosition(Vector3(83.883, 12.3239, 93.4706))
Viewer.camera.lookAt(Vector3(0., 0, 50))
Viewer.saveSnapshot(
os.path.join(SCREENSHOT_DIRPATH, 'Day_{}.png'.format(t / 24 + 1)))
def display(self, color = [205,205,205], add = False):
from openalea.plantgl.all import Scene, Shape, Material, FaceSet, Viewer
from random import randint
s = Scene()
for facedart in self.elements(2):
lastdart = facedart
positions = []
for dart in self.orderedorbit(facedart,[0,1]):
if self.alpha(0, dart) != lastdart:
positions.append(self.get_position(dart))
lastdart = dart
if color is None:
mat = Material((randint(0,255),randint(0,255),randint(0,255)))
else:
mat = Material(tuple(color),diffuse=0.25)
s.add(Shape(FaceSet(positions, [range(len(positions))]) , mat ))
if add : Viewer.add(s)
else : Viewer.display(s)
def dartdisplay(self, add = False, textsize = None):
from openalea.plantgl.all import Viewer
s = self.darts2pglscene(textsize)
if add : Viewer.add(s)
else : Viewer.display(s)
