def get_source_leaf_and_max_height(g,
position='center',
relative_height=2. / 3):
tesselator = pgl.Tesselator()
bbc = pgl.BBoxComputer(tesselator)
leaves = get_leaves(g, label='LeafElement')
centroids = g.property('centroid')
geometries = g.property('geometry')
targets = list(leaf for leaf in leaves if leaf in geometries.iterkeys())
for vid in targets:
if is_iterable(geometries[vid]):
bbc.process(pgl.Scene(geometries[vid]))
else:
bbc.process(pgl.Scene([pgl.Shape(geometries[vid])]))
center = bbc.result.getCenter()
centroids[vid] = center
zmax = max(centroids.items(), key=lambda x: x[1][2])[1][2]
distances = {
vid: pgl.norm(centroids[vid] - (0, 0, relative_height * zmax))
for vid in centroids
}
if position == 'center':
return min(distances.items(), key=lambda x: x[1])[0], zmax
elif position == 'border':
return max(distances.items(), key=lambda x: x[1])[0], zmax
def centroid(vid):
if is_iterable(geometries[vid]):
bbc.process(pgl.Scene(geometries[vid]))
else:
bbc.process(pgl.Scene([pgl.Shape(geometries[vid])]))
center = bbc.result.getCenter()
centroids[vid] = center
def bbox_distance(g1, g2):
bbc.process(pgl.Scene([g1]))
bbox1 = bbc.result
bbc.process(pgl.Scene([g2]))
bbox2 = bbc.result
return bbox1.distance(bbox2)
def bbox_distance(g1, g2):
bbc.process(pgl.Scene([g1]))
bbox1 = bbc.result
bbc.process(pgl.Scene([g2]))
bbox2 = bbc.result
# TODO bbox.lowerLeftCorner, bbox.upperRightCorner
return bbox1.distance(bbox2)
def get_leaf_height(self, leaf_geom):
from openalea.plantgl import all as pgl
tesselator = pgl.Tesselator()
bbc = pgl.BBoxComputer(tesselator)
if self.is_iterable(leaf_geom):
bbc.process(pgl.Scene(leaf_geom))
else:
bbc.process(pgl.Scene([pgl.Shape(leaf_geom)]))
return bbc.result.getCenter()[2]
def scenegraph(rootedgraph):
# traverse the graph
g = deepcopy(rootedgraph)
g = getSMScale(g)
scene = pgl.Scene()
g.add_vertex_property('final_geometry')
final_geometry = g.vertex_property("final_geometry")
traverse2(g.root, g)
scene.merge(pgl.Scene(final_geometry.values()))
return scene
def to_scene(obj):
scene = pgl.Scene()
if obj is None:
pass
elif isinstance(obj, pgl.Scene):
scene = obj
else:
if isinstance(obj, list):
scene = pgl.Scene(obj)
else:
scene = pgl.Scene([obj])
return scene
def representation(self):
mat = pgl.Material('mblue',(0,0,200),transparency=0.8)
mat2 = pgl.Material('mred',(200,0,0),transparency=0.8)
if not self.maxvalue: self.maxvalue = max(self.values)
if self.maxvalue <= 0: return pgl.Scene()
sc = pgl.Scene()
for i, v in enumerate(self.values):
size = v/(2*self.maxvalue)
if size > 1e-2:
sc += pgl.Shape(pgl.Translated(self.getVoxelCenterFromId(i),pgl.Box(self.getVoxelSize()*size)),mat,i)
else:
sc += pgl.Shape(pgl.Translated(self.getVoxelCenterFromId(i),pgl.Box(self.getVoxelSize()*0.1)),mat2,i)
return sc
def parse(cmds):
import openalea.plantgl.all as pgl
objmap = {'Black' : pgl.Color3.BLACK, 'White' : pgl.Color3.WHITE, 'Red' : pgl.Color3.RED, 'Green' : pgl.Color3.GREEN, 'Blue' : pgl.Color3.BLUE, 'Cyan' : pgl.Color3.CYAN, 'Magenta' : pgl.Color3(255,0,255), 'Yellow' : pgl.Color3.YELLOW }
shapes = []
currentid = 0
while currentid < len(cmds):
currentid, obj = parse_object(cmds, currentid, objmap)
if type(obj) == pgl.Shape:
shapes.append(obj)
if len(shapes) > 0 : return pgl.Scene(shapes)
else : return pgl.Scene([pgl.Shape(obj) for obj in objmap if isinstance(obj, pgl.Geometry)])
def build_scene_with_colors(self, colors):
scene = pgl.Scene()
n = len(colors)
for i, (label, count) in enumerate(self.indexes):
pid = plant_id(label)
plant = self.plants[pid]
if is_leaf(label):
lid = leaf_id(label)
geom = plant["leaves"][lid]
elif is_stem(label):
geom = plant["stems"]
else:
geom = self.soil["soil"]
if count == 0:
geom.colorList = []
geom.colorPerVertex = False
assert 3 * len(geom.colorList) == count
if i >= n or type(colors[i]) == float:
geom.colorList.append(pgl.Color4(10, 10, 10, 0))
else:
r, g, b = colors[i]
geom.colorList.append(pgl.Color4(r, g, b, 0))
for plant in list(self.plants.values()):
leaves = plant["leaves"]
stems = plant["stems"]
for leaf in list(leaves.values()):
scene += leaf
if len(stems.pointList) > 0:
scene += stems
if "soil" in self.soil:
scene += self.soil["soil"]
self.scene = scene
def build_scene(self,
leaf_material=None,
stem_material=None,
soil_material=None):
if not leaf_material:
leaf_material = pgl.Material(pgl.Color3(0, 180, 0))
if not stem_material:
stem_material = pgl.Material(pgl.Color3(0, 130, 0))
if not soil_material:
soil_material = pgl.Material(pgl.Color3(170, 85, 0))
scene = pgl.Scene()
for id, plant in self.plants.items():
leaves = plant["leaves"]
stems = plant["stems"]
for lid, leaf in leaves.items():
shape = pgl.Shape(leaf, leaf_material)
shape.name = str(lid)
scene.add(shape)
if len(stems.pointList) > 0:
shape = pgl.Shape(stems, stem_material)
shape.name = str(id)
scene.add(shape)
if "soil" in self.soil:
shape = pgl.Shape(self.soil["soil"], soil_material)
scene.add(shape)
self.scene = scene
def plot(g, prop_cmap='radius', cmap='jet', lognorm=False):
"""
Exemple:
>>> from openalea.plantgl.all import *
>>> s = plot()
>>> shapes = dict( (x.getId(), x.geometry) for x in s)
>>> Viewer.display(s)
"""
visitor = get_root_visitor()
turtle = turt.PglTurtle()
turtle.down(180)
scene = turt.TurtleFrame(g, visitor=visitor, turtle=turtle, gc=False)
# Compute color from radius
color.colormap(g, prop_cmap, cmap=cmap, lognorm=lognorm)
shapes = dict((sh.getId(), sh) for sh in scene)
colors = g.property('color')
for vid in colors:
if vid in shapes:
shapes[vid].appearance = pgl.Material(colors[vid])
scene = pgl.Scene(shapes.values())
return scene
def toPglScene(ptList, mass=None, radius=0.5):
"""generate a box-based scene from a point list"""
scene = pgl.Scene()
x = y = z = 0
if (mass == None):
colors = [gradient(0)] * len(ptList)
else:
colors = []
step = (max(mass) - min(mass)) / 7
if (step == 0):
step = 1
for m in mass:
colors.append(gradient(int((m - min(mass)) / step)))
for i in range(len(ptList)):
pt = ptList[i]
try:
x = pt[0] * 2 * radius
except IndexError:
x = 00.3
try:
y = pt[1] * 2 * radius
except IndexError:
y = 0
try:
z = pt[2] * 2 * radius
except IndexError:
z = 0
#scene.add( disc( x,y,z ) )
#scene.add( sphere( x, y, z , color=colors[ i ]) )
scene.add(box(x, y, z, radius=radius, color=colors[i], id=i + 1))
return scene
def replicate_scene(scene, domain, replicate=None):
""" replicate the scene around the domain
"""
if replicate is None:
newscene = scene
newdomain = domain
else:
dx = abs(domain[0][0] - domain[1][0])
dy = abs(domain[0][1] - domain[1][1])
newscene = pgl.Scene()
for tx in (-dx, 0, dx):
for ty in (-dy, 0, dy):
rep = scene.deepcopy()
for sh in rep:
sh.geometry = pgl.Translated(tx, ty, 0, sh.geometry)
newscene += rep
newdomain = ((domain[0][0] - dx, domain[0][1] - dy),
(domain[1][0] + dx, domain[1][1] + dy))
if replicate == 1:
replicate = None
else:
replicate -= 1
newscene, newdomain = replicate_scene(newscene, newdomain, replicate)
return newscene, newdomain
def plot(pf, length=1.e-4, has_radius=False, r_base=1., r_tip=0.25, visitor=None, prop_cmap=None):
"""
Example:
>>> from openalea.plantgl.all import *
>>> s = plot()
>>> shapes = dict( (x.getId(), x.geometry) for x in s)
>>> Viewer.display(s)
"""
g = pf.g
turtle = turt.PglTurtle()
turtle.down(180)
scene = turt.TurtleFrame(g, visitor=visitor, turtle=turtle, gc=False)
# Compute color from radius
if prop_cmap:
my_colormap(g,prop_cmap)
shapes = dict( (sh.getId(),sh) for sh in scene)
colors = g.property('color')
for vid in colors:
shapes[vid].appearance = pgl.Material(colors[vid])
scene = pgl.Scene(list(shapes.values()))
return scene
def toPglScene( self, geometry=None ):
"""
Generate a PlantGL scene of the MST with the given geometry which size
must be normalized ( < 1), default is a box
"""
if self.dim < 4:
scene = pgl.Scene()
if geometry == None:
geometry = pgl.Box(0.4)
( ptList, size ) = self.absolutePos()
#x = y = z = 0
for pt in ptList :
try:
x = pt[ 0 ]
except IndexError:
x = 0
try:
y = pt[ 1 ]
except IndexError:
y = 0
try:
z = pt[ 2 ]
except IndexError:
z = 0
scene.add( pgl.Translated( (x, y, z), geometry ))
else:
print "Bad dimension"
return scene
def mesh2shapes(scene):
""" Convert all the meshes containing colors into independent shapes.
"""
if isinstance(scene, pgl.Scene):
scene = scene
else:
# Case caribu scene
scene = scene.scene
new_scene = pgl.Scene()
for shape in scene:
g = shape.geometry
if isinstance(g, pgl.TriangleSet) and len(g.colorList) > 0:
# convert the mesh into shapes with different colors
pts = g.pointList
indx = g.indexList
colors = g.colorList
for i, ind in enumerate(indx):
new_geom = pgl.TriangleSet([], [])
new_geom.indexList.append(pgl.Index3(0, 1, 2))
for k in ind:
new_geom.pointList.append(pts[k])
_shape = pgl.Shape(new_geom,
pgl.Material(pgl.Color3(colors[i])))
new_scene.add(_shape)
else:
new_scene.add(shape)
return new_scene,
def view_kdtree(kdtree, bbox=[[-1., 1.], [-1., 1.], [-1., 1.]], radius=0.05):
import numpy as np
scene = pgl.Scene()
sphere = pgl.Sphere(radius, slices=16, stacks=16)
silver = pgl.Material(ambient=(49, 49, 49),
diffuse=3.,
specular=(129, 129, 129),
shininess=0.4)
gold = pgl.Material(ambient=(63, 50, 18),
diffuse=3.,
specular=(160, 141, 93),
shininess=0.4)
if isinstance(kdtree, KDNode):
dim = kdtree.axis
plane_bbox = [b for i, b in enumerate(bbox) if i != dim]
plane_points = []
plane_points += [
np.insert([plane_bbox[0][0], plane_bbox[1][0]], dim,
kdtree.pivot[dim])
]
plane_points += [
np.insert([plane_bbox[0][0], plane_bbox[1][1]], dim,
kdtree.pivot[dim])
]
plane_points += [
np.insert([plane_bbox[0][1], plane_bbox[1][1]], dim,
kdtree.pivot[dim])
]
plane_points += [
np.insert([plane_bbox[0][1], plane_bbox[1][0]], dim,
kdtree.pivot[dim])
]
left_bbox = np.copy(bbox).astype(float)
right_bbox = np.copy(bbox).astype(float)
left_bbox[dim, 1] = kdtree.pivot[dim]
right_bbox[dim, 0] = kdtree.pivot[dim]
scene += pgl.Shape(pgl.Translated(kdtree.pivot, sphere), gold)
scene += view_kdtree(kdtree.left_child, bbox=left_bbox, radius=radius)
scene += view_kdtree(kdtree.right_child,
bbox=right_bbox,
radius=radius)
# scene += pgl.Shape(pgl.Polyline(plane_points+[plane_points[0]],width=2),pgl.Material(ambient=(0,0,0)))
scene += pgl.Shape(
pgl.Polyline(plane_points + [plane_points[0]], width=2),
pgl.Material(ambient=tuple(list(np.insert([0, 0], dim, 255)))))
scene += pgl.Shape(pgl.FaceSet(plane_points, [range(4)]),
pgl.Material(ambient=(0, 0, 0), transparency=0.6))
else:
assert (type(kdtree) == list) or (isinstance(kdtree, np.ndarray))
for p in kdtree:
scene += pgl.Shape(pgl.Translated(p, sphere), silver)
return scene
def to_scene(self, conversion=1.0, name=None):
r"""Create a PlantGL scene from a Ply dictionary.
Args:
conversion (float, optional): Conversion factor that should be
applied to the vertices. Defaults to 1.0.
name (str, optional): Name that should be given to the created
PlantGL symbol. Defaults to None and is ignored.
Returns:
"""
import openalea.plantgl.all as pgl
smb_class, args, kwargs = self.to_geom_args(conversion=conversion,
name=name)
smb = smb_class(*args, **kwargs)
if name is not None:
smb.setName(name)
if self.get('material', None) is not None:
mat = pgl.Material(self['material'])
shp = pgl.Shape(smb, mat)
else:
shp = pgl.Shape(smb)
if name is not None:
shp.setName(name)
scn = pgl.Scene([shp])
return scn
def plot(self, dfvox, dfmap, minval=None, maxval=None):
output = pandas.merge(dfmap, dfvox)
output = output.sort_values(
'primitive_index'
) # sort is needed to ensure matching with triangulation indices
par = output['PAR']
if minval is None:
minval = min(par)
if maxval is None:
maxval = max(par)
cmap = ColorMap()
scene = pgl.Scene()
discretizer = pgl.Discretizer()
for sh in self.scene:
discretizer.process(sh)
mesh = discretizer.result
mesh.colorList = []
mesh.colorPerVertex = False
colors = map(lambda x: cmap(x, minval, maxval, 250., 20.),
par[output['shape_id'] == sh.id])
for color in colors:
r, g, b = color
mesh.colorList.append(pgl.Color4(r, g, b, 0))
scene.add(mesh)
pgl.Viewer.display(scene)
return scene
def visualise_plants(g, vids=[], positions=[]):
max_scale = g.max_scale()
t = pgl.PglTurtle()
if not vids:
vids = g.component_roots_at_scale(g.root, scale=max_scale)
x = -9
y = -12
dx = 2.
dy = 4.
positions = [(x+(count%9)*dx,y+(count/9)*dy,0) for count in range(len(vids))]
else:
vids = [cid for vid in vids for cid in g.component_roots_at_scale_iter(vid, scale=max_scale)]
assert len(vids) == len(positions)
n= len(vids)
scenes = pgl.Scene()
for i, vid in enumerate(vids):
#position = (x+(count%9)*dx,y+(count/9)*dy,0)
position = positions[i]
t = pgl.PglTurtle()
#t.move(position)
scene = turtle.traverse_with_turtle(g, vid, visitor=strawberry_visitor, turtle=t, gc=False)
ds = scene.todict()
for shid in ds:
for sh in ds[shid]:
sh.geometry = pgl.Translated(position, sh.geometry)
scenes.add(sh)
return scenes
def test_class_interface():
scene = pgl.Scene()
scene.add(pgl.Sphere(radius=0.1))
pov = PovRay()
pov.render(scene)
reader = cv2.imread
im = pov.get_image(reader)
return im
def oneScHullScene(scgroup,pointsbyshape):#aka hullscene
"""cree les cvxHull des groupes de scgroup"""
sc = pgl.Scene()
m = color(20,150,20, trans=True)
for ids in scgroup:
pts = ptUnion(pointsbyshape,ids)
sc += pgl.Shape(pgl.fit('convexhull',pgl.Polyline(pts)),m)
return sc
def get_source_leaf(g, position_source=2./3):
tesselator = pgl.Tesselator()
bbc = pgl.BBoxComputer(tesselator)
leaves = get_leaves(g, label='LeafElement')
centroids = g.property('centroid')
geometries = g.property('geometry')
targets = list(leaf for leaf in leaves if leaf in geometries.iterkeys())
for vid in targets:
if isinstance(geometries[vid], collections.Iterable):
bbc.process(pgl.Scene(geometries[vid]))
else:
bbc.process(pgl.Scene([pgl.Shape(geometries[vid])]))
center = bbc.result.getCenter()
centroids[vid] = center
zmax = max(centroids.items(), key=lambda x:x[1][2])[1][2]
distances = {vid:pgl.norm(centroids[vid]-(0,0,position_source*zmax)) for vid in centroids}
return min(distances.items(), key=lambda x:x[1])[0]
def plotSkyTurtle():
pgl.Viewer.start()
sc = pgl.Scene()
for i in range(len(elevations)):
pos = pgl.Vector3(pgl.Vector3.Spherical(30,radians(azimuths[i]),radians(90-elevations[i])))
sc += pgl.Shape(pgl.Translated(pos,pgl.Sphere(0.5)),pgl.Material(),i+1)
pgl.Viewer.display(sc)
return sc
def viewMesures(file):
treeList = treesFromFile(file)
scene = pgl.Scene()
for i in range(len(treeList)):
t = treeList[i]
mes = t.mesures(i)
for sh in mes:
scene.add(sh)
pgl.Viewer.display(scene)
def test_scene():
ds = pgl.Sphere()
t = pgl.Tapered(1., 1., ds)
t2 = pgl.Translated(0., 0., 1., ds)
sc = pgl.Scene([
pgl.Shape(t, pgl.Material((255, 0, 0))),
pgl.Shape(t2, pgl.Material((0, 255, 0)))
])
jsonconversion(sc)
def display_leaves(g):
green = pgl.Material(pgl.Color3(0, 150, 0))
scene = pgl.Scene()
for vid, geom in g.property('geometry').items():
sh = pgl.Shape(geom, green)
sh.id = vid
scene.add(sh)
pgl.Viewer.display(scene)
return scene
def scenegraph(self):
# traverse the graph
g = self._graph
if self._scene:
return self._scene
else:
self._scene = pgl.Scene()
self.visited = set()
self._graph.add_vertex_property('final_geometry')
final_geometry = g.vertex_property("final_geometry")
transfos = [pgl.Matrix4()]
self.traverse2(g.root)
self._scene.merge(pgl.Scene(final_geometry.values()))
return self._scene
def stand_box(domain):
'''
domain: 3D bounding box of the stand
'''
# list of points
z_base = domain[0][2]
z_top = domain[1][2]
sides_points = [
domain[0], # coordinates of bottom right corner
(domain[1][0], domain[0][1], z_base),
(domain[1][0], domain[1][1],
z_base), # coordinates of bottom left corner
(domain[0][0], domain[1][1], z_base),
(domain[0][0], domain[0][1], z_top), # coordinates of top right corner
(domain[1][0], domain[0][1], z_top),
(domain[1][0], domain[1][1], z_top), # coordinates of top left corner
(domain[0][0], domain[1][1], z_top)
]
bottom_points = [
domain[0], # coordinates of bottom right corner
(domain[1][0], domain[0][1], z_base),
(domain[1][0], domain[1][1],
z_base), # coordinates of bottom left corner
(domain[0][0], domain[1][1], z_base)
]
# list of indices to make the quads of the sides from the points
side_indices = [
(0, 1, 5, 4), #
(1, 2, 6, 5), # indices for
(2, 3, 7, 6), # side faces
(3, 0, 4, 7)
] #
# list of indices to make the quads of the bottom from the points
bottom_indices = [(0, 1, 2, 3)] # indices for bottom face
# list of colors
side_color = pgl.Color3(0, 0, 0)
bottom_color = pgl.Color3(255, 255, 255)
# construction of the geometry for the sides
side_box = pgl.QuadSet(sides_points, side_indices)
# construction of the geometry for the bottom
bottom_box = pgl.QuadSet(bottom_points, bottom_indices)
# create 2 shapes: 1 with side_color, 1 with bottom_color
sides_shape = pgl.Shape(side_box, pgl.Material(side_color))
bottom_shape = pgl.Shape(bottom_box, pgl.Material(bottom_color))
scene = pgl.Scene()
scene.add(sides_shape)
scene.add(bottom_shape)
return scene