def np_inertia_axis(points, verbose=False):
assert len(points) > 0
import numpy as np
import openalea.plantgl.all as pgl
if type(points) != pgl.Point3Array:
points = pgl.Point3Array(points)
if verbose: print 'centering points'
center = points.getCenter()
npoints = pgl.Point3Array(points)
if pgl.norm(center) > 1e-5:
npoints.translate(- center)
if verbose: print 'compute covariance'
# compute 1/N*P.P^T
# cov = 1./len(points)*np.dot(npoints.T,npoints)
cov = pgl.pointset_covariance(npoints)
cov = np.array([cov.getRow(i) for i in xrange(3)])
if verbose: print cov
if verbose: print "compute eigen vectors"
# Find the eigen values and vectors.
eig_val, eig_vec = np.linalg.eig(cov)
if verbose:
for i in xrange(3):
print eig_val[i], eig_vec[:, i]
eig_vec = np.array(eig_vec).T
eig_vec = np.array([eig_vec[i] for i in reversed(pgl.get_sorted_element_order(eig_val))])
eig_val = np.array([eig_val[i] for i in reversed(pgl.get_sorted_element_order(eig_val))])
return eig_val, eig_vec, center
def NURBSCurve(self, ctrlpoints, dimension, **kwds):
ctrlpoints = str(ctrlpoints)
ctrlpoints = [float(num) for num in ctrlpoints.split(",")]
dimension = int(dimension)
items, chunk = ctrlpoints, dimension
pointArray = zip(*[iter(items)] * chunk)
if (dimension == 2):
v4array = []
for item in pointArray:
v4array.append(pgl.Vector2(item))
parray = pgl.Point3Array(0)
for item in v4array:
parray.append(Vector3(item,1))
return (pgl.NurbsCurve2D(parray), None)
elif (dimension == 3):
v4array = []
for item in pointArray:
v4array.append(pgl.Vector3(item))
parray = pgl.Point4Array(0)
for item in v4array:
parray.append(Vector4(item,1))
return (pgl.NurbsCurve(parray), None)
def Polygon(self, vertices, **kwds):
""" TODO: Move code to geometry """
points = str(vertices)
points = [float(num) for num in points.split(",")]
items, chunk = points, 3
p3list = zip(*[iter(items)] * chunk)
p2list = project3Dto2D(p3list)
pd2list = []
for i in range(len(p2list)):
pd2list.append({i: p2list[i]})
indexlist = []
poly_orientation = orientation(p2list)
while len(pd2list) >= 3:
for cur in range(len(pd2list)):
prev = cur - 1
nex = (cur + 1) % len(pd2list) # Wrap around on the ends
# By definition, at least there are two ears;
# we will iterate at end only if poly_orientation
# was incorrect.
pcur, pprev, pnex = pd2list[cur].values()[0], pd2list[prev].values()[0], pd2list[nex].values()[0]
det = determinant(pcur, pprev, pnex)
inside = no_interior(pprev, pcur, pnex, pd2list, poly_orientation)
if (det == poly_orientation) and inside:
# Same orientation as polygon
# No points inside
# Add index of this triangle to the index list
index = pd2list[prev].keys()[0], pd2list[cur].keys()[0], pd2list[nex].keys()[0]
indexlist.append(index)
# Remove the triangle from the polygon
del(pd2list[cur])
break
return (pgl.TriangleSet(pgl.Point3Array(p3list), indexlist), None)
def tgl():
return pgl.TriangleSet(
pgl.Point3Array([
pgl.Vector3(1, 0, 0),
pgl.Vector3(-0.2, 1, 0),
pgl.Vector3(-0.2, -1, 0)
]), pgl.Index3Array([pgl.Index3(0, 1, 2)]))
def genericLeaf(allo_length, allo_surf, **kwds):
if kwds.has_key('surface'):
surface = kwds['surface']
length = math.sqrt(surface / (allo_length*allo_surf) )
else:
length = kwds.get('length', 1)
alpha = kwds.get('alpha', 0)
color = kwds.get('color', __niceGreen)
step = length/10.
x = array(arange(step,length,step)) #begin and end are specific
y = (-3.0*allo_length*allo_surf) * (x**2/length - x)
cos = math.cos(math.radians(alpha/2.0))
sin = math.sin(math.radians(alpha/2.0))
list = []
idxList = []
for i in range(len(x)):
list.append(pgl.Vector3(x[i],0,0))
list.append(pgl.Vector3(x[i],y[i]*cos,y[i]*sin))
list.append(pgl.Vector3(x[i],-y[i]*cos,y[i]*sin))
list.append(pgl.Vector3(0,0,0))
list.append(pgl.Vector3(length,0,0))
for i in range(len(x) -1):
idxList.append(pgl.Index(3*(i+1), 3*(i+1)+1, 3*i+1, 3*i ))
idxList.append(pgl.Index(3*i+2, 3*(i+1)+2, 3*(i+1), 3*i ))
idxList.append(pgl.Index(0, 1, len(list)-2 ))
idxList.append(pgl.Index(2, 0, len(list)-2 ))
idxList.append(pgl.Index(3*(len(x)-1)+1, 3*(len(x)-1), len(list)-1 ))
idxList.append(pgl.Index(3*(len(x)-1), 3*(len(x)-1)+2, len(list)-1 ))
p3r = pgl.Point3Array(list)
ir = pgl.IndexArray(idxList)
fs = pgl.FaceSet(p3r, ir)
return pgl.Shape(fs, color)
def pgl_inertia_axis(points):
import openalea.plantgl.all as pgl
if type(points) != pgl.Point3Array:
points = pgl.Point3Array(points)
center = points.getCenter()
u, v, w, s = pgl.Fit.inertiaAxis(points)
return s, [u, v, w], center
def Patch(self, heightValues, usize, vsize, zerolevel, scale, water, **kwds):
usize = int(usize)
vsize = int(vsize)
zerolevel = float(zerolevel)
scale = float(scale)
water = str(water)
water = water.lower() == 'true'
heightValues = str(heightValues)
heightValues = [float(num) for num in heightValues.split(",")]
verts = []
faces = []
nu = usize
nv = vsize
p = (0, 0, 0)
for v in range(nv):
for u in range(nu):
p = heightFieldGetVertex(v*usize + u, usize, vsize, heightValues, zerolevel, scale, water)
verts.append(p)
n = 0
for v in range(nv):
for u in range(nu):
if v < nv-1 and u < nu-1:
face = (n, n+1, n+1+nu, n+nu)
faces.append(face)
n = n+1
return pgl.QuadSet(pgl.Point3Array(verts), faces), None
def ptUnion(pointsbyshape,idList=None):#aka ptsum
"""union des points de la liste ids"""
union = pgl.Point3Array()
if idList is None:
idList = pointsbyshape.keys()
for id in idList:
union += pointsbyshape[id]
return union
def stolon_curve(scale=1.):
v2 = pgl.Vector3
ctrls = pgl.Point3Array([
v2(x * scale, y * scale)
for x, y in [(0, 0), (1, 3), (3, 5), (4, 2), (5, 4)]
])
crv = pgl.BezierCurve2D(ctrls)
return crv
def Supershape(self, a, b, m1, m2, n11, n12, n13, n21, n22, n23, **kwds):
a = float(a)
b = float(b)
m1 = float(m1)
m2 = float(m2)
n11 = float(n11)
n12 = float(n12)
n13 = float(n13)
n21 = float(n21)
n22 = float(n22)
n23 = float(n23)
verts = []
faces = []
scale = 1.0
Unum = 20
Vnum = 20
Uinc = pi / (Unum/2)
Vinc = (pi/2)/(Vnum/2)
#fill verts array
theta = -pi
for i in range (0, Unum + 1):
phi = -pi/2
r1 = Superformula(theta, a, b, m1, n11, n12, n13)
for j in range(0,Vnum + 1):
r2 = Superformula(phi, a, b, m2, n21, n22, n23)
x = scale * (r1 * cos(theta) * r2 * cos(phi))
y = scale * (r1 * sin(theta) * r2 * cos(phi))
z = scale * (r2 * sin(phi))
vert = (x,y,z)
verts.append(vert)
phi = phi + Vinc
theta = theta + Uinc
#define faces
count = 0
for i in range (0, (Vnum + 1) *(Unum)):
if count < Vnum:
A = i
B = i+1
C = (i+(Vnum+1))+1
D = (i+(Vnum+1))
face = (A,B,C,D)
faces.append(face)
count = count + 1
else:
count = 0
return pgl.QuadSet(pgl.Point3Array(verts), faces), None
def to_geom_args(self,
conversion=1.0,
name=None,
_as_obj=False): # pragma: lpy
r"""Get arguments for creating a PlantGL geometry.
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:
tuple: Class, arguments and keyword arguments for PlantGL geometry.
"""
import openalea.plantgl.all as pgl
kwargs = dict()
# Add vertices
obj_points = []
obj_colors = []
for v in self['vertices']:
xarr = conversion * np.array([v[k] for k in ['x', 'y', 'z']])
obj_points.append(
pgl.Vector3(np.float64(xarr[0]), np.float64(xarr[1]),
np.float64(xarr[2])))
c = [v.get(k, None) for k in ['red', 'green', 'blue']]
if None not in c:
cast_type = int
obj_colors.append(
pgl.Color4(cast_type(c[0]), cast_type(c[1]),
cast_type(c[2]), cast_type(1)))
points = pgl.Point3Array(obj_points)
if obj_colors:
colors = pgl.Color4Array(obj_colors)
kwargs['colorList'] = colors
kwargs['colorPerVertex'] = True
# Add indices
obj_indices = []
index_class = pgl.Index
array_class = pgl.IndexArray
smb_class = pgl.FaceSet
# index_class = pgl.Index3
# array_class = pgl.Index3Array
# smb_class = pgl.TriangleSet
for f in self['faces']:
if _as_obj:
f_int = [int(_f['vertex_index']) for _f in f]
else:
f_int = [int(_f) for _f in f['vertex_index']]
obj_indices.append(index_class(*f_int))
indices = array_class(obj_indices)
args = (points, indices)
return smb_class, args, kwargs
def _common_init(self, **keys):
"""
"""
if len(keys["points"]) != 3:
raise Exception(
"ATriangle: triangle must be described by 3 points..")
self._indexes = []
self._points = pgl.Point3Array(keys["points"])
for i in xrange(1, len(keys["points"])):
self._indexes.append(pgl.Index3(0, 1, 2))
self._indexes = pgl.Index3Array(self._indexes)
def stolon_curve(scale=1.):
"""Generates the stolon as curves
:param scale: size of the stolon, defaults to 1.
:type scale: float, optional
:return: return a curve to for symbolise a stolon
:rtype: plf.BezierCurve2D
"""
v2 = pgl.Vector3
ctrls = pgl.Point3Array([v2(x*scale, y*scale) for x,y in [(0,0), (1,3), (3,5), (4,2), (5,4)]])
crv = pgl.BezierCurve2D(ctrls)
return crv
def to_geom_args(self, conversion=1.0, name=None):
r"""Get arguments for creating a PlantGL geometry.
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:
tuple: Class, arguments and keyword arguments for PlantGL geometry.
"""
import openalea.plantgl.all as pgl
kwargs = dict()
# Add vertices
obj_points = []
for v in self['vertices']:
xarr = conversion * np.array(v)
obj_points.append(pgl.Vector3(xarr[0], xarr[1], xarr[2]))
points = pgl.Point3Array(obj_points)
# Add indices
obj_indices = []
nind = None
index_class = pgl.Index3
array_class = pgl.Index3Array
smb_class = pgl.TriangleSet
for f in self['faces']:
if nind is None:
nind = len(f)
if nind == 3:
pass
else:
raise ValueError(
"No PlantGL class for faces with %d vertices." % nind)
else:
if len(f) != nind:
raise ValueError("Faces do not all contain %d vertices." %
nind)
f_int = [int(_f) for _f in f]
obj_indices.append(index_class(*f_int))
indices = array_class(obj_indices)
# Add colors
if self['vertex_colors']:
obj_colors = []
for c in self['vertex_colors']:
assert (len(c) == 3)
obj_colors.append(pgl.Color4(c[0], c[1], c[2], 1))
colors = pgl.Color4Array(obj_colors)
kwargs['colorList'] = colors
kwargs['colorPerVertex'] = True
args = (points, indices)
return smb_class, args, kwargs
def optimizeAlignementPosition(points,
mtg,
distanceratio=10,
nbtests=10,
p_edir=None):
from .mtgmanip import mtg2pgltree
import openalea.plantgl.all as pgl
from .pointprocessing import np_inertia_axis
from math import pi, degrees
nodes, parents, vertex2node = mtg2pgltree(mtg)
dist = pgl.average_distance_to_shape(points, nodes, parents,
[0 for i in range(len(nodes))])
print(dist)
if p_edir is None:
p_eval, p_edir, p_center = np_inertia_axis(points)
mtgextent = pgl.Point3Array(list(
mtg.property('position').values())).getExtent()
def test_shift(cshift, dist, tshift):
print('test shift of', cshift, ':', end=' ')
nnodes = [p + cshift for p in nodes]
ndist = pgl.average_distance_to_shape(points, nnodes, parents,
[0 for j in range(len(nodes))])
print(ndist)
if ndist < dist:
tshift = cshift
dist = ndist
return dist, tshift
for i in range(3):
tshift = None
unitshift = mtgextent[i] * distanceratio / 1000.
for t in range(1, nbtests):
cshift = p_edir[i] * t * unitshift
dist, tshift = test_shift(cshift, dist, tshift)
for t in range(1, nbtests):
cshift = -p_edir[i] * t * unitshift
dist, tshift = test_shift(cshift, dist, tshift)
if not tshift is None:
print('select', tshift, dist)
npos = dict()
for vid, pos in list(mtg.property('position').items()):
npos[vid] = pos + tshift
mtg.property('position').update(npos)
def to_geom_args(self, conversion=1.0, name=None):
r"""Get arguments for creating a PlantGL geometry.
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:
tuple: Class, arguments and keyword arguments for PlantGL geometry.
"""
import openalea.plantgl.all as pgl
smb_class, args, kwargs = super(ObjDict, self).to_geom_args(
conversion=conversion, name=name)
index_class = pgl.Index3
array_class = pgl.Index3Array
# Texture coords
if self.get('texcoords', []):
obj_texcoords = []
for t in self['texcoords']:
obj_texcoords.append(pgl.Vector2(t[0], t[1]))
kwargs['texCoordList'] = pgl.Point2Array(obj_texcoords)
if self.get('face_texcoords', []):
obj_ftexcoords = []
for t in self['face_texcoords']:
if (t is not None) and (t[0] is not None):
entry = [int(_t) for _t in t]
else:
entry = [len(self['texcoords']) for _ in range(3)]
obj_ftexcoords.append(index_class(*entry))
kwargs['texCoordIndexList'] = array_class(obj_ftexcoords)
# Normals
if self.get('normals', []):
obj_normals = []
for n in self['normals']:
obj_normals.append(pgl.Vector3(n[0], n[1], n[2]))
kwargs['normalList'] = pgl.Point3Array(obj_normals)
if self.get('face_normals', []):
obj_fnormals = []
for n in self['face_normals']:
if (n is not None) and (n[0] is not None):
entry = [int(_n) for _n in n]
else:
entry = [len(self['normals']) for _ in range(3)]
obj_fnormals.append(index_class(*entry))
kwargs['normalIndexList'] = array_class(obj_fnormals)
return smb_class, args, kwargs
def __initialiseContext__(context):
import openalea.plantgl.all as pgl
width = pgl.NurbsCurve2D(
ctrlPointList = pgl.Point3Array([(0, 0.0368034, 1),(0.321038, 0.20082, 1),(0.674863, 0.127049, 1),(1, 0.00418017, 1)]) ,
)
width.name = "width"
panel_0 = ({'active': True, 'visible': True, 'name': 'Functions'},[('Function',width)])
import openalea.plantgl.all as pgl
nerve = pgl.NurbsCurve2D(
ctrlPointList = pgl.Point3Array([(-0.5, 0, 1),(-0.223915, 0.114315, 1),(0.121756, 0.0370409, 1),(0.467244, -0.216243, 1)]) ,
)
nerve.name = "nerve"
section = pgl.NurbsCurve2D(
ctrlPointList = pgl.Point3Array([(-0.5, 0, 1),(-0.195355, -0.24554, 1),(0.203326, -0.162142, 1),(0.5, 0, 1)]) ,
)
section.name = "section"
panel_1 = ({'active': True, 'visible': True, 'name': 'Curve2D'},[('Curve2D',nerve),('Curve2D',section)])
parameterset = [panel_0,panel_1,]
context["__functions__"] = [('width',width),]
context["__curves__"] = [('nerve',nerve),('section',section),]
context["__parameterset__"] = parameterset
context["width"] = pgl.QuantisedFunction(width)
context["nerve"] = nerve
context["section"] = section
def fn(change):
if 'new' in change:
value = change['new']
if isinstance(param, BaseScalar):
param.value = value
elif isinstance(param, tuple):
if isinstance(param[1],
(pgl.NurbsCurve2D, pgl.BezierCurve2D)):
param[1].ctrlPointList = pgl.Point3Array(
[pgl.Vector3(p[0], p[1], 1) for p in value])
elif isinstance(param[1], pgl.Polyline2D):
param[1].pointList = pgl.Point2Array(
[pgl.Vector2(p[0], p[1]) for p in value])
lsw.set_parameters(lp.dumps())
def _common_init(self, **keys):
"""
"""
if len(keys["points"]) < 3:
raise Exception("ACenterPolygon: Too few points in..")
self._indexes = []
self._points = pgl.Point3Array([pgl.Vector3()] + keys["points"])
for i in xrange(1, len(keys["points"])):
self._points[0] += self._points[i]
self._indexes.append(pgl.Index([0, i, i + 1]))
self._points[0] += self._points[len(keys["points"])]
self._indexes.append(pgl.Index([0, len(keys["points"]), 1]))
self._points[0] = self._points[0] / len(keys["points"])
self._indexes = pgl.IndexArray(self._indexes)
def pgl_surface_mesh(self,
grid_size=128,
grid_resolution=1,
potential_value=0.5,
color=[190, 205, 205],
transparency=0):
points, triangles = self.surface_mesh(grid_size, grid_resolution,
potential_value)
import openalea.plantgl.all as pgl
if color is None:
color = [np.random.randint(0, 255) for i in xrange(3)]
mat = pgl.Material(tuple(color),
diffuse=0.25,
transparency=transparency)
s = pgl.Scene()
s += pgl.Shape(
pgl.FaceSet(
pgl.Point3Array(points),
pgl.Index3Array([[int(i) for i in tr] for tr in triangles])),
mat)
return s
def mangoLeaf(length=1, alpha=0, color=__niceGreen):
x = array(arange(0.1, length, 0.1))
y = (-3 / (length * 5.)) * (x**2 / length - x)
cos = math.cos(math.radians(alpha / 2.0))
sin = math.sin(math.radians(alpha / 2.0))
list = []
idxList = []
for i in range(len(x)):
list.append(pgl.Vector3(x[i], 0, 0))
list.append(pgl.Vector3(x[i], y[i] * cos, y[i] * sin))
list.append(pgl.Vector3(x[i], -y[i] * cos, y[i] * sin))
list.append(pgl.Vector3(0, 0, 0))
list.append(pgl.Vector3(length, 0, 0))
for i in range(len(x) - 1):
idxList.append(
pgl.Index(3 * (i + 1), 3 * (i + 1) + 1, 3 * i + 1, 3 * i))
idxList.append(
pgl.Index(3 * i + 2, 3 * (i + 1) + 2, 3 * (i + 1), 3 * i))
#idxList.append(pgl.Index(3*i,3*i+1,3*(i+1)+1, 3*(i+1)))
#idxList.append(pgl.Index(3*i,3*(i+1),3*(i+1)+2,3*i+2))
idxList.append(pgl.Index(0, 1, len(list) - 2))
idxList.append(pgl.Index(2, 0, len(list) - 2))
idxList.append(
pgl.Index(3 * (len(x) - 1) + 1, 3 * (len(x) - 1),
len(list) - 1))
idxList.append(
pgl.Index(3 * (len(x) - 1), 3 * (len(x) - 1) + 2,
len(list) - 1))
#idxList.append(pgl.Index(len(list)-2, 1, 0))
#idxList.append(pgl.Index(len(list)-2, 0, 2))
#idxList.append(pgl.Index(len(list)-1, 3*(len(x)-1), 3*(len(x)-1)+1))
#idxList.append(pgl.Index(len(list)-1, 3*(len(x)-1)+2, 3*(len(x)-1)))
p3r = pgl.Point3Array(list)
ir = pgl.IndexArray(idxList)
fs = pgl.FaceSet(p3r, ir)
return pgl.Shape(fs, color)
def scale_and_center(points, mtg):
import openalea.plantgl.all as pgl
if type(mtg) != pgl.Point3Array:
mtgpoints = pgl.Point3Array(list(mtg.property('position').values()))
else:
mtgpoints = mtg
pointextent = pgl.norm(points.getExtent())
mtgextent = pgl.norm(mtgpoints.getExtent())
scaleratio = mtgextent / pointextent
m_center = mtgpoints.getCenter()
p_center = points.getCenter()
from math import log
scale = 1. / pow(10, round(log(scaleratio, 10)))
def transform(v):
return ((v - m_center) * scale) + p_center
npos1 = dict([(vid, transform(pos))
for vid, pos in list(mtg.property('position').items())])
mtg.property('position').update(npos1)
def on_param_changed(change):
if 'new' in change:
value = change['new']
name = change['name']
if isinstance(param, BaseScalar):
if name == 'name':
param.name = value
else:
param.value = value
elif isinstance(param, tuple):
if name == 'value':
if isinstance(param[1],
(pgl.NurbsCurve2D, pgl.BezierCurve2D)):
param[1].ctrlPointList = pgl.Point3Array(
[pgl.Vector3(p[0], p[1], 1) for p in value])
elif isinstance(param[1], pgl.Polyline2D):
param[1].pointList = pgl.Point2Array(
[pgl.Vector2(p[0], p[1]) for p in value])
else:
param[1].name = value
if self.__auto_apply:
self.on_lpy_context_change(self.__lp.dumps())
if self.__auto_save:
self.__save()
def to_geom_args(self, conversion=1.0, name=None): # pragma: lpy
r"""Get arguments for creating a PlantGL geometry.
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:
tuple: Class, arguments and keyword arguments for PlantGL geometry.
"""
import openalea.plantgl.all as pgl
smb_class, args, kwargs = super(ObjDict, self).to_geom_args(
conversion=conversion, name=name, _as_obj=True)
index_class = pgl.Index
array_class = pgl.IndexArray
# Texture coords
if self.get('texcoords', []):
obj_texcoords = []
for t in self['texcoords']:
obj_texcoords.append(
pgl.Vector2(np.float64(t['u']), np.float64(t.get('v',
0.0))))
kwargs['texCoordList'] = pgl.Point2Array(obj_texcoords)
obj_ftexcoords = []
for i, f in enumerate(self['faces']):
entry = []
for _f in f:
if 'texcoord_index' not in _f:
if i > 0:
warnings.warn(
("'texcoord_index' missing from face" +
"%d, texcoord indices will be " + "ignored.")
% i)
obj_ftexcoords = []
entry = []
break
entry.append(int(_f['texcoord_index']))
if not entry:
break
obj_ftexcoords.append(index_class(*entry))
if obj_ftexcoords:
kwargs['texCoordIndexList'] = array_class(obj_ftexcoords)
# Normals
if self.get('normals', []):
obj_normals = []
for n in self['normals']:
obj_normals.append(
pgl.Vector3(np.float64(n['i']), np.float64(n['j']),
np.float64(n['k'])))
kwargs['normalList'] = pgl.Point3Array(obj_normals)
obj_fnormals = []
for i, f in enumerate(self['faces']):
entry = []
for _f in f:
if 'normal_index' not in _f:
if i > 0:
warnings.warn(
("'normal_index' missing from face" +
"%d, normal indices will be " + "ignored.") %
i)
obj_fnormals = []
entry = []
break
entry.append(int(_f['normal_index']))
if not entry:
break
obj_fnormals.append(index_class(*entry))
if obj_fnormals:
kwargs['normalIndexList'] = array_class(obj_fnormals)
return smb_class, args, kwargs
def createDefaultObject(self, subtype=None):
import openalea.plantgl.all as pgl
nbP = 4
return pgl.NurbsCurve2D(
pgl.Point3Array([(float(i) / (nbP - 1), 0) for i in range(nbP)],
1))
try:
def alignGlobally(points, mtg, verbose=False):
import openalea.plantgl.all as pgl
import numpy as np
from .pointprocessing import np_inertia_axis
mtgpoints = pgl.Point3Array(list(mtg.property('position').values()))
axispoints = np_inertia_axis(points, verbose=verbose)
axismtg = np_inertia_axis(mtgpoints, verbose=verbose)
p_eval, p_edir, p_center = axispoints
m_eval, m_edir, m_center = axismtg
pointextent = pgl.norm(points.getExtent())
mtgextent = pgl.norm(mtgpoints.getExtent())
scaleratio = mtgextent / pointextent
from math import log
scale = 1. / pow(10, round(log(scaleratio, 10)))
normalizeorientation = True
checkorientation = True
if normalizeorientation:
def normalize_frame(edir):
a, b = edir[0], edir[1]
c = np.cross(a, b)
return np.array([a, np.cross(c, a), c])
p_edir = normalize_frame(p_edir)
m_edir = normalize_frame(m_edir)
if verbose:
print('Point center :', p_center)
print('MTG center :', m_center)
print('Point axis :', p_edir)
print('MTG axis :', m_edir)
print('Point variance :', p_eval)
print('MTG variance :', m_eval)
def transform(v, t_edir):
v = (v - m_center)
nval = [pgl.dot(v, ed) for ed in m_edir]
nv = sum([val * ed for val, ed in zip(nval, t_edir)],
pgl.Vector3(0, 0, 0))
return (nv + p_center)
ppos = mtg.property('position').copy()
npos1 = dict([(vid, transform(pos, p_edir))
for vid, pos in list(ppos.items())])
#npos1 = dict([(vid, pos*scale) for vid, pos in ppos.items()])
mtg.property('position').update(npos1)
if checkorientation:
if verbose: print('check orientation')
from .mtgmanip import mtg2pgltree
nodes, parents, vertex2node = mtg2pgltree(mtg)
dist1 = pgl.average_distance_to_shape(points, nodes, parents,
[0 for i in range(len(nodes))])
if verbose: print('check flipped orientation')
p_edir2 = np.array(
[-p_edir[0], -p_edir[1],
np.cross(-p_edir[0], -p_edir[1])])
npos2 = dict([(vid, transform(pos, p_edir2))
for vid, pos in list(ppos.items())])
mtg.property('position').update(npos2)
nodes, parents, vertex2node = mtg2pgltree(mtg)
dist2 = pgl.average_distance_to_shape(points, nodes, parents,
[0 for i in range(len(nodes))])
if verbose: print(dist1, dist2)
if dist1 < dist2:
if verbose: print('Use first orientation')
mtg.property('position').update(npos1)
else:
if verbose: print('Use flipped orientation')
