from openalea.plantgl.all import *
from .mtgmanip import pgltree2mtg
[docs]
def xu_method(
mtg,
startfrom,
pointList,
binlength,
k=20,
filter_short_branch=False,
angle_between_trunk_and_lateral=60,
):
"""
Reconstruct a tree skeleton using the Xu method (distance-based clustering).
Parameters
~~~~~~~~~~
mtg: openalea.mtg.MTG
MTG object to add the reconstructed tree to.
startfrom: int
Starting node id in the MTG.
pointList: list of Vector3
Input point cloud.
binlength: float
Bin length for clustering.
k: int
Number of nearest neighbours for connectivity.
filter_short_branch: bool
If True, remove branches with no children.
angle_between_trunk_and_lateral: float
Angle threshold in degrees for edge type determination.
Returns
~~~~~~~
openalea.mtg.MTG
MTG of the reconstructed tree.
"""
rootpos = Vector3(mtg.property("position")[startfrom])
root = len(pointList)
connect_all_points = False if mtg.nb_vertices(mtg.max_scale()) > 1 else True
pointList.append(rootpos)
positions, parents, pointcomponents = skeleton_from_distance_to_root_clusters(
pointList,
root,
binlength,
k,
connect_all_points=connect_all_points,
verbose=True,
)
del pointList[root]
pgltree2mtg(
mtg,
startfrom,
parents,
positions,
None,
filter_short_branch,
angle_between_trunk_and_lateral,
)
return mtg
[docs]
def graphcolonization_method(
mtg,
startfrom,
pointList,
densities,
minbinlength,
maxbinlength,
binlengthfunc,
k=20,
filter_short_branch=False,
angle_between_trunk_and_lateral=60,
):
"""
Reconstruct a tree skeleton using graph colonization with adaptive bin length.
Parameters
~~~~~~~~~~
mtg: openalea.mtg.MTG
MTG object to add the reconstructed tree to.
startfrom: int
Starting node id in the MTG.
pointList: list of Vector3
Input point cloud.
densities: list of float
Density values per point for adaptive bin length.
minbinlength: float
Minimum bin length.
maxbinlength: float
Maximum bin length.
binlengthfunc: callable
Function mapping normalised density to a bin length factor.
k: int
Number of nearest neighbours for connectivity.
filter_short_branch: bool
If True, remove branches with no children.
angle_between_trunk_and_lateral: float
Angle threshold in degrees for edge type determination.
Returns
~~~~~~~
openalea.mtg.MTG
MTG of the reconstructed tree.
"""
rootpos = Vector3(mtg.property("position")[startfrom])
root = len(pointList)
connect_all_points = False if mtg.nb_vertices(mtg.max_scale()) > 1 else True
pointList.append(rootpos)
kclosests = k_closest_points_from_ann(pointList, k, True)
kclosests = connect_all_connex_components(pointList, kclosests, True)
mindensity, maxdensity = densities.getMinAndMax()
deltadensity = maxdensity - mindensity
binlengthfunc.clamped = False
normeddensity = lambda x: binlengthfunc(abs(x - mindensity) / deltadensity)
deltabinlength = maxbinlength - minbinlength
binlength = lambda x: minbinlength + deltabinlength * normeddensity(x)
class CustomSCA(GraphColonization):
def __init__(self, *args):
GraphColonization.__init__(self, *args)
self.use_jonction_points = True
def node_buds_preprocess(self, nid):
# print 'node_buds_preprocess', nid
pos = self.node_position(nid)
components = self.node_components(nid)
# print nid, self.parents[nid], pos, components
self.grid.enable_points(components)
aid = self.grid.closest_point(pos)
self.grid.disable_points(components)
adensity = densities[aid]
l = binlength(adensity)
self.setLengths(l)
sc = GraphColonization(pointList, maxbinlength, kclosests, root)
sc.run()
nodes = sc.nodes
parents = sc.parents
del pointList[root]
pgltree2mtg(
mtg,
startfrom,
parents,
nodes,
None,
filter_short_branch,
angle_between_trunk_and_lateral,
)
return mtg
