from openalea.plantgl.all import *
from .mtgmanip import pgltree2mtg
[docs]
def adaptivespacecolonization_method(
mtg,
startfrom,
pointList,
densities,
mingrowthlength,
maxgrowthlength,
growthlengthfunc,
killradiusratio,
perceptionradiusratio,
min_nb_pt_per_bud,
filter_short_branch=False,
angle_between_trunk_and_lateral=60,
):
"""
Reconstruct a tree skeleton using adaptive space colonization with density-dependent growth.
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 growth length.
mingrowthlength: float
Minimum growth length.
maxgrowthlength: float
Maximum growth length.
growthlengthfunc: callable
Function mapping normalised density to a growth length factor.
killradiusratio: float
Ratio of growth length for the kill radius.
perceptionradiusratio: float
Ratio of growth length for the perception radius.
min_nb_pt_per_bud: int
Minimum number of points per bud.
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])
mindensity, maxdensity = densities.getMinAndMax()
deltadensity = maxdensity - mindensity
growthlengthfunc.clamped = False
normeddensity = lambda x: growthlengthfunc(abs(x - mindensity) / deltadensity)
deltabinlength = maxgrowthlength - mingrowthlength
binlength = lambda x: mingrowthlength + deltabinlength * normeddensity(x)
print(
maxgrowthlength,
maxgrowthlength * killradiusratio,
maxgrowthlength * perceptionradiusratio,
)
class CustomSCA(SpaceColonization):
def __init__(self, *args):
SpaceColonization.__init__(self, *args)
def node_buds_preprocess(self, nid):
pos = self.node_position(nid)
components = self.node_attractors(nid)
# print nid, self.parents[nid], pos, components
aid, aidist = findClosestFromSubset(pos, pointList, components)
adensity = densities[aid]
l = binlength(adensity)
assert l >= mingrowthlength
self.setLengths(l, killradiusratio, perceptionradiusratio)
sc = CustomSCA(
pointList,
maxgrowthlength,
maxgrowthlength * killradiusratio,
maxgrowthlength * perceptionradiusratio,
rootpos,
)
sc.min_nb_pt_per_bud = min_nb_pt_per_bud
sc.run()
nodes = sc.nodes
parents = sc.parents
pgltree2mtg(
mtg,
startfrom,
parents,
nodes,
None,
filter_short_branch,
angle_between_trunk_and_lateral,
)
return mtg
[docs]
def spacecolonization_method(
mtg,
startfrom,
pointList,
growthlength,
killradiusratio,
perceptionradiusratio,
min_nb_pt_per_bud,
filter_short_branch=False,
angle_between_trunk_and_lateral=60,
):
"""
Reconstruct a tree skeleton using space colonization.
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.
growthlength: float
Growth length for each iteration.
killradiusratio: float
Ratio of growth length for the kill radius.
perceptionradiusratio: float
Ratio of growth length for the perception radius.
min_nb_pt_per_bud: int
Minimum number of points per bud.
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])
sc = SpaceColonization(
pointList,
growthlength,
growthlength * killradiusratio,
growthlength * perceptionradiusratio,
rootpos,
)
sc.min_nb_pt_per_bud = min_nb_pt_per_bud
sc.run()
nodes = sc.nodes
parents = sc.parents
pgltree2mtg(
mtg,
startfrom,
parents,
nodes,
None,
filter_short_branch,
angle_between_trunk_and_lateral,
)
return mtg
