def GTreeGPInitializator(genome, **args):
"""This initializator accepts the follow parameters:
*max_depth*
The max depth of the tree
*method*
The method, accepts "grow", "full" or "ramped"
.. versionadded:: 0.6
The *GTreeGPInitializator* function.
"""
max_depth = genome.getParam("max_depth", 5)
method = genome.getParam("method", "grow")
ga_engine = args["ga_engine"]
if method == "grow":
root = GTree.buildGTreeGPGrow(ga_engine, 0, max_depth)
elif method == "full":
root = GTree.buildGTreeGPFull(ga_engine, 0, max_depth)
elif method == "ramped":
if Util.randomFlipCoin(0.5):
root = GTree.buildGTreeGPFull(ga_engine, 0, max_depth)
else:
root = GTree.buildGTreeGPGrow(ga_engine, 0, max_depth)
else:
Util.raiseException("Unknown tree initialization method [%s] !" % method)
genome.setRoot(root)
genome.processNodes()
assert genome.getHeight() <= max_depth
def GTreeGPInitializator(genome, **args):
"""This initializator accepts the follow parameters:
*max_depth*
The max depth of the tree
*method*
The method, accepts "grow", "full" or "ramped"
.. versionadded:: 0.6
The *GTreeGPInitializator* function.
"""
max_depth = genome.getParam("max_depth", 5)
method = genome.getParam("method", "grow")
ga_engine = args["ga_engine"]
if method == "grow":
root = GTree.buildGTreeGPGrow(ga_engine, 0, max_depth)
elif method == "full":
root = GTree.buildGTreeGPFull(ga_engine, 0, max_depth)
elif method == "ramped":
if Util.randomFlipCoin(0.5):
root = GTree.buildGTreeGPFull(ga_engine, 0, max_depth)
else:
root = GTree.buildGTreeGPGrow(ga_engine, 0, max_depth)
else:
Util.raiseException("Unknown tree initialization method [%s] !" %
method)
genome.setRoot(root)
genome.processNodes()
assert genome.getHeight() <= max_depth
def GTreeInitializatorInteger(genome, **args):
""" Integer initialization function of GTree
This initializator accepts the *rangemin* and *rangemax* genome parameters.
It accepts the following parameters too:
*max_depth*
The max depth of the tree
*max_siblings*
The number of maximum siblings of an node
*method*
The method, accepts "grow", "full" or "ramped".
.. versionadded:: 0.6
The *GTreeInitializatorInteger* function.
"""
max_depth = genome.getParam("max_depth", 5)
max_siblings = genome.getParam("max_siblings", 2)
range_min = genome.getParam("rangemin", 0)
range_max = genome.getParam("rangemax", 100)
lambda_generator = lambda: rand_randint(range_min, range_max)
method = genome.getParam("method", "grow")
if method == "grow":
root = GTree.buildGTreeGrow(0, lambda_generator, max_siblings,
max_depth)
elif method == "full":
root = GTree.buildGTreeFull(0, lambda_generator, max_siblings,
max_depth)
elif method == "ramped":
if Util.randomFlipCoin(0.5):
root = GTree.buildGTreeGrow(0, lambda_generator, max_siblings,
max_depth)
else:
root = GTree.buildGTreeFull(0, lambda_generator, max_siblings,
max_depth)
else:
Util.raiseException("Unknown tree initialization method [%s] !" %
method)
genome.setRoot(root)
genome.processNodes()
assert genome.getHeight() <= max_depth
def GTreeInitializatorInteger(genome, **args):
""" Integer initialization function of GTree
This initializator accepts the *rangemin* and *rangemax* genome parameters.
It accepts the following parameters too:
*max_depth*
The max depth of the tree
*max_siblings*
The number of maximum siblings of an node
*method*
The method, accepts "grow", "full" or "ramped".
.. versionadded:: 0.6
The *GTreeInitializatorInteger* function.
"""
max_depth = genome.getParam("max_depth", 5)
max_siblings = genome.getParam("max_siblings", 2)
range_min = genome.getParam("rangemin", 0)
range_max = genome.getParam("rangemax", 100)
lambda_generator = lambda: rand_randint(range_min, range_max)
method = genome.getParam("method", "grow")
if method == "grow":
root = GTree.buildGTreeGrow(
0, lambda_generator, max_siblings, max_depth)
elif method == "full":
root = GTree.buildGTreeFull(
0, lambda_generator, max_siblings, max_depth)
elif method == "ramped":
if Util.randomFlipCoin(0.5):
root = GTree.buildGTreeGrow(
0, lambda_generator, max_siblings, max_depth)
else:
root = GTree.buildGTreeFull(
0, lambda_generator, max_siblings, max_depth)
else:
Util.raiseException(
"Unknown tree initialization method [%s] !" % method)
genome.setRoot(root)
genome.processNodes()
assert genome.getHeight() <= max_depth
def GTreeInitializatorAllele(genome, **args):
""" Allele initialization function of GTree
To use this initializator, you must specify the *allele* genome parameter with the
:class:`GAllele.GAlleles` instance.
.. warning:: the :class:`GAllele.GAlleles` instance **must** have the homogeneous flag enabled
.. versionadded:: 0.6
The *GTreeInitializatorAllele* function.
"""
max_depth = genome.getParam("max_depth", 5)
max_siblings = genome.getParam("max_siblings", 2)
method = genome.getParam("method", "grow")
allele = genome.getParam("allele", None)
if allele is None:
Util.raiseException(
"to use the GTreeInitializatorAllele, you must specify the 'allele' parameter"
)
if not allele.homogeneous:
Util.raiseException(
"to use the GTreeInitializatorAllele, the 'allele' must be homogeneous"
)
if method == "grow":
root = GTree.buildGTreeGrow(0, allele[0].getRandomAllele, max_siblings,
max_depth)
elif method == "full":
root = GTree.buildGTreeFull(0, allele[0].getRandomAllele, max_siblings,
max_depth)
elif method == "ramped":
if Util.randomFlipCoin(0.5):
root = GTree.buildGTreeGrow(0, allele[0].getRandomAllele,
max_siblings, max_depth)
else:
root = GTree.buildGTreeFull(0, allele[0].getRandomAllele,
max_siblings, max_depth)
else:
Util.raiseException("Unknown tree initialization method [%s] !" %
method)
genome.setRoot(root)
genome.processNodes()
assert genome.getHeight() <= max_depth
def GTreeInitializatorAllele(genome, **args):
""" Allele initialization function of GTree
To use this initializator, you must specify the *allele* genome parameter with the
:class:`GAllele.GAlleles` instance.
.. warning:: the :class:`GAllele.GAlleles` instance **must** have the homogeneous flag enabled
.. versionadded:: 0.6
The *GTreeInitializatorAllele* function.
"""
max_depth = genome.getParam("max_depth", 5)
max_siblings = genome.getParam("max_siblings", 2)
method = genome.getParam("method", "grow")
allele = genome.getParam("allele", None)
if allele is None:
Util.raiseException(
"to use the GTreeInitializatorAllele, you must specify the 'allele' parameter")
if not allele.homogeneous:
Util.raiseException(
"to use the GTreeInitializatorAllele, the 'allele' must be homogeneous")
if method == "grow":
root = GTree.buildGTreeGrow(
0, allele[0].getRandomAllele, max_siblings, max_depth)
elif method == "full":
root = GTree.buildGTreeFull(
0, allele[0].getRandomAllele, max_siblings, max_depth)
elif method == "ramped":
if Util.randomFlipCoin(0.5):
root = GTree.buildGTreeGrow(
0, allele[0].getRandomAllele, max_siblings, max_depth)
else:
root = GTree.buildGTreeFull(
0, allele[0].getRandomAllele, max_siblings, max_depth)
else:
Util.raiseException(
"Unknown tree initialization method [%s] !" % method)
genome.setRoot(root)
genome.processNodes()
assert genome.getHeight() <= max_depth
def getMatrixDirectly_and_feature(ind):
import GTree
arrays = []
feature = []
prefixnum = 0
features = gol.get_val("feature_method")
classes = gol.get_val("classes")
MaxDeapth = gol.get_val("maxDeap")
New_Ind = GTree.GTreeGP()
for i in xrange(len(ind.nodes_list)):
if ind.nodes_list[i].getType() == nodeType["NONTERMINAL"]:
prefixnum = prefixnum + 1
for j in xrange(0, len(classes)):
locals()[classes[j]] = classes[j]
New_Ind.setRoot(ind.nodes_list[i])
array = eval(New_Ind.getCompiledCode())
arrays.append(list(array))
else:
arrays.append(list(ind.nodes_list[i].getData()))
for i in xrange(len(arrays)):
for j in xrange(len(features)):
if features[j] in arrays[i]:
feature.append(features[j])
arrays[i].remove(features[j])
pre_order = ind.nodes_list
cem = CEM(MaxDeapth, classes, prefixnum)
cem.construct_tree(pre_order, arrays)
ecocMatrix = np.array(cem.getMatrix())
feature = np.array(feature)
#1.There being a column with all 0 or 1 or -1
deletes = LC.zeroColumn(ecocMatrix)
ecocMatrix = np.delete(ecocMatrix, deletes, axis=1)
feature = np.delete(feature, deletes, axis=0)
#2.There being a column that is lack of 1 or -1
deletes = LC.onlyOneColumn(ecocMatrix)
ecocMatrix = np.delete(ecocMatrix, deletes, axis=1)
feature = np.delete(feature, deletes, axis=0)
#3.Two columns having the same numbers
deletes = LC.sameColumns(ecocMatrix, feature)
ecocMatrix = np.delete(ecocMatrix, deletes, axis=1)
feature = np.delete(feature, deletes, axis=0)
#4.Two columns having the opposite numbers
deletes = LC.opstColumns(ecocMatrix, feature)
ecocMatrix = np.delete(ecocMatrix, deletes, axis=1)
feature = np.delete(feature, deletes, axis=0)
#############################
return ecocMatrix, feature
def GTreeGPMutatorSubtree(genome, **args):
""" The mutator of GTreeGP, Subtree Mutator
This mutator will recreate random subtree of the tree using the grow algorithm.
.. versionadded:: 0.6
The *GTreeGPMutatorSubtree* function
"""
if args["pmut"] <= 0.0:
return 0
ga_engine = args["ga_engine"]
max_depth = genome.getParam("max_depth", None)
mutations = 0
if max_depth is None:
Util.raiseException(
"You must specify the max_depth genome parameter !", ValueError)
if max_depth < 0:
Util.raiseException(
"The max_depth must be >= 1, if you want to use GTreeGPMutatorSubtree crossover !",
ValueError)
branch_list = genome.nodes_branch
elements = len(branch_list)
for i in xrange(elements):
node = branch_list[i]
assert node is not None
if Util.randomFlipCoin(args["pmut"]):
depth = genome.getNodeDepth(node)
mutations += 1
root_subtree = GTree.buildGTreeGPGrow(ga_engine, 0,
max_depth - depth)
node_parent = node.getParent()
if node_parent is None:
genome.setRoot(root_subtree)
genome.processNodes()
return mutations
else:
root_subtree.setParent(node_parent)
node_parent.replaceChild(node, root_subtree)
genome.processNodes()
return int(mutations)
def GTreeGPMutatorSubtree(genome, **args):
""" The mutator of GTreeGP, Subtree Mutator
This mutator will recreate random subtree of the tree using the grow algorithm.
.. versionadded:: 0.6
The *GTreeGPMutatorSubtree* function
"""
if args["pmut"] <= 0.0:
return 0
ga_engine = args["ga_engine"]
max_depth = genome.getParam("max_depth", None)
mutations = 0
if max_depth is None:
Util.raiseException(
"You must specify the max_depth genome parameter !", ValueError)
if max_depth < 0:
Util.raiseException(
"The max_depth must be >= 1, if you want to use GTreeGPMutatorSubtree crossover !", ValueError)
branch_list = genome.nodes_branch
elements = len(branch_list)
for i in xrange(elements):
node = branch_list[i]
assert node is not None
if Util.randomFlipCoin(args["pmut"]):
depth = genome.getNodeDepth(node)
mutations += 1
root_subtree = GTree.buildGTreeGPGrow(
ga_engine, 0, max_depth - depth)
node_parent = node.getParent()
if node_parent is None:
genome.setRoot(root_subtree)
genome.processNodes()
return mutations
else:
root_subtree.setParent(node_parent)
node_parent.replaceChild(node, root_subtree)
genome.processNodes()
return int(mutations)
