def make_tree(X, C, method='single'):
if method == 'single':
tree = to_tree(single(C))
elif method == 'ward':
tree = to_tree(ward(X))
elif method == 'average':
tree = to_tree(average(C))
return Tree(root=construct_node(tree))
def preorder_indent(tree: Tree, position: Tree.Position, depth: int):
"""
Print preorder representation of subtree of T rooted at p at depth depth
:param tree: tree
:param position: root
:param depth: depth
"""
print(2 * depth * " ", str(position.element()))
for c in tree.children(position):
preorder_indent(tree, c, depth + 1)
def parenthesis(tree: Tree, position: Tree.Position):
"""
Print parenthesized representation of tree rooted at the position
:param tree: tree
:param position: position
:return:
"""
print(position.element(), end="")
if not tree.is_leaf(position):
first_time = Tree
for c in tree.children(position):
if first_time:
print("(", end="")
else:
print(",", end=" ")
first_time = False
parenthesis(tree, c)
print(")", end="")
def preorder_label(tree: Tree, position: Tree.Position, depth: int, path: [int]):
"""
Print preorder representation of subtree of T rooted at p at depth depth
:param tree: tree
:param position: root
:param depth: depth
:param path: a list of ints to represent the path of the position
"""
label = ".".join([str(j+1) for j in path])
print(2 * depth * " ", label, str(position.element()))
path.append(0)
for c in tree.children(position):
preorder_label(tree, c, depth + 1, path)
path[-1] += 1
path.pop()
def test__tree__given_root__is_not_empty(self):
root = Node(0)
tree = Tree(root)
assert not tree.is_empty()
def test__tree__given_no_root__is_empty(self):
tree = Tree(root=None)
assert tree.is_empty()
X += np.random.normal(scale=0.01, size=X.shape)
pca = PCA(2)
pca.fit(X)
# X = pca.transform(X)
N, D = X.shape
C = pdist(X)
tree = to_tree(single(C))
def construct_node(snode):
if snode.left is None and snode.right is None:
return TreeLeaf(snode.get_id())
node = TreeNode()
node.add_child(construct_node(snode.left))
node.add_child(construct_node(snode.right))
return node
root = construct_node(tree)
linkage_tree = Tree(root=root)
plot_tree(linkage_tree, 'linkage_induced')
if args.tree:
with open(args.tree, 'r') as fp:
ddt_tree = Tree.from_newick(fp.read())
plot_tree(ddt_tree, 'ddt_induced')
def __init__(self):
self.x_dict = LabelDictionary(
["write", "that", "code", "ROOT", "don't"])
self.train_trees = TreeList()
tree_ex1 = Tree() # container for node_list and edge_list
idx = self.x_dict.get_label_id("write")
n0 = Node(len(tree_ex1), idx) # len is 0
tree_ex1.add_node(n0)
idx = self.x_dict.get_label_id("that")
n1 = Node(len(tree_ex1), idx)
tree_ex1.add_node(n1)
idx = self.x_dict.get_label_id("code")
n2 = Node(len(tree_ex1), idx)
tree_ex1.add_node(n2)
idx = self.x_dict.get_label_id("ROOT")
n3 = Node(len(tree_ex1), idx)
tree_ex1.add_node(n3)
tree_ex1.add_edge(Edge(n0, n2))
tree_ex1.add_edge(Edge(n2, n1))
tree_ex1.add_edge(Edge(n3, n0))
self.train_trees.add_tree(tree_ex1)
tree_ex2 = Tree()
idx = self.x_dict.get_label_id("don't")
n0 = Node(len(tree_ex1), idx) # len is 0
tree_ex2.add_node(n0)
idx = self.x_dict.get_label_id("write")
n1 = Node(len(tree_ex1), idx)
tree_ex2.add_node(n1)
idx = self.x_dict.get_label_id("code")
n2 = Node(len(tree_ex1), idx)
tree_ex2.add_node(n2)
idx = self.x_dict.get_label_id("ROOT")
n3 = Node(len(tree_ex1), idx)
tree_ex2.add_node(n3)
tree_ex2.add_edge(Edge(n0, n1))
tree_ex2.add_edge(Edge(n1, n2))
tree_ex2.add_edge(Edge(n3, n0))
self.train_trees.add_tree(tree_ex2)
X += np.random.normal(scale=0.01, size=X.shape)
pca = PCA(2)
pca.fit(X)
# X = pca.transform(X)
N, D = X.shape
C = pdist(X)
tree = to_tree(single(C))
def construct_node(snode):
if snode.left is None and snode.right is None:
return TreeLeaf(snode.get_id())
node = TreeNode()
node.add_child(construct_node(snode.left))
node.add_child(construct_node(snode.right))
return node
root = construct_node(tree)
linkage_tree = Tree(root=root)
plot_tree(linkage_tree, 'linkage_induced')
if args.tree:
with open(args.tree, 'r') as fp:
ddt_tree = Tree.from_newick(fp.read())
plot_tree(ddt_tree, 'ddt_induced')
def __init__(self, file="", json=""):
"""
Constructor.
It simply calls GeneralTree constructor.
"""
Tree.__init__(self, file, json)