"""
=========================================
Understanding the decision tree structure
=========================================
The decision tree structure can be analysed to gain further insight on the
relation between the features and the target to predict. In this example, we
show how to retrieve:
- the binary tree structure;
- the depth of each node and whether or not it's a leaf;
- the nodes that were reached by a sample using the ``decision_path`` method;
- the leaf that was reached by a sample using the apply method;
- the rules that were used to predict a sample;
- the decision path shared by a group of samples.
"""
import numpy as np
from matplotlib import pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.datasets import load_iris
from sklearn.tree import DecisionTreeClassifier
from sklearn import tree
##############################################################################
# Train tree classifier
# ---------------------
# First, we fit a :class:`~sklearn.tree.DecisionTreeClassifier` using the
# :func:`~sklearn.datasets.load_iris` dataset.
iris = load_iris()
X = iris.data
y = iris.target
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
clf = DecisionTreeClassifier(max_leaf_nodes=3, random_state=0)
clf.fit(X_train, y_train)
##############################################################################
# Tree structure
# --------------
#
# The decision classifier has an attribute called ``tree_`` which allows access
# to low level attributes such as ``node_count``, the total number of nodes,
# and ``max_depth``, the maximal depth of the tree. It also stores the
# entire binary tree structure, represented as a number of parallel arrays. The
# i-th element of each array holds information about the node ``i``. Node 0 is
# the tree's root. Some of the arrays only apply to either leaves or split
# nodes. In this case the values of the nodes of the other type is arbitrary.
# For example, the arrays ``feature`` and ``threshold`` only apply to split
# nodes. The values for leaf nodes in these arrays are therefore arbitrary.
#
# Among these arrays, we have:
#
# - ``children_left[i]``: id of the left child of node ``i`` or -1 if leaf
# node
# - ``children_right[i]``: id of the right child of node ``i`` or -1 if leaf
# node
# - ``feature[i]``: feature used for splitting node ``i``
# - ``threshold[i]``: threshold value at node ``i``
# - ``n_node_samples[i]``: the number of of training samples reaching node
# ``i``
# - ``impurity[i]``: the impurity at node ``i``
#
# Using the arrays, we can traverse the tree structure to compute various
# properties. Below, we will compute the depth of each node and whether or not
# it is a leaf.
n_nodes = clf.tree_.node_count
children_left = clf.tree_.children_left
children_right = clf.tree_.children_right
feature = clf.tree_.feature
threshold = clf.tree_.threshold
node_depth = np.zeros(shape=n_nodes, dtype=np.int64)
is_leaves = np.zeros(shape=n_nodes, dtype=bool)
stack = [(0, 0)] # start with the root node id (0) and its depth (0)
while len(stack) > 0:
# `pop` ensures each node is only visited once
node_id, depth = stack.pop()
node_depth[node_id] = depth
# If the left and right child of a node is not the same we have a split
# node
is_split_node = children_left[node_id] != children_right[node_id]
# If a split node, append left and right children and depth to `stack`
# so we can loop through them
if is_split_node:
stack.append((children_left[node_id], depth + 1))
stack.append((children_right[node_id], depth + 1))
else:
is_leaves[node_id] = True
print("The binary tree structure has {n} nodes and has "
"the following tree structure:\n".format(n=n_nodes))
for i in range(n_nodes):
if is_leaves[i]:
print("{space}node={node} is a leaf node.".format(
space=node_depth[i] * "\t", node=i))
else:
print("{space}node={node} is a split node: "
"go to node {left} if X[:, {feature}] <= {threshold} "
"else to node {right}.".format(
space=node_depth[i] * "\t",
node=i,
left=children_left[i],
feature=feature[i],
threshold=threshold[i],
right=children_right[i]))
##############################################################################
# We can compare the above output to the plot of the decision tree.
tree.plot_tree(clf)
plt.show()
##############################################################################
# Decision path
# -------------
#
# We can also retrieve the decision path of samples of interest. The
# ``decision_path`` method outputs an indicator matrix that allows us to
# retrieve the nodes the samples of interest traverse through. A non zero
# element in the indicator matrix at position ``(i, j)`` indicates that
# the sample ``i`` goes through the node ``j``. Or, for one sample ``i``, the
# positions of the non zero elements in row ``i`` of the indicator matrix
# designate the ids of the nodes that sample goes through.
#
# The leaf ids reached by samples of interest can be obtained with the
# ``apply`` method. This returns an array of the node ids of the leaves
# reached by each sample of interest. Using the leaf ids and the
# ``decision_path`` we can obtain the splitting conditions that were used to
# predict a sample or a group of samples. First, let's do it for one sample.
# Note that ``node_index`` is a sparse matrix.
node_indicator = clf.decision_path(X_test)
leaf_id = clf.apply(X_test)
sample_id = 0
# obtain ids of the nodes `sample_id` goes through, i.e., row `sample_id`
node_index = node_indicator.indices[node_indicator.indptr[sample_id]:
node_indicator.indptr[sample_id + 1]]
print('Rules used to predict sample {id}:\n'.format(id=sample_id))
for node_id in node_index:
# continue to the next node if it is a leaf node
if leaf_id[sample_id] == node_id:
continue
# check if value of the split feature for sample 0 is below threshold
if (X_test[sample_id, feature[node_id]] <= threshold[node_id]):
threshold_sign = "<="
else:
threshold_sign = ">"
print("decision node {node} : (X_test[{sample}, {feature}] = {value}) "
"{inequality} {threshold})".format(
node=node_id,
sample=sample_id,
feature=feature[node_id],
value=X_test[sample_id, feature[node_id]],
inequality=threshold_sign,
threshold=threshold[node_id]))
##############################################################################
# For a group of samples, we can determine the common nodes the samples go
# through.
sample_ids = [0, 1]
# boolean array indicating the nodes both samples go through
common_nodes = (node_indicator.toarray()[sample_ids].sum(axis=0) ==
len(sample_ids))
# obtain node ids using position in array
common_node_id = np.arange(n_nodes)[common_nodes]
print("\nThe following samples {samples} share the node(s) {nodes} in the "
"tree.".format(samples=sample_ids, nodes=common_node_id))
print("This is {prop}% of all nodes.".format(
prop=100 * len(common_node_id) / n_nodes))