479 lines
18 KiB
Python
479 lines
18 KiB
Python
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"""
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This module defines export functions for decision trees.
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"""
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# Authors: Gilles Louppe <g.louppe@gmail.com>
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# Peter Prettenhofer <peter.prettenhofer@gmail.com>
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# Brian Holt <bdholt1@gmail.com>
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# Noel Dawe <noel@dawe.me>
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# Satrajit Gosh <satrajit.ghosh@gmail.com>
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# Trevor Stephens <trev.stephens@gmail.com>
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# Li Li <aiki.nogard@gmail.com>
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# License: BSD 3 clause
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from numbers import Integral
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import numpy as np
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import warnings
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from ..externals import six
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from ..utils.validation import check_is_fitted
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from . import _criterion
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from . import _tree
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def _color_brew(n):
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"""Generate n colors with equally spaced hues.
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Parameters
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----------
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n : int
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The number of colors required.
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Returns
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-------
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color_list : list, length n
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List of n tuples of form (R, G, B) being the components of each color.
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"""
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color_list = []
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# Initialize saturation & value; calculate chroma & value shift
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s, v = 0.75, 0.9
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c = s * v
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m = v - c
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for h in np.arange(25, 385, 360. / n).astype(int):
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# Calculate some intermediate values
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h_bar = h / 60.
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x = c * (1 - abs((h_bar % 2) - 1))
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# Initialize RGB with same hue & chroma as our color
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rgb = [(c, x, 0),
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(x, c, 0),
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(0, c, x),
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(0, x, c),
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(x, 0, c),
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(c, 0, x),
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(c, x, 0)]
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r, g, b = rgb[int(h_bar)]
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# Shift the initial RGB values to match value and store
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rgb = [(int(255 * (r + m))),
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(int(255 * (g + m))),
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(int(255 * (b + m)))]
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color_list.append(rgb)
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return color_list
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class Sentinel(object):
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def __repr__(self):
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return '"tree.dot"'
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SENTINEL = Sentinel()
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def export_graphviz(decision_tree, out_file=SENTINEL, max_depth=None,
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feature_names=None, class_names=None, label='all',
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filled=False, leaves_parallel=False, impurity=True,
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node_ids=False, proportion=False, rotate=False,
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rounded=False, special_characters=False, precision=3):
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"""Export a decision tree in DOT format.
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This function generates a GraphViz representation of the decision tree,
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which is then written into `out_file`. Once exported, graphical renderings
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can be generated using, for example::
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$ dot -Tps tree.dot -o tree.ps (PostScript format)
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$ dot -Tpng tree.dot -o tree.png (PNG format)
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The sample counts that are shown are weighted with any sample_weights that
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might be present.
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Read more in the :ref:`User Guide <tree>`.
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Parameters
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----------
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decision_tree : decision tree classifier
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The decision tree to be exported to GraphViz.
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out_file : file object or string, optional (default='tree.dot')
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Handle or name of the output file. If ``None``, the result is
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returned as a string. This will the default from version 0.20.
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max_depth : int, optional (default=None)
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The maximum depth of the representation. If None, the tree is fully
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generated.
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feature_names : list of strings, optional (default=None)
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Names of each of the features.
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class_names : list of strings, bool or None, optional (default=None)
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Names of each of the target classes in ascending numerical order.
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Only relevant for classification and not supported for multi-output.
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If ``True``, shows a symbolic representation of the class name.
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label : {'all', 'root', 'none'}, optional (default='all')
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Whether to show informative labels for impurity, etc.
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Options include 'all' to show at every node, 'root' to show only at
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the top root node, or 'none' to not show at any node.
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filled : bool, optional (default=False)
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When set to ``True``, paint nodes to indicate majority class for
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classification, extremity of values for regression, or purity of node
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for multi-output.
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leaves_parallel : bool, optional (default=False)
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When set to ``True``, draw all leaf nodes at the bottom of the tree.
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impurity : bool, optional (default=True)
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When set to ``True``, show the impurity at each node.
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node_ids : bool, optional (default=False)
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When set to ``True``, show the ID number on each node.
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proportion : bool, optional (default=False)
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When set to ``True``, change the display of 'values' and/or 'samples'
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to be proportions and percentages respectively.
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rotate : bool, optional (default=False)
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When set to ``True``, orient tree left to right rather than top-down.
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rounded : bool, optional (default=False)
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When set to ``True``, draw node boxes with rounded corners and use
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Helvetica fonts instead of Times-Roman.
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special_characters : bool, optional (default=False)
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When set to ``False``, ignore special characters for PostScript
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compatibility.
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precision : int, optional (default=3)
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Number of digits of precision for floating point in the values of
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impurity, threshold and value attributes of each node.
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Returns
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-------
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dot_data : string
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String representation of the input tree in GraphViz dot format.
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Only returned if ``out_file`` is None.
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.. versionadded:: 0.18
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Examples
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--------
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>>> from sklearn.datasets import load_iris
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>>> from sklearn import tree
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>>> clf = tree.DecisionTreeClassifier()
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>>> iris = load_iris()
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>>> clf = clf.fit(iris.data, iris.target)
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>>> tree.export_graphviz(clf,
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... out_file='tree.dot') # doctest: +SKIP
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"""
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def get_color(value):
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# Find the appropriate color & intensity for a node
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if colors['bounds'] is None:
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# Classification tree
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color = list(colors['rgb'][np.argmax(value)])
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sorted_values = sorted(value, reverse=True)
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if len(sorted_values) == 1:
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alpha = 0
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else:
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alpha = int(np.round(255 * (sorted_values[0] -
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sorted_values[1]) /
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(1 - sorted_values[1]), 0))
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else:
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# Regression tree or multi-output
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color = list(colors['rgb'][0])
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alpha = int(np.round(255 * ((value - colors['bounds'][0]) /
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(colors['bounds'][1] -
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colors['bounds'][0])), 0))
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# Return html color code in #RRGGBBAA format
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color.append(alpha)
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hex_codes = [str(i) for i in range(10)]
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hex_codes.extend(['a', 'b', 'c', 'd', 'e', 'f'])
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color = [hex_codes[c // 16] + hex_codes[c % 16] for c in color]
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return '#' + ''.join(color)
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def node_to_str(tree, node_id, criterion):
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# Generate the node content string
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if tree.n_outputs == 1:
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value = tree.value[node_id][0, :]
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else:
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value = tree.value[node_id]
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# Should labels be shown?
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labels = (label == 'root' and node_id == 0) or label == 'all'
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# PostScript compatibility for special characters
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if special_characters:
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characters = ['#', '<SUB>', '</SUB>', '≤', '<br/>', '>']
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node_string = '<'
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else:
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characters = ['#', '[', ']', '<=', '\\n', '"']
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node_string = '"'
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# Write node ID
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if node_ids:
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if labels:
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node_string += 'node '
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node_string += characters[0] + str(node_id) + characters[4]
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# Write decision criteria
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if tree.children_left[node_id] != _tree.TREE_LEAF:
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# Always write node decision criteria, except for leaves
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if feature_names is not None:
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feature = feature_names[tree.feature[node_id]]
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else:
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feature = "X%s%s%s" % (characters[1],
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tree.feature[node_id],
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characters[2])
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node_string += '%s %s %s%s' % (feature,
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characters[3],
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round(tree.threshold[node_id],
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precision),
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characters[4])
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# Write impurity
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if impurity:
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if isinstance(criterion, _criterion.FriedmanMSE):
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criterion = "friedman_mse"
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elif not isinstance(criterion, six.string_types):
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criterion = "impurity"
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if labels:
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node_string += '%s = ' % criterion
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node_string += (str(round(tree.impurity[node_id], precision)) +
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characters[4])
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# Write node sample count
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if labels:
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node_string += 'samples = '
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if proportion:
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percent = (100. * tree.n_node_samples[node_id] /
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float(tree.n_node_samples[0]))
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node_string += (str(round(percent, 1)) + '%' +
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characters[4])
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else:
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node_string += (str(tree.n_node_samples[node_id]) +
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characters[4])
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# Write node class distribution / regression value
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if proportion and tree.n_classes[0] != 1:
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# For classification this will show the proportion of samples
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value = value / tree.weighted_n_node_samples[node_id]
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if labels:
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node_string += 'value = '
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if tree.n_classes[0] == 1:
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# Regression
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value_text = np.around(value, precision)
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elif proportion:
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# Classification
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value_text = np.around(value, precision)
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elif np.all(np.equal(np.mod(value, 1), 0)):
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# Classification without floating-point weights
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value_text = value.astype(int)
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else:
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# Classification with floating-point weights
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value_text = np.around(value, precision)
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# Strip whitespace
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value_text = str(value_text.astype('S32')).replace("b'", "'")
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value_text = value_text.replace("' '", ", ").replace("'", "")
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if tree.n_classes[0] == 1 and tree.n_outputs == 1:
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value_text = value_text.replace("[", "").replace("]", "")
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value_text = value_text.replace("\n ", characters[4])
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node_string += value_text + characters[4]
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# Write node majority class
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if (class_names is not None and
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tree.n_classes[0] != 1 and
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tree.n_outputs == 1):
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# Only done for single-output classification trees
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if labels:
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node_string += 'class = '
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if class_names is not True:
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class_name = class_names[np.argmax(value)]
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else:
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class_name = "y%s%s%s" % (characters[1],
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np.argmax(value),
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characters[2])
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node_string += class_name
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# Clean up any trailing newlines
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if node_string[-2:] == '\\n':
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node_string = node_string[:-2]
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if node_string[-5:] == '<br/>':
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node_string = node_string[:-5]
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return node_string + characters[5]
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def recurse(tree, node_id, criterion, parent=None, depth=0):
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if node_id == _tree.TREE_LEAF:
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raise ValueError("Invalid node_id %s" % _tree.TREE_LEAF)
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left_child = tree.children_left[node_id]
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right_child = tree.children_right[node_id]
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# Add node with description
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if max_depth is None or depth <= max_depth:
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# Collect ranks for 'leaf' option in plot_options
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if left_child == _tree.TREE_LEAF:
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ranks['leaves'].append(str(node_id))
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elif str(depth) not in ranks:
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ranks[str(depth)] = [str(node_id)]
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else:
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ranks[str(depth)].append(str(node_id))
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out_file.write('%d [label=%s'
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% (node_id,
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node_to_str(tree, node_id, criterion)))
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if filled:
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# Fetch appropriate color for node
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if 'rgb' not in colors:
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# Initialize colors and bounds if required
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colors['rgb'] = _color_brew(tree.n_classes[0])
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if tree.n_outputs != 1:
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# Find max and min impurities for multi-output
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colors['bounds'] = (np.min(-tree.impurity),
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np.max(-tree.impurity))
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elif (tree.n_classes[0] == 1 and
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len(np.unique(tree.value)) != 1):
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# Find max and min values in leaf nodes for regression
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colors['bounds'] = (np.min(tree.value),
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np.max(tree.value))
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if tree.n_outputs == 1:
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node_val = (tree.value[node_id][0, :] /
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tree.weighted_n_node_samples[node_id])
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if tree.n_classes[0] == 1:
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# Regression
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node_val = tree.value[node_id][0, :]
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else:
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# If multi-output color node by impurity
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node_val = -tree.impurity[node_id]
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out_file.write(', fillcolor="%s"' % get_color(node_val))
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out_file.write('] ;\n')
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if parent is not None:
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# Add edge to parent
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out_file.write('%d -> %d' % (parent, node_id))
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if parent == 0:
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# Draw True/False labels if parent is root node
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angles = np.array([45, -45]) * ((rotate - .5) * -2)
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out_file.write(' [labeldistance=2.5, labelangle=')
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if node_id == 1:
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out_file.write('%d, headlabel="True"]' % angles[0])
|
||
|
|
else:
|
||
|
|
out_file.write('%d, headlabel="False"]' % angles[1])
|
||
|
|
out_file.write(' ;\n')
|
||
|
|
|
||
|
|
if left_child != _tree.TREE_LEAF:
|
||
|
|
recurse(tree, left_child, criterion=criterion, parent=node_id,
|
||
|
|
depth=depth + 1)
|
||
|
|
recurse(tree, right_child, criterion=criterion, parent=node_id,
|
||
|
|
depth=depth + 1)
|
||
|
|
|
||
|
|
else:
|
||
|
|
ranks['leaves'].append(str(node_id))
|
||
|
|
|
||
|
|
out_file.write('%d [label="(...)"' % node_id)
|
||
|
|
if filled:
|
||
|
|
# color cropped nodes grey
|
||
|
|
out_file.write(', fillcolor="#C0C0C0"')
|
||
|
|
out_file.write('] ;\n' % node_id)
|
||
|
|
|
||
|
|
if parent is not None:
|
||
|
|
# Add edge to parent
|
||
|
|
out_file.write('%d -> %d ;\n' % (parent, node_id))
|
||
|
|
|
||
|
|
check_is_fitted(decision_tree, 'tree_')
|
||
|
|
own_file = False
|
||
|
|
return_string = False
|
||
|
|
try:
|
||
|
|
if out_file == SENTINEL:
|
||
|
|
warnings.warn("out_file can be set to None starting from 0.18. "
|
||
|
|
"This will be the default in 0.20.",
|
||
|
|
DeprecationWarning)
|
||
|
|
out_file = "tree.dot"
|
||
|
|
|
||
|
|
if isinstance(out_file, six.string_types):
|
||
|
|
if six.PY3:
|
||
|
|
out_file = open(out_file, "w", encoding="utf-8")
|
||
|
|
else:
|
||
|
|
out_file = open(out_file, "wb")
|
||
|
|
own_file = True
|
||
|
|
|
||
|
|
if out_file is None:
|
||
|
|
return_string = True
|
||
|
|
out_file = six.StringIO()
|
||
|
|
|
||
|
|
if isinstance(precision, Integral):
|
||
|
|
if precision < 0:
|
||
|
|
raise ValueError("'precision' should be greater or equal to 0."
|
||
|
|
" Got {} instead.".format(precision))
|
||
|
|
else:
|
||
|
|
raise ValueError("'precision' should be an integer. Got {}"
|
||
|
|
" instead.".format(type(precision)))
|
||
|
|
|
||
|
|
# Check length of feature_names before getting into the tree node
|
||
|
|
# Raise error if length of feature_names does not match
|
||
|
|
# n_features_ in the decision_tree
|
||
|
|
if feature_names is not None:
|
||
|
|
if len(feature_names) != decision_tree.n_features_:
|
||
|
|
raise ValueError("Length of feature_names, %d "
|
||
|
|
"does not match number of features, %d"
|
||
|
|
% (len(feature_names),
|
||
|
|
decision_tree.n_features_))
|
||
|
|
|
||
|
|
# The depth of each node for plotting with 'leaf' option
|
||
|
|
ranks = {'leaves': []}
|
||
|
|
# The colors to render each node with
|
||
|
|
colors = {'bounds': None}
|
||
|
|
|
||
|
|
out_file.write('digraph Tree {\n')
|
||
|
|
|
||
|
|
# Specify node aesthetics
|
||
|
|
out_file.write('node [shape=box')
|
||
|
|
rounded_filled = []
|
||
|
|
if filled:
|
||
|
|
rounded_filled.append('filled')
|
||
|
|
if rounded:
|
||
|
|
rounded_filled.append('rounded')
|
||
|
|
if len(rounded_filled) > 0:
|
||
|
|
out_file.write(', style="%s", color="black"'
|
||
|
|
% ", ".join(rounded_filled))
|
||
|
|
if rounded:
|
||
|
|
out_file.write(', fontname=helvetica')
|
||
|
|
out_file.write('] ;\n')
|
||
|
|
|
||
|
|
# Specify graph & edge aesthetics
|
||
|
|
if leaves_parallel:
|
||
|
|
out_file.write('graph [ranksep=equally, splines=polyline] ;\n')
|
||
|
|
if rounded:
|
||
|
|
out_file.write('edge [fontname=helvetica] ;\n')
|
||
|
|
if rotate:
|
||
|
|
out_file.write('rankdir=LR ;\n')
|
||
|
|
|
||
|
|
# Now recurse the tree and add node & edge attributes
|
||
|
|
if isinstance(decision_tree, _tree.Tree):
|
||
|
|
recurse(decision_tree, 0, criterion="impurity")
|
||
|
|
else:
|
||
|
|
recurse(decision_tree.tree_, 0, criterion=decision_tree.criterion)
|
||
|
|
|
||
|
|
# If required, draw leaf nodes at same depth as each other
|
||
|
|
if leaves_parallel:
|
||
|
|
for rank in sorted(ranks):
|
||
|
|
out_file.write("{rank=same ; " +
|
||
|
|
"; ".join(r for r in ranks[rank]) + "} ;\n")
|
||
|
|
out_file.write("}")
|
||
|
|
|
||
|
|
if return_string:
|
||
|
|
return out_file.getvalue()
|
||
|
|
|
||
|
|
finally:
|
||
|
|
if own_file:
|
||
|
|
out_file.close()
|