Make project python package friendly

- Add setup.py
- Move classes to module files
- Move tests folder inside module folder

.travis.yml

@@ -10,4 +10,4 @@ notifications:
     on_success: never # default: change
     on_failure: always # default: always
 # command to run tests
-script: python -m unittest tests.Stree_test tests.Snode_test
+script: python -m unittest stree.tests

README.md

@@ -4,7 +4,13 @@
 
 Oblique Tree classifier based on SVM nodes
 
-![Stree](example.png)
+![Stree](https://raw.github.com/doctorado-ml/stree/master/example.png)
+
+## Installation
+
+```bash
+pip install git+https://github.com/doctorado-ml/stree
+```
 
 ## Examples
 
@@ -24,12 +30,12 @@ Oblique Tree classifier based on SVM nodes
 
 ### Command line
 
-```python
+```bash
 python main.py
 ```
 
 ## Tests
 
-```python
-python -m unittest -v tests.Stree_test tests.Snode_test
+```bash
+python -m unittest -v stree.tests
 ```

main.py

@@ -1,6 +1,6 @@
 import time
 from sklearn.model_selection import train_test_split
-from trees.Stree import Stree
+from stree import Stree
 
 random_state=1
 

setup.py

@@ -0,0 +1,40 @@
+import setuptools
+
+from stree import __author__, __version__
+
+
+def readme():
+    with open('README.md') as f:
+        return f.read()
+
+
+setuptools.setup(
+    name='STree',
+    version=__version__,
+    license='MIT License',
+    description='a python interface to oblique decision tree implementations',
+    long_description=readme(),
+    long_description_content_type='text/markdown',
+    packages=['stree'],
+    url='https://github.com/doctorado-ml/stree',
+    author=__author__,
+    author_email='ricardo.montanana@alu.uclm.es',
+    keywords='scikit-learn oblique-classifier oblique-decision-tree decision-tree svm svc',
+    classifiers=[
+        'Development Status :: 4 - Beta',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 3.7',
+        'Natural Language :: English',
+        'Topic :: Scientific/Engineering :: Artificial Intelligence',
+        'Intended Audience :: Science/Research'
+    ],
+    install_requires=[
+        'scikit-learn>=0.23.0',
+        'numpy',
+        'matplotlib',
+        'ipympl'
+    ],
+    data_files=[('data', ['data/.gitignore'])],
+    test_suite="stree.tests",
+    zip_safe=False
+)

stree/Strees.py

@@ -8,20 +8,100 @@ Uses LinearSVC
 '''
 
 import typing
+import os
 
 import numpy as np
 from sklearn.base import BaseEstimator, ClassifierMixin
 from sklearn.svm import LinearSVC
 from sklearn.utils.validation import check_X_y, check_array, check_is_fitted
-from trees.Snode import Snode
-from trees.Siterator import Siterator
 
+class Snode:
+    def __init__(self, clf: LinearSVC, X: np.ndarray, y: np.ndarray, title: str):
+        self._clf = clf
+        self._vector = None if clf is None else clf.coef_
+        self._interceptor = 0. if clf is None else clf.intercept_
+        self._title = title
+        self._belief = 0.  # belief of the prediction in a leaf node based on samples
+        # Only store dataset in Testing 
+        self._X = X if os.environ.get('TESTING', 'NS') != 'NS' else None
+        self._y = y
+        self._down = None
+        self._up = None
+        self._class = None
+
+    @classmethod
+    def copy(cls, node: 'Snode') -> 'Snode':
+        return cls(node._clf, node._X, node._y, node._title)
+
+    def set_down(self, son):
+        self._down = son
+
+    def set_up(self, son):
+        self._up = son
+
+    def is_leaf(self) -> bool:
+        return self._up is None and self._down is None
+
+    def get_down(self) -> 'Snode':
+        return self._down
+
+    def get_up(self) -> 'Snode':
+        return self._up
+
+    def make_predictor(self):
+        """Compute the class of the predictor and its belief based on the subdataset of the node
+        only if it is a leaf
+        """
+        if not self.is_leaf():
+            return
+        classes, card = np.unique(self._y, return_counts=True)
+        if len(classes) > 1:
+            max_card = max(card)
+            min_card = min(card)
+            try:
+                self._belief = max_card / (max_card + min_card)
+            except:
+                self._belief = 0.
+            self._class = classes[card == max_card][0]
+        else:
+            self._belief = 1
+            self._class = classes[0]
+
+    def __str__(self) -> str:
+        if self.is_leaf():
+            return f"{self._title} - Leaf class={self._class} belief={self._belief:.6f} counts={np.unique(self._y, return_counts=True)}"
+        else:
+            return f"{self._title}"
+
+
+class Siterator:
+    """Stree preorder iterator
+    """
+
+    def __init__(self, tree: Snode):
+        self._stack = []
+        self._push(tree)
+
+    def __iter__(self):
+        return self
+
+    def _push(self, node: Snode):
+        if node is not None:
+            self._stack.append(node)
+
+    def __next__(self) -> Snode:
+        if len(self._stack) == 0:
+            raise StopIteration()
+        node = self._stack.pop()
+        self._push(node.get_up())
+        self._push(node.get_down())
+        return node
 
 class Stree(BaseEstimator, ClassifierMixin):
     """
     """
 
-    def __init__(self, C: float=1.0, max_iter: int = 1000, random_state: int = 0, use_predictions: bool = False):
+    def __init__(self, C: float = 1.0, max_iter: int = 1000, random_state: int = 0, use_predictions: bool = False):
         self._max_iter = max_iter
         self._C = C
         self._random_state = random_state
@@ -77,12 +157,14 @@ class Stree(BaseEstimator, ClassifierMixin):
     def _build_predictor(self):
         """Process the leaves to make them predictors
         """
+
         def run_tree(node: Snode):
             if node.is_leaf():
                 node.make_predictor()
                 return
             run_tree(node.get_down())
             run_tree(node.get_up())
+
         run_tree(self._tree)
 
     def train(self, X: np.ndarray, y: np.ndarray, title: str = 'root') -> Snode:
@@ -121,6 +203,7 @@ class Stree(BaseEstimator, ClassifierMixin):
             k, l = predict_class(d, i_d, node.get_down())
             m, n = predict_class(u, i_u, node.get_up())
             return np.append(k, m), np.append(l, n)
+
         # sklearn check
         check_is_fitted(self)
         # Input validation
@@ -136,6 +219,7 @@ class Stree(BaseEstimator, ClassifierMixin):
         :param X: dataset
         :type X: np.array
         """
+
         def predict_class(xp: np.array, indices: np.array, dist: np.array, node: Snode) -> np.array:
             """Run the tree to compute predictions
 
@@ -161,6 +245,7 @@ class Stree(BaseEstimator, ClassifierMixin):
             k, l = predict_class(d, i_d, r_d, node.get_down())
             m, n = predict_class(u, i_u, r_u, node.get_up())
             return np.append(k, m), np.append(l, n)
+
         # sklearn check
         check_is_fitted(self)
         # Input validation
@@ -217,5 +302,10 @@ class Stree(BaseEstimator, ClassifierMixin):
     def save_sub_datasets(self):
         """Save the every dataset stored in the tree to check with manual classifier
         """
+        if not os.path.isdir(self.__folder):
+            os.mkdir(self.__folder)
         with open(self.get_catalog_name(), 'w', encoding='utf-8') as catalog:
             self._save_datasets(self._tree, catalog, 1)
+
+
+

stree/Strees_grapher.py

@@ -6,12 +6,14 @@ __version__ = "0.9"
 Plot 3D views of nodes in Stree
 '''
 
-import numpy as np
-import matplotlib.pyplot as plt
-from mpl_toolkits.mplot3d import Axes3D
-from trees.Snode import Snode
-from trees.Stree import Stree
+import os
 
+import matplotlib.pyplot as plt
+import numpy as np
+from sklearn.decomposition import PCA
+from mpl_toolkits.mplot3d import Axes3D
+
+from .Strees import Stree, Snode, Siterator
 
 class Snode_graph(Snode):
 
@@ -68,6 +70,7 @@ class Snode_graph(Snode):
             # get the splitting hyperplane
             def hyperplane(x, y): return (-self._interceptor - self._vector[0][0] * x
                                           - self._vector[0][1] * y) / self._vector[0][2]
+
             tmpx = np.linspace(self._X[:, 0].min(), self._X[:, 0].max())
             tmpy = np.linspace(self._X[:, 1].min(), self._X[:, 1].max())
             xx, yy = np.meshgrid(tmpx, tmpy)
@@ -93,3 +96,87 @@ class Snode_graph(Snode):
         ax.set_ylabel('X1')
         ax.set_zlabel('X2')
         plt.show()
+
+class Stree_grapher(Stree):
+    """Build 3d graphs of any dataset, if it's more than 3 features PCA shall
+    make its magic
+    """
+
+    def __init__(self, params: dict):
+        self._plot_size = (8, 8)
+        self._tree_gr = None
+        # make Snode store X's
+        os.environ['TESTING'] = '1'
+        self._fitted = False
+        self._pca = None
+        super().__init__(**params)
+
+    def __del__(self):
+        try:
+            os.environ.pop('TESTING')
+        except:
+            pass
+        plt.close('all')
+
+    def _copy_tree(self, node: Snode) -> Snode_graph:
+        mirror = Snode_graph(node)
+        # clone node
+        mirror._class = node._class
+        mirror._belief = node._belief
+        if node.get_down() is not None:
+            mirror.set_down(self._copy_tree(node.get_down()))
+        if node.get_up() is not None:
+            mirror.set_up(self._copy_tree(node.get_up()))
+        return mirror
+
+    def fit(self, X: np.array, y: np.array) -> Stree:
+        """Fit the Stree and copy the tree in a Snode_graph tree
+
+        :param X: Dataset
+        :type X: np.array
+        :param y: Labels
+        :type y: np.array
+        :return: Stree model
+        :rtype: Stree
+        """
+        if X.shape[1] != 3:
+            self._pca = PCA(n_components=3)
+            X = self._pca.fit_transform(X)
+        res = super().fit(X, y)
+        self._tree_gr = self._copy_tree(self._tree)
+        self._fitted = True
+        return res
+
+    def score(self, X: np.array, y: np.array) -> float:
+        self._check_fitted()
+        if X.shape[1] != 3:
+            X = self._pca.transform(X)
+        return super().score(X, y)
+
+    def _check_fitted(self):
+        if not self._fitted:
+            raise Exception('Have to fit the grapher first!')
+
+    def save_all(self, save_folder: str = './', save_prefix: str = ''):
+        """Save all the node plots in png format, each with a sequence number
+
+        :param save_folder: folder where the plots are saved, defaults to './'
+        :type save_folder: str, optional
+        """
+        self._check_fitted()
+        seq = 1
+        for node in self:
+            node.save_hyperplane(save_folder=save_folder,
+                                 save_prefix=save_prefix, save_seq=seq)
+            seq += 1
+
+    def plot_all(self):
+        """Plots all the nodes
+        """
+        self._check_fitted()
+        for node in self:
+            node.plot_hyperplane()
+
+    def __iter__(self):
+        return Siterator(self._tree_gr)
+

stree/__init__.py

@@ -0,0 +1,4 @@
+__version__ = "0.9rc1"
+__author__ = "Ricardo Montañana Gómez"
+from .Strees import Stree, Snode, Siterator
+from .Strees_grapher import Stree_grapher, Snode_graph

stree/tests/Strees_test.py

@@ -5,7 +5,7 @@ import unittest
 import numpy as np
 from sklearn.datasets import make_classification
 
-from trees.Stree import Stree, Snode
+from stree import Stree, Snode
 
 
 class Stree_test(unittest.TestCase):
@@ -14,7 +14,7 @@ class Stree_test(unittest.TestCase):
         os.environ['TESTING'] = '1'
         self._random_state = 1
         self._clf = Stree(random_state=self._random_state,
-                            use_predictions=False)
+                          use_predictions=False)
         self._clf.fit(*self._get_Xy())
         super().__init__(*args, **kwargs)
 
@@ -163,10 +163,10 @@ class Stree_test(unittest.TestCase):
         yp = self._clf.predict_proba(X[:num, :])
         self.assertListEqual(y[:num].tolist(), yp[:, 0].tolist())
         expected_proba = [0.88395641, 0.36746962, 0.84158767, 0.34106833, 0.14269291, 0.85193236,
-                        0.29876058, 0.7282164,  0.85958616, 0.89517877, 0.99745224, 0.18860349,
-                        0.30756427, 0.8318412,  0.18981198, 0.15564624, 0.25740655, 0.22923355,
-                        0.87365959, 0.49928689, 0.95574351, 0.28761257, 0.28906333, 0.32643692,
-                        0.29788483, 0.01657364, 0.81149083]
+                          0.29876058, 0.7282164, 0.85958616, 0.89517877, 0.99745224, 0.18860349,
+                          0.30756427, 0.8318412, 0.18981198, 0.15564624, 0.25740655, 0.22923355,
+                          0.87365959, 0.49928689, 0.95574351, 0.28761257, 0.28906333, 0.32643692,
+                          0.29788483, 0.01657364, 0.81149083]
         expected = np.round(expected_proba, decimals=decimals).tolist()
         computed = np.round(yp[:, 1], decimals=decimals).tolist()
         for i in range(len(expected)):
@@ -178,9 +178,9 @@ class Stree_test(unittest.TestCase):
         coefficients to compute both predictions and splitted data
         """
         model_clf = Stree(random_state=self._random_state,
-                            use_predictions=True)
+                          use_predictions=True)
         model_computed = Stree(random_state=self._random_state,
-                            use_predictions=False)
+                               use_predictions=False)
         X, y = self._get_Xy()
         model_clf.fit(X, y)
         model_computed.fit(X, y)
@@ -201,7 +201,7 @@ class Stree_test(unittest.TestCase):
         b = use_math.score(X, y)
         self.assertEqual(
             use_clf.score(X, y),
-           b
+            b
         )
         self.assertGreater(b, .95)
 
@@ -243,7 +243,71 @@ class Stree_test(unittest.TestCase):
             computed.append(str(node))
         self.assertListEqual(expected, computed)
 
+class Snode_test(unittest.TestCase):
 
+    def __init__(self, *args, **kwargs):
+        os.environ['TESTING'] = '1'
+        self._random_state = 1
+        self._clf = Stree(random_state=self._random_state,
+                          use_predictions=True)
+        self._clf.fit(*self._get_Xy())
+        super().__init__(*args, **kwargs)
 
+    @classmethod
+    def tearDownClass(cls):
+        try:
+            os.environ.pop('TESTING')
+        except:
+            pass
 
+    def _get_Xy(self):
+        X, y = make_classification(n_samples=1500, n_features=3, n_informative=3,
+                                   n_redundant=0, n_repeated=0, n_classes=2, n_clusters_per_class=2,
+                                   class_sep=1.5, flip_y=0, weights=[0.5, 0.5], random_state=self._random_state)
+        return X, y
+
+    def test_attributes_in_leaves(self):
+        """Check if the attributes in leaves have correct values so they form a predictor
+        """
+
+        def check_leave(node: Snode):
+            if not node.is_leaf():
+                check_leave(node.get_down())
+                check_leave(node.get_up())
+                return
+            # Check Belief in leave
+            classes, card = np.unique(node._y, return_counts=True)
+            max_card = max(card)
+            min_card = min(card)
+            if len(classes) > 1:
+                try:
+                    belief = max_card / (max_card + min_card)
+                except:
+                    belief = 0.
+            else:
+                belief = 1
+            self.assertEqual(belief, node._belief)
+            # Check Class
+            class_computed = classes[card == max_card]
+            self.assertEqual(class_computed, node._class)
+
+        check_leave(self._clf._tree)
+
+    def test_nodes_coefs(self):
+        """Check if the nodes of the tree have the right attributes filled
+        """
+
+        def run_tree(node: Snode):
+            if node._belief < 1:
+                # only exclude pure leaves
+                self.assertIsNotNone(node._clf)
+                self.assertIsNotNone(node._clf.coef_)
+                self.assertIsNotNone(node._vector)
+                self.assertIsNotNone(node._interceptor)
+            if node.is_leaf():
+                return
+            run_tree(node.get_down())
+            run_tree(node.get_up())
+
+        run_tree(self._clf._tree)
 

stree/tests/__init__.py

@@ -0,0 +1 @@
+from .Strees_test import Stree_test, Snode_test

test2.ipynb

@@ -26,7 +26,8 @@
     "from sklearn.svm import LinearSVC\n",
     "from sklearn.tree import DecisionTreeClassifier\n",
     "from sklearn.datasets import make_classification, load_iris, load_wine\n",
-    "from trees.Stree import Stree\n",
+    "from sklearn.model_selection import train_test_split\n",
+    "from stree import Stree\n",
     "import time"
    ]
   },
@@ -50,14 +51,10 @@
     {
      "output_type": "stream",
      "name": "stdout",
-     "text": "Fraud: 0.173% 492\nValid: 99.827% 284315\nX.shape (1492, 28)  y.shape (1492,)\nFraud: 32.976% 492\nValid: 67.024% 1000\n"
+     "text": "Fraud: 0.173% 492\nValid: 99.827% 284315\nX.shape (1492, 28)  y.shape (1492,)\nFraud: 33.110% 494\nValid: 66.890% 998\n"
     }
    ],
    "source": [
-    "import time\n",
-    "from sklearn.model_selection import train_test_split\n",
-    "from trees.Stree import Stree\n",
-    "\n",
     "random_state=1\n",
     "\n",
     "def load_creditcard(n_examples=0):\n",
@@ -105,7 +102,7 @@
     {
      "output_type": "stream",
      "name": "stdout",
-     "text": "************** C=0.001 ****************************\nClassifier's accuracy (train): 0.9559\nClassifier's accuracy (test) : 0.9442\nroot\nroot - Down, <cgaf> - Leaf class=1 belief=0.986928 counts=(array([0, 1]), array([  4, 302]))\nroot - Up, <cgaf> - Leaf class=0 belief=0.943089 counts=(array([0, 1]), array([696,  42]))\n\n**************************************************\n************** C=0.01 ****************************\nClassifier's accuracy (train): 0.9588\nClassifier's accuracy (test) : 0.9397\nroot\nroot - Down, <cgaf> - Leaf class=1 belief=0.993443 counts=(array([0, 1]), array([  2, 303]))\nroot - Up, <cgaf> - Leaf class=0 belief=0.944520 counts=(array([0, 1]), array([698,  41]))\n\n**************************************************\n************** C=1 ****************************\nClassifier's accuracy (train): 0.9703\nClassifier's accuracy (test) : 0.9531\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([313]))\nroot - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([4]))\nroot - Up, <cgaf> - Leaf class=0 belief=0.957359 counts=(array([0, 1]), array([696,  31]))\n\n**************************************************\n************** C=5 ****************************\nClassifier's accuracy (train): 0.9703\nClassifier's accuracy (test) : 0.9531\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([313]))\nroot - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([7]))\nroot - Up, <cgaf> - Leaf class=0 belief=0.957182 counts=(array([0, 1]), array([693,  31]))\n\n**************************************************\n************** C=17 ****************************\nClassifier's accuracy (train): 0.9789\nClassifier's accuracy (test) : 0.9509\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([313]))\nroot - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([10]))\nroot - Up\nroot - Up - Down, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([4]))\nroot - Up - Up\nroot - Up - Up - Down, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([4]))\nroot - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([5]))\nroot - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([3]))\nroot - Up - Up - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([1]))\nroot - Up - Up - Up - Up - Up - Up - Up, <cgaf> - Leaf class=0 belief=0.968481 counts=(array([0, 1]), array([676,  22]))\n\n**************************************************\n0.6609 secs\n"
+     "text": "************** C=0.001 ****************************\nClassifier's accuracy (train): 0.9521\nClassifier's accuracy (test) : 0.9598\nroot\nroot - Down, <cgaf> - Leaf class=1 belief=0.980519 counts=(array([0, 1]), array([  6, 302]))\nroot - Up, <cgaf> - Leaf class=0 belief=0.940217 counts=(array([0, 1]), array([692,  44]))\n\n**************************************************\n************** C=0.01 ****************************\nClassifier's accuracy (train): 0.9521\nClassifier's accuracy (test) : 0.9643\nroot\nroot - Down\nroot - Down - Down, <cgaf> - Leaf class=1 belief=0.986842 counts=(array([0, 1]), array([  4, 300]))\nroot - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([1]))\nroot - Up, <cgaf> - Leaf class=0 belief=0.937754 counts=(array([0, 1]), array([693,  46]))\n\n**************************************************\n************** C=1 ****************************\nClassifier's accuracy (train): 0.9636\nClassifier's accuracy (test) : 0.9688\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([308]))\nroot - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([8]))\nroot - Up, <cgaf> - Leaf class=0 belief=0.947802 counts=(array([0, 1]), array([690,  38]))\n\n**************************************************\n************** C=5 ****************************\nClassifier's accuracy (train): 0.9665\nClassifier's accuracy (test) : 0.9621\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([308]))\nroot - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([11]))\nroot - Up\nroot - Up - Down\nroot - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([1]))\nroot - Up - Up\nroot - Up - Up - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Up, <cgaf> - Leaf class=0 belief=0.951456 counts=(array([0, 1]), array([686,  35]))\n\n**************************************************\n************** C=17 ****************************\nClassifier's accuracy (train): 0.9741\nClassifier's accuracy (test) : 0.9576\nroot\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([306]))\nroot - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([10]))\nroot - Up\nroot - Up - Down\nroot - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([3]))\nroot - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up\nroot - Up - Up - Down\nroot - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([3]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down\nroot - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([7]))\nroot - Up - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([4]))\nroot - Up - Up - Up - Up - Up - Up, <cgaf> - Leaf class=0 belief=0.961538 counts=(array([0, 1]), array([675,  27]))\n\n**************************************************\n0.7816 secs\n"
     }
    ],
    "source": [
@@ -146,7 +143,7 @@
     {
      "output_type": "stream",
      "name": "stdout",
-     "text": "root\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([313]))\nroot - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([10]))\nroot - Up\nroot - Up - Down, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([4]))\nroot - Up - Up\nroot - Up - Up - Down, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([4]))\nroot - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([5]))\nroot - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([3]))\nroot - Up - Up - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([1]))\nroot - Up - Up - Up - Up - Up - Up - Up, <cgaf> - Leaf class=0 belief=0.968481 counts=(array([0, 1]), array([676,  22]))\n"
+     "text": "root\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([306]))\nroot - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([10]))\nroot - Up\nroot - Up - Down\nroot - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([3]))\nroot - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up\nroot - Up - Up - Down\nroot - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([3]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down\nroot - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([7]))\nroot - Up - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([4]))\nroot - Up - Up - Up - Up - Up - Up, <cgaf> - Leaf class=0 belief=0.961538 counts=(array([0, 1]), array([675,  27]))\n"
     }
    ],
    "source": [
@@ -163,7 +160,7 @@
     {
      "output_type": "stream",
      "name": "stdout",
-     "text": "root\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([313]))\nroot - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([10]))\nroot - Up\nroot - Up - Down, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([4]))\nroot - Up - Up\nroot - Up - Up - Down, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([4]))\nroot - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([5]))\nroot - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([3]))\nroot - Up - Up - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([1]))\nroot - Up - Up - Up - Up - Up - Up - Up, <cgaf> - Leaf class=0 belief=0.968481 counts=(array([0, 1]), array([676,  22]))\n"
+     "text": "root\nroot - Down\nroot - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([306]))\nroot - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([10]))\nroot - Up\nroot - Up - Down\nroot - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([3]))\nroot - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up\nroot - Up - Up - Down\nroot - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([3]))\nroot - Up - Up - Up\nroot - Up - Up - Up - Down\nroot - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([1]))\nroot - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([2]))\nroot - Up - Up - Up - Up - Up\nroot - Up - Up - Up - Up - Up - Down\nroot - Up - Up - Up - Up - Up - Down - Down, <pure> - Leaf class=1 belief=1.000000 counts=(array([1]), array([7]))\nroot - Up - Up - Up - Up - Up - Down - Up, <pure> - Leaf class=0 belief=1.000000 counts=(array([0]), array([4]))\nroot - Up - Up - Up - Up - Up - Up, <cgaf> - Leaf class=0 belief=0.961538 counts=(array([0, 1]), array([675,  27]))\n"
     }
    ],
    "source": [

tests/Snode_test.py

@@ -1,72 +0,0 @@
-import os
-import unittest
-
-import numpy as np
-from sklearn.datasets import make_classification
-
-from trees.Stree import Stree, Snode
-
-
-class Snode_test(unittest.TestCase):
-
-    def __init__(self, *args, **kwargs):
-        os.environ['TESTING'] = '1'
-        self._random_state = 1
-        self._clf = Stree(random_state=self._random_state,
-                            use_predictions=True)
-        self._clf.fit(*self._get_Xy())
-        super().__init__(*args, **kwargs)
-
-    @classmethod
-    def tearDownClass(cls):
-        try:
-            os.environ.pop('TESTING')
-        except:
-            pass
-
-    def _get_Xy(self):
-        X, y = make_classification(n_samples=1500, n_features=3, n_informative=3,
-                                   n_redundant=0, n_repeated=0, n_classes=2, n_clusters_per_class=2,
-                                   class_sep=1.5, flip_y=0, weights=[0.5, 0.5], random_state=self._random_state)
-        return X, y
-
-    def test_attributes_in_leaves(self):
-        """Check if the attributes in leaves have correct values so they form a predictor
-        """
-        def check_leave(node: Snode):
-            if not node.is_leaf():
-                check_leave(node.get_down())
-                check_leave(node.get_up())
-                return
-            # Check Belief in leave
-            classes, card = np.unique(node._y, return_counts=True)
-            max_card = max(card)
-            min_card = min(card)
-            if len(classes) > 1:
-                try:
-                    belief = max_card / (max_card + min_card)
-                except:
-                    belief = 0.
-            else:
-                belief = 1
-            self.assertEqual(belief, node._belief)
-            # Check Class
-            class_computed = classes[card == max_card]
-            self.assertEqual(class_computed, node._class)
-        check_leave(self._clf._tree)
-    
-    def test_nodes_coefs(self):
-        """Check if the nodes of the tree have the right attributes filled
-        """
-        def run_tree(node: Snode):
-            if node._belief < 1:
-                # only exclude pure leaves
-                self.assertIsNotNone(node._clf)
-                self.assertIsNotNone(node._clf.coef_)
-                self.assertIsNotNone(node._vector)
-                self.assertIsNotNone(node._interceptor)
-            if node.is_leaf():
-                return
-            run_tree(node.get_down())
-            run_tree(node.get_up())
-        run_tree(self._clf._tree)

trees/Siterator.py

@@ -1,33 +0,0 @@
-'''
-__author__ = "Ricardo Montañana Gómez"
-__copyright__ = "Copyright 2020, Ricardo Montañana Gómez"
-__license__ = "MIT"
-__version__ = "0.9"
-Inorder iterator for the binary tree of Snodes
-'''
-
-from trees.Snode import Snode
-
-
-class Siterator:
-    """Stree preorder iterator
-    """
-
-    def __init__(self, tree: Snode):
-        self._stack = []
-        self._push(tree)
-
-    def __iter__(self):
-        return self
-
-    def _push(self, node: Snode):
-        if node is not None:
-            self._stack.append(node)
-
-    def __next__(self) -> Snode:
-        if len(self._stack) == 0:
-            raise StopIteration()
-        node = self._stack.pop()
-        self._push(node.get_up())
-        self._push(node.get_down())
-        return node

trees/Snode.py

@@ -1,70 +0,0 @@
-'''
-__author__ = "Ricardo Montañana Gómez"
-__copyright__ = "Copyright 2020, Ricardo Montañana Gómez"
-__license__ = "MIT"
-__version__ = "0.9"
-Node of the Stree (binary tree)
-'''
-
-import os
-
-import numpy as np
-from sklearn.svm import LinearSVC
-
-class Snode:
-    def __init__(self, clf: LinearSVC, X: np.ndarray, y: np.ndarray, title: str):
-        self._clf = clf
-        self._vector = None if clf is None else clf.coef_
-        self._interceptor = 0. if clf is None else clf.intercept_
-        self._title = title
-        self._belief = 0.  # belief of the prediction in a leaf node based on samples
-        # Only store dataset in Testing 
-        self._X = X if os.environ.get('TESTING', 'NS') != 'NS' else None
-        self._y = y
-        self._down = None
-        self._up = None
-        self._class = None
-
-    @classmethod
-    def copy(cls, node: 'Snode') -> 'Snode':
-        return cls(node._clf, node._X, node._y, node._title)
-
-    def set_down(self, son):
-        self._down = son
-
-    def set_up(self, son):
-        self._up = son
-
-    def is_leaf(self,) -> bool:
-        return self._up is None and self._down is None
-
-    def get_down(self) -> 'Snode':
-        return self._down
-
-    def get_up(self) -> 'Snode':
-        return self._up
-
-    def make_predictor(self):
-        """Compute the class of the predictor and its belief based on the subdataset of the node
-        only if it is a leaf
-        """
-        if not self.is_leaf():
-            return
-        classes, card = np.unique(self._y, return_counts=True)
-        if len(classes) > 1:
-            max_card = max(card)
-            min_card = min(card)
-            try:
-                self._belief = max_card / (max_card + min_card)
-            except:
-                self._belief = 0.
-            self._class = classes[card == max_card][0]
-        else:
-            self._belief = 1
-            self._class = classes[0]
-
-    def __str__(self) -> str:
-        if self.is_leaf():
-            return f"{self._title} - Leaf class={self._class} belief={self._belief:.6f} counts={np.unique(self._y, return_counts=True)}"
-        else:
-            return f"{self._title}"

trees/Stree_grapher.py

@@ -1,101 +0,0 @@
-'''
-__author__ = "Ricardo Montañana Gómez"
-__copyright__ = "Copyright 2020, Ricardo Montañana Gómez"
-__license__ = "MIT"
-__version__ = "0.9"
-Plot 3D views of nodes in Stree
-'''
-
-import os
-import numpy as np
-from sklearn.decomposition import PCA
-import trees
-import matplotlib.pyplot as plt
-from trees.Snode import Snode
-from trees.Snode_graph import Snode_graph
-from trees.Stree import Stree
-from trees.Siterator import Siterator
-
-
-class Stree_grapher(Stree):
-    """Build 3d graphs of any dataset, if it's more than 3 features PCA shall
-    make its magic
-    """
-
-    def __init__(self, params: dict):
-        self._plot_size = (8, 8)
-        self._tree_gr = None
-        # make Snode store X's
-        os.environ['TESTING'] = '1'
-        self._fitted = False
-        self._pca = None
-        super().__init__(**params)
-
-    def __del__(self):
-        try:
-            os.environ.pop('TESTING')
-        except:
-            pass
-        plt.close('all')
-
-    def _copy_tree(self, node: Snode) -> Snode_graph:
-        mirror = Snode_graph(node)
-        # clone node
-        mirror._class = node._class
-        mirror._belief = node._belief
-        if node.get_down() is not None:
-            mirror.set_down(self._copy_tree(node.get_down()))
-        if node.get_up() is not None:
-            mirror.set_up(self._copy_tree(node.get_up()))
-        return mirror
-
-    def fit(self, X: np.array, y: np.array) -> Stree:
-        """Fit the Stree and copy the tree in a Snode_graph tree
-
-        :param X: Dataset
-        :type X: np.array
-        :param y: Labels
-        :type y: np.array
-        :return: Stree model
-        :rtype: Stree
-        """
-        if X.shape[1] != 3:
-            self._pca = PCA(n_components=3)
-            X = self._pca.fit_transform(X)
-        res = super().fit(X, y)
-        self._tree_gr = self._copy_tree(self._tree)
-        self._fitted = True
-        return res
-
-    def score(self, X: np.array, y: np.array) -> float:
-        self._check_fitted()
-        if X.shape[1] != 3:
-            X = self._pca.transform(X)
-        return super().score(X, y)
-
-    def _check_fitted(self):
-        if not self._fitted:
-            raise Exception('Have to fit the grapher first!')
-
-    def save_all(self, save_folder: str = './', save_prefix: str = ''):
-        """Save all the node plots in png format, each with a sequence number
-
-        :param save_folder: folder where the plots are saved, defaults to './'
-        :type save_folder: str, optional
-        """
-        self._check_fitted()
-        seq = 1
-        for node in self:
-            node.save_hyperplane(save_folder=save_folder,
-                                 save_prefix=save_prefix, save_seq=seq)
-            seq += 1
-
-    def plot_all(self):
-        """Plots all the nodes
-        """
-        self._check_fitted()
-        for node in self:
-            node.plot_hyperplane()
-
-    def __iter__(self):
-        return Siterator(self._tree_gr)