From 9b4de0e29a01552b4bb3f47fe0d3f01f5601c000 Mon Sep 17 00:00:00 2001
From: martinroyer <16647869+martinroyer@users.noreply.github.com>
Date: Tue, 9 Jun 2020 08:42:30 +0200
Subject: Apply suggestions from code review

---
 src/python/gudhi/representations/vector_methods.py | 45 ++++++++++++++++------
 1 file changed, 33 insertions(+), 12 deletions(-)

(limited to 'src/python/gudhi/representations')

diff --git a/src/python/gudhi/representations/vector_methods.py b/src/python/gudhi/representations/vector_methods.py
index df66ffc3..a09b9356 100644
--- a/src/python/gudhi/representations/vector_methods.py
+++ b/src/python/gudhi/representations/vector_methods.py
@@ -577,26 +577,26 @@ class ComplexPolynomial(BaseEstimator, TransformerMixin):
         return self.fit_transform([diag])[0,:]
 
 def _lapl_contrast(measure, centers, inertias, eps=1e-8):
-	"""contrast function for vectorising `measure` in ATOL"""
+    """contrast function for vectorising `measure` in ATOL"""
     return np.exp(-np.sqrt(pairwise.pairwise_distances(measure, Y=centers) / (inertias + eps)))
 
 def _gaus_contrast(measure, centers, inertias, eps=1e-8):
-	"""contrast function for vectorising `measure` in ATOL"""
+    """contrast function for vectorising `measure` in ATOL"""
     return np.exp(-pairwise.pairwise_distances(measure, Y=centers) / (inertias + eps))
 
 def _indicator_contrast(diags, centers, inertias, eps=1e-8):
-	"""contrast function for vectorising `measure` in ATOL"""
+    """contrast function for vectorising `measure` in ATOL"""
     pair_dist = pairwise.pairwise_distances(diags, Y=centers)
     flat_circ = (pair_dist < (inertias+eps)).astype(int)
     robe_curve = np.positive((2-pair_dist/(inertias+eps))*((inertias+eps) < pair_dist).astype(int))
     return flat_circ + robe_curve
 
 def _cloud_weighting(measure):
-	"""automatic uniform weighting with mass 1 for `measure` in ATOL"""
+    """automatic uniform weighting with mass 1 for `measure` in ATOL"""
     return np.ones(shape=measure.shape[0])
 
 def _iidproba_weighting(measure):
-	"""automatic uniform weighting with mass 1/N for `measure` in ATOL"""
+    """automatic uniform weighting with mass 1/N for `measure` in ATOL"""
     return np.ones(shape=measure.shape[0]) / measure.shape[0]
 
 class Atol(BaseEstimator, TransformerMixin):
@@ -611,20 +611,41 @@ class Atol(BaseEstimator, TransformerMixin):
 
         Parameters:
             quantiser (Object): Object with `fit` (sklearn API consistent) and `cluster_centers` and `n_clusters`
-                attributes (default: MiniBatchKMeans()). This object will be fitted by the function `fit`.
-            weighting_method (function): constant generic function for weighting the measure points
+                attributes. This object will be fitted by the function `fit`.
+            weighting_method (string): constant generic function for weighting the measure points
 			    choose from {"cloud", "iidproba"}
                 (default: constant function, i.e. the measure is seen as a point cloud by default).
                 This will have no impact if weights are provided along with measures all the way: `fit` and `transform`.
             contrast (string): constant function for evaluating proximity of a measure with respect to centers
-			    choose from {"gaus", "lapl", "indi"}
+			    choose from {"gaussian", "laplacian", "indicator"}
                 (default: laplacian contrast function, see page 3 in the ATOL paper).
-        """
+
+    Example
+    --------
+    >>> from sklearn.cluster import KMeans
+    >>> import numpy as np
+    >>> a = np.array([[1, 2, 4], [1, 4, 0], [1, 0, 4]])
+    >>> b = np.array([[4, 2, 0], [4, 4, 0], [4, 0, 2]])
+    >>> c = np.array([[3, 2, -1], [1, 2, -1]])
+    >>> atol_vectoriser = Atol(quantiser=KMeans(n_clusters=2))
+    >>> atol_vectoriser.fit(X=[a, b, c])
+    >>> atol_vectoriser.centers
+    array([[ 2.6       ,  2.8       , -0.4       ],
+       [ 2.        ,  0.66666667,  3.33333333]])
+    >>> atol_vectoriser(a)
+    array([0.58394704, 1.0769395 ])
+    >>> atol_vectoriser(c)
+    array([1.02816136, 0.23559623])
+    >>> atol_vectoriser.transform(X=[a, b, c])
+    array([[0.58394704, 1.0769395 ],
+       [1.04696684, 0.56203292],
+       [1.02816136, 0.23559623]])
+    """
         self.quantiser = quantiser
         self.contrast = {
-            "gaus": _gaus_contrast,
-            "lapl": _lapl_contrast,
-            "indi": _indicator_contrast,
+            "gaussian": _gaus_contrast,
+            "laplacian": _lapl_contrast,
+            "indicator": _indicator_contrast,
         }.get(contrast, _gaus_contrast)
         self.centers = np.ones(shape=(self.quantiser.n_clusters, 2))*np.inf
         self.inertias = np.full(self.quantiser.n_clusters, np.nan)
-- 
cgit v1.2.3