Merge pull request #173 from MathieuCarriere/master

Example in doc + fix on Landscape
Fix #166 

2 files changed, 43 insertions, 12 deletions

diff --git a/src/python/doc/representations.rst b/src/python/doc/representations.rst
index b3131a25..11dcbcf9 100644
--- a/src/python/doc/representations.rst
+++ b/src/python/doc/representations.rst
@@ -8,7 +8,7 @@ Representations manual
 
 .. include:: representations_sum.inc
 
-This module, originally named sklearn_tda, aims at bridging the gap between persistence diagrams and machine learning tools, in particular scikit-learn. It provides tools, using the scikit-learn standard interface, to compute distances and kernels on diagrams, and to convert diagrams into vectors.
+This module, originally available at https://github.com/MathieuCarriere/sklearn-tda and named sklearn_tda, aims at bridging the gap between persistence diagrams and machine learning, by providing implementations of most of the vector representations for persistence diagrams in the literature, in a scikit-learn format. More specifically, it provides tools, using the scikit-learn standard interface, to compute distances and kernels on persistence diagrams, and to convert these diagrams into vectors in Euclidean space.
 
 A diagram is represented as a numpy array of shape (n,2), as can be obtained from :func:`~gudhi.SimplexTree.persistence_intervals_in_dimension` for instance. Points at infinity are represented as a numpy array of shape (n,1), storing only the birth time.
 
@@ -46,3 +46,27 @@ Metrics
    :members:
    :special-members:
    :show-inheritance:
+
+Basic example
+-------------
+
+This example computes the first two Landscapes associated to a persistence diagram with four points. The landscapes are evaluated on ten samples, leading to two vectors with ten coordinates each, that are eventually concatenated in order to produce a single vector representation.
+
+.. testcode::
+
+    import numpy as np
+    from gudhi.representations import Landscape
+    # A single diagram with 4 points
+    D = np.array([[0.,4.],[1.,2.],[3.,8.],[6.,8.]])
+    diags = [D]
+    l=Landscape(num_landscapes=2,resolution=10).fit_transform(diags)
+    print(l) 
+
+The output is:
+
+.. testoutput::
+
+    [[1.02851895 2.05703791 2.57129739 1.54277843 0.89995409 1.92847304
+      2.95699199 3.08555686 2.05703791 1.02851895 0.         0.64282435
+      0.         0.         0.51425948 0.         0.         0.
+      0.77138922 1.02851895]]
diff --git a/src/python/gudhi/representations/vector_methods.py b/src/python/gudhi/representations/vector_methods.py
index 61c4fb84..fe26dbe2 100644
--- a/src/python/gudhi/representations/vector_methods.py
+++ b/src/python/gudhi/representations/vector_methods.py
@@ -95,6 +95,8 @@ class Landscape(BaseEstimator, TransformerMixin):
             sample_range ([double, double]): minimum and maximum of all piecewise-linear function domains, of the form [x_min, x_max] (default [numpy.nan, numpy.nan]). It is the interval on which samples will be drawn evenly. If one of the values is numpy.nan, it can be computed from the persistence diagrams with the fit() method.
         """
         self.num_landscapes, self.resolution, self.sample_range = num_landscapes, resolution, sample_range
+        self.nan_in_range = np.isnan(np.array(self.sample_range))
+        self.new_resolution = self.resolution + self.nan_in_range.sum()
 
     def fit(self, X, y=None):
         """
@@ -104,10 +106,10 @@ class Landscape(BaseEstimator, TransformerMixin):
             X (list of n x 2 numpy arrays): input persistence diagrams.
             y (n x 1 array): persistence diagram labels (unused).
         """
-        if np.isnan(np.array(self.sample_range)).any():
+        if self.nan_in_range.any():
             pre = DiagramScaler(use=True, scalers=[([0], MinMaxScaler()), ([1], MinMaxScaler())]).fit(X,y)
             [mx,my],[Mx,My] = [pre.scalers[0][1].data_min_[0], pre.scalers[1][1].data_min_[0]], [pre.scalers[0][1].data_max_[0], pre.scalers[1][1].data_max_[0]]
-            self.sample_range = np.where(np.isnan(np.array(self.sample_range)), np.array([mx, My]), np.array(self.sample_range))
+            self.sample_range = np.where(self.nan_in_range, np.array([mx, My]), np.array(self.sample_range))
         return self
 
     def transform(self, X):
@@ -121,26 +123,26 @@ class Landscape(BaseEstimator, TransformerMixin):
             numpy array with shape (number of diagrams) x (number of samples = **num_landscapes** x **resolution**): output persistence landscapes.
         """
         num_diag, Xfit = len(X), []
-        x_values = np.linspace(self.sample_range[0], self.sample_range[1], self.resolution)
+        x_values = np.linspace(self.sample_range[0], self.sample_range[1], self.new_resolution)
         step_x = x_values[1] - x_values[0]
 
         for i in range(num_diag):
 
             diagram, num_pts_in_diag = X[i], X[i].shape[0]
 
-            ls = np.zeros([self.num_landscapes, self.resolution])
+            ls = np.zeros([self.num_landscapes, self.new_resolution])
 
             events = []
-            for j in range(self.resolution):
+            for j in range(self.new_resolution):
                 events.append([])
 
             for j in range(num_pts_in_diag):
                 [px,py] = diagram[j,:2]
-                min_idx = np.clip(np.ceil((px          - self.sample_range[0]) / step_x).astype(int), 0, self.resolution)
-                mid_idx = np.clip(np.ceil((0.5*(py+px) - self.sample_range[0]) / step_x).astype(int), 0, self.resolution)
-                max_idx = np.clip(np.ceil((py          - self.sample_range[0]) / step_x).astype(int), 0, self.resolution)
+                min_idx = np.clip(np.ceil((px          - self.sample_range[0]) / step_x).astype(int), 0, self.new_resolution)
+                mid_idx = np.clip(np.ceil((0.5*(py+px) - self.sample_range[0]) / step_x).astype(int), 0, self.new_resolution)
+                max_idx = np.clip(np.ceil((py          - self.sample_range[0]) / step_x).astype(int), 0, self.new_resolution)
 
-                if min_idx < self.resolution and max_idx > 0:
+                if min_idx < self.new_resolution and max_idx > 0:
 
                     landscape_value = self.sample_range[0] + min_idx * step_x - px
                     for k in range(min_idx, mid_idx):
@@ -152,12 +154,17 @@ class Landscape(BaseEstimator, TransformerMixin):
                         events[k].append(landscape_value)
                         landscape_value -= step_x
 
-            for j in range(self.resolution):
+            for j in range(self.new_resolution):
                 events[j].sort(reverse=True)
                 for k in range( min(self.num_landscapes, len(events[j])) ):
                     ls[k,j] = events[j][k]
 
-            Xfit.append(np.sqrt(2)*np.reshape(ls,[1,-1]))
+            if self.nan_in_range[0]:
+                ls = ls[:,1:]
+            if self.nan_in_range[1]:
+                ls = ls[:,:-1]
+            ls = np.sqrt(2)*np.reshape(ls,[1,-1])
+            Xfit.append(ls)
 
         Xfit = np.concatenate(Xfit,0)