fixed useless coordinates in Landscape if min and max are computed from data

3 files changed, 35 insertions, 8 deletions

diff --git a/src/python/doc/representations.rst b/src/python/doc/representations.rst
index b3131a25..b338f7f0 100644
--- a/src/python/doc/representations.rst
+++ b/src/python/doc/representations.rst
@@ -8,9 +8,9 @@ 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.
+A diagram is represented as a numpy array of shape (n,2), as can be obtained from `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.
 
 A small example is provided
 
@@ -46,3 +46,24 @@ 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::
+
+    [[0.         1.25707872 2.51415744 1.88561808 0.7856742  2.04275292 3.29983165 2.51415744 1.25707872 0.         0.         0.         0.31426968 0.         0.62853936 0.         0.         0.31426968 1.25707872 0.        ]] 
diff --git a/src/python/example/diagram_vectorizations_distances_kernels.py b/src/python/example/diagram_vectorizations_distances_kernels.py
index 119072eb..f777984c 100755
--- a/src/python/example/diagram_vectorizations_distances_kernels.py
+++ b/src/python/example/diagram_vectorizations_distances_kernels.py
@@ -26,9 +26,9 @@ plt.show()
 
 LS = Landscape(resolution=1000)
 L = LS.fit_transform(diags)
-plt.plot(L[0][:1000])
-plt.plot(L[0][1000:2000])
-plt.plot(L[0][2000:3000])
+plt.plot(L[0][:999])
+plt.plot(L[0][999:2*999])
+plt.plot(L[0][2*999:3*999])
 plt.title("Landscape")
 plt.show()
 
diff --git a/src/python/gudhi/representations/vector_methods.py b/src/python/gudhi/representations/vector_methods.py
index 61c4fb84..083551a4 100644
--- a/src/python/gudhi/representations/vector_methods.py
+++ b/src/python/gudhi/representations/vector_methods.py
@@ -104,10 +104,11 @@ class Landscape(BaseEstimator, TransformerMixin):
             X (list of n x 2 numpy arrays): input persistence diagrams.
             y (n x 1 array): persistence diagram labels (unused).
         """
+        self.nan_in_range = np.isnan(np.array(self.sample_range))
         if np.isnan(np.array(self.sample_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):
@@ -121,7 +122,7 @@ 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.resolution + self.nan_in_range.sum())
         step_x = x_values[1] - x_values[0]
 
         for i in range(num_diag):
@@ -157,7 +158,12 @@ class Landscape(BaseEstimator, TransformerMixin):
                 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)