Merge branch 'master' of https://github.com/GUDHI/gudhi-devel into diff

3 files changed, 21 insertions, 23 deletions

diff --git a/src/python/gudhi/__init__.py.in b/src/python/gudhi/__init__.py.in
index 3043201a..79e12fbc 100644
--- a/src/python/gudhi/__init__.py.in
+++ b/src/python/gudhi/__init__.py.in
@@ -23,10 +23,6 @@ __all__ = [@GUDHI_PYTHON_MODULES@ @GUDHI_PYTHON_MODULES_EXTRA@]
 __available_modules = ''
 __missing_modules = ''
 
-# For unitary tests purpose
-# could use "if 'collapse_edges' in gudhi.__all__" when collapse edges will have a python module
-__GUDHI_USE_EIGEN3 = @GUDHI_USE_EIGEN3@
-
 # Try to import * from gudhi.__module_name for default modules.
 # Extra modules require an explicit import by the user (mostly because of
 # unusual dependencies, but also to avoid cluttering namespace gudhi and
diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py
index 604018d1..7ed11360 100644
--- a/src/python/gudhi/persistence_graphical_tools.py
+++ b/src/python/gudhi/persistence_graphical_tools.py
@@ -193,6 +193,7 @@ def plot_persistence_barcode(
         x=[birth for (dim,(birth,death)) in persistence]
         y=[(death - birth) if death != float("inf") else (infinity - birth) for (dim,(birth,death)) in persistence]
         c=[colormap[dim] for (dim,(birth,death)) in persistence]
+
         axes.barh(list(reversed(range(len(x)))), y, height=0.8, left=x, alpha=alpha, color=c, linewidth=0)
 
         if legend:
@@ -324,6 +325,7 @@ def plot_persistence_diagram(
         x=[birth for (dim,(birth,death)) in persistence]
         y=[death if death != float("inf") else infinity for (dim,(birth,death)) in persistence]
         c=[colormap[dim] for (dim,(birth,death)) in persistence]
+
         axes.scatter(x,y,alpha=alpha,color=c)
         if float("inf") in (death for (dim,(birth,death)) in persistence):
             # infinity line and text
@@ -449,16 +451,15 @@ def plot_persistence_density(
             _, axes = plt.subplots(1, 1)
 
         try:
-            if len(persistence) > 0:
-                # if not read from file but given by an argument
-                persistence = _array_handler(persistence)
-                persistence_dim = np.array(
-                    [
-                        (dim_interval[1][0], dim_interval[1][1])
-                        for dim_interval in persistence
-                        if (dim_interval[0] == dimension) or (dimension is None)
-                    ]
-                )
+            # if not read from file but given by an argument
+            persistence = _array_handler(persistence)
+            persistence_dim = np.array(
+                [
+                    (dim_interval[1][0], dim_interval[1][1])
+                    for dim_interval in persistence
+                    if (dim_interval[0] == dimension) or (dimension is None)
+                ]
+            )
             persistence_dim = persistence_dim[np.isfinite(persistence_dim[:, 1])]
             persistence_dim = np.array(
                 _limit_to_max_intervals(
@@ -482,6 +483,7 @@ def plot_persistence_density(
             zi = k(np.vstack([xi.flatten(), yi.flatten()]))
             # Make the plot
             img = axes.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap, shading="auto")
+            plot_success = True
 
         # IndexError on empty diagrams, ValueError on only inf death values
         except (IndexError, ValueError):
@@ -489,6 +491,7 @@ def plot_persistence_density(
             birth_max = 1.0
             death_min = 0.0
             death_max = 1.0
+            plot_success = False
             pass
 
         # line display of equation : birth = death
@@ -504,7 +507,7 @@ def plot_persistence_density(
                 )
             )
 
-        if legend:
+        if plot_success and legend:
             plt.colorbar(img, ax=axes)
 
         axes.set_xlabel("Birth", fontsize=fontsize)
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index a4914184..2c53a872 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -676,18 +676,17 @@ cdef class SimplexTree:
         return (normal0, normals, infinite0, infinites)
 
     def collapse_edges(self, nb_iterations = 1):
-        """Assuming the simplex tree is a 1-skeleton graph, this method collapse edges (simplices of higher dimension
-        are ignored) and resets the simplex tree from the remaining edges.
-        A good candidate is to build a simplex tree on top of a :class:`~gudhi.RipsComplex` of dimension 1 before
-        collapsing edges
+        """Assuming the complex is a graph (simplices of higher dimension are ignored), this method implicitly
+        interprets it as the 1-skeleton of a flag complex, and replaces it with another (smaller) graph whose
+        expansion has the same persistent homology, using a technique known as edge collapses
+        (see :cite:`edgecollapsearxiv`).
+
+        A natural application is to get a simplex tree of dimension 1 from :class:`~gudhi.RipsComplex`,
+        then collapse edges, perform :meth:`expansion()` and finally compute persistence
         (cf. :download:`rips_complex_edge_collapse_example.py <../example/rips_complex_edge_collapse_example.py>`).
-        For implementation details, please refer to :cite:`edgecollapsesocg2020`.
 
         :param nb_iterations: The number of edge collapse iterations to perform. Default is 1.
         :type nb_iterations: int
-
-        :note: collapse_edges method requires `Eigen <installation.html#eigen>`_ >= 3.1.0 and an exception is thrown
-            if this method is not available.
         """
         # Backup old pointer
         cdef Simplex_tree_interface_full_featured* ptr = self.get_ptr()