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

7 files changed, 36 insertions, 49 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 3e7f5d97..2c682437 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -149,10 +149,6 @@ if(PYTHONINTERP_FOUND)
       add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}")
       # No problem, even if no CGAL found
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
-      set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_EIGEN3', ")
-      set(GUDHI_USE_EIGEN3 "True")
-    else (EIGEN3_FOUND)
-      set(GUDHI_USE_EIGEN3 "False")
     endif (EIGEN3_FOUND)
 
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'off_reader', ")
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()
diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h
index aa3dac18..7f9b0067 100644
--- a/src/python/include/Simplex_tree_interface.h
+++ b/src/python/include/Simplex_tree_interface.h
@@ -15,9 +15,7 @@
 #include <gudhi/distance_functions.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Points_off_io.h>
-#ifdef GUDHI_USE_EIGEN3
 #include <gudhi/Flag_complex_edge_collapser.h>
-#endif
 
 #include <iostream>
 #include <vector>
@@ -165,7 +163,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   }
 
   Simplex_tree_interface* collapse_edges(int nb_collapse_iteration) {
-#ifdef GUDHI_USE_EIGEN3
     using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>;
     std::vector<Filtered_edge> edges;
     for (Simplex_handle sh : Base::skeleton_simplex_range(1)) {
@@ -179,7 +176,7 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     }
 
     for (int iteration = 0; iteration < nb_collapse_iteration; iteration++) {
-      edges = Gudhi::collapse::flag_complex_collapse_edges(edges);
+      edges = Gudhi::collapse::flag_complex_collapse_edges(std::move(edges));
     }
     Simplex_tree_interface* collapsed_stree_ptr = new Simplex_tree_interface();
     // Copy the original 0-skeleton
@@ -191,9 +188,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
       collapsed_stree_ptr->insert({std::get<0>(remaining_edge), std::get<1>(remaining_edge)}, std::get<2>(remaining_edge));
     }
     return collapsed_stree_ptr;
-#else
-    throw std::runtime_error("Unable to collapse edges as it requires Eigen3 >= 3.1.0.");
-#endif
   }
 
   void expansion_with_blockers_callback(int dimension, blocker_func_t user_func, void *user_data) {
diff --git a/src/python/test/test_persistence_graphical_tools.py b/src/python/test/test_persistence_graphical_tools.py
index 7d9bae90..c19836b7 100644
--- a/src/python/test/test_persistence_graphical_tools.py
+++ b/src/python/test/test_persistence_graphical_tools.py
@@ -15,7 +15,7 @@ import pytest
 
 
 def test_array_handler():
-    diags = np.array([[1, 2], [3, 4], [5, 6]], np.float)
+    diags = np.array([[1, 2], [3, 4], [5, 6]], float)
     arr_diags = gd.persistence_graphical_tools._array_handler(diags)
     for idx in range(len(diags)):
         assert arr_diags[idx][0] == 0
@@ -96,10 +96,14 @@ def test_limit_to_max_intervals():
 
 
 def _limit_plot_persistence(function):
-    pplot = function(persistence=[()])
-    assert issubclass(type(pplot), plt.axes.SubplotBase)
+    pplot = function(persistence=[])
+    assert isinstance(pplot, plt.axes.SubplotBase)
+    pplot = function(persistence=[], legend=True)
+    assert isinstance(pplot, plt.axes.SubplotBase)
     pplot = function(persistence=[(0, float("inf"))])
-    assert issubclass(type(pplot), plt.axes.SubplotBase)
+    assert isinstance(pplot, plt.axes.SubplotBase)
+    pplot = function(persistence=[(0, float("inf"))], legend=True)
+    assert isinstance(pplot, plt.axes.SubplotBase)
 
 
 def test_limit_plot_persistence():
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index eb481a49..688f4fd6 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -8,7 +8,7 @@
       - YYYY/MM Author: Description of the modification
 """
 
-from gudhi import SimplexTree, __GUDHI_USE_EIGEN3
+from gudhi import SimplexTree
 import numpy as np
 import pytest
 
@@ -354,16 +354,11 @@ def test_collapse_edges():
 
     assert st.num_simplices() == 10
 
-    if __GUDHI_USE_EIGEN3:
-        st.collapse_edges()
-        assert st.num_simplices() == 9
-        assert st.find([1, 3]) == False
-        for simplex in st.get_skeleton(0):
-            assert simplex[1] == 1.
-    else:
-        # If no Eigen3, collapse_edges throws an exception
-        with pytest.raises(RuntimeError):
-            st.collapse_edges()
+    st.collapse_edges()
+    assert st.num_simplices() == 9
+    assert st.find([0, 2]) == False # [1, 3] would be fine as well
+    for simplex in st.get_skeleton(0):
+        assert simplex[1] == 1.
 
 def test_reset_filtration():
     st = SimplexTree()