From 2b5586fd60848b159fb4fa4481e61bab0e0cd766 Mon Sep 17 00:00:00 2001
From: MathieuCarriere <mathieu.carriere3@gmail.com>
Date: Wed, 29 Apr 2020 18:31:24 -0400
Subject: small modifs

---
 .../include/gudhi/Bitmap_cubical_complex_base.h    |  4 +--
 src/python/gudhi/cubical_complex.pyx               | 42 +++++++++++-----------
 .../include/Persistent_cohomology_interface.h      |  7 +++-
 3 files changed, 29 insertions(+), 24 deletions(-)

(limited to 'src')

diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
index 248ebdb6..eaf8a0b6 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
@@ -116,7 +116,7 @@ class Bitmap_cubical_complex_base {
    * be an edge or vertex of a cube. On the other hand, the output is always indicating the position of
    * a cube in the data structure. 
    **/
-  inline int get_top_dimensional_coface_of_a_cell(int splx);
+  inline int get_top_dimensional_coface_of_a_cell(size_t splx);
 
   /**
   * This procedure compute incidence numbers between cubes. For a cube \f$A\f$ of
@@ -612,7 +612,7 @@ void Bitmap_cubical_complex_base<T>::setup_bitmap_based_on_top_dimensional_cells
 }
 
 template <typename T>
-int Bitmap_cubical_complex_base<T>::get_top_dimensional_coface_of_a_cell(int splx) {
+int Bitmap_cubical_complex_base<T>::get_top_dimensional_coface_of_a_cell(size_t splx) {
   if (this->get_dimension_of_a_cell(splx) == this->dimension()){return splx;}
   else{  
     for (auto v : this->get_coboundary_of_a_cell(splx)){
diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 884b0664..b16a037f 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -199,28 +199,28 @@ cdef class CubicalComplex:
             The indices of the arrays in the list correspond to the homological dimensions, and the 
             integers of each row in each array correspond to: (index of positive top-dimensional cell).
         """
+
+        assert self.pcohptr != NULL, "cofaces_of_persistence_pairs function requires persistence function to be launched first."
+
         cdef vector[vector[int]] persistence_result
-        if self.pcohptr != NULL:
-            output = [[],[]]
-            persistence_result = self.pcohptr.cofaces_of_cubical_persistence_pairs()
-            pr = np.array(persistence_result)
-
-            ess_ind = np.argwhere(pr[:,2] == -1)[:,0]
-            ess = pr[ess_ind]
-            max_h = max(ess[:,0])+1
-            for h in range(max_h):
-                hidxs = np.argwhere(ess[:,0] == h)[:,0]
-                output[1].append(ess[hidxs][:,1])
-
-            reg_ind = np.setdiff1d(np.array(range(len(pr))), ess_ind)
-            reg = pr[reg_ind]
-            max_h = max(reg[:,0])+1
-            for h in range(max_h):
-                hidxs = np.argwhere(reg[:,0] == h)[:,0]
-                output[0].append(reg[hidxs][:,1:])
-        else:
-            print("cofaces_of_persistence_pairs function requires persistence function"
-                  " to be launched first.")
+        output = [[],[]]
+        persistence_result = self.pcohptr.cofaces_of_cubical_persistence_pairs()
+        pr = np.array(persistence_result)
+
+        ess_ind = np.argwhere(pr[:,2] == -1)[:,0]
+        ess = pr[ess_ind]
+        max_h = max(ess[:,0])+1
+        for h in range(max_h):
+            hidxs = np.argwhere(ess[:,0] == h)[:,0]
+            output[1].append(ess[hidxs][:,1])
+
+        reg_ind = np.setdiff1d(np.array(range(len(pr))), ess_ind)
+        reg = pr[reg_ind]
+        max_h = max(reg[:,0])+1
+        for h in range(max_h):
+            hidxs = np.argwhere(reg[:,0] == h)[:,0]
+            output[0].append(reg[hidxs][:,1:])
+
         return output
 
     def betti_numbers(self):
diff --git a/src/python/include/Persistent_cohomology_interface.h b/src/python/include/Persistent_cohomology_interface.h
index c4e60a27..cec18546 100644
--- a/src/python/include/Persistent_cohomology_interface.h
+++ b/src/python/include/Persistent_cohomology_interface.h
@@ -68,11 +68,16 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
     return persistence;
   }
 
+  // This function computes the top-dimensional cofaces associated to the positive and negative
+  // simplices of a cubical complex. The output format is a vector of vectors of three integers,
+  // which are [homological dimension, index of top-dimensional coface of positive simplex,
+  // index of top-dimensional coface of negative simplex]. If the topological feature is essential,
+  // then the index of top-dimensional coface of negative simplex is arbitrarily set to -1.
   std::vector<std::vector<int>> cofaces_of_cubical_persistence_pairs() {
 
     // Warning: this function is meant to be used with CubicalComplex only!!
 
-    auto pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex,
+    auto&& pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex,
       persistent_cohomology::Field_Zp>::get_persistent_pairs();
 
     // Gather all top-dimensional cells and store their simplex handles
-- 
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