From c5c565dfd92ce1ad5b318dca40edf9429d6334c2 Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Mon, 30 Mar 2020 20:46:56 +0200
Subject: Streamline initialize_filtration

---
 src/Persistent_cohomology/example/custom_persistence_sort.cpp       | 3 ---
 src/Persistent_cohomology/example/persistence_from_file.cpp         | 3 ---
 src/Persistent_cohomology/example/plain_homology.cpp                | 3 ---
 src/Persistent_cohomology/example/rips_multifield_persistence.cpp   | 3 ---
 src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp | 3 ---
 src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h     | 2 --
 6 files changed, 17 deletions(-)

(limited to 'src/Persistent_cohomology')

diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
index 87e9c207..410cd987 100644
--- a/src/Persistent_cohomology/example/custom_persistence_sort.cpp
+++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
@@ -86,9 +86,6 @@ int main(int argc, char **argv) {
         " - " << simplex.num_simplices() << " simplices - " <<
         simplex.num_vertices() << " vertices." << std::endl;
 
-    // Sort the simplices in the order of the filtration
-    simplex.initialize_filtration();
-
     std::clog << "Simplex_tree dim: " << simplex.dimension() << std::endl;
 
     Persistent_cohomology pcoh(simplex);
diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp
index 79108730..38c44514 100644
--- a/src/Persistent_cohomology/example/persistence_from_file.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_file.cpp
@@ -59,9 +59,6 @@ int main(int argc, char * argv[]) {
   std::clog << std::endl;
   }*/
 
-  // Sort the simplices in the order of the filtration
-  simplex_tree.initialize_filtration();
-
   // Compute the persistence diagram of the complex
   Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree);
   // initializes the coefficient field for homology
diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp
index 4d329020..236b67de 100644
--- a/src/Persistent_cohomology/example/plain_homology.cpp
+++ b/src/Persistent_cohomology/example/plain_homology.cpp
@@ -59,9 +59,6 @@ int main() {
   st.insert_simplex_and_subfaces(edge35);
   st.insert_simplex(vertex4);
 
-  // Sort the simplices in the order of the filtration
-  st.initialize_filtration();
-
   // Class for homology computation
   // By default, since the complex has dimension 1, only 0-dimensional homology would be computed.
   // Here we also want persistent homology to be computed for the maximal dimension in the complex (persistence_dim_max = true)
diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index e2e2c0a5..2edf5bc4 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -59,9 +59,6 @@ int main(int argc, char * argv[]) {
   std::clog << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
   std::clog << "   and has dimension " << simplex_tree.dimension() << " \n";
 
-  // Sort the simplices in the order of the filtration
-  simplex_tree.initialize_filtration();
-
   // Compute the persistence diagram of the complex
   Persistent_cohomology pcoh(simplex_tree);
   // initializes the coefficient field for homology
diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
index 7da9f15d..a503d983 100644
--- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
@@ -76,9 +76,6 @@ int main(int argc, char * argv[]) {
   std::clog << "The complex contains " << st.num_simplices() << " simplices \n";
   std::clog << "   and has dimension " << st.dimension() << " \n";
 
-  // Sort the simplices in the order of the filtration
-  st.initialize_filtration();
-
   // Compute the persistence diagram of the complex
   Persistent_cohomology pcoh(st);
   // initializes the coefficient field for homology
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index ca4bc10d..bc111f94 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -561,7 +561,6 @@ class Persistent_cohomology {
   void output_diagram(std::ostream& ostream = std::cout) {
     cmp_intervals_by_length cmp(cpx_);
     std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp);
-    bool has_infinity = std::numeric_limits<Filtration_value>::has_infinity;
     for (auto pair : persistent_pairs_) {
       ostream << get<2>(pair) << "  " << cpx_->dimension(get<0>(pair)) << " "
         << cpx_->filtration(get<0>(pair)) << " "
@@ -573,7 +572,6 @@ class Persistent_cohomology {
     std::ofstream diagram_out(diagram_name.c_str());
     cmp_intervals_by_length cmp(cpx_);
     std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp);
-    bool has_infinity = std::numeric_limits<Filtration_value>::has_infinity;
     for (auto pair : persistent_pairs_) {
       diagram_out << cpx_->dimension(get<0>(pair)) << " "
             << cpx_->filtration(get<0>(pair)) << " "
-- 
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