Rename enum.

10 files changed, 23 insertions, 27 deletions

diff --git a/matching/include/bifiltration.h b/matching/include/bifiltration.h
index 2b4950f..bdb7a4e 100644
--- a/matching/include/bifiltration.h
+++ b/matching/include/bifiltration.h
@@ -85,12 +85,12 @@ namespace md {
 
         void rivet_format_reader(std::ifstream&);
 
-        void rene_format_reader(std::ifstream&);
+        void phat_like_format_reader(std::ifstream&);
 
         // in Rene format each simplex knows IDs of its boundary facets
-        // postprocess_rene_format fills vector of IDs of boundary facets
+        // postprocess_phat_like_format fills vector of IDs of boundary facets
         // in each simplex
-        void postprocess_rene_format();
+        void postprocess_phat_like_format();
 
         // in Rivet format each simplex knows its vertices,
         // postprocess_rivet_format fills vector of IDs of boundary facets
diff --git a/matching/include/matching_distance.h b/matching/include/matching_distance.h
index 72743a4..bb1dfea 100644
--- a/matching/include/matching_distance.h
+++ b/matching/include/matching_distance.h
@@ -77,13 +77,11 @@ namespace md {
 #endif
     };
 
+
     template<class DiagramProvider>
     class DistanceCalculator {
 
-//        using DiagramProvider = md::Bifiltration;
-//        using DiagramProvider = md::ModulePresentation;
         using DualBox = md::DualBox;
-
         using CellValueVector = std::vector<CellWithValue>;
 
     public:
diff --git a/matching/include/simplex.h b/matching/include/simplex.h
index e0a654b..e9d0e30 100644
--- a/matching/include/simplex.h
+++ b/matching/include/simplex.h
@@ -12,7 +12,7 @@ namespace md {
     class Bifiltration;
 
     enum class BifiltrationFormat {
-        rene, rivet
+        phat_like, rivet
     };
 
     class AbstractSimplex {
@@ -85,7 +85,7 @@ namespace md {
 
         void init_rivet(std::string s);
 
-        void init_rene(std::string s);
+        void init_phat_like(std::string s);
 
         Index id() const { return id_; }
 
diff --git a/matching/src/bifiltration.cpp b/matching/src/bifiltration.cpp
index b0d4248..676b0cc 100644
--- a/matching/src/bifiltration.cpp
+++ b/matching/src/bifiltration.cpp
@@ -42,8 +42,8 @@ namespace md {
             case BifiltrationFormat::rivet :
                 rivet_format_reader(ifstr);
                 break;
-            case BifiltrationFormat::rene :
-                rene_format_reader(ifstr);
+            case BifiltrationFormat::phat_like :
+                phat_like_format_reader(ifstr);
                 break;
         }
         init();
@@ -64,9 +64,9 @@ namespace md {
         }
     }
 
-    void Bifiltration::rene_format_reader(std::ifstream& ifstr)
+    void Bifiltration::phat_like_format_reader(std::ifstream& ifstr)
     {
-        spd::debug("Enter rene_format_reader");
+        spd::debug("Enter phat_like_format_reader");
         // read stream line by line; do not use >> operator
         std::string s;
         std::getline(ifstr, s);
@@ -74,7 +74,7 @@ namespace md {
 
         for(Index index = 0; index < n_simplices; index++) {
             std::getline(ifstr, s);
-            simplices_.emplace_back(index, s, BifiltrationFormat::rene);
+            simplices_.emplace_back(index, s, BifiltrationFormat::phat_like);
         }
         spd::debug("Read {} simplices from file", n_simplices);
     }
@@ -245,7 +245,7 @@ namespace md {
             case BifiltrationFormat::rivet:
                 throw std::runtime_error("Not implemented");
                 break;
-            case BifiltrationFormat::rene: {
+            case BifiltrationFormat::phat_like: {
                 std::ofstream f(filename);
                 if (not f.good()) {
                     std::cerr << "Bifiltration::save: cannot open file " << filename << std::endl;
diff --git a/matching/src/main.cpp b/matching/src/main.cpp
index 34c4240..7e74475 100644
--- a/matching/src/main.cpp
+++ b/matching/src/main.cpp
@@ -176,8 +176,8 @@ int main(int argc, char** argv)
     auto bounds_list = split_by_delim(bounds_list_str, ',');

     auto traverse_list = split_by_delim(traverse_list_str, ',');

 

-    Bifiltration bif_a(fname_a, BifiltrationFormat::rene);

-    Bifiltration bif_b(fname_b, BifiltrationFormat::rene);

+    Bifiltration bif_a(fname_a, BifiltrationFormat::phat_like);

+    Bifiltration bif_b(fname_b, BifiltrationFormat::phat_like);

 

     bif_a.sanity_check();

     bif_b.sanity_check();

diff --git a/matching/src/simplex.cpp b/matching/src/simplex.cpp
index 661dcb1..b490db0 100644
--- a/matching/src/simplex.cpp
+++ b/matching/src/simplex.cpp
@@ -76,16 +76,16 @@ namespace md {
             dim++;
             vertices_.push_back(vertex);
         }
-        // 
+        //
         std::sort(vertices_.begin(), vertices_.end());
         assert(dim > 0);
-        
+
         std::stringstream pos_ss(pos_str);
         // TODO: get rid of 1-criticaltiy assumption
         pos_ss >> pos_.x >> pos_.y;
     }
 
-    void Simplex::init_rene(std::string s)
+    void Simplex::init_phat_like(std::string s)
     {
         facet_indices_.clear();
         std::stringstream ss(s);
@@ -104,8 +104,8 @@ namespace md {
             :id_(_id)
     {
         switch (input_format) {
-            case BifiltrationFormat::rene :
-                init_rene(s);
+            case BifiltrationFormat::phat_like :
+                init_phat_like(s);
                 break;
             case BifiltrationFormat::rivet :
                 init_rivet(s);
diff --git a/matching/src/test_generator.cpp b/matching/src/test_generator.cpp
index a0d8fc7..e8f128f 100644
--- a/matching/src/test_generator.cpp
+++ b/matching/src/test_generator.cpp
@@ -201,7 +201,7 @@ int main(int argc, char** argv)
 
     auto bif1 = get_random_bifiltration(n_vertices, max_dim, n_top_simplices);
     std::cout << "Generated bifiltration." << std::endl;
-    bif1.save(fname, md::BifiltrationFormat::rene);
+    bif1.save(fname, md::BifiltrationFormat::phat_like);
     std::cout << "Saved to file " << fname << std::endl;
     return 0;
 }
diff --git a/matching/src/tests/test_bifiltration.cpp b/matching/src/tests/test_bifiltration.cpp
index caa50ac..742dab8 100644
--- a/matching/src/tests/test_bifiltration.cpp
+++ b/matching/src/tests/test_bifiltration.cpp
@@ -11,7 +11,7 @@ using namespace md;
 
 //TEST_CASE("Small check", "[bifiltration][dim2]")
 //{
-//    Bifiltration bif("/home/narn/code/matching_distance/code/src/tests/test_bifiltration_full_triangle_rene.txt", BifiltrationFormat::rene);
+//    Bifiltration bif("/home/narn/code/matching_distance/code/src/tests/test_bifiltration_full_triangle_phat_like.txt", BifiltrationFormat::phat_like);
 //    auto simplices = bif.simplices();
 //    bif.sanity_check();
 //
diff --git a/matching/src/tests/test_common.cpp b/matching/src/tests/test_common.cpp
index 30465e4..c55577e 100644
--- a/matching/src/tests/test_common.cpp
+++ b/matching/src/tests/test_common.cpp
@@ -167,8 +167,6 @@ TEST_CASE("Flat Line with positive slope", "[flat_line]")
     Point p_4(6, 4.5);
     Point p_5(2, 2);
 
-    std::cout << "AHOY " << l_flat.y_from_x(p_2.x) << std::endl;
-
     REQUIRE((not l_flat.contains(p_1) and
             not l_flat.contains(p_2) and
             not l_flat.contains(p_3) and
diff --git a/matching/src/tests/test_matching_distance.cpp b/matching/src/tests/test_matching_distance.cpp
index caf32cd..90baa0f 100644
--- a/matching/src/tests/test_matching_distance.cpp
+++ b/matching/src/tests/test_matching_distance.cpp
@@ -115,8 +115,8 @@ TEST_CASE("Bifiltrations from file", "[matching_distance][small_example][lesnick
     fname_a = "/home/narn/code/matching_distance/code/python_scripts/prism_1_lesnick.bif";
     fname_b = "/home/narn/code/matching_distance/code/python_scripts/prism_2_lesnick.bif";
 
-    Bifiltration bif_a(fname_a, BifiltrationFormat::rene);
-    Bifiltration bif_b(fname_b, BifiltrationFormat::rene);
+    Bifiltration bif_a(fname_a, BifiltrationFormat::phat_like);
+    Bifiltration bif_b(fname_b, BifiltrationFormat::phat_like);
 
     CalculationParams params;