fixed code to enable cached diameters without coefficients

1 files changed, 92 insertions, 82 deletions

diff --git a/ripser.cpp b/ripser.cpp
index 5c29022..3b0acae 100644
--- a/ripser.cpp
+++ b/ripser.cpp
@@ -18,20 +18,20 @@ typedef long coefficient_t;
 //#define PRECOMPUTE_DIAMETERS
 //#define PRECOMPUTE_DIAMETERS_IN_TOP_DIMENSION
 
-#define STORE_DIAMETERS
+//#define STORE_DIAMETERS
 
 #define USE_BINARY_SEARCH
 //#define USE_EXPONENTIAL_SEARCH
 
-#define ASSEMBLE_REDUCTION_MATRIX
-#define USE_COEFFICIENTS
+//#define ASSEMBLE_REDUCTION_MATRIX
+//#define USE_COEFFICIENTS
 
 //#define INDICATE_PROGRESS
-#define PRINT_PERSISTENCE_PAIRS
+//#define PRINT_PERSISTENCE_PAIRS
 
 //#define FILE_FORMAT_DIPHA
-//#define FILE_FORMAT_UPPER_TRIANGULAR_CSV
-#define FILE_FORMAT_LOWER_TRIANGULAR_CSV
+#define FILE_FORMAT_UPPER_TRIANGULAR_CSV
+//#define FILE_FORMAT_LOWER_TRIANGULAR_CSV
 
 class binomial_coeff_table {
     std::vector<std::vector<index_t> > B;
@@ -124,63 +124,7 @@ std::vector<index_t> vertices_of_simplex(const index_t simplex_index, const inde
     return vertices;
 }
 
-template <typename DistanceMatrix>
-class rips_filtration_comparator {
-public:
-    const DistanceMatrix& dist;
-    
-    const index_t dim;
-
-private:
-    mutable std::vector<index_t> vertices;
-    
-    const binomial_coeff_table& binomial_coeff;
-    
-public:
-    rips_filtration_comparator(
-        const DistanceMatrix& _dist,
-        const index_t _dim,
-        const binomial_coeff_table& _binomial_coeff
-    ): dist(_dist), dim(_dim), vertices(_dim + 1), binomial_coeff(_binomial_coeff) {};
-    
-    inline value_t diameter(const index_t index) const {
-        value_t diam = 0;
-        get_simplex_vertices(index, dim, dist.size(), binomial_coeff, vertices.begin() );
-        
-        for (index_t i = 0; i <= dim; ++i)
-            for (index_t j = 0; j < i; ++j) {
-                diam = std::max(diam, dist(vertices[i], vertices[j]));
-            }
-        return diam;
-    }
-
-    inline bool operator()(const index_t a, const index_t b) const
-    {
-        assert(a < binomial_coeff(dist.size(), dim + 1));
-        assert(b < binomial_coeff(dist.size(), dim + 1));
-        
-        value_t a_diam = 0, b_diam = 0;
-    
-        b_diam = diameter(b);
-        
-        get_simplex_vertices(a, dim, dist.size(), binomial_coeff, vertices.begin() );
-        for (index_t i = 0; i <= dim; ++i)
-            for (index_t j = i + 1; j <= dim; ++j) {
-                a_diam = std::max(a_diam, dist(vertices[i], vertices[j]));
-                if (a_diam > b_diam)
-                    return true;
-            }
-       
-        return (a_diam == b_diam) && (a > b);
-    }
-    
-    template <typename Entry>
-    inline bool operator()(const Entry& a, const Entry& b) const
-    {
-        return operator()(get_index(a), get_index(b));
-    }
 
-};
 
 #ifdef USE_COEFFICIENTS
 struct entry_t {
@@ -225,7 +169,7 @@ std::ostream& operator<< (std::ostream& stream, const entry_t& e) {
 
 typedef index_t entry_t;
 
-inline index_t get_index(entry_t i) {
+inline const index_t get_index(entry_t i) {
     return i;
 }
 
@@ -237,6 +181,8 @@ inline entry_t make_entry(index_t _index, coefficient_t _value) {
     return entry_t(_index);
 }
 
+inline void set_coefficient(index_t& e, const coefficient_t c) { e = c; }
+
 #endif
 
 inline const entry_t& get_entry(const entry_t& e) { return e; }
@@ -248,6 +194,89 @@ struct greater_index {
 };
 
 
+
+#ifdef STORE_DIAMETERS
+typedef std::pair<entry_t, value_t> entry_diameter_t;
+
+inline const entry_t& get_entry(const entry_diameter_t& p) { return p.first; }
+inline entry_t& get_entry(entry_diameter_t& p) { return p.first; }
+inline const index_t get_index(const entry_diameter_t& p) { return get_index(get_entry(p)); }
+inline const coefficient_t get_coefficient(const entry_diameter_t& p) { return get_coefficient(get_entry(p)); }
+inline const value_t& get_diameter(const entry_diameter_t& p) { return p.second; }
+inline void set_coefficient(entry_diameter_t& p, const coefficient_t c) { set_coefficient(get_entry(p), c); }
+
+
+struct greater_diameter_or_index {
+    inline bool operator() (const entry_diameter_t& a, const entry_diameter_t& b) {
+        return (get_diameter(a) > get_diameter(b)) ||
+            ((get_diameter(a) == get_diameter(b)) && (get_index(a) > get_index(b)));
+    }
+};
+#else
+typedef entry_t entry_diameter_t;
+#endif
+
+
+
+template <typename DistanceMatrix>
+class rips_filtration_comparator {
+public:
+    const DistanceMatrix& dist;
+    
+    const index_t dim;
+
+private:
+    mutable std::vector<index_t> vertices;
+    
+    const binomial_coeff_table& binomial_coeff;
+    
+public:
+    rips_filtration_comparator(
+        const DistanceMatrix& _dist,
+        const index_t _dim,
+        const binomial_coeff_table& _binomial_coeff
+    ): dist(_dist), dim(_dim), vertices(_dim + 1), binomial_coeff(_binomial_coeff) {};
+    
+    inline value_t diameter(const index_t index) const {
+        value_t diam = 0;
+        get_simplex_vertices(index, dim, dist.size(), binomial_coeff, vertices.begin() );
+        
+        for (index_t i = 0; i <= dim; ++i)
+            for (index_t j = 0; j < i; ++j) {
+                diam = std::max(diam, dist(vertices[i], vertices[j]));
+            }
+        return diam;
+    }
+
+    inline bool operator()(const index_t a, const index_t b) const
+    {
+        assert(a < binomial_coeff(dist.size(), dim + 1));
+        assert(b < binomial_coeff(dist.size(), dim + 1));
+        
+        value_t a_diam = 0, b_diam = 0;
+    
+        b_diam = diameter(b);
+        
+        get_simplex_vertices(a, dim, dist.size(), binomial_coeff, vertices.begin() );
+        for (index_t i = 0; i <= dim; ++i)
+            for (index_t j = i + 1; j <= dim; ++j) {
+                a_diam = std::max(a_diam, dist(vertices[i], vertices[j]));
+                if (a_diam > b_diam)
+                    return true;
+            }
+       
+        return (a_diam == b_diam) && (a > b);
+    }
+    
+    template <typename Entry>
+    inline bool operator()(const Entry& a, const Entry& b) const
+    {
+        return operator()(get_index(a), get_index(b));
+    }
+
+};
+
+
 class simplex_coboundary_enumerator {
 private:
     index_t idx, modified_idx, dim, n, k;
@@ -499,25 +528,6 @@ public:
 
 
 
-#ifdef STORE_DIAMETERS
-typedef std::pair<entry_t, value_t> entry_diameter_t;
-
-inline const entry_t& get_entry(const entry_diameter_t& p) { return p.first; }
-inline const index_t get_index(const entry_diameter_t& p) { return get_index(get_entry(p)); }
-inline const coefficient_t get_coefficient(const entry_diameter_t& p) { return get_coefficient(get_entry(p)); }
-inline const value_t& get_diameter(const entry_diameter_t& p) { return p.second; }
-inline void set_coefficient(entry_diameter_t& p, const coefficient_t c) { set_coefficient(p.first, c); }
-
-
-struct greater_diameter_or_index {
-    inline bool operator() (const entry_diameter_t& a, const entry_diameter_t& b) {
-        return (get_diameter(a) > get_diameter(b)) ||
-            ((get_diameter(a) == get_diameter(b)) && (get_index(a) > get_index(b)));
-    }
-};
-#else
-typedef entry_t entry_diameter_t;
-#endif
 
 
 #ifdef USE_COEFFICIENTS