Reorganize matching_dist code, minor fixes.

14 files changed, 36 insertions, 243 deletions

diff --git a/matching/CMakeLists.txt b/matching/CMakeLists.txt
index 121e25c..3ee0f6b 100644
--- a/matching/CMakeLists.txt
+++ b/matching/CMakeLists.txt
@@ -22,7 +22,6 @@ set(CMAKE_CXX_STANDARD 14)
 
 if (NOT WIN32)
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-    #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}  ${OpenMP_CXX_FLAGS} -Wall pedantic -Wextra ")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}  ${OpenMP_CXX_FLAGS} -Wall -Wextra ")
     set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -D_GLIBCXX_DEBUG")
     set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELEASE} -O2 -g -ggdb")
@@ -31,32 +30,23 @@ endif (NOT WIN32)
 file(GLOB BT_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/../bottleneck/include/*.h ${CMAKE_CURRENT_SOURCE_DIR}/../bottleneck/include/*.hpp)
 file(GLOB MD_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/include/*.h ${CMAKE_CURRENT_SOURCE_DIR}/include/*.hpp)
 
-file(GLOB SRC_FILES ${CMAKE_CURRENT_SOURCE_DIR}/src/*.cpp)
-
-file(GLOB SRC_TEST_FILES ${CMAKE_CURRENT_SOURCE_DIR}/src/tests/*.cpp)
-
+file(GLOB SRC_TEST_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tests/*.cpp)
+ 
 find_package(Threads)
 set(libraries ${libraries} "stdc++fs" ${CMAKE_THREAD_LIBS_INIT})
 
 
 find_package(OpenMP)
 if (OPENMP_FOUND)
-set(libraries ${libraries} ${OpenMP_CXX_LIBRARIES})
-set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+    set(libraries ${libraries} ${OpenMP_CXX_LIBRARIES})
+    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+    set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
 endif()
 
 
-add_executable(matching_distance "src/main.cpp" ${MD_HEADERS} ${BT_HEADERS} )
-target_link_libraries(matching_distance PUBLIC ${libraries})
+add_executable(matching_dist "example/matching_dist.cpp" ${MD_HEADERS} ${BT_HEADERS} )
+target_link_libraries(matching_dist PUBLIC ${libraries})
 
 add_executable(matching_distance_test ${SRC_TEST_FILES} ${BT_HEADERS} ${MD_HEADERS})
 target_link_libraries(matching_distance_test PUBLIC ${libraries})
-
-add_executable(test_generator "src/test_generator.cpp"
-        ${MD_HEADERS}
-        ${BT_HEADERS})
-target_link_libraries(test_generator PUBLIC ${libraries})
-
-#add_executable(matching_distance "include/main.cpp" "src/box.cpp" "src/common_util.cpp" "src/line.cpp" "src/persistence_module.hpp" ${BT_HEADERS} ${MD_HEADERS})
diff --git a/matching/README b/matching/README.md
index 7dc1874..7dc1874 100644
--- a/matching/README
+++ b/matching/README.md
diff --git a/matching/src/main.cpp b/matching/example/matching_dist.cpp
index 2093457..13e5c6d 100644
--- a/matching/src/main.cpp
+++ b/matching/example/matching_dist.cpp
@@ -5,7 +5,7 @@
 #include <cassert>

 #include <experimental/filesystem>

 

-#ifdef EXPERIMENTAL_TIMING

+#ifdef MD_EXPERIMENTAL_TIMING

 #include <chrono>

 #endif

 

@@ -24,12 +24,6 @@ using namespace md;
 

 namespace fs = std::experimental::filesystem;

 

-void force_instantiation()

-{

-    DualBox<Real> db;

-    std::cout << db;

-}

-

 #ifdef PRINT_HEAT_MAP

 void print_heat_map(const md::HeatMaps<Real>& hms, std::string fname, const CalculationParams<Real>& params)

 {

@@ -149,14 +143,25 @@ int main(int argc, char** argv)
     using opts::PosOption;

     opts::Options ops;

 

+    CalculationParams<Real> params;

+

     bool help = false;

+

+#ifdef MD_EXPERIMENTAL_TIMING

     bool no_stop_asap = false;

-    CalculationParams<Real> params;

+#endif

+

 

 #ifdef PRINT_HEAT_MAP

     bool heatmap_only = false;

 #endif

 

+    // default values are the best for practical use

+    // if compiled with MD_EXPERIMENTAL_TIMING, user can supply

+    // different bounds and traverse strategies

+    // separated by commas, all combinations will be timed.

+    // See corresponding >> operators in matching_distance.h

+    // for possible values.

     std::string bounds_list_str = "local_combined";

     std::string traverse_list_str = "BFS";

 

@@ -164,10 +169,12 @@ int main(int argc, char** argv)
         >> Option('e', "max-error", params.delta, "error threshold")

         >> Option('d', "dim", params.dim, "dim")

         >> Option('i', "initial-depth", params.initialization_depth, "initialization depth")

+#ifdef MD_EXPERIMENTAL_TIMING

         >> Option("no-stop-asap", no_stop_asap,

                 "don't stop looping over points, if cell cannot be pruned (asap is on by default)")

         >> Option("bounds", bounds_list_str, "bounds to use, separated by ,")

-        >> Option("traverse", traverse_list_str, "traverse to use, separated by ,")

+        >> Option("traverse", traverse_list_str, "traverse strategy to use, separated by ,")

+#endif

 #ifdef PRINT_HEAT_MAP

         >> Option("heatmap-only", heatmap_only, "only save heatmap (bruteforce)")

 #endif

@@ -177,11 +184,15 @@ int main(int argc, char** argv)
     std::string fname_b;

 

     if (!ops.parse(argc, argv) || help || !(ops >> PosOption(fname_a) >> PosOption(fname_b))) {

-        std::cerr << "Usage: " << argv[0] << "bifiltration-file-1 bifiltration-file-2\n" << ops << std::endl;

+        std::cerr << "Usage: " << argv[0] << " bifiltration-file-1 bifiltration-file-2\n" << ops << std::endl;

         return 1;

     }

 

+#ifdef MD_EXPERIMENTAL_TIMING

     params.stop_asap = not no_stop_asap;

+#else

+    params.stop_asap = true;

+#endif

 

     auto bounds_list = split_by_delim(bounds_list_str, ',');

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

@@ -206,7 +217,7 @@ int main(int argc, char** argv)
     }

 

 

-#ifdef EXPERIMENTAL_TIMING

+#ifdef MD_EXPERIMENTAL_TIMING

 

     for(auto bs : bound_strategies) {

         for(auto ts : traverse_strategies) {

@@ -215,7 +226,7 @@ int main(int argc, char** argv)
     }

 

     struct ExperimentResult {

-        CalculationParams<Real> params {CalculationParams()};

+        CalculationParams<Real> params {CalculationParams<Real>()};

         int n_hera_calls {0};

         double total_milliseconds_elapsed {0};

         Real distance {0};

@@ -265,12 +276,14 @@ int main(int argc, char** argv)
 

     const int n_repetitions = 1;

 

+#ifdef PRINT_HEAT_MAP

     if (heatmap_only) {

         bound_strategies.clear();

         bound_strategies.push_back(BoundStrategy::bruteforce);

         traverse_strategies.clear();

         traverse_strategies.push_back(TraverseStrategy::breadth_first);

     }

+#endif

 

     std::map<std::tuple<BoundStrategy, TraverseStrategy>, ExperimentResult> results;

     for(BoundStrategy bound_strategy : bound_strategies) {

@@ -293,9 +306,11 @@ int main(int argc, char** argv)
             // remember: params is passed by reference to return real relative error and heat map

 

             int user_max_iters = params.max_depth;

+#ifdef PRINT_HEAT_MAP

             if (bound_strategy == BoundStrategy::bruteforce and not heatmap_only) {

                 params_experiment.max_depth = std::min(7, params.max_depth);

             }

+#endif

             double total_milliseconds_elapsed = 0;

             int total_n_hera_calls = 0;

             Real dist;

@@ -377,6 +392,5 @@ int main(int argc, char** argv)
     Real dist = matching_distance<Real>(bif_a, bif_b, params);

     std::cout << dist << std::endl;

 #endif

-    force_instantiation();

     return 0;

 }

diff --git a/matching/include/matching_distance.h b/matching/include/matching_distance.h
index 5be34c7..276cc3a 100644
--- a/matching/include/matching_distance.h
+++ b/matching/include/matching_distance.h
@@ -169,7 +169,7 @@ namespace md {
         bool print_stats { false };
 
 #ifdef MD_PRINT_HEAT_MAP
-        HeatMaps heat_maps;
+        HeatMaps<Real> heat_maps;
 #endif
     };
 
diff --git a/matching/src/test_generator.cpp b/matching/src/test_generator.cpp
deleted file mode 100644
index a2f0625..0000000
--- a/matching/src/test_generator.cpp
+++ /dev/null
@@ -1,211 +0,0 @@
-#include <map>
-#include <vector>
-#include <random>
-#include <iostream>
-#include <algorithm>
-
-#include "opts/opts.h"
-#include "spdlog/spdlog.h"
-#include "spdlog/fmt/ostr.h"
-
-#include "common_util.h"
-#include "bifiltration.h"
-
-using Real = double;
-using Index = md::Index;
-using Point = md::Point<Real>;
-using Bifiltration = md::Bifiltration<Real>;
-using Column = md::Column;
-using Simplex = md::Simplex<Real>;
-
-int g_max_coord = 100;
-
-using ASimplex = md::AbstractSimplex;
-
-using ASimplexToBirthMap = std::map<ASimplex, Point>;
-
-namespace spd = spdlog;
-
-// random generator is global
-std::random_device rd;
-std::mt19937_64 gen(rd());
-
-//std::mt19937_64 gen(42);
-
-Point get_random_position(int max_coord)
-{
-    assert(max_coord > 0);
-    std::uniform_int_distribution<int> distr(0, max_coord);
-    return Point(distr(gen), distr(gen));
-
-}
-
-Point get_random_position_less_than(Point ub)
-{
-    std::uniform_int_distribution<int> distr_x(0, ub.x);
-    std::uniform_int_distribution<int> distr_y(0, ub.y);
-    return Point(distr_x(gen), distr_y(gen));
-}
-
-Point get_random_position_greater_than(Point lb)
-{
-    std::uniform_int_distribution<int> distr_x(lb.x, g_max_coord);
-    std::uniform_int_distribution<int> distr_y(lb.y, g_max_coord);
-    return Point(distr_x(gen), distr_y(gen));
-}
-
-// non-proper faces (empty and simplex itself) are also faces
-bool is_face(const ASimplex& face_candidate, const ASimplex& coface_candidate)
-{
-    return std::includes(coface_candidate.begin(), coface_candidate.end(), face_candidate.begin(),
-            face_candidate.end());
-}
-
-bool is_top_simplex(const ASimplex& candidate_simplex, const std::vector<ASimplex>& current_top_simplices)
-{
-    return std::none_of(current_top_simplices.begin(), current_top_simplices.end(),
-            [&candidate_simplex](const ASimplex& ts) { return is_face(candidate_simplex, ts); });
-}
-
-void add_if_top(const ASimplex& candidate_simplex, std::vector<ASimplex>& current_top_simplices)
-{
-    // check that candidate simplex is not face of someone in current_top_simplices
-    if (!is_top_simplex(candidate_simplex, current_top_simplices))
-        return;
-
-    spd::debug("candidate_simplex is top, will be added to top_simplices");
-    // remove s from currrent_top_simplices, if s is face of candidate_simplex
-    current_top_simplices.erase(std::remove_if(current_top_simplices.begin(), current_top_simplices.end(),
-            [candidate_simplex](const ASimplex& s) { return is_face(s, candidate_simplex); }),
-            current_top_simplices.end());
-
-    current_top_simplices.push_back(candidate_simplex);
-}
-
-ASimplex get_random_simplex(int n_vertices, int dim)
-{
-    std::vector<int> all_vertices(n_vertices, 0);
-    // fill in with 0..n-1
-    std::iota(all_vertices.begin(), all_vertices.end(), 0);
-    std::shuffle(all_vertices.begin(), all_vertices.end(), gen);
-    return ASimplex(all_vertices.begin(), all_vertices.begin() + dim + 1, true);
-}
-
-void generate_positions(const ASimplex& s, ASimplexToBirthMap& simplex_to_birth, Point upper_bound)
-{
-    auto pos = get_random_position_less_than(upper_bound);
-    auto curr_pos_iter = simplex_to_birth.find(s);
-    if (curr_pos_iter != simplex_to_birth.end())
-        pos = md::greatest_lower_bound(pos, curr_pos_iter->second);
-    simplex_to_birth[s] = pos;
-    for(const ASimplex& facet : s.facets()) {
-        generate_positions(facet, simplex_to_birth, pos);
-    }
-}
-
-Bifiltration get_random_bifiltration(int n_vertices, int max_dim, int n_top_simplices)
-{
-    ASimplexToBirthMap simplex_to_birth;
-
-    // generate vertices
-    for(int i = 0; i < n_vertices; ++i) {
-        Point vertex_birth = get_random_position(g_max_coord / 10);
-        ASimplex vertex;
-        vertex.push_back(i);
-        simplex_to_birth[vertex] = vertex_birth;
-    }
-
-    std::vector<ASimplex> top_simplices;
-    // generate top simplices
-    while((int)top_simplices.size() < n_top_simplices) {
-        std::uniform_int_distribution<int> dimension_distr(1, max_dim);
-        int dim = dimension_distr(gen);
-        auto candidate_simplex = get_random_simplex(n_vertices, dim);
-        spd::debug("candidate_simplex = {}", candidate_simplex);
-        add_if_top(candidate_simplex, top_simplices);
-    }
-
-    Point upper_bound{static_cast<Real>(g_max_coord), static_cast<Real>(g_max_coord)};
-    for(const auto& top_simplex : top_simplices) {
-        generate_positions(top_simplex, simplex_to_birth, upper_bound);
-    }
-
-    std::vector<std::pair<ASimplex, Point>> simplex_birth_pairs{simplex_to_birth.begin(), simplex_to_birth.end()};
-    std::vector<Column> boundaries{simplex_to_birth.size(), Column()};
-
-// assign ids and save boundaries
-    int id = 0;
-
-    for(int dim = 0; dim <= max_dim; ++dim) {
-        for(int i = 0; i < (int) simplex_birth_pairs.size(); ++i) {
-            ASimplex& simplex = simplex_birth_pairs[i].first;
-            if (simplex.dim() == dim) {
-                simplex.id = id++;
-                Column bdry;
-                for(auto& facet : simplex.facets()) {
-                    auto facet_iter = std::find_if(simplex_birth_pairs.begin(), simplex_birth_pairs.end(),
-                            [facet](const std::pair<ASimplex, Point>& sbp) { return facet == sbp.first; });
-                    assert(facet_iter != simplex_birth_pairs.end());
-                    assert(facet_iter->first.id >= 0);
-                    bdry.push_back(facet_iter->first.id);
-                }
-                std::sort(bdry.begin(), bdry.end());
-                boundaries[i] = bdry;
-            }
-        }
-    }
-
-// create vector of Simplex-es
-    std::vector<Simplex> simplices;
-    for(int i = 0; i < (int) simplex_birth_pairs.size(); ++i) {
-        int id = simplex_birth_pairs[i].first.id;
-        int dim = simplex_birth_pairs[i].first.dim();
-        Point birth = simplex_birth_pairs[i].second;
-        Column bdry = boundaries[i];
-        simplices.emplace_back(id, birth, dim, bdry);
-    }
-
-// sort by id
-    std::sort(simplices.begin(), simplices.end(),
-            [](const Simplex& s1, const Simplex& s2) { return s1.id() < s2.id(); });
-    for(int i = 0; i < (int)simplices.size(); ++i) {
-        assert(simplices[i].id() == i);
-        assert(i == 0 || simplices[i].dim() >= simplices[i - 1].dim());
-    }
-
-    return Bifiltration(simplices.begin(), simplices.end());
-}
-
-int main(int argc, char** argv)
-{
-    spd::set_level(spd::level::info);
-    int n_vertices;
-    int max_dim;
-    int n_top_simplices;
-    std::string fname;
-
-    using opts::Option;
-    using opts::PosOption;
-    opts::Options ops;
-
-    bool help = false;
-
-    ops >> Option('v', "n-vertices", n_vertices, "number of vertices")
-        >> Option('d', "max-dim", max_dim, "maximal dim")
-        >> Option('m', "max-coord", g_max_coord, "maximal coordinate")
-        >> Option('t', "n-top-simplices", n_top_simplices, "number of top simplices")
-        >> Option('h', "help", help, "show help message");
-
-    if (!ops.parse(argc, argv) || help || !(ops >> PosOption(fname))) {
-        std::cerr << "Usage: " << argv[0] << "\n" << ops << std::endl;
-        return 1;
-    }
-
-
-    auto bif1 = get_random_bifiltration(n_vertices, max_dim, n_top_simplices);
-    std::cout << "Generated bifiltration." << std::endl;
-    bif1.save(fname, md::BifiltrationFormat::phat_like);
-    std::cout << "Saved to file " << fname << std::endl;
-    return 0;
-}
-
diff --git a/matching/src/tests/prism_1.bif b/matching/tests/prism_1.bif
index b37e807..b37e807 100644
--- a/matching/src/tests/prism_1.bif
+++ b/matching/tests/prism_1.bif
diff --git a/matching/src/tests/prism_2.bif b/matching/tests/prism_2.bif
index 49885e6..49885e6 100644
--- a/matching/src/tests/prism_2.bif
+++ b/matching/tests/prism_2.bif
diff --git a/matching/src/tests/test_bifiltration.cpp b/matching/tests/test_bifiltration.cpp
index 742dab8..742dab8 100644
--- a/matching/src/tests/test_bifiltration.cpp
+++ b/matching/tests/test_bifiltration.cpp
diff --git a/matching/src/tests/test_bifiltration_1.txt b/matching/tests/test_bifiltration_1.txt
index ddd23e9..ddd23e9 120000
--- a/matching/src/tests/test_bifiltration_1.txt
+++ b/matching/tests/test_bifiltration_1.txt
diff --git a/matching/src/tests/test_bifiltration_full_triangle_rene.txt b/matching/tests/test_bifiltration_full_triangle_rene.txt
index 47f49fd..47f49fd 120000
--- a/matching/src/tests/test_bifiltration_full_triangle_rene.txt
+++ b/matching/tests/test_bifiltration_full_triangle_rene.txt
diff --git a/matching/src/tests/test_common.cpp b/matching/tests/test_common.cpp
index 9079a56..9079a56 100644
--- a/matching/src/tests/test_common.cpp
+++ b/matching/tests/test_common.cpp
diff --git a/matching/src/tests/test_list.txt b/matching/tests/test_list.txt
index 1984606..1984606 100644
--- a/matching/src/tests/test_list.txt
+++ b/matching/tests/test_list.txt
diff --git a/matching/src/tests/test_matching_distance.cpp b/matching/tests/test_matching_distance.cpp
index 82da530..82da530 100644
--- a/matching/src/tests/test_matching_distance.cpp
+++ b/matching/tests/test_matching_distance.cpp
diff --git a/matching/src/tests/tests_main.cpp b/matching/tests/tests_main.cpp
index 1c77b13..1c77b13 100644
--- a/matching/src/tests/tests_main.cpp
+++ b/matching/tests/tests_main.cpp