multipers 2.3.3b6__cp311-cp311-manylinux_2_39_x86_64.whl

multipers/gudhi/gudhi/Flag_complex_edge_collapser.h

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+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Siddharth Pritam, Marc Glisse
+ *
+ *    Copyright (C) 2020 Inria
+ *
+ *    Modification(s):
+ *      - 2020/03 Vincent Rouvreau: integration to the gudhi library
+ *      - 2021 Marc Glisse: complete rewrite
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#ifndef FLAG_COMPLEX_EDGE_COLLAPSER_H_
+#define FLAG_COMPLEX_EDGE_COLLAPSER_H_
+
+#include <gudhi/Debug_utils.h>
+
+#include <boost/container/flat_map.hpp>
+#include <boost/container/flat_set.hpp>
+
+#ifdef GUDHI_USE_TBB
+#include <tbb/parallel_sort.h>
+#endif
+
+#include <utility>
+#include <vector>
+#include <tuple>
+#include <algorithm>
+#include <limits>
+
+namespace Gudhi {
+
+namespace collapse {
+
+/** \private
+ *
+ * \brief Flag complex sparse matrix data structure.
+ *
+ * \tparam Vertex type must be an integer type.
+ * \tparam Filtration type for the value of the filtration function.
+ */
+template<typename Vertex, typename Filtration_value>
+struct Flag_complex_edge_collapser {
+  using Filtered_edge = std::tuple<Vertex, Vertex, Filtration_value>;
+  typedef std::pair<Vertex,Vertex> Edge;
+  struct Cmpi { template<class T, class U> bool operator()(T const&a, U const&b)const{return b<a; } };
+  typedef boost::container::flat_map<Vertex, Filtration_value> Ngb_list;
+  typedef std::vector<Ngb_list> Neighbors;
+  Neighbors neighbors; // closed neighborhood
+  std::size_t num_vertices;
+  std::vector<std::tuple<Vertex, Vertex, Filtration_value>> res;
+
+#ifdef GUDHI_COLLAPSE_USE_DENSE_ARRAY
+  // Minimal matrix interface
+  // Using this matrix generally helps performance, but the memory use may be excessive for a very sparse graph
+  // (and in extreme cases the constant initialization of the matrix may start to dominate the running time).
+  // Are there cases where the matrix is too big but a hash table would help?
+  std::vector<Filtration_value> neighbors_data;
+  void init_neighbors_dense(){
+    neighbors_data.clear();
+    neighbors_data.resize(num_vertices*num_vertices, std::numeric_limits<Filtration_value>::infinity());
+  }
+  Filtration_value& neighbors_dense(Vertex i, Vertex j){return neighbors_data[num_vertices*j+i];}
+#endif
+
+  // This does not touch the events list, only the adjacency matrix(es)
+  void delay_neighbor(Vertex u, Vertex v, Filtration_value f) {
+    neighbors[u][v]=f;
+    neighbors[v][u]=f;
+#ifdef GUDHI_COLLAPSE_USE_DENSE_ARRAY
+    neighbors_dense(u,v)=f;
+    neighbors_dense(v,u)=f;
+#endif
+  }
+  void remove_neighbor(Vertex u, Vertex v) {
+    neighbors[u].erase(v);
+    neighbors[v].erase(u);
+#ifdef GUDHI_COLLAPSE_USE_DENSE_ARRAY
+    neighbors_dense(u,v)=std::numeric_limits<Filtration_value>::infinity();
+    neighbors_dense(v,u)=std::numeric_limits<Filtration_value>::infinity();
+#endif
+  }
+
+  template<class FilteredEdgeRange>
+  void read_edges(FilteredEdgeRange const&r){
+    neighbors.resize(num_vertices);
+#ifdef GUDHI_COLLAPSE_USE_DENSE_ARRAY
+    init_neighbors_dense();
+#endif
+    // Use the raw sequence to avoid maintaining the order
+    std::vector<typename Ngb_list::sequence_type> neighbors_seq(num_vertices);
+    for(auto&&e : r){
+      using std::get;
+      Vertex u = get<0>(e);
+      Vertex v = get<1>(e);
+      Filtration_value f = get<2>(e);
+      neighbors_seq[u].emplace_back(v, f);
+      neighbors_seq[v].emplace_back(u, f);
+#ifdef GUDHI_COLLAPSE_USE_DENSE_ARRAY
+      neighbors_dense(u,v)=f;
+      neighbors_dense(v,u)=f;
+#endif
+    }
+    for(std::size_t i=0;i<neighbors_seq.size();++i){
+      neighbors_seq[i].emplace_back(i, -std::numeric_limits<Filtration_value>::infinity());
+      neighbors[i].adopt_sequence(std::move(neighbors_seq[i])); // calls sort
+#ifdef GUDHI_COLLAPSE_USE_DENSE_ARRAY
+      neighbors_dense(i,i)=-std::numeric_limits<Filtration_value>::infinity();
+#endif
+    }
+  }
+
+  // Open neighborhood
+  // At some point it helped gcc to add __attribute__((noinline)) here, otherwise we had +50% on the running time
+  // on one example. It looks ok now, or I forgot which example that was.
+  void common_neighbors(boost::container::flat_set<Vertex>& e_ngb,
+      std::vector<std::pair<Filtration_value, Vertex>>& e_ngb_later,
+      Vertex u, Vertex v, Filtration_value f_event){
+    // Using neighbors_dense here seems to hurt, even if we loop on the smaller of nu and nv.
+    Ngb_list const&nu = neighbors[u];
+    Ngb_list const&nv = neighbors[v];
+    auto ui = nu.begin();
+    auto ue = nu.end();
+    auto vi = nv.begin();
+    auto ve = nv.end();
+    assert(ui != ue && vi != ve);
+    while(ui != ue && vi != ve){
+      Vertex w = ui->first;
+      if(w < vi->first) { ++ui; continue; }
+      if(w > vi->first) { ++vi; continue; }
+      // nu and nv are closed, so we need to exclude e here.
+      if(w != u && w != v) {
+        Filtration_value f = std::max(ui->second, vi->second);
+        if(f > f_event)
+          e_ngb_later.emplace_back(f, w);
+        else
+          e_ngb.insert(e_ngb.end(), w);
+      }
+      ++ui; ++vi;
+    }
+  }
+
+  // Test if the neighborhood of e is included in the closed neighborhood of c
+  template<class Ngb>
+  bool is_dominated_by(Ngb const& e_ngb, Vertex c, Filtration_value f){
+    // The best strategy probably depends on the distribution, how sparse / dense the adjacency matrix is,
+    // how (un)balanced the sizes of e_ngb and nc are.
+    // Some efficient operations on sets work best with bitsets, although the need for a map complicates things.
+#ifdef GUDHI_COLLAPSE_USE_DENSE_ARRAY
+    for(auto v : e_ngb) {
+      // if(v==c)continue;
+      if(neighbors_dense(v,c) > f) return false;
+    }
+    return true;
+#else
+    auto&&nc = neighbors[c];
+    // if few neighbors, use dichotomy? Seems slower.
+    // I tried storing a copy of neighbors as a vector<absl::flat_hash_map> and using it for nc, but it was
+    // a bit slower here. It did help with neighbors[dominator].find(w) in the main function though,
+    // sometimes enough, sometimes not.
+    auto ci = nc.begin();
+    auto ce = nc.end();
+    auto eni = e_ngb.begin();
+    auto ene = e_ngb.end();
+    assert(eni != ene);
+    assert(ci != ce);
+    // if(*eni == c && ++eni == ene) return true;
+    for(;;){
+      Vertex ve = *eni;
+      Vertex vc = ci->first;
+      while(ve > vc) {
+        // try a gallop strategy (exponential search)? Seems slower
+        if(++ci == ce) return false;
+        vc = ci->first;
+      }
+      if(ve < vc) return false;
+      // ve == vc
+      if(ci->second > f) return false;
+      if(++eni == ene)return true;
+      // If we stored an open neighborhood of c (excluding c), we would need to test for c here and before the loop
+      // if(*eni == c && ++eni == ene)return true;
+      if(++ci == ce) return false;
+    }
+#endif
+  }
+
+  template<class FilteredEdgeRange, class Delay>
+  void process_edges(FilteredEdgeRange const& edges, Delay&& delay) {
+    {
+      Vertex maxi = 0, maxj = 0;
+      for(auto& fe : edges) {
+        Vertex i = std::get<0>(fe);
+        Vertex j = std::get<1>(fe);
+        if (i > maxi) maxi = i;
+        if (j > maxj) maxj = j;
+      }
+      num_vertices = std::max(maxi, maxj) + 1;
+    }
+
+    read_edges(edges);
+
+    boost::container::flat_set<Vertex> e_ngb;
+    e_ngb.reserve(num_vertices);
+    std::vector<std::pair<Filtration_value, Vertex>> e_ngb_later;
+    for(auto&e:edges) {
+      {
+        Vertex u = std::get<0>(e);
+        Vertex v = std::get<1>(e);
+        Filtration_value input_time = std::get<2>(e);
+        auto time = delay(input_time);
+        auto start_time = time;
+        e_ngb.clear();
+        e_ngb_later.clear();
+        common_neighbors(e_ngb, e_ngb_later, u, v, time);
+        // If we identify a good candidate (the first common neighbor) for being a dominator of e until infinity,
+        // we could check that a bit more cheaply. It does not seem to help though.
+        auto cmp1=[](auto const&a, auto const&b){return a.first > b.first;};
+        auto e_ngb_later_begin=e_ngb_later.begin();
+        auto e_ngb_later_end=e_ngb_later.end();
+        bool heapified = false;
+
+        bool dead = false;
+        while(true) {
+          Vertex dominator = -1;
+          // special case for size 1
+          // if(e_ngb.size()==1){dominator=*e_ngb.begin();}else
+          // It is tempting to test the dominators in increasing order of filtration value, which is likely to reduce
+          // the number of calls to is_dominated_by before finding a dominator, but sorting, even partially / lazily,
+          // is very expensive.
+          for(auto c : e_ngb){
+            if(is_dominated_by(e_ngb, c, time)){
+              dominator = c;
+              break;
+            }
+          }
+          if(dominator==-1) break;
+          // Push as long as dominator remains a dominator.
+          // Iterate on times where at least one neighbor appears.
+          for (bool still_dominated = true; still_dominated; ) {
+            if(e_ngb_later_begin == e_ngb_later_end) {
+              dead = true; goto end_move;
+            }
+            if(!heapified) {
+              // Eagerly sorting can be slow
+              std::make_heap(e_ngb_later_begin, e_ngb_later_end, cmp1);
+              heapified=true;
+            }
+            time = e_ngb_later_begin->first; // first place it may become critical
+            // Update the neighborhood for this new time, while checking if any of the new neighbors break domination.
+            while (e_ngb_later_begin != e_ngb_later_end && e_ngb_later_begin->first <= time) {
+              Vertex w = e_ngb_later_begin->second;
+#ifdef GUDHI_COLLAPSE_USE_DENSE_ARRAY
+              if (neighbors_dense(dominator,w) > e_ngb_later_begin->first)
+                still_dominated = false;
+#else
+              auto& ngb_dom = neighbors[dominator];
+              auto wit = ngb_dom.find(w); // neighborhood may be open or closed, it does not matter
+              if (wit == ngb_dom.end() || wit->second > e_ngb_later_begin->first)
+                still_dominated = false;
+#endif
+              e_ngb.insert(w);
+              std::pop_heap(e_ngb_later_begin, e_ngb_later_end--, cmp1);
+            }
+          } // this doesn't seem to help that much...
+        }
+end_move:
+        if(dead) {
+          remove_neighbor(u, v);
+        } else if(start_time != time) {
+          delay_neighbor(u, v, time);
+          res.emplace_back(u, v, time);
+        } else {
+          res.emplace_back(u, v, input_time);
+        }
+      }
+    }
+  }
+
+  std::vector<Filtered_edge> output() {
+    return std::move(res);
+  }
+
+};
+
+template<class R> R to_range(R&& r) { return std::move(r); }
+template<class R, class T> R to_range(T const& t) { R r; r.insert(r.end(), t.begin(), t.end()); return r; }
+
+template<class FilteredEdgeRange, class Delay>
+auto flag_complex_collapse_edges(FilteredEdgeRange&& edges, Delay&&delay) {
+  // Would it help to label the points according to some spatial sorting?
+  auto first_edge_itr = std::begin(edges);
+  using Vertex = std::decay_t<decltype(std::get<0>(*first_edge_itr))>;
+  using Filtration_value = std::decay_t<decltype(std::get<2>(*first_edge_itr))>;
+  using Edge_collapser = Flag_complex_edge_collapser<Vertex, Filtration_value>;
+  if (first_edge_itr != std::end(edges)) {
+    auto edges2 = to_range<std::vector<typename Edge_collapser::Filtered_edge>>(std::forward<FilteredEdgeRange>(edges));
+#ifdef GUDHI_USE_TBB
+    // I think this sorting is always negligible compared to the collapse, but parallelizing it shouldn't hurt.
+    tbb::parallel_sort(edges2.begin(), edges2.end(),
+        [](auto const&a, auto const&b){return std::get<2>(a)>std::get<2>(b);});
+#else
+    std::sort(edges2.begin(), edges2.end(), [](auto const&a, auto const&b){return std::get<2>(a)>std::get<2>(b);});
+#endif
+    Edge_collapser edge_collapser;
+    edge_collapser.process_edges(edges2, std::forward<Delay>(delay));
+    return edge_collapser.output();
+  }
+  return std::vector<typename Edge_collapser::Filtered_edge>();
+}
+
+/** \brief Implicitly constructs a flag complex from edges as an input, collapses edges while preserving the persistent
+ * homology and returns the remaining edges as a range. The filtration value of vertices is irrelevant to this function.
+ *
+ * \param[in] edges Range of Filtered edges. There is no need for the range to be sorted, as it will be done internally.
+ *
+ * \tparam FilteredEdgeRange Range of `std::tuple<Vertex_handle, Vertex_handle, Filtration_value>`
+ * where `Vertex_handle` is the type of a vertex index.
+ *
+ * \return Remaining edges after collapse as a range of
+ * `std::tuple<Vertex_handle, Vertex_handle, Filtration_value>`.
+ *
+ * \ingroup edge_collapse
+ *
+ * \note
+ * Advanced: Defining the macro GUDHI_COLLAPSE_USE_DENSE_ARRAY tells gudhi to allocate a square table of size the
+ * maximum vertex index. This usually speeds up the computation for dense graphs. However, for sparse graphs, the memory
+ * use may be problematic and initializing this large table may be slow.
+ */
+template<class FilteredEdgeRange> auto flag_complex_collapse_edges(const FilteredEdgeRange& edges) {
+  return flag_complex_collapse_edges(edges, [](auto const&d){return d;});
+}
+
+}  // namespace collapse
+
+}  // namespace Gudhi
+
+#endif  // FLAG_COMPLEX_EDGE_COLLAPSER_H_