diff options
Diffstat (limited to 'src/Simplex_tree/include')
-rw-r--r-- | src/Simplex_tree/include/gudhi/Simplex_tree.h | 113 |
1 files changed, 113 insertions, 0 deletions
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 7b39a500..7be14bce 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -125,6 +125,8 @@ class Simplex_tree { private: typedef typename Dictionary::iterator Dictionary_it; typedef typename Dictionary_it::value_type Dit_value_t; + double minval_; + double maxval_; struct return_first { Vertex_handle operator()(const Dit_value_t& p_sh) const { @@ -1469,6 +1471,117 @@ class Simplex_tree { } } + /** \brief Retrieve good values for extended persistence, and separate the + * diagrams into the ordinary, relative, extended+ and extended- subdiagrams. + * Need extend_filtration to be called first! + * @param[in] dgm Persistence diagram obtained after calling this->extend_filtration + * and this->get_persistence. + * @return A vector of four persistence diagrams. The first one is Ordinary, the + * second one is Relative, the third one is Extended+ and the fourth one is Extended-. + */ + std::vector<std::vector<std::pair<int, std::pair<double, double>>>> compute_extended_persistence_subdiagrams(const std::vector<std::pair<int, std::pair<double, double>>>& dgm){ + std::vector<std::vector<std::pair<int, std::pair<double, double>>>> new_dgm(4); + double x, y; + for(unsigned int i = 0; i < dgm.size(); i++){ + int h = dgm[i].first; + double px = dgm[i].second.first; + double py = dgm[i].second.second; + if(std::isinf(py)) continue; + else{ + if ((px <= -1) & (py <= -1)){ + x = minval_ + (maxval_-minval_)*(px + 2); + y = minval_ + (maxval_-minval_)*(py + 2); + new_dgm[0].push_back(std::make_pair(h, std::make_pair(x,y))); + } + if ((px >= 1) & (py >= 1)){ + x = minval_ - (maxval_-minval_)*(px - 2); + y = minval_ - (maxval_-minval_)*(py - 2); + new_dgm[1].push_back(std::make_pair(h, std::make_pair(x,y))); + } + if ((px <= -1) & (py >= 1)){ + x = minval_ + (maxval_-minval_)*(px + 2); + y = minval_ - (maxval_-minval_)*(py - 2); + if (x <= y){ + new_dgm[2].push_back(std::make_pair(h, std::make_pair(x,y))); + } + else{ + new_dgm[3].push_back(std::make_pair(h, std::make_pair(x,y))); + } + } + } + } + return new_dgm; + } + + /** \brief Extend filtration for computing extended persistence. + * This function only uses the filtration values at the 0-dimensional simplices, + * and computes the extended persistence diagram induced by the lower-star filtration + * computed with these values. Note that after calling this function, the filtration + * values are actually modified. The function compute_extended_persistence_subdiagrams + * retrieves the original values and separates the extended persistence diagram points + * w.r.t. their types (Ord, Rel, Ext+, Ext-) and should always be called after + * computing the persistent homology of the extended simplicial complex. + */ + void extend_filtration() { + + // Compute maximum and minimum of filtration values + int maxvert = -std::numeric_limits<int>::infinity(); + std::vector<double> filt; + for (auto sh : this->complex_simplex_range()) { + if (this->dimension(sh) == 0){ + filt.push_back(this->filtration(sh)); + maxvert = std::max(*this->simplex_vertex_range(sh).begin(), maxvert); + } + } + minval_ = *std::min_element(filt.begin(), filt.end()); + maxval_ = *std::max_element(filt.begin(), filt.end()); + maxvert += 1; + + // Compute vectors of integers corresponding to the Simplex handles + std::vector<std::vector<int> > splxs; + for (auto sh : this->complex_simplex_range()) { + std::vector<int> vr; + for (auto vh : this->simplex_vertex_range(sh)){ + vr.push_back(vh); + } + splxs.push_back(vr); + } + + // Add point for coning the simplicial complex + int count = this->num_simplices(); + std::vector<int> cone; + cone.push_back(maxvert); + auto ins = this->insert_simplex(cone, -3); + this->assign_key(ins.first, count); + count++; + + // For each simplex + for (auto vr : splxs){ + // Create cone on simplex + auto sh = this->find(vr); vr.push_back(maxvert); + if (this->dimension(sh) == 0){ + // Assign ascending value between -2 and -1 to vertex + double v = this->filtration(sh); + this->assign_filtration(sh, -2 + (v-minval_)/(maxval_-minval_)); + // Assign descending value between 1 and 2 to cone on vertex + auto ins = this->insert_simplex(vr, 2 - (v-minval_)/(maxval_-minval_)); + this->assign_key(ins.first, count); + } + else{ + // Assign value -3 to simplex and cone on simplex + this->assign_filtration(sh, -3); + auto ins = this->insert_simplex(vr, -3); + this->assign_key(ins.first, count); + } + count++; + } + + this->make_filtration_non_decreasing(); + this->initialize_filtration(); + + } + + private: Vertex_handle null_vertex_; /** \brief Total number of simplices in the complex, without the empty simplex.*/ |