diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-02-02 15:45:06 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-02-02 15:45:06 +0000 |
commit | 5ae31a73253f6b29f5cbf1e04af17acf62741d9e (patch) | |
tree | 512041b9bf0835f2520e5b6b2fde0f972998efc4 /src/common/include | |
parent | 4a5332dfb88ec27157c82f77df87f588f7016736 (diff) | |
parent | 265484997185f3bf900744406206a2d64ca0a20d (diff) |
Merge last trunk modificat
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@3212 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: ea6296547b67ad82f5983d4309493e9131da7dd0
Diffstat (limited to 'src/common/include')
-rw-r--r-- | src/common/include/gudhi/Debug_utils.h | 4 | ||||
-rw-r--r-- | src/common/include/gudhi/Unitary_tests_utils.h | 40 | ||||
-rw-r--r-- | src/common/include/gudhi/distance_functions.h | 32 | ||||
-rw-r--r-- | src/common/include/gudhi/graph_simplicial_complex.h | 63 |
4 files changed, 130 insertions, 9 deletions
diff --git a/src/common/include/gudhi/Debug_utils.h b/src/common/include/gudhi/Debug_utils.h index 8ed3b7b3..90d3cf47 100644 --- a/src/common/include/gudhi/Debug_utils.h +++ b/src/common/include/gudhi/Debug_utils.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -32,7 +32,7 @@ // GUDHI_CHECK throw an exception if expression is false in debug mode, but does nothing in release mode // Could assert in release mode, but cmake sets NDEBUG (for "NO DEBUG") in this mode, means assert does nothing. #ifdef GUDHI_DEBUG - #define GUDHI_CHECK(expression, excpt) if ((expression) == 0) throw excpt + #define GUDHI_CHECK(expression, excpt) ((expression) ? (void) 0 : (throw excpt)) #define GUDHI_CHECK_code(CODE) CODE #else #define GUDHI_CHECK(expression, excpt) (void) 0 diff --git a/src/common/include/gudhi/Unitary_tests_utils.h b/src/common/include/gudhi/Unitary_tests_utils.h new file mode 100644 index 00000000..8394a062 --- /dev/null +++ b/src/common/include/gudhi/Unitary_tests_utils.h @@ -0,0 +1,40 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2017 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ +#ifndef UNITARY_TESTS_UTILS_H_ +#define UNITARY_TESTS_UTILS_H_ + +#include <boost/test/unit_test.hpp> + +#include <iostream> +#include <limits> // for std::numeric_limits<> + +template<typename FloatingType > +void GUDHI_TEST_FLOAT_EQUALITY_CHECK(FloatingType a, FloatingType b, + FloatingType epsilon = std::numeric_limits<FloatingType>::epsilon()) { +#ifdef DEBUG_TRACES + std::cout << "GUDHI_TEST_FLOAT_EQUALITY_CHECK - " << a << " versus " << b + << " | diff = " << std::fabs(a - b) << " - epsilon = " << epsilon << std::endl; +#endif + BOOST_CHECK(std::fabs(a - b) < epsilon); +} + +#endif // UNITARY_TESTS_UTILS_H_ diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index f6e2ab5a..3a5d1fd5 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -23,9 +23,14 @@ #ifndef DISTANCE_FUNCTIONS_H_ #define DISTANCE_FUNCTIONS_H_ +#include <gudhi/Debug_utils.h> + +#include <boost/range/metafunctions.hpp> + #include <cmath> // for std::sqrt #include <type_traits> // for std::decay #include <iterator> // for std::begin, std::end +#include <utility> namespace Gudhi { @@ -37,16 +42,29 @@ namespace Gudhi { * have the same dimension. */ class Euclidean_distance { public: + // boost::range_value is not SFINAE-friendly so we cannot use it in the return type template< typename Point > - auto operator()(const Point& p1, const Point& p2) const -> typename std::decay<decltype(*std::begin(p1))>::type { - auto it1 = p1.begin(); - auto it2 = p2.begin(); - typename Point::value_type dist = 0.; - for (; it1 != p1.end(); ++it1, ++it2) { - typename Point::value_type tmp = (*it1) - (*it2); + typename std::iterator_traits<typename boost::range_iterator<Point>::type>::value_type + operator()(const Point& p1, const Point& p2) const { + auto it1 = std::begin(p1); + auto it2 = std::begin(p2); + typedef typename boost::range_value<Point>::type NT; + NT dist = 0; + for (; it1 != std::end(p1); ++it1, ++it2) { + GUDHI_CHECK(it2 != std::end(p2), "inconsistent point dimensions"); + NT tmp = *it1 - *it2; dist += tmp*tmp; } - return std::sqrt(dist); + GUDHI_CHECK(it2 == std::end(p2), "inconsistent point dimensions"); + using std::sqrt; + return sqrt(dist); + } + template< typename T > + T operator() (const std::pair< T, T >& f, const std::pair< T, T >& s) const { + T dx = f.first - s.first; + T dy = f.second - s.second; + using std::sqrt; + return sqrt(dx*dx + dy*dy); } }; diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index 5fe7c826..d84421b2 100644 --- a/src/common/include/gudhi/graph_simplicial_complex.h +++ b/src/common/include/gudhi/graph_simplicial_complex.h @@ -28,6 +28,9 @@ #include <utility> // for pair<> #include <vector> #include <map> +#include <tuple> // for std::tie + +namespace Gudhi { /* Edge tag for Boost PropertyGraph. */ struct edge_filtration_t { @@ -39,4 +42,64 @@ struct vertex_filtration_t { typedef boost::vertex_property_tag kind; }; +template <typename SimplicialComplexForProximityGraph> +using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS +, boost::property < vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value > +, boost::property < edge_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >>; + +/** \brief Computes the proximity graph of the points. + * + * If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the + * distance function between points u and v is smaller than threshold. + * + * \tparam ForwardPointRange furnishes `.begin()` and `.end()` methods. + * + * \tparam Distance furnishes `operator()(const Point& p1, const Point& p2)`, where + * `Point` is a point from the `ForwardPointRange`, and that returns a `Filtration_value`. + */ +template< typename SimplicialComplexForProximityGraph + , typename ForwardPointRange + , typename Distance > +Proximity_graph<SimplicialComplexForProximityGraph> compute_proximity_graph( + const ForwardPointRange& points, + typename SimplicialComplexForProximityGraph::Filtration_value threshold, + Distance distance) { + using Vertex_handle = typename SimplicialComplexForProximityGraph::Vertex_handle; + using Filtration_value = typename SimplicialComplexForProximityGraph::Filtration_value; + + std::vector<std::pair< Vertex_handle, Vertex_handle >> edges; + std::vector< Filtration_value > edges_fil; + std::map< Vertex_handle, Filtration_value > vertices; + + Vertex_handle idx_u, idx_v; + Filtration_value fil; + idx_u = 0; + for (auto it_u = points.begin(); it_u != points.end(); ++it_u) { + idx_v = idx_u + 1; + for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) { + fil = distance(*it_u, *it_v); + if (fil <= threshold) { + edges.emplace_back(idx_u, idx_v); + edges_fil.push_back(fil); + } + } + ++idx_u; + } + + // Points are labeled from 0 to idx_u-1 + Proximity_graph<SimplicialComplexForProximityGraph> skel_graph(edges.begin(), edges.end(), edges_fil.begin(), idx_u); + + auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph); + + typename boost::graph_traits<Proximity_graph<SimplicialComplexForProximityGraph>>::vertex_iterator vi, vi_end; + for (std::tie(vi, vi_end) = boost::vertices(skel_graph); + vi != vi_end; ++vi) { + boost::put(vertex_prop, *vi, 0.); + } + + return skel_graph; +} + +} // namespace Gudhi + #endif // GRAPH_SIMPLICIAL_COMPLEX_H_ |