multipers 2.2.3__cp312-cp312-win_amd64.whl → 2.3.1__cp312-cp312-win_amd64.whl

multipers/gudhi/gudhi/Simplex_tree_multi.h

@@ -1,163 +1,152 @@
-/*    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): David
- * Loiseaux, Hannah Schreiber
- *
- *    Copyright (C) 2023 Inria
- *
- *    Modification(s):
- *      - YYYY/MM Author: Description of the modification
- */
-#ifndef SIMPLEX_TREE_MULTI_H_
-#define SIMPLEX_TREE_MULTI_H_
-
-#include <algorithm>
-#include <gudhi/Simplex_tree.h>
-
-namespace Gudhi {
-namespace multi_persistence {
-
-/** Model of SimplexTreeOptions, with a multiparameter filtration.
- * \ingroup multi_persistence
- * */
-template <typename Filtration>
-struct Simplex_tree_options_multidimensional_filtration {
-public:
-  typedef linear_indexing_tag Indexing_tag;
-  typedef int Vertex_handle;
-  using Filtration_value = Filtration;
-  typedef typename Filtration::value_type value_type;
-  typedef std::uint32_t Simplex_key;
-  static const bool store_key = true;
-  static const bool store_filtration = true;
-  static const bool contiguous_vertices = false;
-  static const bool link_nodes_by_label = false;
-  static const bool stable_simplex_handles = false;
-  static const bool is_multi_parameter = true;
-};
-
-/**
- * \brief Turns a 1-parameter simplextree into a multiparameter simplextree,
- * and keeps the 1-filtration in the 1st axis.
- * Default values can be specified.
- * \ingroup multi_persistence
- * \tparam simplextree_std A non-multi simplextree
- * \tparam simplextree_multi A multi simplextree
- * \param st Simplextree to copy
- * \param st_multi Multiparameter simplextree container to fill.
- * \param default_values If given, this vector is assume to be of size `num_parameters-1` and contains the default
- * values of axes `1` to `num_parameters`.
- * */
-template <class simplextree_std, class simplextree_multi>
-void multify(simplextree_std &st, simplextree_multi &st_multi,
-             const int num_parameters,
-             const typename simplextree_multi::Options::Filtration_value
-                 &default_values = {}) {
-  typename simplextree_multi::Options::Filtration_value f(num_parameters);
-  static_assert(
-      !simplextree_std::Options::is_multi_parameter &&
-          simplextree_multi::Options::is_multi_parameter,
-      "Can only convert non-multiparameter to multiparameter simplextree.");
-  unsigned int num_default_values = 0;
-  if constexpr (simplextree_multi::Options::Filtration_value::
-                    is_multi_critical) {
-    num_default_values = default_values[0].size();
-  } else {
-    num_default_values = default_values.size();
-  }
-  for (auto i = 0u; i < std::min(num_default_values,
-                                 num_parameters < 1 ? 0u : static_cast<unsigned int>(num_parameters - 1));
-       i++) {
-    if constexpr (simplextree_multi::Options::Filtration_value::
-                      is_multi_critical) {
-      f[0][i + 1] = default_values[0][i];
-    } else {
-      f[i + 1] = default_values[i];
-    }
-  }
-
-  std::vector<int> simplex;
-  simplex.reserve(st.dimension() + 1);
-  for (auto &simplex_handle : st.complex_simplex_range()) {
-    simplex.clear();
-    for (auto vertex : st.simplex_vertex_range(simplex_handle))
-      simplex.push_back(vertex);
-
-    if (num_parameters > 0) {
-      if constexpr (simplextree_multi::Options::Filtration_value::
-                        is_multi_critical) {
-        f[0][0] = st.filtration(simplex_handle);
-      } else {
-        f[0] = st.filtration(simplex_handle);
-      }
-    }
-    st_multi.insert_simplex(simplex, f);
-  }
-  st_multi.set_number_of_parameters(num_parameters);
-}
-
-/**
- * \brief Turns a multiparameter-parameter simplextree into a 1-parameter
- * simplextree.
- * \ingroup multi_persistence
- * \tparam simplextree_std A non-multi simplextree
- * \tparam simplextree_multi A multi simplextree
- * \param st Simplextree to fill.
- * \param st_multi Multiparameter simplextree to convert into a 1 parameter simplex tree.
- * \param dimension The filtration parameter to put into the 1 parameter simplextree.
- * */
-template <class simplextree_std, class simplextree_multi>
-void flatten(simplextree_std &st, simplextree_multi &st_multi,
-             const int dimension = 0) {
-  static_assert(
-      !simplextree_std::Options::is_multi_parameter &&
-          simplextree_multi::Options::is_multi_parameter,
-      "Can only convert multiparameter to non-multiparameter simplextree.");
-  for (const auto &simplex_handle : st_multi.complex_simplex_range()) {
-    std::vector<int> simplex;
-    typename simplextree_multi::Options::value_type f;
-    for (auto vertex : st_multi.simplex_vertex_range(simplex_handle))
-      simplex.push_back(vertex);
-    if constexpr (simplextree_multi::Filtration_value::is_multi_critical) {
-      f = dimension >= 0 ? st_multi.filtration(simplex_handle)[0][dimension]
-                         : 0;
-    } else {
-      f = dimension >= 0 ? st_multi.filtration(simplex_handle)[dimension] : 0;
-    }
-    st.insert_simplex(simplex, f);
-  }
-}
-
-// TODO: following not in the planned version in Gudhi. So either remove from here, or add there.
-
-/**
- * \brief Applies a linear form (given by a scalar product, via Riesz
- * representation) to the filtration values of the multiparameter simplextree to
- * get a 1 parameter simplextree. \ingroup multiparameter \tparam
- * simplextree_std A non-multi simplextree \tparam simplextree_multi A multi
- * simplextree \param st Simplextree, with the same simplicial complex as
- * st_multi, whose filtration has to be filled. \param st_multi Multiparameter
- * simplextree to convert into a 1 parameter simplex tree. \param linear_form
- * the linear form to apply.
- * */
-template <class simplextree_std, class simplextree_multi>
-void linear_projection(simplextree_std &st, simplextree_multi &st_multi,
-                       const std::vector<double> &linear_form) {
-  static_assert(
-      !simplextree_std::Options::is_multi_parameter &&
-          simplextree_multi::Options::is_multi_parameter,
-      "Can only convert multiparameter to non-multiparameter simplextree.");
-  auto sh = st.complex_simplex_range().begin();
-  auto sh_multi = st_multi.complex_simplex_range().begin();
-  auto end = st.complex_simplex_range().end();
-  typename simplextree_multi::Options::Filtration_value multi_filtration;
-  for (; sh != end; ++sh, ++sh_multi) {
-    multi_filtration = st_multi.filtration(*sh_multi);
-    auto projected_filtration = compute_linear_projection(multi_filtration, linear_form);
-    st.assign_filtration(*sh, projected_filtration);
-  }
-}
-
-}} // namespace Gudhi::multi_persistence
-
-#endif // SIMPLEX_TREE_MULTI_H_
+/*    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): David
+ * Loiseaux, Hannah Schreiber
+ *
+ *    Copyright (C) 2023 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+#ifndef SIMPLEX_TREE_MULTI_H_
+#define SIMPLEX_TREE_MULTI_H_
+
+#include <algorithm>
+#include <cstdint>
+#include <vector>
+#include <gudhi/Simplex_tree.h>
+
+namespace Gudhi {
+namespace multi_persistence {
+
+/** Model of SimplexTreeOptions, with a multiparameter filtration.
+ * \ingroup multi_persistence
+ * */
+template <typename Filtration>
+struct Simplex_tree_options_multidimensional_filtration {
+ public:
+  typedef linear_indexing_tag Indexing_tag;
+  typedef int Vertex_handle;
+  using Filtration_value = Filtration;
+  typedef typename Filtration::value_type value_type;
+  typedef std::uint32_t Simplex_key;
+  static const bool store_key = true;
+  static const bool store_filtration = true;
+  static const bool contiguous_vertices = false;
+  static const bool link_nodes_by_label = false;
+  static const bool stable_simplex_handles = false;
+  static const bool is_multi_parameter = true;
+};
+
+/**
+ * \brief Turns a 1-parameter simplextree into a multiparameter simplextree,
+ * and keeps the 1-filtration in the 1st axis.
+ * Default values can be specified.
+ * \ingroup multi_persistence
+ * \tparam simplextree_std A non-multi simplextree
+ * \tparam simplextree_multi A multi simplextree
+ * \param st Simplextree to copy
+ * \param st_multi Multiparameter simplextree container to fill.
+ * \param default_values If given, this vector is assume to be of size `num_parameters-1` and contains the default
+ * values of axes `1` to `num_parameters`.
+ * */
+template <class simplextree_std, class simplextree_multi>
+void multify(simplextree_std &st,
+             simplextree_multi &st_multi,
+             const int num_parameters,
+             const typename simplextree_multi::Options::Filtration_value &default_values = {}) {
+  typename simplextree_multi::Options::Filtration_value f(num_parameters);
+  static_assert(!simplextree_std::Options::is_multi_parameter && simplextree_multi::Options::is_multi_parameter,
+                "Can only convert non-multiparameter to multiparameter simplextree.");
+  unsigned int num_default_values = 0;
+  if constexpr (simplextree_multi::Options::Filtration_value::is_multi_critical) {
+    num_default_values = default_values[0].size();
+  } else {
+    num_default_values = default_values.size();
+  }
+  for (auto i = 0u;
+       i < std::min(num_default_values, num_parameters < 1 ? 0u : static_cast<unsigned int>(num_parameters - 1));
+       i++) {
+    if constexpr (simplextree_multi::Options::Filtration_value::is_multi_critical) {
+      f[0][i + 1] = default_values[0][i];
+    } else {
+      f[i + 1] = default_values[i];
+    }
+  }
+
+  std::vector<int> simplex;
+  simplex.reserve(st.dimension() + 1);
+  for (auto &simplex_handle : st.complex_simplex_range()) {
+    simplex.clear();
+    for (auto vertex : st.simplex_vertex_range(simplex_handle)) simplex.push_back(vertex);
+
+    if (num_parameters > 0) {
+      if constexpr (simplextree_multi::Options::Filtration_value::is_multi_critical) {
+        f[0][0] = st.filtration(simplex_handle);
+      } else {
+        f[0] = st.filtration(simplex_handle);
+      }
+    }
+    st_multi.insert_simplex(simplex, f);
+  }
+  st_multi.set_number_of_parameters(num_parameters);
+}
+
+/**
+ * \brief Turns a multiparameter-parameter simplextree into a 1-parameter
+ * simplextree.
+ * \ingroup multi_persistence
+ * \tparam simplextree_std A non-multi simplextree
+ * \tparam simplextree_multi A multi simplextree
+ * \param st Simplextree to fill.
+ * \param st_multi Multiparameter simplextree to convert into a 1 parameter simplex tree.
+ * \param dimension The filtration parameter to put into the 1 parameter simplextree.
+ * */
+template <class simplextree_std, class simplextree_multi>
+void flatten(simplextree_std &st, simplextree_multi &st_multi, const int dimension = 0) {
+  static_assert(!simplextree_std::Options::is_multi_parameter && simplextree_multi::Options::is_multi_parameter,
+                "Can only convert multiparameter to non-multiparameter simplextree.");
+  for (const auto &simplex_handle : st_multi.complex_simplex_range()) {
+    std::vector<int> simplex;
+    typename simplextree_multi::Options::value_type f;
+    for (auto vertex : st_multi.simplex_vertex_range(simplex_handle)) simplex.push_back(vertex);
+    if constexpr (simplextree_multi::Filtration_value::is_multi_critical) {
+      f = dimension >= 0 ? st_multi.filtration(simplex_handle)[0][dimension] : 0;
+    } else {
+      f = dimension >= 0 ? st_multi.filtration(simplex_handle)[dimension] : 0;
+    }
+    st.insert_simplex(simplex, f);
+  }
+}
+
+// TODO: following not in the planned version in Gudhi. So either remove from here, or add there.
+
+/**
+ * \brief Applies a linear form (given by a scalar product, via Riesz
+ * representation) to the filtration values of the multiparameter simplextree to
+ * get a 1 parameter simplextree. \ingroup multiparameter \tparam
+ * simplextree_std A non-multi simplextree \tparam simplextree_multi A multi
+ * simplextree \param st Simplextree, with the same simplicial complex as
+ * st_multi, whose filtration has to be filled. \param st_multi Multiparameter
+ * simplextree to convert into a 1 parameter simplex tree. \param linear_form
+ * the linear form to apply.
+ * */
+template <class simplextree_std, class simplextree_multi>
+void linear_projection(simplextree_std &st, simplextree_multi &st_multi, const std::vector<double> &linear_form) {
+  static_assert(!simplextree_std::Options::is_multi_parameter && simplextree_multi::Options::is_multi_parameter,
+                "Can only convert multiparameter to non-multiparameter simplextree.");
+  auto sh = st.complex_simplex_range().begin();
+  auto sh_multi = st_multi.complex_simplex_range().begin();
+  auto end = st.complex_simplex_range().end();
+  typename simplextree_multi::Options::Filtration_value multi_filtration;
+  for (; sh != end; ++sh, ++sh_multi) {
+    multi_filtration = st_multi.filtration(*sh_multi);
+    auto projected_filtration = compute_linear_projection(multi_filtration, linear_form);
+    st.assign_filtration(*sh, projected_filtration);
+  }
+}
+
+}  // namespace multi_persistence
+}  // namespace Gudhi
+
+#endif  // SIMPLEX_TREE_MULTI_H_

multipers/gudhi/gudhi/distance_functions.h

@@ -1,62 +1,62 @@
-/*    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):       Clément Maria
- *
- *    Copyright (C) 2014 Inria
- *
- *    Modification(s):
- *      - YYYY/MM Author: Description of the modification
- */
-
-#ifndef DISTANCE_FUNCTIONS_H_
-#define DISTANCE_FUNCTIONS_H_
-
-#include <gudhi/Debug_utils.h>
-
-#include <boost/range/metafunctions.hpp>
-#include <boost/range/size.hpp>
-
-#include <cmath>  // for std::sqrt
-#include <type_traits>  // for std::decay
-#include <iterator>  // for std::begin, std::end
-#include <utility>
-
-namespace Gudhi {
-
-/** @file
- * @brief Global distance functions
- */
-
-/** @brief Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to
- * 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 >
-  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;
-    }
-    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);
-  }
-};
-
-}  // namespace Gudhi
-
-#endif  // DISTANCE_FUNCTIONS_H_
+/*    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):       Clément Maria
+ *
+ *    Copyright (C) 2014 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#ifndef DISTANCE_FUNCTIONS_H_
+#define DISTANCE_FUNCTIONS_H_
+
+#include <gudhi/Debug_utils.h>
+
+#include <boost/range/metafunctions.hpp>
+#include <boost/range/size.hpp>
+
+#include <cmath>  // for std::sqrt
+#include <type_traits>  // for std::decay
+#include <iterator>  // for std::begin, std::end
+#include <utility>
+
+namespace Gudhi {
+
+/** @file
+ * @brief Global distance functions
+ */
+
+/** @brief Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to
+ * 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 >
+  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;
+    }
+    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);
+  }
+};
+
+}  // namespace Gudhi
+
+#endif  // DISTANCE_FUNCTIONS_H_