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-rw-r--r--src/common/include/gudhi/Clock.h2
-rw-r--r--src/common/include/gudhi/Debug_utils.h2
-rw-r--r--src/common/include/gudhi/Null_output_iterator.h2
-rw-r--r--src/common/include/gudhi/Off_reader.h4
-rw-r--r--src/common/include/gudhi/Point.h2
-rw-r--r--src/common/include/gudhi/Points_3D_off_io.h2
-rw-r--r--src/common/include/gudhi/Points_off_io.h2
-rw-r--r--src/common/include/gudhi/Simple_object_pool.h2
-rw-r--r--src/common/include/gudhi/Unitary_tests_utils.h2
-rw-r--r--src/common/include/gudhi/allocator.h2
-rw-r--r--src/common/include/gudhi/console_color.h2
-rw-r--r--src/common/include/gudhi/distance_functions.h52
-rw-r--r--src/common/include/gudhi/graph_simplicial_complex.h8
-rw-r--r--src/common/include/gudhi/random_point_generators.h5
-rw-r--r--src/common/include/gudhi/reader_utils.h2
-rw-r--r--src/common/include/gudhi/writing_persistence_to_file.h117
16 files changed, 191 insertions, 17 deletions
diff --git a/src/common/include/gudhi/Clock.h b/src/common/include/gudhi/Clock.h
index b83de2f5..cdf18cb2 100644
--- a/src/common/include/gudhi/Clock.h
+++ b/src/common/include/gudhi/Clock.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
diff --git a/src/common/include/gudhi/Debug_utils.h b/src/common/include/gudhi/Debug_utils.h
index 90d3cf47..3f5cb04f 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
+ * 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
diff --git a/src/common/include/gudhi/Null_output_iterator.h b/src/common/include/gudhi/Null_output_iterator.h
index 42e6e449..c700af5f 100644
--- a/src/common/include/gudhi/Null_output_iterator.h
+++ b/src/common/include/gudhi/Null_output_iterator.h
@@ -4,7 +4,7 @@
*
* Author(s): Marc Glisse
*
- * Copyright (C) 2017 INRIA
+ * 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
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index 32320e4d..05a1e145 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.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
@@ -137,7 +137,7 @@ class Off_reader {
if (!std::ifstream::sentry(stream_)) return false;
std::getline(stream_, uncomment_line);
} while (uncomment_line[0] == '#');
- return (bool)stream_;
+ return static_cast<bool>(stream_);
}
template<typename OffVisitor>
diff --git a/src/common/include/gudhi/Point.h b/src/common/include/gudhi/Point.h
index 0479e71e..345a8465 100644
--- a/src/common/include/gudhi/Point.h
+++ b/src/common/include/gudhi/Point.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
diff --git a/src/common/include/gudhi/Points_3D_off_io.h b/src/common/include/gudhi/Points_3D_off_io.h
index b0d24998..704f73a7 100644
--- a/src/common/include/gudhi/Points_3D_off_io.h
+++ b/src/common/include/gudhi/Points_3D_off_io.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * Copyright (C) 2015 INRIA Saclay (France)
+ * Copyright (C) 2015 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
diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h
index 08f324c6..38029658 100644
--- a/src/common/include/gudhi/Points_off_io.h
+++ b/src/common/include/gudhi/Points_off_io.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * Copyright (C) 2015 INRIA Saclay (France)
+ * Copyright (C) 2015 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
diff --git a/src/common/include/gudhi/Simple_object_pool.h b/src/common/include/gudhi/Simple_object_pool.h
index fb9c8e23..47283521 100644
--- a/src/common/include/gudhi/Simple_object_pool.h
+++ b/src/common/include/gudhi/Simple_object_pool.h
@@ -4,7 +4,7 @@
*
* Author(s): Marc Glisse
*
- * Copyright (C) 2015 INRIA Saclay - Ile de France
+ * Copyright (C) 2015 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
diff --git a/src/common/include/gudhi/Unitary_tests_utils.h b/src/common/include/gudhi/Unitary_tests_utils.h
index 8394a062..e07c8d42 100644
--- a/src/common/include/gudhi/Unitary_tests_utils.h
+++ b/src/common/include/gudhi/Unitary_tests_utils.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * Copyright (C) 2017 INRIA
+ * 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
diff --git a/src/common/include/gudhi/allocator.h b/src/common/include/gudhi/allocator.h
index 4ede14e4..3de16a49 100644
--- a/src/common/include/gudhi/allocator.h
+++ b/src/common/include/gudhi/allocator.h
@@ -4,7 +4,7 @@
*
* Author(s): Marc Glisse
*
- * Copyright (C) 2015 INRIA Saclay - Ile de France
+ * Copyright (C) 2015 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
diff --git a/src/common/include/gudhi/console_color.h b/src/common/include/gudhi/console_color.h
index c4671da3..a493e0d0 100644
--- a/src/common/include/gudhi/console_color.h
+++ b/src/common/include/gudhi/console_color.h
@@ -4,7 +4,7 @@
*
* Author(s): Clement Jamin
*
- * Copyright (C) 2016 INRIA Sophia-Antipolis (France)
+ * Copyright (C) 2016 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
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index 3a5d1fd5..5ef12f2e 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -4,7 +4,7 @@
*
* Author(s): Clément Maria
*
- * Copyright (C) 2014 INRIA
+ * 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
@@ -25,7 +25,10 @@
#include <gudhi/Debug_utils.h>
+#include <gudhi/Miniball.hpp>
+
#include <boost/range/metafunctions.hpp>
+#include <boost/range/size.hpp>
#include <cmath> // for std::sqrt
#include <type_traits> // for std::decay
@@ -68,6 +71,53 @@ class Euclidean_distance {
}
};
+/** @brief Compute the radius of the minimal enclosing ball between Points given by a range of coordinates.
+ * The points are assumed to have the same dimension. */
+class Minimal_enclosing_ball_radius {
+ public:
+ /** \brief Minimal_enclosing_ball_radius from two points.
+ *
+ * @param[in] point_1 First point.
+ * @param[in] point_2 second point.
+ * @return The minimal enclosing ball radius for the two points (aka. Euclidean distance / 2.).
+ *
+ * \tparam Point must be a range of Cartesian coordinates.
+ *
+ */
+ template< typename Point >
+ typename std::iterator_traits<typename boost::range_iterator<Point>::type>::value_type
+ operator()(const Point& point_1, const Point& point_2) const {
+ return Euclidean_distance()(point_1, point_2) / 2.;
+ }
+ /** \brief Minimal_enclosing_ball_radius from a point cloud.
+ *
+ * @param[in] point_cloud The points.
+ * @return The minimal enclosing ball radius for the points.
+ *
+ * \tparam Point_cloud must be a range of points with Cartesian coordinates.
+ * Point_cloud is a range over a range of Coordinate.
+ *
+ */
+ template< typename Point_cloud,
+ typename Point_iterator = typename boost::range_const_iterator<Point_cloud>::type,
+ typename Point = typename std::iterator_traits<Point_iterator>::value_type,
+ typename Coordinate_iterator = typename boost::range_const_iterator<Point>::type,
+ typename Coordinate = typename std::iterator_traits<Coordinate_iterator>::value_type>
+ Coordinate
+ operator()(const Point_cloud& point_cloud) const {
+ using Min_sphere = Miniball::Miniball<Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>;
+
+ Min_sphere ms(boost::size(*point_cloud.begin()), point_cloud.begin(), point_cloud.end());
+#ifdef DEBUG_TRACES
+ std::cout << "Minimal_enclosing_ball_radius = " << std::sqrt(ms.squared_radius()) << " | nb points = "
+ << boost::size(point_cloud) << " | dimension = "
+ << boost::size(*point_cloud.begin()) << std::endl;
+#endif // DEBUG_TRACES
+
+ return std::sqrt(ms.squared_radius());
+ }
+};
+
} // namespace Gudhi
#endif // DISTANCE_FUNCTIONS_H_
diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h
index d84421b2..49fe56cc 100644
--- a/src/common/include/gudhi/graph_simplicial_complex.h
+++ b/src/common/include/gudhi/graph_simplicial_complex.h
@@ -4,7 +4,7 @@
*
* Author(s): Clément Maria
*
- * Copyright (C) 2014 INRIA
+ * 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
@@ -42,6 +42,12 @@ struct vertex_filtration_t {
typedef boost::vertex_property_tag kind;
};
+/** \brief Proximity_graph contains the vertices and edges with their filtration values in order to store the result
+ * of `Gudhi::compute_proximity_graph` function.
+ *
+ * \tparam SimplicialComplexForProximityGraph furnishes `Filtration_value` type definition.
+ *
+ */
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 >
diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h
index 9df77760..f8107c8b 100644
--- a/src/common/include/gudhi/random_point_generators.h
+++ b/src/common/include/gudhi/random_point_generators.h
@@ -4,7 +4,7 @@
*
* Author(s): Clement Jamin
*
- * Copyright (C) 2016 INRIA
+ * Copyright (C) 2016 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
@@ -190,7 +190,8 @@ template <typename Kernel, typename OutputIterator>
static void generate_uniform_points_on_torus_d(const Kernel &k, int dim, std::size_t num_slices,
OutputIterator out,
double radius_noise_percentage = 0.,
- std::vector<typename Kernel::FT> current_point = std::vector<typename Kernel::FT>()) {
+ std::vector<typename Kernel::FT> current_point =
+ std::vector<typename Kernel::FT>()) {
CGAL::Random rng;
int point_size = static_cast<int>(current_point.size());
if (point_size == 2 * dim) {
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 90be4fc7..26eeb76d 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -4,7 +4,7 @@
*
* Author(s): Clement Maria, Pawel Dlotko, Clement Jamin
*
- * Copyright (C) 2014 INRIA
+ * 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
diff --git a/src/common/include/gudhi/writing_persistence_to_file.h b/src/common/include/gudhi/writing_persistence_to_file.h
new file mode 100644
index 00000000..34448576
--- /dev/null
+++ b/src/common/include/gudhi/writing_persistence_to_file.h
@@ -0,0 +1,117 @@
+/* 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): Pawel Dlotko
+ *
+ * Copyright (C) 2017 Swansea University, UK
+ *
+ * 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 WRITING_PERSISTENCE_TO_FILE_H_
+#define WRITING_PERSISTENCE_TO_FILE_H_
+
+#include <iostream>
+#include <string>
+#include <limits>
+
+namespace Gudhi {
+
+/**
+* This is a class to store persistence intervals. Its main purpose is to
+* exchange data in between different packages and provide unified way
+* of writing a collection of persistence intervals to file.
+**/
+template <typename Filtration_type, typename Coefficient_field>
+class Persistence_interval_common {
+ public:
+ /**
+ * Constructor taking as an input birth and death of the pair.
+ **/
+ Persistence_interval_common(Filtration_type birth, Filtration_type death)
+ : birth_(birth),
+ death_(death),
+ dimension_(std::numeric_limits<unsigned>::max()),
+ arith_element_(std::numeric_limits<Coefficient_field>::max()) {}
+
+ /**
+ * Constructor taking as an input birth, death and dimension of the pair.
+ **/
+ Persistence_interval_common(Filtration_type birth, Filtration_type death, unsigned dim)
+ : birth_(birth), death_(death), dimension_(dim), arith_element_(std::numeric_limits<Coefficient_field>::max()) {}
+
+ /**
+* Constructor taking as an input birth, death, dimension of the pair as well
+* as the number p such that this interval is present over Z_p field.
+**/
+ Persistence_interval_common(Filtration_type birth, Filtration_type death, unsigned dim, Coefficient_field field)
+ : birth_(birth), death_(death), dimension_(dim), arith_element_(field) {}
+
+ /**
+ * Operator to compare two persistence pairs. During the comparision all the
+ * fields: birth, death, dimensiona and arith_element_ are taken into account
+ * and they all have to be equal for two pairs to be equal.
+ **/
+ bool operator==(const Persistence_interval_common& i2) const {
+ return ((this->birth_ == i2.birth_) && (this->death_ == i2.death_) && (this->dimension_ == i2.dimension_) &&
+ (this->arith_element_ == i2.arith_element_));
+ }
+
+ /**
+ * Check if two persistence paris are not equal.
+ **/
+ bool operator!=(const Persistence_interval_common& i2) const { return (!((*this) == i2)); }
+
+ /**
+ * Operator to compare objects of a type Persistence_interval_common.
+ * One intervals is smaller than the other if it has lower persistence.
+ * Note that this operator do not take Arith_element into account when doing comparisions.
+ **/
+ bool operator<(const Persistence_interval_common& i2) const {
+ return fabs(this->death_ - this->birth_) < fabs(i2.death_ - i2.birth_);
+ }
+
+ friend std::ostream& operator<<(std::ostream& out, const Persistence_interval_common& it) {
+ if (it.arith_element_ != std::numeric_limits<Coefficient_field>::max()) {
+ out << it.arith_element_ << " ";
+ }
+ if (it.dimension_ != std::numeric_limits<unsigned>::max()) {
+ out << it.dimension_ << " ";
+ }
+ out << it.birth_ << " " << it.death_ << " ";
+ return out;
+ }
+
+ private:
+ Filtration_type birth_;
+ Filtration_type death_;
+ unsigned dimension_;
+ Coefficient_field arith_element_;
+};
+
+/**
+ * This function write a vector<Persistence_interval_common> to a stream
+**/
+template <typename Persistence_interval_range>
+void write_persistence_intervals_to_stream(const Persistence_interval_range& intervals,
+ std::ostream& out = std::cout) {
+ for (auto interval : intervals) {
+ out << interval << "\n";
+ }
+}
+
+} // namespace Gudhi
+
+#endif // WRITING_PERSISTENCE_TO_FILE_H_
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-04 13:29:30 +0000