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-rw-r--r--src/cython/include/Alpha_complex_interface.h4
-rw-r--r--src/cython/include/Bottleneck_distance_interface.h2
-rw-r--r--src/cython/include/Cubical_complex_interface.h8
-rw-r--r--src/cython/include/Euclidean_strong_witness_complex_interface.h2
-rw-r--r--src/cython/include/Euclidean_witness_complex_interface.h2
-rw-r--r--src/cython/include/Nerve_gic_interface.h61
-rw-r--r--src/cython/include/Off_reader_interface.h2
-rw-r--r--src/cython/include/Persistent_cohomology_interface.h28
-rw-r--r--src/cython/include/Reader_utils_interface.h2
-rw-r--r--src/cython/include/Rips_complex_interface.h19
-rw-r--r--src/cython/include/Simplex_tree_interface.h6
-rw-r--r--src/cython/include/Strong_witness_complex_interface.h2
-rw-r--r--src/cython/include/Subsampling_interface.h2
-rw-r--r--src/cython/include/Tangential_complex_interface.h19
-rw-r--r--src/cython/include/Witness_complex_interface.h2
15 files changed, 117 insertions, 44 deletions
diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h
index d47db71f..faa059d1 100644
--- a/src/cython/include/Alpha_complex_interface.h
+++ b/src/cython/include/Alpha_complex_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
@@ -60,7 +60,7 @@ class Alpha_complex_interface {
Point_d ph = alpha_complex_->get_point(vh);
for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
vd.push_back(*coord);
- } catch (std::out_of_range outofrange) {
+ } catch (std::out_of_range const&) {
// std::out_of_range is thrown in case not found. Other exceptions must be re-thrown
}
return vd;
diff --git a/src/cython/include/Bottleneck_distance_interface.h b/src/cython/include/Bottleneck_distance_interface.h
index d5fbf6ea..5ad9d77d 100644
--- a/src/cython/include/Bottleneck_distance_interface.h
+++ b/src/cython/include/Bottleneck_distance_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
diff --git a/src/cython/include/Cubical_complex_interface.h b/src/cython/include/Cubical_complex_interface.h
index 7c0148f1..85b717b3 100644
--- a/src/cython/include/Cubical_complex_interface.h
+++ b/src/cython/include/Cubical_complex_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
@@ -43,6 +43,12 @@ class Cubical_complex_interface : public Bitmap_cubical_complex<CubicalComplexOp
: Bitmap_cubical_complex<CubicalComplexOptions>(dimensions, top_dimensional_cells) {
}
+ Cubical_complex_interface(const std::vector<unsigned>& dimensions,
+ const std::vector<double>& top_dimensional_cells,
+ const std::vector<bool>& periodic_dimensions)
+ : Bitmap_cubical_complex<CubicalComplexOptions>(dimensions, top_dimensional_cells, periodic_dimensions) {
+ }
+
Cubical_complex_interface(const std::string& perseus_file)
: Bitmap_cubical_complex<CubicalComplexOptions>(perseus_file.c_str()) {
}
diff --git a/src/cython/include/Euclidean_strong_witness_complex_interface.h b/src/cython/include/Euclidean_strong_witness_complex_interface.h
index b9dd8177..d86355d6 100644
--- a/src/cython/include/Euclidean_strong_witness_complex_interface.h
+++ b/src/cython/include/Euclidean_strong_witness_complex_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
diff --git a/src/cython/include/Euclidean_witness_complex_interface.h b/src/cython/include/Euclidean_witness_complex_interface.h
index 2a09b3b5..dc303533 100644
--- a/src/cython/include/Euclidean_witness_complex_interface.h
+++ b/src/cython/include/Euclidean_witness_complex_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
diff --git a/src/cython/include/Nerve_gic_interface.h b/src/cython/include/Nerve_gic_interface.h
new file mode 100644
index 00000000..aa71e2a6
--- /dev/null
+++ b/src/cython/include/Nerve_gic_interface.h
@@ -0,0 +1,61 @@
+/* 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) 2018 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 INCLUDE_NERVE_GIC_INTERFACE_H_
+#define INCLUDE_NERVE_GIC_INTERFACE_H_
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/GIC.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <iostream>
+#include <vector>
+#include <string>
+
+namespace Gudhi {
+
+namespace cover_complex {
+
+class Nerve_gic_interface : public Cover_complex<std::vector<double>> {
+ public:
+ void create_simplex_tree(Simplex_tree_interface<>* simplex_tree) {
+ create_complex(*simplex_tree);
+ simplex_tree->initialize_filtration();
+ }
+ void set_cover_from_Euclidean_Voronoi(int m) {
+ set_cover_from_Voronoi(Gudhi::Euclidean_distance(), m);
+ }
+ double set_graph_from_automatic_euclidean_rips(int N) {
+ return set_graph_from_automatic_rips(Gudhi::Euclidean_distance(), N);
+ }
+ void set_graph_from_euclidean_rips(double threshold) {
+ set_graph_from_rips(threshold, Gudhi::Euclidean_distance());
+ }
+};
+
+} // namespace cover_complex
+
+} // namespace Gudhi
+
+#endif // INCLUDE_NERVE_GIC_INTERFACE_H_
diff --git a/src/cython/include/Off_reader_interface.h b/src/cython/include/Off_reader_interface.h
index 0ca55500..f6b14f38 100644
--- a/src/cython/include/Off_reader_interface.h
+++ b/src/cython/include/Off_reader_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h
index 55028fd0..8cf71a4e 100644
--- a/src/cython/include/Persistent_cohomology_interface.h
+++ b/src/cython/include/Persistent_cohomology_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
@@ -85,6 +85,32 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
return persistence;
}
+ std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs() {
+ auto pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex,
+ persistent_cohomology::Field_Zp>::get_persistent_pairs();
+
+ std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs;
+ persistence_pairs.reserve(pairs.size());
+ for (auto pair : pairs) {
+ std::vector<int> birth;
+ if (get<0>(pair) != stptr_->null_simplex()) {
+ for (auto vertex : stptr_->simplex_vertex_range(get<0>(pair))) {
+ birth.push_back(vertex);
+ }
+ }
+
+ std::vector<int> death;
+ if (get<1>(pair) != stptr_->null_simplex()) {
+ for (auto vertex : stptr_->simplex_vertex_range(get<1>(pair))) {
+ death.push_back(vertex);
+ }
+ }
+
+ persistence_pairs.push_back(std::make_pair(birth, death));
+ }
+ return persistence_pairs;
+ }
+
private:
// A copy
FilteredComplex* stptr_;
diff --git a/src/cython/include/Reader_utils_interface.h b/src/cython/include/Reader_utils_interface.h
index 8ec34f61..5f7527d9 100644
--- a/src/cython/include/Reader_utils_interface.h
+++ b/src/cython/include/Reader_utils_interface.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/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
index 02985727..8b6c9c35 100644
--- a/src/cython/include/Rips_complex_interface.h
+++ b/src/cython/include/Rips_complex_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
@@ -25,9 +25,7 @@
#include <gudhi/Simplex_tree.h>
#include <gudhi/Rips_complex.h>
-#include <gudhi/Points_off_io.h>
#include <gudhi/distance_functions.h>
-#include <gudhi/reader_utils.h>
#include "Simplex_tree_interface.h"
@@ -56,21 +54,6 @@ class Rips_complex_interface {
}
}
- Rips_complex_interface(const std::string& file_name, double threshold, bool euclidean, bool from_file = true) {
- if (euclidean) {
- // Rips construction where file_name is an OFF file
- Gudhi::Points_off_reader<Point_d> off_reader(file_name);
- rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(off_reader.get_point_cloud(),
- threshold,
- Gudhi::Euclidean_distance());
- } else {
- // Rips construction where values is a distance matrix
- Distance_matrix distances =
- Gudhi::read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
- rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(distances, threshold);
- }
- }
-
~Rips_complex_interface() {
delete rips_complex_;
}
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index 09e7e992..3481eeff 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
@@ -52,6 +52,10 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
return (Base::find(vh) != Base::null_simplex());
}
+ void assign_simplex_filtration(const Simplex& vh, Filtration_value filtration) {
+ Base::assign_filtration(Base::find(vh), filtration);
+ }
+
bool insert(const Simplex& simplex, Filtration_value filtration = 0) {
Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration);
return (result.second);
diff --git a/src/cython/include/Strong_witness_complex_interface.h b/src/cython/include/Strong_witness_complex_interface.h
index d05eaac5..3c72c916 100644
--- a/src/cython/include/Strong_witness_complex_interface.h
+++ b/src/cython/include/Strong_witness_complex_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
diff --git a/src/cython/include/Subsampling_interface.h b/src/cython/include/Subsampling_interface.h
index b0f4a50a..f990da0c 100644
--- a/src/cython/include/Subsampling_interface.h
+++ b/src/cython/include/Subsampling_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index 5e9dc0e4..71418886 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
@@ -45,24 +45,19 @@ class Tangential_complex_interface {
using TC = Tangential_complex<Dynamic_kernel, CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>;
public:
- Tangential_complex_interface(const std::vector<std::vector<double>>& points) {
+ Tangential_complex_interface(int intrisic_dim, const std::vector<std::vector<double>>& points) {
Dynamic_kernel k;
- unsigned intrisic_dim = 0;
- if (points.size() > 0)
- intrisic_dim = points[0].size() - 1;
tangential_complex_ = new TC(points, intrisic_dim, k);
tangential_complex_->compute_tangential_complex();
num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
}
- Tangential_complex_interface(const std::string& off_file_name, bool from_file = true) {
- Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
+ Tangential_complex_interface(int intrisic_dim, const std::string& off_file_name, bool from_file = true) {
Dynamic_kernel k;
- unsigned intrisic_dim = 0;
+
+ Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
std::vector<Point_d> points = off_reader.get_point_cloud();
- if (points.size() > 0)
- intrisic_dim = points[0].size() - 1;
tangential_complex_ = new TC(points, intrisic_dim, k);
tangential_complex_->compute_tangential_complex();
@@ -105,9 +100,7 @@ class Tangential_complex_interface {
}
void create_simplex_tree(Simplex_tree<>* simplex_tree) {
- int max_dim = tangential_complex_->create_complex<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>(*simplex_tree);
- // FIXME
- simplex_tree->set_dimension(max_dim);
+ tangential_complex_->create_complex<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>(*simplex_tree);
simplex_tree->initialize_filtration();
}
diff --git a/src/cython/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h
index 6501cc35..01b372e7 100644
--- a/src/cython/include/Witness_complex_interface.h
+++ b/src/cython/include/Witness_complex_interface.h
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * 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
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-15 07:19:03 +0000