GUDHI 2.2.0 as released by upstream in a tarball.upstream/2.2.0

20 files changed, 107 insertions, 35 deletions

diff --git a/concept/Alpha_complex/SimplicialComplexForAlpha.h b/concept/Alpha_complex/SimplicialComplexForAlpha.h
index 2b8bff94..a51df127 100644
--- a/concept/Alpha_complex/SimplicialComplexForAlpha.h
+++ b/concept/Alpha_complex/SimplicialComplexForAlpha.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/concept/Bottleneck_distance/Persistence_diagram.h b/concept/Bottleneck_distance/Persistence_diagram.h
index b157f22a..d016faf4 100644
--- a/concept/Bottleneck_distance/Persistence_diagram.h
+++ b/concept/Bottleneck_distance/Persistence_diagram.h
@@ -4,7 +4,7 @@
  *
  *    Author:       François Godi
  *
- *    Copyright (C) 2015  INRIA
+ *    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/concept/Cech_complex/SimplicialComplexForCech.h b/concept/Cech_complex/SimplicialComplexForCech.h
new file mode 100644
index 00000000..89231eec
--- /dev/null
+++ b/concept/Cech_complex/SimplicialComplexForCech.h
@@ -0,0 +1,66 @@
+/*    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 CONCEPT_CECH_COMPLEX_SIMPLICIAL_COMPLEX_FOR_CECH_H_
+#define CONCEPT_CECH_COMPLEX_SIMPLICIAL_COMPLEX_FOR_CECH_H_
+
+namespace Gudhi {
+
+namespace cech_complex {
+
+/** \brief The concept SimplicialComplexForCech describes the requirements for a type to implement a simplicial
+ * complex, that can be created from a `Cech_complex`.
+ */
+struct SimplicialComplexForCech {
+  /** Handle to specify a simplex. */
+  typedef unspecified Simplex_handle;
+  /** Handle to specify a vertex. Must be a non-negative integer. */
+  typedef unspecified Vertex_handle;
+  /** Handle to specify the simplex filtration value. */
+  typedef unspecified Filtration_value;
+
+  /** Assigns the 'simplex' with the given 'filtration' value. */
+  int assign_filtration(Simplex_handle simplex, Filtration_value filtration);
+
+  /** \brief Returns a range over vertices of a given
+   *  simplex. */
+  Simplex_vertex_range simplex_vertex_range(Simplex_handle const & simplex);
+
+  /** \brief Inserts a given `Gudhi::ProximityGraph` in the simplicial complex. */
+  template<class ProximityGraph>
+  void insert_graph(const ProximityGraph& proximity_graph);
+
+  /** \brief Expands the simplicial complex containing only its one skeleton until a given maximal dimension.
+   * expansion can be blocked by the blocker oracle. */
+  template< typename Blocker >
+  void expansion_with_blockers(int max_dim, Blocker block_simplex);
+
+  /** Returns the number of vertices in the simplicial complex. */
+  std::size_t num_vertices();
+
+};
+
+}  // namespace alpha_complex
+
+}  // namespace Gudhi
+
+#endif  // CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_H_
diff --git a/concept/Persistence_representations/Real_valued_topological_data.h b/concept/Persistence_representations/Real_valued_topological_data.h
index 1d3595ad..22ef6d72 100644
--- a/concept/Persistence_representations/Real_valued_topological_data.h
+++ b/concept/Persistence_representations/Real_valued_topological_data.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Pawel Dlotko
  *
- *    Copyright (C) 2016  INRIA (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/concept/Persistence_representations/Topological_data_with_averages.h b/concept/Persistence_representations/Topological_data_with_averages.h
index 9ebd105f..aa64467f 100644
--- a/concept/Persistence_representations/Topological_data_with_averages.h
+++ b/concept/Persistence_representations/Topological_data_with_averages.h
@@ -5,7 +5,7 @@
  *
  *    Author(s):       Pawel Dlotko
  *
- *    Copyright (C) 2016  INRIA (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/concept/Persistence_representations/Topological_data_with_distances.h b/concept/Persistence_representations/Topological_data_with_distances.h
index a6a62307..c8eb2b34 100644
--- a/concept/Persistence_representations/Topological_data_with_distances.h
+++ b/concept/Persistence_representations/Topological_data_with_distances.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Pawel Dlotko
  *
- *    Copyright (C) 2016  INRIA (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/concept/Persistence_representations/Topological_data_with_scalar_product.h b/concept/Persistence_representations/Topological_data_with_scalar_product.h
index 2e506ca9..0f08b8c6 100644
--- a/concept/Persistence_representations/Topological_data_with_scalar_product.h
+++ b/concept/Persistence_representations/Topological_data_with_scalar_product.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Pawel Dlotko
  *
- *    Copyright (C) 2016  INRIA (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/concept/Persistence_representations/Vectorized_topological_data.h b/concept/Persistence_representations/Vectorized_topological_data.h
index b6b5b109..365105d6 100644
--- a/concept/Persistence_representations/Vectorized_topological_data.h
+++ b/concept/Persistence_representations/Vectorized_topological_data.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Pawel Dlotko
  *
- *    Copyright (C) 2016  INRIA (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/concept/Persistent_cohomology/CoefficientField.h b/concept/Persistent_cohomology/CoefficientField.h
index 953b06c2..9d066cca 100644
--- a/concept/Persistent_cohomology/CoefficientField.h
+++ b/concept/Persistent_cohomology/CoefficientField.h
@@ -4,7 +4,7 @@
   *
   *    Author(s):       Clément Maria
   *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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/concept/Persistent_cohomology/FilteredComplex.h b/concept/Persistent_cohomology/FilteredComplex.h
index c19698df..62b9002f 100644
--- a/concept/Persistent_cohomology/FilteredComplex.h
+++ b/concept/Persistent_cohomology/FilteredComplex.h
@@ -4,7 +4,7 @@
   *
   *    Author(s):       Clément Maria
   *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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
@@ -29,10 +29,6 @@ struct FilteredComplex
 {
 /** Handle to specify a simplex. */
   typedef unspecified      Simplex_handle;
-/** \brief Key associated to each simplex. 
-  *
-  * Must be a signed integer type. */
-  typedef unspecified      Simplex_key;
 /** \brief Type for the value of the filtration function.
   *
   * Must be comparable with <. */
@@ -58,20 +54,10 @@ struct FilteredComplex
   * filtration function on the complex. */
   Filtration_value         filtration(Simplex_handle sh);
 
-/** \brief Returns a key that is different from the keys associated 
-  * to the simplices. */
-  Simplex_key              null_key ();
-/** \brief Returns the key associated to a simplex.
- *
- * This is never called on null_simplex(). */
-  Simplex_key              key      ( Simplex_handle sh );
 /** \brief Returns the simplex that has index idx in the filtration.
  *
- * This is never called on null_key(). */
-  Simplex_handle           simplex  ( Simplex_key idx );
-/** \brief Assign a key to a simplex. */
-  void                     assign_key(Simplex_handle sh, Simplex_key key);
- 
+ * This is only called on valid indices. */
+  Simplex_handle           simplex  ( size_t idx );
 /** \brief Iterator on the simplices belonging to the
   * boundary of a simplex.
   *
@@ -115,6 +101,26 @@ typedef unspecified Filtration_simplex_range;
   * .begin() and .end() return type Filtration_simplex_iterator.*/
 Filtration_simplex_range filtration_simplex_range();
 
+/** \name Map interface
+  * Conceptually a `std::unordered_map<Simplex_handle,std::size_t>`.
+  *  @{ */
+/** \brief Data stored for each simplex. 
+  *
+  * Must be an integer type. */
+  typedef unspecified      Simplex_key;
+/** \brief Returns a constant dummy number that is either negative,
+  * or at least as large as `num_simplices()`.  Suggested value: -1.  */
+  Simplex_key              null_key ();
+/** \brief Returns the number stored for a simplex by `assign_key`.
+  *
+  * This is never called on null_simplex(). */
+  Simplex_key              key      ( Simplex_handle sh );
+/** \brief Store a number for a simplex, which can later be retrieved with `key(sh)`.
+  *
+  * This is never called on null_simplex(). */
+  void                     assign_key(Simplex_handle sh, Simplex_key n);
+/** @} */
+ 
 
 /* \brief Iterator over the simplices of the complex,
   * in an arbitrary order.
diff --git a/concept/Persistent_cohomology/PersistentHomology.h b/concept/Persistent_cohomology/PersistentHomology.h
index 111723a5..f9a78763 100644
--- a/concept/Persistent_cohomology/PersistentHomology.h
+++ b/concept/Persistent_cohomology/PersistentHomology.h
@@ -4,7 +4,7 @@
   *
   *    Author(s):       Clément Maria
   *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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/concept/Rips_complex/SimplicialComplexForRips.h b/concept/Rips_complex/SimplicialComplexForRips.h
index 7dab0615..3c5acecf 100644
--- a/concept/Rips_complex/SimplicialComplexForRips.h
+++ b/concept/Rips_complex/SimplicialComplexForRips.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/concept/Simplex_tree/FiltrationValue.h b/concept/Simplex_tree/FiltrationValue.h
index 79ca06cc..f4dcf985 100644
--- a/concept/Simplex_tree/FiltrationValue.h
+++ b/concept/Simplex_tree/FiltrationValue.h
@@ -4,7 +4,7 @@
   *
   *    Author(s):       Clément Maria
   *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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/concept/Simplex_tree/IndexingTag.h b/concept/Simplex_tree/IndexingTag.h
index 1dcdd756..37e7e294 100644
--- a/concept/Simplex_tree/IndexingTag.h
+++ b/concept/Simplex_tree/IndexingTag.h
@@ -4,7 +4,7 @@
   *
   *    Author(s):       Clément Maria
   *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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/concept/Simplex_tree/SimplexKey.h b/concept/Simplex_tree/SimplexKey.h
index 9fbed401..c03f7da1 100644
--- a/concept/Simplex_tree/SimplexKey.h
+++ b/concept/Simplex_tree/SimplexKey.h
@@ -4,7 +4,7 @@
   *
   *    Author(s):       Clément Maria
   *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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/concept/Simplex_tree/SimplexTreeOptions.h b/concept/Simplex_tree/SimplexTreeOptions.h
index 89acdc18..6638da26 100644
--- a/concept/Simplex_tree/SimplexTreeOptions.h
+++ b/concept/Simplex_tree/SimplexTreeOptions.h
@@ -4,7 +4,7 @@
   *
   *    Author(s):       Marc Glisse
   *
-  *    Copyright (C) 2015  INRIA Saclay - Ile-de-France (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/concept/Simplex_tree/VertexHandle.h b/concept/Simplex_tree/VertexHandle.h
index 3efbba61..9d0642c3 100644
--- a/concept/Simplex_tree/VertexHandle.h
+++ b/concept/Simplex_tree/VertexHandle.h
@@ -4,7 +4,7 @@
   *
   *    Author(s):       Clément Maria
   *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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/concept/Skeleton_blocker/SkeletonBlockerDS.h b/concept/Skeleton_blocker/SkeletonBlockerDS.h
index d82425a0..fd806ff1 100644
--- a/concept/Skeleton_blocker/SkeletonBlockerDS.h
+++ b/concept/Skeleton_blocker/SkeletonBlockerDS.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/concept/Skeleton_blocker/SkeletonBlockerGeometricDS.h b/concept/Skeleton_blocker/SkeletonBlockerGeometricDS.h
index 477464c4..d8521343 100644
--- a/concept/Skeleton_blocker/SkeletonBlockerGeometricDS.h
+++ b/concept/Skeleton_blocker/SkeletonBlockerGeometricDS.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/concept/Witness_complex/SimplicialComplexForWitness.h b/concept/Witness_complex/SimplicialComplexForWitness.h
index d78cc83f..8b85f4e4 100644
--- a/concept/Witness_complex/SimplicialComplexForWitness.h
+++ b/concept/Witness_complex/SimplicialComplexForWitness.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Siargey Kachanovich
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (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