Initial import of upstream's 1.3.1.upstream/1.3.1

5 files changed, 163 insertions, 0 deletions

diff --git a/concept/Simplex_tree/FiltrationValue.h b/concept/Simplex_tree/FiltrationValue.h
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+++ b/concept/Simplex_tree/FiltrationValue.h
@@ -0,0 +1,35 @@
+ /*    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):       Clément Maria
+  *
+  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+  *
+  *    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/>.
+  */
+
+/** \brief Value type for a filtration function on a cell complex.
+  *
+  * A <EM>filtration</EM> of a cell complex (see FilteredComplex) is
+  * a function \f$f:\mathbf{K} \rightarrow \mathbb{R}\f$ satisfying \f$f(\tau)\leq 
+  * f(\sigma)\f$ whenever \f$\tau \subseteq \sigma\f$. Ordering the simplices 
+  * by increasing filtration values (breaking ties so as a simplex appears after 
+  * its subsimplices of same filtration value) provides an indexing scheme 
+  * (see IndexingTag).
+  */
+  struct FiltrationValue {
+    /** \brief Operator < is a StrictWeakOrdering. */
+    bool operator<(FiltrationValue f1, FiltrationValue f2);
+  };
diff --git a/concept/Simplex_tree/IndexingTag.h b/concept/Simplex_tree/IndexingTag.h
new file mode 100644
index 00000000..1dcdd756
--- /dev/null
+++ b/concept/Simplex_tree/IndexingTag.h
@@ -0,0 +1,30 @@
+ /*    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):       Clément Maria
+  *
+  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+  *
+  *    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/>.
+  */
+
+/** \brief Concept describing an indexing scheme (see FilteredComplex) 
+  * for applying 
+  * continuous maps to a cell complex, and compute its persistent
+  * homology.
+  *
+  * Must be `Gudhi::linear_indexing_tag`. 
+  */
+struct IndexingTag {};
diff --git a/concept/Simplex_tree/SimplexKey.h b/concept/Simplex_tree/SimplexKey.h
new file mode 100644
index 00000000..9fbed401
--- /dev/null
+++ b/concept/Simplex_tree/SimplexKey.h
@@ -0,0 +1,28 @@
+ /*    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):       Clément Maria
+  *
+  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+  *
+  *    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/>.
+  */
+
+ /** \brief Key type used as simplex identifier.
+  *
+  * Must be an integer type.
+  */
+ struct SimplexKey {};
+ 
diff --git a/concept/Simplex_tree/SimplexTreeOptions.h b/concept/Simplex_tree/SimplexTreeOptions.h
new file mode 100644
index 00000000..89acdc18
--- /dev/null
+++ b/concept/Simplex_tree/SimplexTreeOptions.h
@@ -0,0 +1,43 @@
+ /*    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):       Marc Glisse
+  *
+  *    Copyright (C) 2015  INRIA Saclay - Ile-de-France (France)
+  *
+  *    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/>.
+  */
+  
+/** \brief Concept of the template parameter for the class `Gudhi::Simplex_tree<SimplexTreeOptions>`.
+ *
+ * One model for this is `Gudhi::Simplex_tree_options_full_featured`. If you want to provide your own, it is recommended that you derive from it and override some parts instead of writing a class from scratch.
+ */
+struct SimplexTreeOptions {
+  /// Forced for now.
+  typedef IndexingTag Indexing_tag;
+  /// Must be a signed integer type. It admits a total order <.
+  typedef VertexHandle Vertex_handle;
+  /// Must be comparable with operator<.
+  typedef FiltrationValue Filtration_value;
+  /// Must be an integer type.
+  typedef SimplexKey Simplex_key;
+  /// If true, each simplex has extra storage for one `Simplex_key`. Necessary for `Persistent_cohomology`.
+  static const bool store_key;
+  /// If true, each simplex has extra storage for one `Filtration_value`, and this value is propagated by operations like `Gudhi::Simplex_tree::expansion`. Without it, `Persistent_cohomology` degenerates to computing usual (non-persistent) cohomology.
+  static const bool store_filtration;
+  /// If true, the list of vertices present in the complex must always be 0, ..., num_vertices-1, without any hole.
+  static constexpr bool contiguous_vertices;
+};
+
diff --git a/concept/Simplex_tree/VertexHandle.h b/concept/Simplex_tree/VertexHandle.h
new file mode 100644
index 00000000..3efbba61
--- /dev/null
+++ b/concept/Simplex_tree/VertexHandle.h
@@ -0,0 +1,27 @@
+ /*    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):       Clément Maria
+  *
+  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+  *
+  *    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/>.
+  */
+  
+/** \brief Handle type for the vertices of a cell complex.
+  * 
+  * Must be a signed integer type. <code>operator&lt;</code> defines a total order on it.
+  */
+struct VertexHandle {};