Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_nerve_gic_vincent@3656 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1f02e2f3b3e716d6578be49437e7d0b33fa99e5b

20 files changed, 51 insertions, 36 deletions

diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt
index 8b135ba1..2bb3b0c7 100644
--- a/src/Persistent_cohomology/benchmark/CMakeLists.txt
+++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt
@@ -1,6 +1,4 @@
-cmake_minimum_required(VERSION 2.6)
 project(Persistent_cohomology_benchmark)
-
   
 if(GMP_FOUND)
    if(GMPXX_FOUND)
diff --git a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
index 252e8aef..3b00d7a9 100644
--- a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
+++ b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
@@ -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/src/Persistent_cohomology/concept/CoefficientField.h b/src/Persistent_cohomology/concept/CoefficientField.h
index 953b06c2..9d066cca 100644
--- a/src/Persistent_cohomology/concept/CoefficientField.h
+++ b/src/Persistent_cohomology/concept/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/src/Persistent_cohomology/concept/FilteredComplex.h b/src/Persistent_cohomology/concept/FilteredComplex.h
index d6b662e9..62b9002f 100644
--- a/src/Persistent_cohomology/concept/FilteredComplex.h
+++ b/src/Persistent_cohomology/concept/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 an 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 only called on valid indices. */
   Simplex_handle           simplex  ( size_t idx );
-/** \brief Assign a key to a simplex. */
-  void                     assign_key(Simplex_handle sh, Simplex_key key);
- 
 /** \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/src/Persistent_cohomology/concept/PersistentHomology.h b/src/Persistent_cohomology/concept/PersistentHomology.h
index 111723a5..f9a78763 100644
--- a/src/Persistent_cohomology/concept/PersistentHomology.h
+++ b/src/Persistent_cohomology/concept/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/src/Persistent_cohomology/doc/COPYRIGHT b/src/Persistent_cohomology/doc/COPYRIGHT
index 34345bef..6cde9520 100644
--- a/src/Persistent_cohomology/doc/COPYRIGHT
+++ b/src/Persistent_cohomology/doc/COPYRIGHT
@@ -4,7 +4,7 @@ computational topology.
 
 Author(s):       Clément Maria
 
-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 the Free Software
diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
index 4dbe82c7..5fb9d4d2 100644
--- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
+++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.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
@@ -162,6 +162,19 @@ persistence diagram with a family of field coefficients.
 Rips_complex/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and
 outputs its persistence diagram.
 
+The file should contain square or lower triangular distance matrix with semicolons as separators.
+The code do not check if it is dealing with a distance matrix. It is the user responsibility to provide a valid input.
+Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an example of a file.
+
+\li <a href="_rips_complex_2rips_correlation_matrix_persistence_8cpp-example.html">
+Rips_complex/rips_correlation_matrix_persistence.cpp</a>
+computes the Rips complex of a correlation matrix and outputs its persistence diagram.
+
+Note that no check is performed if the matrix given as the input is a correlation matrix.
+It is the user responsibility to ensure that this is the case. The input is to be given either as a square or a lower
+triangular matrix.
+Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv for an example of a file.
+
 \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
 Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
 \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file.
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 18e2913b..0f731519 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Persistent_cohomology_examples)
 
 add_executable(plain_homology plain_homology.cpp)
diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
index 64f2a4dc..35366144 100644
--- a/src/Persistent_cohomology/example/custom_persistence_sort.cpp
+++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA Saclay (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/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp
index eafa3fd5..c40434a4 100644
--- a/src/Persistent_cohomology/example/persistence_from_file.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_file.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA Saclay (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/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
index 8ef479d4..ffccfd86 100644
--- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    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/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp
index a5ae09c8..a2256060 100644
--- a/src/Persistent_cohomology/example/plain_homology.cpp
+++ b/src/Persistent_cohomology/example/plain_homology.cpp
@@ -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/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index dae36ed2..626ec2ef 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -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
diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
index c1de0ef8..7c81fcfb 100644
--- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
@@ -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/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
index 9618f278..c7607dce 100644
--- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria, Marc Glisse
  *
- *    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/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index e0a147b3..c68b5c0b 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.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
@@ -285,7 +285,7 @@ class Persistent_cohomology {
         }
       }
       cpx_->assign_key(sigma, cpx_->null_key());
-    } else {  // If ku == kv, same connected component: create a 1-cocycle class.
+    } else if (dim_max_ > 1) {  // If ku == kv, same connected component: create a 1-cocycle class.
       create_cocycle(sigma, coeff_field_.multiplicative_identity(), coeff_field_.characteristic());
     }
   }
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
index 6db16e69..e98b4bb4 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.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/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
index 38bc08d1..2bae8654 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.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/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h
index 5deb2d88..de6c0750 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.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/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt
index 45f53eb9..f8baf861 100644
--- a/src/Persistent_cohomology/test/CMakeLists.txt
+++ b/src/Persistent_cohomology/test/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Persistent_cohomology_tests)
 
 include(GUDHI_test_coverage)