Merge from trunk.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/qt5@1848 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c8e1376894207c8c08896f750f71c115e07f6d95

16 files changed, 513 insertions, 438 deletions

diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index c852c43f..d3a52b60 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -33,25 +33,6 @@ if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
 
   SET(Boost_USE_STATIC_LIBS ON)
   SET(Boost_USE_MULTITHREAD OFF)
-  INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
-  LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-  
-  include(${CGAL_USE_FILE})
-  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-  # A workaround is to add "-std=c++11" again.
-  # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-  # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-  # but it implies to use cmake version 3.1 at least.
-  if(NOT MSVC)
-    include(CheckCXXCompilerFlag)
-    CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-    if(COMPILER_SUPPORTS_CXX11)
-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-    endif()
-  endif()
-  # - End of workaround
-
   include_directories (${QGLVIEWER_INCLUDE_DIR})
  
   #####################################################################
@@ -69,6 +50,11 @@ if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
   target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL )
   target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} )
   target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )	
+if (TBB_FOUND)
+  target_link_libraries( GudhUI ${TBB_LIBRARIES})
+endif()
+
+###############################################################################
 
 else()
   message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt5, and will not be compiled.")
diff --git a/src/GudhUI/gui/MainWindow.h b/src/GudhUI/gui/MainWindow.h
index 7e11ddd6..15664dcb 100644
--- a/src/GudhUI/gui/MainWindow.h
+++ b/src/GudhUI/gui/MainWindow.h
@@ -23,6 +23,9 @@
 #ifndef GUI_MAINWINDOW_H_
 #define GUI_MAINWINDOW_H_
 
+// Workaround https://svn.boost.org/trac/boost/ticket/12534
+#include <boost/container/flat_map.hpp>
+
 #include <QMainWindow>
 #include "ui_main_window.h"
 #include "model/Model.h"
diff --git a/src/GudhUI/gui/MenuEdgeContraction.ui b/src/GudhUI/gui/MenuEdgeContraction.ui
index da2e5c82..b1696431 100644
--- a/src/GudhUI/gui/MenuEdgeContraction.ui
+++ b/src/GudhUI/gui/MenuEdgeContraction.ui
@@ -1,118 +1,118 @@
-<?xml version="1.0" encoding="UTF-8"?>

-<ui version="4.0">

- <class>MenuEdgeContraction</class>

- <widget class="QDialog" name="MenuEdgeContraction">

-  <property name="geometry">

-   <rect>

-    <x>0</x>

-    <y>0</y>

-    <width>362</width>

-    <height>209</height>

-   </rect>

-  </property>

-  <property name="windowTitle">

-   <string>Edge contraction</string>

-  </property>

-  <layout class="QGridLayout" name="gridLayout">

-   <item row="5" column="2">

-    <widget class="QSpinBox" name="spinBox_nb_remaining_vertices">

-     <property name="minimum">

-      <number>1</number>

-     </property>

-     <property name="maximum">

-      <number>999999999</number>

-     </property>

-     <property name="value">

-      <number>1</number>

-     </property>

-    </widget>

-   </item>

-   <item row="7" column="2">

-    <widget class="QCheckBox" name="checkBox_link_condition">

-     <property name="enabled">

-      <bool>false</bool>

-     </property>

-     <property name="text">

-      <string>Link condition</string>

-     </property>

-     <property name="checked">

-      <bool>true</bool>

-     </property>

-    </widget>

-   </item>

-   <item row="3" column="2" alignment="Qt::AlignRight">

-    <widget class="QLabel" name="txt_nb_collapses">

-     <property name="text">

-      <string>1</string>

-     </property>

-    </widget>

-   </item>

-   <item row="6" column="0">

-    <widget class="QLabel" name="label">

-     <property name="text">

-      <string>Policy</string>

-     </property>

-    </widget>

-   </item>

-   <item row="6" column="2">

-    <widget class="QComboBox" name="m_simplificationMethod">

-     <item>

-      <property name="text">

-       <string>Length_midpoint</string>

-      </property>

-     </item>

-    </widget>

-   </item>

-   <item row="2" column="2" alignment="Qt::AlignRight">

-    <widget class="QLabel" name="txt_nb_vertices">

-     <property name="text">

-      <string>0</string>

-     </property>

-    </widget>

-   </item>

-   <item row="2" column="0">

-    <widget class="QLabel" name="label_5">

-     <property name="text">

-      <string>Number of vertices</string>

-     </property>

-    </widget>

-   </item>

-   <item row="3" column="0" colspan="2">

-    <widget class="QLabel" name="label_3">

-     <property name="text">

-      <string>Number of contractions</string>

-     </property>

-    </widget>

-   </item>

-   <item row="5" column="0" colspan="2">

-    <widget class="QLabel" name="label_4">

-     <property name="text">

-      <string>Number of vertices after </string>

-     </property>

-    </widget>

-   </item>

-   <item row="1" column="0">

-    <widget class="QSlider" name="horizontalSlider">

-     <property name="minimum">

-      <number>0</number>

-     </property>

-     <property name="maximum">

-      <number>100</number>

-     </property>

-     <property name="orientation">

-      <enum>Qt::Horizontal</enum>

-     </property>

-    </widget>

-   </item>

-   <item row="1" column="2">

-    <widget class="QPushButton" name="pushButton_collapse">

-     <property name="text">

-      <string>Perform collapse</string>

-     </property>

-    </widget>

-   </item>

-  </layout>

- </widget>

- <resources/>

- <connections/>

-</ui>

+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>MenuEdgeContraction</class>
+ <widget class="QDialog" name="MenuEdgeContraction">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>362</width>
+    <height>209</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Edge contraction</string>
+  </property>
+  <layout class="QGridLayout" name="gridLayout">
+   <item row="5" column="2">
+    <widget class="QSpinBox" name="spinBox_nb_remaining_vertices">
+     <property name="minimum">
+      <number>1</number>
+     </property>
+     <property name="maximum">
+      <number>999999999</number>
+     </property>
+     <property name="value">
+      <number>1</number>
+     </property>
+    </widget>
+   </item>
+   <item row="7" column="2">
+    <widget class="QCheckBox" name="checkBox_link_condition">
+     <property name="enabled">
+      <bool>false</bool>
+     </property>
+     <property name="text">
+      <string>Link condition</string>
+     </property>
+     <property name="checked">
+      <bool>true</bool>
+     </property>
+    </widget>
+   </item>
+   <item row="3" column="2" alignment="Qt::AlignRight">
+    <widget class="QLabel" name="txt_nb_collapses">
+     <property name="text">
+      <string>1</string>
+     </property>
+    </widget>
+   </item>
+   <item row="6" column="0">
+    <widget class="QLabel" name="label">
+     <property name="text">
+      <string>Policy</string>
+     </property>
+    </widget>
+   </item>
+   <item row="6" column="2">
+    <widget class="QComboBox" name="m_simplificationMethod">
+     <item>
+      <property name="text">
+       <string>Length_midpoint</string>
+      </property>
+     </item>
+    </widget>
+   </item>
+   <item row="2" column="2" alignment="Qt::AlignRight">
+    <widget class="QLabel" name="txt_nb_vertices">
+     <property name="text">
+      <string>0</string>
+     </property>
+    </widget>
+   </item>
+   <item row="2" column="0">
+    <widget class="QLabel" name="label_5">
+     <property name="text">
+      <string>Number of vertices</string>
+     </property>
+    </widget>
+   </item>
+   <item row="3" column="0" colspan="2">
+    <widget class="QLabel" name="label_3">
+     <property name="text">
+      <string>Number of contractions</string>
+     </property>
+    </widget>
+   </item>
+   <item row="5" column="0" colspan="2">
+    <widget class="QLabel" name="label_4">
+     <property name="text">
+      <string>Number of vertices after </string>
+     </property>
+    </widget>
+   </item>
+   <item row="1" column="0">
+    <widget class="QSlider" name="horizontalSlider">
+     <property name="minimum">
+      <number>0</number>
+     </property>
+     <property name="maximum">
+      <number>100</number>
+     </property>
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
+     </property>
+    </widget>
+   </item>
+   <item row="1" column="2">
+    <widget class="QPushButton" name="pushButton_collapse">
+     <property name="text">
+      <string>Perform collapse</string>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>
diff --git a/src/GudhUI/gui/gudhui.cpp b/src/GudhUI/gui/gudhui.cpp
index 377cd2f2..276c4a5f 100644
--- a/src/GudhUI/gui/gudhui.cpp
+++ b/src/GudhUI/gui/gudhui.cpp
@@ -1,38 +1,38 @@
-/* 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):       David Salinas

- *

- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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/>.

- * 

- */

-

-#include "MainWindow.h"

-#include <QApplication>

-#include <CGAL/Qt/resources.h>

-

-int main(int argc, char** argv) {

-  QApplication application(argc, argv);

-  application.setOrganizationDomain("inria.fr");

-  application.setOrganizationName("INRIA");

-  application.setApplicationName("GudhUI");

-

-  MainWindow mw;

-  application.setQuitOnLastWindowClosed(false);

-  mw.show();

-  return application.exec();

-}

+/* 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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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/>.
+ * 
+ */
+
+#include "MainWindow.h"
+#include <QApplication>
+#include <CGAL/Qt/resources.h>
+
+int main(int argc, char** argv) {
+  QApplication application(argc, argv);
+  application.setOrganizationDomain("inria.fr");
+  application.setOrganizationName("INRIA");
+  application.setApplicationName("GudhUI");
+
+  MainWindow mw;
+  application.setQuitOnLastWindowClosed(false);
+  mw.show();
+  return application.exec();
+}
diff --git a/src/GudhUI/model/Complex_typedefs.h b/src/GudhUI/model/Complex_typedefs.h
index c310d4a6..a4df2c94 100644
--- a/src/GudhUI/model/Complex_typedefs.h
+++ b/src/GudhUI/model/Complex_typedefs.h
@@ -41,7 +41,7 @@ struct Geometry_trait : public CGAL::Cartesian_d<double> {
 typedef Geometry_trait::Point Point;
 
 using namespace Gudhi;
-using namespace Gudhi::skbl;
+using namespace Gudhi::skeleton_blocker;
 
 typedef Skeleton_blocker_simple_geometric_traits<Geometry_trait> Complex_geometric_traits;
 typedef Skeleton_blocker_geometric_complex< Complex_geometric_traits > Complex;
diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h
index d78cbad9..fc284cc6 100644
--- a/src/GudhUI/model/Model.h
+++ b/src/GudhUI/model/Model.h
@@ -71,9 +71,9 @@ class CGAL_geometric_flag_complex_wrapper {
 
   void maximal_face(std::vector<int> vertices) {
     if (!load_only_points_) {
-      std::cout << "size:" << vertices.size() << std::endl;
-      for (int i = 0; i < vertices.size(); ++i)
-        for (int j = i + 1; j < vertices.size(); ++j)
+      // std::cout << "size:" << vertices.size() << std::endl;
+      for (std::size_t i = 0; i < vertices.size(); ++i)
+        for (std::size_t j = i + 1; j < vertices.size(); ++j)
           complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j]));
     }
   }
@@ -187,7 +187,7 @@ class Model {
   }
 
   void contract_edges(unsigned num_contractions) {
-    Clock c;
+    Gudhi::Clock c;
     Edge_contractor<Complex> contractor(complex_, num_contractions);
     std::cout << "Time to simplify: " << c.num_seconds() << "s" << std::endl;
   }
@@ -248,8 +248,8 @@ class Model {
     unsigned num_simplices = 0;
     int euler = 0;
     int dimension = 0;
-    Clock clock;
-    for (const auto &s : complex_.simplex_range()) {
+    Gudhi::Clock clock;
+    for (const auto &s : complex_.complex_simplex_range()) {
       num_simplices++;
       dimension = (std::max)(s.dimension(), dimension);
       if (s.dimension() % 2 == 0)
@@ -271,7 +271,7 @@ class Model {
 #ifdef _WIN32
     std::cout << "Works only on linux x64 for the moment\n";
 #else
-    Clock clock;
+    Gudhi::Clock clock;
     run_chomp();
     clock.end();
 #endif
@@ -281,7 +281,7 @@ class Model {
     unsigned num_simplices = 0;
     int euler = 0;
     int dimension = 0;
-    for (const auto &s : complex_.simplex_range()) {
+    for (const auto &s : complex_.complex_simplex_range()) {
       num_simplices++;
       dimension = (std::max)(s.dimension(), dimension);
       if (s.dimension() % 2 == 0)
@@ -328,7 +328,7 @@ class Model {
   void save_complex_in_file_for_chomp() {
     std::ofstream file;
     file.open("chomp.sim");
-    for (const auto &s : complex_.simplex_range()) {
+    for (const auto &s : complex_.complex_simplex_range()) {
       bool first = true;
       file << "(";
       for (auto x : s) {
diff --git a/src/GudhUI/utils/Bar_code_persistence.h b/src/GudhUI/utils/Bar_code_persistence.h
new file mode 100644
index 00000000..b527d684
--- /dev/null
+++ b/src/GudhUI/utils/Bar_code_persistence.h
@@ -0,0 +1,90 @@
+#include <math.h>  // isfinite
+
+#include <QtGui/QApplication>
+
+#include <QGraphicsView>
+#include <QGraphicsScene>
+#include <QPointF>
+#include <QVector>
+#include <QGraphicsTextItem>
+
+#include <iostream>
+#include <vector>
+#include <limits>  // NaN, infinity
+#include <utility>  // for pair
+#include <string>
+
+#ifndef UTILS_BAR_CODE_PERSISTENCE_H_
+#define UTILS_BAR_CODE_PERSISTENCE_H_
+
+class Bar_code_persistence {
+ private:
+  typedef std::vector<std::pair<double, double>> Persistence;
+  Persistence persistence_vector;
+  double min_birth;
+  double max_death;
+
+ public:
+  Bar_code_persistence()
+      : min_birth(std::numeric_limits<double>::quiet_NaN()),
+      max_death(std::numeric_limits<double>::quiet_NaN()) { }
+
+  void insert(double birth, double death) {
+    persistence_vector.push_back(std::make_pair(birth, death));
+    if (std::isfinite(birth)) {
+      if ((birth < min_birth) || (std::isnan(min_birth)))
+        min_birth = birth;
+      if ((birth > max_death) || (std::isnan(max_death)))
+        max_death = birth;
+    }
+    if (std::isfinite(death))
+      if ((death > max_death) || (std::isnan(max_death)))
+        max_death = death;
+  }
+
+  void show(const std::string& window_title) {
+    // Create a view, put a scene in it
+    QGraphicsView * view = new QGraphicsView();
+    QGraphicsScene * scene = new QGraphicsScene();
+    view->setScene(scene);
+    double ratio = 600.0 / (max_death - min_birth);
+    // std::cout << "min_birth=" << min_birth << " - max_death=" << max_death << " - ratio=" << ratio << std::endl;
+
+    double height = 0.0, birth = 0.0, death = 0.0;
+    int pers_num = 1;
+    for (auto& persistence : persistence_vector) {
+      height = 5.0 * pers_num;
+      // std::cout << "[" << pers_num << "] birth=" << persistence.first << " - death=" << persistence.second << std::endl;
+      if (std::isfinite(persistence.first))
+        birth = ((persistence.first - min_birth) * ratio) + 50.0;
+      else
+        birth = 0.0;
+
+      if (std::isfinite(persistence.second))
+        death = ((persistence.second - min_birth) * ratio) + 50.0;
+      else
+        death = 700.0;
+
+      scene->addLine(birth, height, death, height, QPen(Qt::blue, 2));
+      pers_num++;
+    }
+    height += 10.0;
+    // scale line
+    scene->addLine(0, height, 700.0, height, QPen(Qt::black, 1));
+    int modulo = 0;
+    for (double scale = 50.0; scale < 700.0; scale += 50.0) {
+      modulo++;
+      // scale small dash
+      scene->addLine(scale, height - 3.0, scale, height + 3.0, QPen(Qt::black, 1));
+      // scale text
+      QString scale_value = QString::number(((scale - 50.0) / ratio) + min_birth);
+      QGraphicsTextItem* dimText = scene->addText(scale_value, QFont("Helvetica", 8));
+      dimText->setPos(scale - (3.0 * scale_value.size()), height + 9.0 * (modulo % 2));
+    }
+    view->setWindowTitle(window_title.c_str());
+    // Show the view
+    view->show();
+  }
+};
+
+#endif  // UTILS_BAR_CODE_PERSISTENCE_H_
diff --git a/src/GudhUI/utils/Edge_contractor.h b/src/GudhUI/utils/Edge_contractor.h
index 45079a40..8a29ff4b 100644
--- a/src/GudhUI/utils/Edge_contractor.h
+++ b/src/GudhUI/utils/Edge_contractor.h
@@ -65,7 +65,7 @@ template<typename SkBlComplex> class Edge_contractor {
 
     Placement_type operator()(const EdgeProfile& profile) const override {
       std::vector<double> mid_coords(profile.p0().dimension(), 0);
-      for (size_t i = 0; i < profile.p0().dimension(); ++i) {
+      for (int i = 0; i < profile.p0().dimension(); ++i) {
         mid_coords[i] = (profile.p0()[i] + profile.p1()[i]) / 2.;
       }
       return Point(profile.p0().dimension(), mid_coords.begin(), mid_coords.end());
diff --git a/src/GudhUI/utils/Furthest_point_epsilon_net.h b/src/GudhUI/utils/Furthest_point_epsilon_net.h
index f2a216f6..98346daa 100644
--- a/src/GudhUI/utils/Furthest_point_epsilon_net.h
+++ b/src/GudhUI/utils/Furthest_point_epsilon_net.h
@@ -73,7 +73,7 @@ template<typename SkBlComplex> class Furthest_point_epsilon_net {
       complex_(complex) {
     if (!complex.empty()) {
       init_filtration();
-      for (int k = 2; k < net_filtration_.size(); ++k) {
+      for (std::size_t k = 2; k < net_filtration_.size(); ++k) {
         update_radius_value(k);
       }
     }
diff --git a/src/GudhUI/utils/Is_manifold.h b/src/GudhUI/utils/Is_manifold.h
index b6b19ee0..0640ea47 100644
--- a/src/GudhUI/utils/Is_manifold.h
+++ b/src/GudhUI/utils/Is_manifold.h
@@ -69,7 +69,7 @@ template<typename SkBlComplex> class Is_manifold {
  private:
   unsigned local_dimension(Vertex_handle v) {
     unsigned dim = 0;
-    for (const auto& s : input_complex_.simplex_range(v))
+    for (const auto& s : input_complex_.star_simplex_range(v))
       dim = (std::max)(dim, (unsigned) s.dimension());
     return dim;
   }
diff --git a/src/GudhUI/utils/K_nearest_builder.h b/src/GudhUI/utils/K_nearest_builder.h
index cab24b7c..7be0a4f4 100644
--- a/src/GudhUI/utils/K_nearest_builder.h
+++ b/src/GudhUI/utils/K_nearest_builder.h
@@ -29,12 +29,10 @@
 #include <CGAL/Search_traits_d.h>
 #include <CGAL/Search_traits_adapter.h>
 #include <CGAL/property_map.h>
-#include <boost/iterator/iterator_facade.hpp>
-#include <boost/iterator/zip_iterator.hpp>
 
 #include <unordered_map>
-#include <tuple>
 #include <list>
+#include <utility>
 
 #include "utils/UI_utils.h"
 #include "model/Complex_typedefs.h"
@@ -43,9 +41,9 @@ template<typename SkBlComplex> class K_nearest_builder {
  private:
   typedef Geometry_trait Kernel;
   typedef Point Point_d;
-  typedef boost::tuple<Point_d, unsigned> Point_d_with_id;
+  typedef std::pair<Point_d, unsigned> Point_d_with_id;
   typedef CGAL::Search_traits_d<Kernel> Traits_base;
-  typedef CGAL::Search_traits_adapter<Point_d_with_id, CGAL::Nth_of_tuple_property_map<0, Point_d_with_id>,
+  typedef CGAL::Search_traits_adapter<Point_d_with_id, CGAL::First_of_pair_property_map<Point_d_with_id>,
       Traits_base> Traits;
   typedef CGAL::Orthogonal_k_neighbor_search<Traits> Neighbor_search;
   typedef Neighbor_search::Tree Tree;
@@ -81,7 +79,7 @@ template<typename SkBlComplex> class K_nearest_builder {
     for (auto p : complex_.vertex_range()) {
       Neighbor_search search(tree, complex_.point(p), k + 1);
       for (auto it = ++search.begin(); it != search.end(); ++it) {
-        Vertex_handle q(boost::get<1>(it->first));
+        Vertex_handle q(std::get<1>(it->first));
         if (p != q && complex_.contains_vertex(p) && complex_.contains_vertex(q))
           complex_.add_edge(p, q);
       }
diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h
index 0b9961d3..97165490 100644
--- a/src/GudhUI/utils/Persistence_compute.h
+++ b/src/GudhUI/utils/Persistence_compute.h
@@ -46,10 +46,6 @@ struct Persistence_params {
  * Show persistence into output stream
  */
 template<typename SkBlComplex> class Persistence_compute {
- private:
-  SkBlComplex& complex_;
-  std::ostream& stream_;
-
  public:
   typedef typename SkBlComplex::Vertex_handle Vertex_handle;
   typedef typename SkBlComplex::Edge_handle Edge_handle;
@@ -61,9 +57,7 @@ template<typename SkBlComplex> class Persistence_compute {
    * double threshold
    * int p for coefficient Z_p
    */
-  Persistence_compute(SkBlComplex& complex, std::ostream& stream, const Persistence_params& params) :
-      // double threshold = 0.5,unsigned dim_max = 8):
-      complex_(complex), stream_(stream) {
+  Persistence_compute(SkBlComplex& complex, std::ostream& stream, const Persistence_params& params) {
     // for now everything is copied, todo boost adapt iterators to points of SkBlComplex instead of copying to an
     // initial vector
     typedef std::vector<double> Point_t;
@@ -87,10 +81,10 @@ template<typename SkBlComplex> class Persistence_compute {
     pcoh.init_coefficients(params.p);
     // put params.min_pers
     pcoh.compute_persistent_cohomology(params.min_pers);
-    stream_ << "persistence: \n";
-    stream_ << "p dimension birth death: \n";
+    stream << "persistence: \n";
+    stream << "p dimension birth death: \n";
 
-    pcoh.output_diagram(stream_);
+    pcoh.output_diagram(stream);
   }
 };
 
diff --git a/src/GudhUI/view/FirstCoordProjector.h b/src/GudhUI/view/FirstCoordProjector.h
index 529d2d42..1333f5d3 100644
--- a/src/GudhUI/view/FirstCoordProjector.h
+++ b/src/GudhUI/view/FirstCoordProjector.h
@@ -32,8 +32,12 @@ class FirstCoordProjector3D : public Projector3D {
   typedef Projector3D::Point_3 Point_3;
 
   Point_3 operator()(const Point& p) const {
-    assert(p.dimension() >= 3);
-    return Point_3(p.x(), p.y(), p.z());
+    if (p.dimension() >= 3)
+      return Point_3(p.x(), p.y(), p.z());
+    else if  (p.dimension() >= 2)
+      return Point_3(p.x(), p.y(), 0.0);
+    else
+      return Point_3(0.0, 0.0, 0.0);
   }
 };
 
diff --git a/src/GudhUI/view/Viewer.h b/src/GudhUI/view/Viewer.h
index 48427099..797ddc53 100644
--- a/src/GudhUI/view/Viewer.h
+++ b/src/GudhUI/view/Viewer.h
@@ -1,117 +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):       David Salinas

- *

- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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/>.

- * 

- */

-

-#ifndef VIEW_VIEWER_H_

-#define VIEW_VIEWER_H_

-

-#include <QGLViewer/qglviewer.h>

-

-#include <vector>

-

-#include "View_parameter.h"

-#include "model/Complex_typedefs.h"

-#include "Color.h"

-#include "Viewer_instructor.h"

-

-class Viewer_instructor;

-

-class Viewer : public QGLViewer {

-  Q_OBJECT

-

-  Viewer_instructor * instructor;

-

-  /**

-   * light angles

-   */

-  double theta, phi;

-  typedef Complex::GT Gudhi_kernel;

-  typedef Gudhi_kernel::Point_3 Point_3;

-

- public:

-  Viewer(QWidget* parent);

-

-  void set_instructor(Viewer_instructor* instructor_);

-

-  void show_entire_scene();

-

-  void draw();

-

-  void set_bounding_box(const Point_3 & lower_left, const Point_3 & upper_right);

-

-  void update_GL();

-

-  void init_scene();

-

-  void init_light();

-

-  void set_light();

-

-  void set_light_direction(double theta, double phi);

-

-  /**

-   * set the light in the direction of the observer

-   */

-  void set_light_direction();

-

- protected:

-  virtual void postSelection(const QPoint& point);

-

- public:

-  ////////////////////////

-  // draw

-  ////////////////////////

-  void set_size_point(double size_points);

-

-  void set_color(const Color& color);

-

-  void draw_point(const Point_3& p, const Color& color, double size_points);

-

-  void begin_draw_points(double size, bool light = false);

-

-  void draw_points(const Point_3 & point);

-

-  void end_draw_points();

-

-  void draw_edge(const Point_3 &a, const Point_3 &b, const Color& color, double size);

-

-  void begin_draw_edges(double size, bool light = false);

-

-  void draw_edges(const Point_3 &a, const Point_3 &b);

-

-  void end_draw_edges();

-

-  void begin_draw_triangles(double size, bool light, bool transparent = false);

-

-  void draw_triangles(const Point_3& p1, const Point_3& p2, const Point_3& p3);

-

-  // todo remove

-  void draw_triangles(const std::vector<Point_3*>& points);

-

-  void end_draw_triangles();

-

-

- signals:

-  void click(const Point_3& position);

-};

-

-#endif  // VIEW_VIEWER_H_

+/* 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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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/>.
+ * 
+ */
+
+#ifndef VIEW_VIEWER_H_
+#define VIEW_VIEWER_H_
+
+#include <QGLViewer/qglviewer.h>
+
+#include <vector>
+
+#include "View_parameter.h"
+#include "model/Complex_typedefs.h"
+#include "Color.h"
+#include "Viewer_instructor.h"
+
+class Viewer_instructor;
+
+class Viewer : public QGLViewer {
+  Q_OBJECT
+
+  Viewer_instructor * instructor;
+
+  /**
+   * light angles
+   */
+  double theta, phi;
+  typedef Complex::GT Gudhi_kernel;
+  typedef Gudhi_kernel::Point_3 Point_3;
+
+ public:
+  Viewer(QWidget* parent);
+
+  void set_instructor(Viewer_instructor* instructor_);
+
+  void show_entire_scene();
+
+  void draw();
+
+  void set_bounding_box(const Point_3 & lower_left, const Point_3 & upper_right);
+
+  void update_GL();
+
+  void init_scene();
+
+  void init_light();
+
+  void set_light();
+
+  void set_light_direction(double theta, double phi);
+
+  /**
+   * set the light in the direction of the observer
+   */
+  void set_light_direction();
+
+ protected:
+  virtual void postSelection(const QPoint& point);
+
+ public:
+  ////////////////////////
+  // draw
+  ////////////////////////
+  void set_size_point(double size_points);
+
+  void set_color(const Color& color);
+
+  void draw_point(const Point_3& p, const Color& color, double size_points);
+
+  void begin_draw_points(double size, bool light = false);
+
+  void draw_points(const Point_3 & point);
+
+  void end_draw_points();
+
+  void draw_edge(const Point_3 &a, const Point_3 &b, const Color& color, double size);
+
+  void begin_draw_edges(double size, bool light = false);
+
+  void draw_edges(const Point_3 &a, const Point_3 &b);
+
+  void end_draw_edges();
+
+  void begin_draw_triangles(double size, bool light, bool transparent = false);
+
+  void draw_triangles(const Point_3& p1, const Point_3& p2, const Point_3& p3);
+
+  // todo remove
+  void draw_triangles(const std::vector<Point_3*>& points);
+
+  void end_draw_triangles();
+
+
+ signals:
+  void click(const Point_3& position);
+};
+
+#endif  // VIEW_VIEWER_H_
diff --git a/src/GudhUI/view/Viewer_instructor.cpp b/src/GudhUI/view/Viewer_instructor.cpp
index 4446d209..1ddd4d8b 100644
--- a/src/GudhUI/view/Viewer_instructor.cpp
+++ b/src/GudhUI/view/Viewer_instructor.cpp
@@ -159,7 +159,7 @@ void Viewer_instructor::set_color_edge(Edge_handle eh) {
   viewer_->set_color(Color(view_params_.light_edges, view_params_.light_edges, view_params_.light_edges));
 }
 
-void Viewer_instructor::set_color_triangle(const Simplex_handle& triangle) {
+void Viewer_instructor::set_color_triangle(const Simplex& triangle) {
   viewer_->set_color(Color(view_params_.light_triangles, view_params_.light_triangles, view_params_.light_triangles));
 }
 
diff --git a/src/GudhUI/view/Viewer_instructor.h b/src/GudhUI/view/Viewer_instructor.h
index 96b25c77..05c5c1fc 100644
--- a/src/GudhUI/view/Viewer_instructor.h
+++ b/src/GudhUI/view/Viewer_instructor.h
@@ -1,114 +1,114 @@
-/* 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):       David Salinas

- *

- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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/>.

- * 

- */

-

-#ifndef VIEW_VIEWER_INSTRUCTOR_H_

-#define VIEW_VIEWER_INSTRUCTOR_H_

-

-// todo do a viewer instructor that have directely a pointer to a QGLviewer and buffer ot not triangles

-

-#include <QFileDialog>

-#include <QKeyEvent>

-#include <QGLViewer/camera.h>

-

-#include <memory>

-#include <utility>  // for pair<>

-

-#include "model/Complex_typedefs.h"

-

-#include "Projector3D.h"

-#include "View_parameter.h"

-#include "Viewer.h"

-

-class Viewer;

-class Viewer_parameter;

-

-class Viewer_instructor : public QWidget {

-  Q_OBJECT

-

-  typedef Geometry_trait::Point_3 Point_3;

-  typedef Complex::Point Point;

-  typedef Complex::Vertex_handle Vertex_handle;

-  typedef Complex::Edge_handle Edge_handle;

-  typedef Complex::Simplex_handle Simplex_handle;

-

-  Viewer* viewer_;

-  View_parameter view_params_;

-  const Complex& mesh_;

-  std::unique_ptr<Projector3D> projector_;

-

- public:

-  Viewer_instructor(QWidget* parent, Viewer* viewer, const Complex& mesh);

-

-  void initialize_bounding_box();

-

-  std::pair<Point, Point> compute_bounding_box_corners();

-

-  void show_entire_scene();

-

-  const qglviewer::Camera* camera() const;

-

-  int width() const;

-  int height() const;

-

-  /**

-   * to change display parameters

-   */

-  View_parameter& view_params();

-

- public:

-  /**

-   * gives instructions to the viewer

-   */

-  void give_instructions();

-

-  void draw_edges();

-  void draw_triangles();

-  void draw_points();

-

-  void draw_edge(const Point&, const Point&);

-

-  void draw_point(const Point&);

-

-  /**

-   * set the right color of vertex/edge/triangle considering the view_params choice

-   */

-  void set_color_vertex(Vertex_handle vh);

-  void set_color_edge(Edge_handle eh);

-

-  void set_color_triangle(const Simplex_handle& triangle);

-

- private:

-  /**

-   * Projection to 3D needed for the viewer.

-   */

-  Point_3 proj(const Point& p) const;

-

- public slots:

-  void sceneChanged();

-  void change_draw_vertices();

-  void change_draw_edges();

-  void change_draw_triangles();

-  void change_light();

-};

-

-#endif  // VIEW_VIEWER_INSTRUCTOR_H_

+/* 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):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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/>.
+ * 
+ */
+
+#ifndef VIEW_VIEWER_INSTRUCTOR_H_
+#define VIEW_VIEWER_INSTRUCTOR_H_
+
+// todo do a viewer instructor that have directely a pointer to a QGLviewer and buffer ot not triangles
+
+#include <QFileDialog>
+#include <QKeyEvent>
+#include <QGLViewer/camera.h>
+
+#include <memory>
+#include <utility>  // for pair<>
+
+#include "model/Complex_typedefs.h"
+
+#include "Projector3D.h"
+#include "View_parameter.h"
+#include "Viewer.h"
+
+class Viewer;
+class Viewer_parameter;
+
+class Viewer_instructor : public QWidget {
+  Q_OBJECT
+
+  typedef Geometry_trait::Point_3 Point_3;
+  typedef Complex::Point Point;
+  typedef Complex::Vertex_handle Vertex_handle;
+  typedef Complex::Edge_handle Edge_handle;
+  typedef Complex::Simplex Simplex;
+
+  Viewer* viewer_;
+  View_parameter view_params_;
+  const Complex& mesh_;
+  std::unique_ptr<Projector3D> projector_;
+
+ public:
+  Viewer_instructor(QWidget* parent, Viewer* viewer, const Complex& mesh);
+
+  void initialize_bounding_box();
+
+  std::pair<Point, Point> compute_bounding_box_corners();
+
+  void show_entire_scene();
+
+  const qglviewer::Camera* camera() const;
+
+  int width() const;
+  int height() const;
+
+  /**
+   * to change display parameters
+   */
+  View_parameter& view_params();
+
+ public:
+  /**
+   * gives instructions to the viewer
+   */
+  void give_instructions();
+
+  void draw_edges();
+  void draw_triangles();
+  void draw_points();
+
+  void draw_edge(const Point&, const Point&);
+
+  void draw_point(const Point&);
+
+  /**
+   * set the right color of vertex/edge/triangle considering the view_params choice
+   */
+  void set_color_vertex(Vertex_handle vh);
+  void set_color_edge(Edge_handle eh);
+
+  void set_color_triangle(const Simplex& triangle);
+
+ private:
+  /**
+   * Projection to 3D needed for the viewer.
+   */
+  Point_3 proj(const Point& p) const;
+
+ public slots:
+  void sceneChanged();
+  void change_draw_vertices();
+  void change_draw_edges();
+  void change_draw_triangles();
+  void change_light();
+};
+
+#endif  // VIEW_VIEWER_INSTRUCTOR_H_