Merge of alpha complex feature from trunk

Add Eigen3 in installation
Add alpha complex in introduction
All examples directory moved to example (was example/common, example/Alpha_complex)


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Doxygen_for_GUDHI_1.3.0@1110 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0b88a4f2b102e2189f4b916b8358ffb2458a72f0

5 files changed, 100 insertions, 12 deletions

diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index fd7397ea..a7e64319 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -61,6 +61,8 @@ if (TBB_FOUND)
   target_link_libraries( GudhUI ${TBB_RELEASE_LIBRARY})
 endif()
 
+###############################################################################
+
 else()
   message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.")
 endif()
diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h
index 07a67a0c..1c39c0d7 100644
--- a/src/GudhUI/model/Model.h
+++ b/src/GudhUI/model/Model.h
@@ -71,7 +71,7 @@ class CGAL_geometric_flag_complex_wrapper {
 
   void maximal_face(std::vector<int> vertices) {
     if (!load_only_points_) {
-      std::cout << "size:" << vertices.size() << std::endl;
+      // std::cout << "size:" << vertices.size() << std::endl;
       for (int i = 0; i < vertices.size(); ++i)
         for (int j = i + 1; j < vertices.size(); ++j)
           complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j]));
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/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..a4027b7f 100644
--- a/src/GudhUI/view/FirstCoordProjector.h
+++ b/src/GudhUI/view/FirstCoordProjector.h
@@ -32,8 +32,10 @@ class FirstCoordProjector3D : public Projector3D {
   typedef Projector3D::Point_3 Point_3;
 
   Point_3 operator()(const Point& p) const {
-    assert(p.dimension() >= 3);
+    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);
   }
 };