Fix alpha complex remarks and bugs

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@957 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: fa837fd1a4373c2322db16353d98767907f34c79

3 files changed, 7 insertions, 89 deletions

diff --git a/src/GudhUI/alpha_complex_persistence.cpp b/src/GudhUI/alpha_complex_persistence.cpp
deleted file mode 100644
index 4f85459a..00000000
--- a/src/GudhUI/alpha_complex_persistence.cpp
+++ /dev/null
@@ -1,78 +0,0 @@
-#include <iostream>
-#include <string>
-
-
-#include <QtGui/QApplication>
-
-// to construct a Delaunay_triangulation from a OFF file
-#include <gudhi/Delaunay_triangulation_off_io.h>
-#include <gudhi/Alpha_complex.h>
-#include <gudhi/Persistent_cohomology.h>
-
-#include "utils/Bar_code_persistence.h"
-
-void usage(char * const progName) {
-  std::cerr << "Usage: " << progName << " filename.off " <<  // alpha_square_max_value[double] " <<
-      "coeff_field_characteristic[integer > 0] min_persistence[double >= -1.0]" << std::endl;
-  std::cerr << "       i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0 2 0.02" << std::endl;
-  exit(-1); // ----- >>
-}
-
-int main(int argc, char **argv) {
-  if (argc != 4) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
-    usage(argv[0]);
-  }
-  
-  QApplication qtapp(argc, argv);
-
-  std::string off_file_name(argv[1]);
-  // double alpha_square_max_value = atof(argv[2]);
-  double alpha_square_max_value = 1e20;
-  int coeff_field_characteristic = atoi(argv[2]);  // argv[3]
-  double min_persistence = atof(argv[3]);  // argv[4]
-  
-  // ----------------------------------------------------------------------------
-  // Init of an alpha complex from an OFF file
-  // ----------------------------------------------------------------------------
-  typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
-  Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name, alpha_square_max_value);
-
-  // ----------------------------------------------------------------------------
-  // Display information about the alpha complex
-  // ----------------------------------------------------------------------------
-  std::cout << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() <<
-      " - " << alpha_complex_from_file.num_simplices() << " simplices - " <<
-      alpha_complex_from_file.num_vertices() << " vertices." << std::endl;
-
-  // Sort the simplices in the order of the filtration
-  alpha_complex_from_file.initialize_filtration();
-
-  std::cout << "Simplex_tree dim: " << alpha_complex_from_file.dimension() << std::endl;
-  // Compute the persistence diagram of the complex
-  Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::alphacomplex::Alpha_complex<Kernel>,
-      Gudhi::persistent_cohomology::Field_Zp > pcoh(alpha_complex_from_file);
-  
-  std::cout << "coeff_field_characteristic " << coeff_field_characteristic <<
-      " - min_persistence " << min_persistence << std::endl;
-
-  // initializes the coefficient field for homology
-  pcoh.init_coefficients(coeff_field_characteristic);
-
-  pcoh.compute_persistent_cohomology(min_persistence);
-
-  pcoh.output_diagram();
-  
-  std::vector<std::pair<double, double>> persistence_vector;
-  pcoh.get_persistence(persistence_vector);
-
-  Bar_code_persistence bc_persistence;
-  
-  for (auto persistence : persistence_vector) {
-    bc_persistence.insert(persistence.first, persistence.second);
-  }
-
-  bc_persistence.show();
-
-  return qtapp.exec();
-}
diff --git a/src/GudhUI/utils/Bar_code_persistence.h b/src/GudhUI/utils/Bar_code_persistence.h
index a1a46ea8..a4cd8156 100644
--- a/src/GudhUI/utils/Bar_code_persistence.h
+++ b/src/GudhUI/utils/Bar_code_persistence.h
@@ -39,7 +39,7 @@ class Bar_code_persistence {
         max_death = death;
   }
 
-  void show() {
+  void show(const std::string& window_title) {
     // Create a view, put a scene in it
     QGraphicsView * view = new QGraphicsView();
     QGraphicsScene * scene = new QGraphicsScene();
@@ -78,6 +78,7 @@ class Bar_code_persistence {
       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();
   }
diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h
index 0b9961d3..1f04cc6b 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 +81,11 @@ 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);
+    
   }
 };