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

11 files changed, 191 insertions, 247 deletions

diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index d7c13da0..fa24e1b1 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -18,8 +18,6 @@ if(CGAL_FOUND)
       add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
       target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-      add_executable ( cerr cerr.cpp )
-
       # Do not forget to copy test files in current binary dir
       file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
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);
+    
   }
 };
 
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index eb4ee3e3..9e96adc0 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -22,63 +22,61 @@ add_executable(persistence_from_file persistence_from_file.cpp)
 target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0)
 add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
-   
-if(GMPXX_FOUND AND GMP_FOUND)
-   message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
-   message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
-
-   add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
-   target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
-   add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100)
-
-   add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
-   target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
-
-   if(CGAL_FOUND)
-     add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp)
-     target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
-     add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5)
-     #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
-
-
 
-
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-    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")
+if(GMPXX_FOUND AND GMP_FOUND)
+  message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
+  message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
+
+  add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
+  target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+  add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100)
+
+  add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
+  target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+
+  if(CGAL_FOUND)
+    add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp)
+    target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
+    add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5)
+    #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
+
+    if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+      message(STATUS "CGAL version: ${CGAL_VERSION}.")
+
+      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()
-    endif()
-    # - End of workaround
+      # - End of workaround
 
-    find_package(Eigen3 3.1.0)
-    if (EIGEN3_FOUND)
-      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-      include( ${EIGEN3_USE_FILE} )
+      find_package(Eigen3 3.1.0)
+      if (EIGEN3_FOUND)
+        message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+        include( ${EIGEN3_USE_FILE} )
       
-      add_executable (alphacomplexpersistence alpha_complex_persistence.cpp)
-      target_link_libraries(alphacomplexpersistence  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+        add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
+        target_link_libraries(alpha_complex_persistence  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
+      else()
+        message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
+      endif()
     else()
-      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
-    endif()
+      message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+    endif ()
   else()
-    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
-  endif ()
-
-
-
-   endif()
+    # message(WARNING "CGAL not found.")
+  endif()
    
+else()
+  # message(WARNING "GMP not found.")
 endif()
diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
index fbadf673..0dabdeac 100644
--- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
@@ -1,34 +1,35 @@
 #include <iostream>
 #include <string>
 
+#include <boost/program_options.hpp>
+
 // 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>
 
-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); // ----- >>
-}
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , std::string & output_file_diag
+                     , Filtration_value & alpha_square_max_value
+                     , int & coeff_field_characteristic
+                     , Filtration_value & min_persistence);
 
 int main(int argc, char **argv) {
-  if (argc != 5) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
-    usage(argv[0]);
-  }
+  std::string off_file_points;
+  std::string output_file_diag;
+  Filtration_value alpha_square_max_value;
+  int coeff_field_characteristic;
+  Filtration_value min_persistence;
+  
+  program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, coeff_field_characteristic, min_persistence);
 
-  std::string off_file_name(argv[1]);
-  double alpha_square_max_value = atof(argv[2]);
-  int coeff_field_characteristic = atoi(argv[3]);
-  double min_persistence = atof(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);
+  Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points, alpha_square_max_value);
 
   // ----------------------------------------------------------------------------
   // Display information about the alpha complex
@@ -49,7 +50,66 @@ int main(int argc, char **argv) {
 
   pcoh.compute_persistent_cohomology(min_persistence);
 
-  pcoh.output_diagram();
+  // Output the diagram in filediag
+  if (output_file_diag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::cout << "Result in file: " << output_file_diag << std::endl;
+    std::ofstream out(output_file_diag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
 
   return 0;
 }
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , std::string & output_file_diag
+                     , Filtration_value & alpha_square_max_value
+                     , int & coeff_field_characteristic
+                     , Filtration_value & min_persistence) {
+  namespace po = boost::program_options;
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&off_file_points),
+       "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");
+
+  po::options_description visible("Allowed options", 100);
+  visible.add_options()
+      ("help,h", "produce help message")
+      ("output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
+       "Name of file in which the persistence diagram is written. Default print in std::cout")
+      ("max-alpha-square-value,r", po::value<Filtration_value>(&alpha_square_max_value)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+       "Maximal alpha square value for the Alpha complex construction.")
+      ("field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11),
+       "Characteristic p of the coefficient field Z/pZ for computing homology.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+
+  po::positional_options_description pos;
+  pos.add("input-file", 1);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
+
+  po::variables_map vm;
+  po::store(po::command_line_parser(argc, argv).
+            options(all).positional(pos).run(), vm);
+  po::notify(vm);
+
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of an Alpha complex defined on a set of input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index 9b1ef42f..fa0449a8 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -30,6 +30,7 @@
 
 #include <string>
 #include <vector>
+#include <limits>  // infinity
 
 using namespace Gudhi;
 using namespace Gudhi::persistent_cohomology;
@@ -114,7 +115,7 @@ void program_options(int argc, char * argv[]
       ("help,h", "produce help message")
       ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
        "Name of file in which the persistence diagram is written. Default print in std::cout")
-      ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
+      ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
        "Maximal length of an edge for the Rips complex construction.")
       ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
        "Maximal dimension of the Rips complex we want to compute.")
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 4b04e75a..d4f9aeae 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1160,43 +1160,28 @@ std::cout << "prune_above_filtration - filtration=" << filtration << std::endl;
         threshold_ = filtration;
         // Initialize filtration_vect_ if required
         if (filtration_vect_.empty()) {
-std::cout << "prune_above_filtration - initialize_filtration" << std::endl;
           initialize_filtration();
         }
-
-std::cout << "prune_above_filtration - after initialize_filtration ";
-for(auto sh : filtration_vect_) {
-for (auto vertex : simplex_vertex_range(sh)) {
-std::cout << (int) vertex << ", ";
-}
-std::cout <<  " - filtration=" << sh->second.filtration() <<  " - " << &(sh->second) << std::endl;
-}
-    
         
+        std::vector<std::vector<Vertex_handle>> simplex_list_to_removed;
         // Loop in reverse mode until threshold is reached
-        auto f_simplex = filtration_vect_.rbegin();
-        for (; (f_simplex != filtration_vect_.rend()) && ((*f_simplex)->second.filtration() > threshold_); f_simplex++) {
-          
-std::cout << "prune_above_filtration - remove ";
-for (auto vertex : simplex_vertex_range(*f_simplex)) {
-std::cout << (int) vertex << ", ";
-}
-std::cout <<  " - " << &((*f_simplex)->second) << std::endl;
-
-          remove_maximal_simplex(*f_simplex);
+        // Do not erase while looping, because removing is shifting data in a flat_map
+        for (auto f_simplex = filtration_vect_.rbegin();
+             (f_simplex != filtration_vect_.rend()) && ((*f_simplex)->second.filtration() > threshold_);
+             f_simplex++) {
+          std::vector<Vertex_handle> simplex_to_remove;
+          for (auto vertex : simplex_vertex_range(*f_simplex))
+            simplex_to_remove.insert(simplex_to_remove.begin(), vertex);
+          simplex_list_to_removed.push_back(simplex_to_remove);
         }
-std::cout << "prune_above_filtration - remove STOPPED ON ";
-for (auto vertex : simplex_vertex_range(*f_simplex)) {
-std::cout << (int) vertex << ", ";
-}
-std::cout <<  " - filtration=" << (*f_simplex)->second.filtration() <<  " - " << &(*f_simplex->second) << std::endl;
-        if (f_simplex != filtration_vect_.rbegin()) {
-          // Do not forget to update filtration_vect_ - resize is enough
-          std::size_t new_size = filtration_vect_.size() - (f_simplex - filtration_vect_.rbegin());
-std::cout << "prune_above_filtration - resize" << new_size << std::endl;
-          filtration_vect_.resize(new_size);
+        for (auto simplex_to_remove : simplex_list_to_removed) {
+          Simplex_handle sh = find_simplex(simplex_to_remove);
+          if (sh != null_simplex())
+            remove_maximal_simplex(sh);
         }
-
+        // Re-initialize filtration_vect_ if dta were removed, because removing is shifting data in a flat_map
+        if (simplex_list_to_removed.size() > 0)
+          initialize_filtration();
       }
     }
   }
@@ -1205,6 +1190,7 @@ std::cout << "prune_above_filtration - resize" << new_size << std::endl;
    * @param[in] sh Simplex handle on the maximal simplex to remove.
    * \pre Please check the simplex has no coface before removing it.
    * \warning In debug mode, the exception std::invalid_argument is thrown if sh has children.
+   * \warning Be aware that removing is shifting data in a flat_map (initialize_filtration to be done).
    */
   void remove_maximal_simplex(Simplex_handle sh) {
     // Guarantee the simplex has no children
@@ -1213,49 +1199,18 @@ std::cout << "prune_above_filtration - resize" << new_size << std::endl;
     
     // Simplex is a leaf, it means the child is the Siblings owning the leaf
     Siblings* child = sh->second.children();
+
     if ((child->size() > 1) || (child == root())) {
       // Not alone, just remove it from members
       // Special case when child is the root of the simplex tree, just remove it from members
-std::cout << "remove_maximal_simplex - members removal" << std::endl;
       child->erase(sh->first);
     } else {
       // Sibling is emptied : must be deleted, and its parent must point on his own Sibling
-std::cout << "remove_maximal_simplex - members is empty" << std::endl;
       child->oncles()->members().at(child->parent()).assign_children(child->oncles());
       delete child;
     }
   }
-/***************************************************************************************************************/  
-   public:
-  /** \brief Prints the simplex_tree hierarchically. 
-   * Since it prints the vertices recursively, one can watch its tree shape.
-   */
-  void print_tree() {
-    for (auto sh = root_.members().begin(); sh != root_.members().end(); ++sh) {
-      std::cout << sh->first << " ";
-      if (has_children(sh)) {
-        std::cout << "(";
-        rec_print(sh->second.children());
-        std::cout << ")";
-      }
-      std::cout << std::endl;
-    }
-  }
-
 
-  /** \brief Recursively prints the simplex_tree, using depth first search. */
- private:
-  void rec_print(Siblings * sib) {
-    for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) {
-      std::cout << " " << sh->first << " ";
-      if (has_children(sh)) {
-        std::cout << "(";
-        rec_print(sh->second.children());
-        std::cout << ")";
-      }
-    }
-  }
-/*****************************************************************************************************************/
  private:
   Vertex_handle null_vertex_;
   /** \brief Upper bound on the filtration values of the simplices.*/
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index f6bd5411..0d73d347 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -351,7 +351,7 @@ BOOST_AUTO_TEST_CASE(simplex_tree_insertion) {
   // Display the Simplex_tree - Can not be done in the middle of 2 inserts
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
   std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
-  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
   for (auto f_simplex : st.filtration_simplex_range()) {
     std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
     for (auto vertex : st.simplex_vertex_range(f_simplex)) {
@@ -549,7 +549,7 @@ BOOST_AUTO_TEST_CASE(NSimplexAndSubfaces_tree_insertion) {
   // Display the Simplex_tree - Can not be done in the middle of 2 inserts
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
   std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
-  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
   for (auto f_simplex : st.filtration_simplex_range()) {
     std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
     for (auto vertex : st.simplex_vertex_range(f_simplex)) {
@@ -805,7 +805,7 @@ struct MyOptions : Simplex_tree_options_full_featured {
 };
 typedef Simplex_tree<MyOptions> miniST;
 
-/*BOOST_AUTO_TEST_CASE(remove_maximal_simplex) {
+BOOST_AUTO_TEST_CASE(remove_maximal_simplex) {
   std::cout << "********************************************************************" << std::endl;
   std::cout << "REMOVE MAXIMAL SIMPLEX" << std::endl;
 
@@ -887,7 +887,7 @@ typedef Simplex_tree<MyOptions> miniST;
   st.remove_maximal_simplex(st.find({7}));
   
   BOOST_CHECK(st == st_wo_seven);
-}*/
+}
 
 BOOST_AUTO_TEST_CASE(prune_above_filtration) {
   std::cout << "********************************************************************" << std::endl;
@@ -939,10 +939,10 @@ BOOST_AUTO_TEST_CASE(prune_above_filtration) {
   st.prune_above_filtration(5.0);
   BOOST_CHECK(st == st_complete);
 
-  // Display the Simplex_tree - Can not be done in the middle of 2 inserts
+  // Display the Simplex_tree
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
   std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
-  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
   for (auto f_simplex : st.filtration_simplex_range()) {
     std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
     for (auto vertex : st.simplex_vertex_range(f_simplex)) {
@@ -955,35 +955,45 @@ BOOST_AUTO_TEST_CASE(prune_above_filtration) {
   // Set the st_pruned filtration for operator==
   st_pruned.set_filtration(2.5);
   st.prune_above_filtration(2.5);
-  /*BOOST_CHECK(st == st_pruned);
+  BOOST_CHECK(st == st_pruned);
+
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 2.5 contains " << st.num_simplices() << " simplices" << std::endl;
+  std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
+  std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << (int) vertex << " ";
+    }
+    std::cout << std::endl;
+  }
 
   st_pruned.set_filtration(2.0);
   st.prune_above_filtration(2.0);
   BOOST_CHECK(st == st_pruned);
-*/
-/*  std::cout << "The complex contains " << st.num_simplices() << " simplices --------------------------" << std::endl;
-  std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
-  st.print_tree();
 
-  std::cout << "The pruned complex contains " << st_pruned.num_simplices() << " simplices --------------------------" << std::endl;
-  std::cout << "   - dimension " << st_pruned.dimension() << "   - filtration " << st_pruned.filtration() << std::endl;
-  st_pruned.print_tree();
-  
   typeST st_empty;
   // FIXME
   st_empty.set_dimension(3);
   st.prune_above_filtration(0.0);
- */
-  /*BOOST_CHECK(st == st_empty);
+
+    // Display the Simplex_tree
+  std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices" << std::endl;
+  std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
+  std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << (int) vertex << " ";
+    }
+    std::cout << std::endl;
+  }
+
+  BOOST_CHECK(st == st_empty);
 
   // Test case to the limit
   st.prune_above_filtration(-1.0);
   st_empty.set_filtration(-1.0);
   BOOST_CHECK(st == st_empty);
-*/
 }
-
-/*BOOST_AUTO_TEST_CASE(sanitizer) {
-  int a[2] = {1, 0};
-  int b=a[2];
-}*/
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index e5c79ded..cd518581 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -23,6 +23,8 @@
 #ifndef DISTANCE_FUNCTIONS_H_
 #define DISTANCE_FUNCTIONS_H_
 
+#include <cmath>  // for std::sqrt
+
 /* Compute the Euclidean distance between two Points given
  * by a range of coordinates. The points are assumed to have 
  * the same dimension. */
@@ -35,7 +37,7 @@ double euclidean_distance(Point &p1, Point &p2) {
     double tmp = *it1 - *it2;
     dist += tmp*tmp;
   }
-  return sqrt(dist);
+  return std::sqrt(dist);
 }
 
 #endif  // DISTANCE_FUNCTIONS_H_
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index e05714c7..da2c2c36 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -58,7 +58,9 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
     while (iss >> x) {
       point.push_back(x);
     }
-    points.push_back(point);
+    // Check for empty lines
+    if (!point.empty())
+      points.push_back(point);
   }
   in_file.close();
 }