Alpha complex fix for only inserting when alpha is less than

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@736 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0bc6560fa08b72d823681d36c49e80f0437d99f1

1 files changed, 131 insertions, 43 deletions

diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
index b7aceb5e..aa9500e7 100644
--- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
+++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
@@ -24,15 +24,17 @@
 #include <boost/test/included/unit_test.hpp>
 #include <boost/system/error_code.hpp>
 #include <boost/chrono/thread_clock.hpp>
-// to construct a Delaunay_triangulation from a OFF file
-#include "gudhi/Delaunay_triangulation_off_io.h"
-#include "gudhi/Alpha_complex.h"
-
 #include <CGAL/Delaunay_triangulation.h>
 #include <CGAL/Epick_d.h>
 
-#include <cmath> // float comparison
+#include <cmath>  // float comparison
 #include <limits>
+#include <string>
+#include <vector>
+
+// to construct a Delaunay_triangulation from a OFF file
+#include "gudhi/Delaunay_triangulation_off_io.h"
+#include "gudhi/Alpha_complex.h"
 
 // Use dynamic_dimension_tag for the user to be able to set dimension
 typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel_d;
@@ -45,9 +47,11 @@ BOOST_AUTO_TEST_CASE(S4_100_OFF_file) {
   //
   // ----------------------------------------------------------------------------
   std::string off_file_name("S4_100.off");
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " ==========" << std::endl;
+  double max_alpha_square_value = 1e10;
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
+      max_alpha_square_value << "==========" << std::endl;
 
-  Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name);
+  Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value);
 
   const int DIMENSION = 4;
   std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
@@ -59,8 +63,51 @@ BOOST_AUTO_TEST_CASE(S4_100_OFF_file) {
 
   const int NUMBER_OF_SIMPLICES = 6879;
   std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+  // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+
+  // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [
+  int num_simplices = 0;
+  for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
+    num_simplices++;
+  }
+  std::cout << "num_simplices=" << num_simplices << std::endl;
+  BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES);
+  // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ]
+}
+
+BOOST_AUTO_TEST_CASE(S4_100_OFF_file_filtered) {
+  // ----------------------------------------------------------------------------
+  //
+  // Init of an alpha-complex from a OFF file
+  //
+  // ----------------------------------------------------------------------------
+  std::string off_file_name("S4_100.off");
+  double max_alpha_square_value = 0.999;
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
+      max_alpha_square_value << "==========" << std::endl;
+
+  Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value);
+
+  const int DIMENSION = 4;
+  std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION);
+
+  const int NUMBER_OF_VERTICES = 13;  // Versus 100, because of filtered alpha value
+  std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES);
+
+  const int NUMBER_OF_SIMPLICES = 90;  // Versus 6879, because of filtered alpha value
+  std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
+  // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
 
+  // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [
+  int num_simplices = 0;
+  for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
+    num_simplices++;
+  }
+  std::cout << "num_simplices=" << num_simplices << std::endl;
+  BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES);
+  // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ]
 }
 
 BOOST_AUTO_TEST_CASE(S8_10_OFF_file) {
@@ -70,9 +117,11 @@ BOOST_AUTO_TEST_CASE(S8_10_OFF_file) {
   //
   // ----------------------------------------------------------------------------
   std::string off_file_name("S8_10.off");
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " ==========" << std::endl;
+  double max_alpha_square_value = 1e10;
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
+      max_alpha_square_value << "==========" << std::endl;
 
-  Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name);
+  Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value);
 
   const int DIMENSION = 8;
   std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
@@ -84,7 +133,51 @@ BOOST_AUTO_TEST_CASE(S8_10_OFF_file) {
 
   const int NUMBER_OF_SIMPLICES = 1007;
   std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+  // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+
+  // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [
+  int num_simplices = 0;
+  for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
+    num_simplices++;
+  }
+  std::cout << "num_simplices=" << num_simplices << std::endl;
+  BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES);
+  // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ]
+}
+
+BOOST_AUTO_TEST_CASE(S8_10_OFF_file_filtered) {
+  // ----------------------------------------------------------------------------
+  //
+  // Init of an alpha-complex from a OFF file
+  //
+  // ----------------------------------------------------------------------------
+  std::string off_file_name("S8_10.off");
+  double max_alpha_square_value = 1.0;
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
+      max_alpha_square_value << "==========" << std::endl;
+
+  Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value);
+
+  const int DIMENSION = 8;
+  std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION);
+
+  const int NUMBER_OF_VERTICES = 10;
+  std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES);
+
+  const int NUMBER_OF_SIMPLICES = 895;  // Versus 1007, because of filtered alpha value
+  std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
+  // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+
+  // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [
+  int num_simplices = 0;
+  for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
+    num_simplices++;
+  }
+  std::cout << "num_simplices=" << num_simplices << std::endl;
+  BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES);
+  // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ]
 }
 
 bool are_almost_the_same(float a, float b) {
@@ -100,57 +193,53 @@ typedef std::vector<Point> Vector_of_points;
 bool is_point_in_list(Vector_of_points points_list, Point point) {
   for (auto& point_in_list : points_list) {
     if (point_in_list == point) {
-      return true; // point found
+      return true;  // point found
     }
   }
-  return false; // point not found
+  return false;  // point not found
 }
 
 BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
-
   // ----------------------------------------------------------------------------
   // Init of a list of points
   // ----------------------------------------------------------------------------
   Vector_of_points points;
-  std::vector<double> coords;
-
-  points.clear();
-  coords.clear();
-  coords.push_back(0.0);
-  coords.push_back(0.0);
-  coords.push_back(0.0);
-  coords.push_back(1.0);
+  std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 };
   points.push_back(Point(coords.begin(), coords.end()));
-  coords.clear();
-  coords.push_back(0.0);
-  coords.push_back(0.0);
-  coords.push_back(1.0);
-  coords.push_back(0.0);
+  coords = { 0.0, 0.0, 1.0, 0.0 };
   points.push_back(Point(coords.begin(), coords.end()));
-  coords.clear();
-  coords.push_back(0.0);
-  coords.push_back(1.0);
-  coords.push_back(0.0);
-  coords.push_back(0.0);
+  coords = { 0.0, 1.0, 0.0, 0.0 };
   points.push_back(Point(coords.begin(), coords.end()));
-  coords.clear();
-  coords.push_back(1.0);
-  coords.push_back(0.0);
-  coords.push_back(0.0);
-  coords.push_back(0.0);
+  coords = { 1.0, 0.0, 0.0, 0.0 };
   points.push_back(Point(coords.begin(), coords.end()));
 
   // ----------------------------------------------------------------------------
   // Init of an alpha complex from the list of points
   // ----------------------------------------------------------------------------
-  Gudhi::alphacomplex::Alpha_complex<Kernel_s> alpha_complex_from_points(3, points.size(), points.begin(), points.end());
+  double max_alpha_square_value = 1e10;
+  Gudhi::alphacomplex::Alpha_complex<Kernel_s> alpha_complex_from_points(3, points.size(), points.begin(), points.end(),
+                                                                         max_alpha_square_value);
 
   std::cout << "========== Alpha_complex_from_points ==========" << std::endl;
 
+  std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  int num_simplices = 0;  // TODO(VR) : in wait of num_simplices fix in Simplex_tree
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    num_simplices++;  // TODO(VR) : in wait of num_simplices fix in Simplex_tree
+    std::cout << "   ( ";
+    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+
   std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl;
   BOOST_CHECK(alpha_complex_from_points.dimension() == 4);
-  std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_complex_from_points.num_simplices() == 15);
+  // TODO(VR) : std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices()
+  // << std::endl;
+  // TODO(VR) : BOOST_CHECK(alpha_complex_from_points.num_simplices() == 15);
+  BOOST_CHECK(num_simplices == 15);  // TODO(VR) : in wait of num_simplices fix in Simplex_tree
   std::cout << "alpha_complex_from_points.num_vertices()=" << alpha_complex_from_points.num_vertices() << std::endl;
   BOOST_CHECK(alpha_complex_from_points.num_vertices() == 4);
 
@@ -169,11 +258,11 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
         BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 3.0/4.0));
         break;
       default:
-        BOOST_CHECK(false); // Shall not happen
+        BOOST_CHECK(false);  // Shall not happen
         break;
     }
   }
-  
+
   Point p1 = alpha_complex_from_points.get_point(1);
   std::cout << "alpha_complex_from_points.get_point(1)=" << p1 << std::endl;
   BOOST_CHECK(4 == p1.dimension());
@@ -205,5 +294,4 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
   Point p1234 = alpha_complex_from_points.get_point(1234);
   std::cout << "alpha_complex_from_points.get_point(1234)=" << p1234.dimension() << std::endl;
   BOOST_CHECK(!is_point_in_list(points, p1234));
-
 }