alpha off reader test strategy modification

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@995 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: aa4ba97eecefb03e01a53ae1e2b50248a0857043

7 files changed, 78 insertions, 33 deletions

diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index 12d62ac0..8eea6ba7 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -67,7 +67,7 @@ namespace alphacomplex {
  * 
  * When launching:
  * 
- * \code $> ./alphapoints 60.0
+ * \code $> ./alphapoints
  * \endcode
  *
  * the program output is:
diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
index 780f904b..80445a22 100644
--- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp
+++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
@@ -5,14 +5,14 @@
 #include <string>
 
 void usage(char * const progName) {
-  std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value" << std::endl;
-  std::cerr << "       i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0" << std::endl;
+  std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value [ouput_file.txt]\n";
+  std::cerr << "       i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0\n";
   exit(-1);  // ----- >>
 }
 
 int main(int argc, char **argv) {
-  if (argc != 3) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+  if ((argc != 3) && (argc != 4)) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
     usage(argv[0]);
   }
 
@@ -25,21 +25,34 @@ int main(int argc, char **argv) {
   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);
 
+  std::streambuf* streambufffer;
+  std::ofstream ouput_file_stream;
+  
+  if (argc == 4) {
+    ouput_file_stream.open(std::string(argv[3]));
+    streambufffer = ouput_file_stream.rdbuf();
+  } else {
+    streambufffer = std::cout.rdbuf();
+  }
+
+  std::ostream output_stream(streambufffer);
+
   // ----------------------------------------------------------------------------
   // Display information about the alpha complex
   // ----------------------------------------------------------------------------
-  std::cout << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() <<
+  output_stream << "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;
 
-  std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
   for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
-    std::cout << "   ( ";
+    output_stream << "   ( ";
     for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) {
-      std::cout << vertex << " ";
+      output_stream << vertex << " ";
     }
-    std::cout << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] ";
-    std::cout << std::endl;
+    output_stream << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] ";
+    output_stream << std::endl;
   }
+  ouput_file_stream.close();
   return 0;
 }
diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
index dab161c9..815e40d7 100644
--- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp
+++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
@@ -10,7 +10,7 @@ typedef Kernel::Point_d Point;
 typedef std::vector<Point> Vector_of_points;
 
 int main(int argc, char **argv) {
-  double alpha_square_max_value = 32.0;
+  double alpha_square_max_value = 60.0;
 
   // ----------------------------------------------------------------------------
   // Init of a list of points
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index 33ff6805..d93dd436 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -27,12 +27,25 @@ if(CGAL_FOUND)
     if (EIGEN3_FOUND)
       message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
       include( ${EIGEN3_USE_FILE} )
-      
-      add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
-      target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
 
       add_executable ( alphapoints Alpha_complex_from_points.cpp )
       target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints)
+
+      # Do not forget to copy test files in current binary dir
+      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+      # Do not forget to copy test results files in current binary dir
+      file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+      file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+      add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
+      target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt)
+      add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt)
+      if (DIFF_PATH)
+        add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
+        add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
+      endif()
     else()
       message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
     endif()
diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt
index 553431a9..13183e86 100644
--- a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt
+++ b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt
@@ -7,16 +7,16 @@ Iterator on alpha complex simplices in the filtration order, with [filtration va
    ( 4 ) -> [0] 
    ( 5 ) -> [0] 
    ( 6 ) -> [0] 
-   ( 5 4 ) -> [6.25] 
-   ( 4 1 ) -> [20] 
-   ( 4 2 ) -> [8.5] 
-   ( 6 2 ) -> [9.25] 
-   ( 6 5 ) -> [10] 
-   ( 6 4 ) -> [11.25] 
-   ( 6 5 4 ) -> [12.5] 
-   ( 6 4 2 ) -> [12.9959] 
-   ( 3 0 ) -> [13.25] 
-   ( 4 1 ) -> [20] 
-   ( 1 0 ) -> [22.7367] 
-   ( 3 1 0 ) -> [22.7367] 
-   ( 5 0 ) -> [30.25] 
+   ( 3 2 ) -> [6.25] 
+   ( 5 4 ) -> [7.25] 
+   ( 2 0 ) -> [8.5] 
+   ( 1 0 ) -> [9.25] 
+   ( 3 1 ) -> [10] 
+   ( 2 1 ) -> [11.25] 
+   ( 3 2 1 ) -> [12.5] 
+   ( 2 1 0 ) -> [12.9959] 
+   ( 6 5 ) -> [13.25] 
+   ( 4 2 ) -> [20] 
+   ( 6 4 ) -> [22.7367] 
+   ( 6 5 4 ) -> [22.7367] 
+   ( 6 3 ) -> [30.25] 
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index fa24e1b1..52ec0a78 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -8,6 +8,20 @@ if(CGAL_FOUND)
     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()
+    # - End of workaround
  
     find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index dbef8517..3911f497 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -307,7 +307,8 @@ class Simplex_tree {
    * of the simplex.
    *
    * @param[in] sh Simplex for which the boundary is computed. */
-  Boundary_simplex_range boundary_simplex_range(Simplex_handle sh) {
+  template<class DictionaryIterator>
+  Boundary_simplex_range boundary_simplex_range(DictionaryIterator sh) {
     return Boundary_simplex_range(Boundary_simplex_iterator(this, sh),
                                   Boundary_simplex_iterator(this));
   }
@@ -528,7 +529,11 @@ class Simplex_tree {
 
   /** \brief Returns true if the node in the simplex tree pointed by
    * sh has children.*/
-  bool has_children(Simplex_handle sh) const {
+  /*bool has_children(Simplex_handle sh) const {
+    return (sh->second.children()->parent() == sh->first);
+  }*/
+  template<class DictionaryIterator>
+  bool has_children(DictionaryIterator sh) const {
     return (sh->second.children()->parent() == sh->first);
   }
 
@@ -1128,7 +1133,7 @@ class Simplex_tree {
   bool make_filtration_non_decreasing() {
     bool modified = false;
     // Loop must be from the end to the beginning, as higher dimension simplex are always on the left part of the tree
-    for (auto sh = (root_.members().end() - 1); sh >= root_.members().begin(); --sh) {
+    for (auto sh = root_.members().rbegin(); sh != root_.members().rend(); ++sh) {
       if (has_children(sh)) {
         modified |= rec_make_filtration_non_decreasing(sh->second.children());
       }
@@ -1144,10 +1149,11 @@ class Simplex_tree {
   bool rec_make_filtration_non_decreasing(Siblings * sib) {
     bool modified = false;
 
+    // Loop must be from the end to the beginning, as higher dimension simplex are always on the left part of the tree
     for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) {
       // Find the maximum filtration value in the border
       Boundary_simplex_range boundary = boundary_simplex_range(sh);
-      Boundary_simplex_iterator max_border = std::max_element( std::begin(boundary), std::end(boundary),
+      Boundary_simplex_iterator max_border = std::max_element(std::begin(boundary), std::end(boundary),
                                                               [](Simplex_handle sh1, Simplex_handle sh2) {
                                                                 return filtration(sh1) < filtration(sh2);
                                                               } );
@@ -1175,7 +1181,6 @@ class Simplex_tree {
    * call `initialize_filtration()` to recompute it.
    */
   void prune_above_filtration(Filtration_value filtration) {
-std::cout << "prune_above_filtration - filtration=" << filtration << std::endl;
     // No action if filtration is not stored
     if (Options::store_filtration) {
       if (filtration < threshold_) {