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, 127 insertions, 68 deletions

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.")