Add MPFR dependency for python module. Use Epeck_d by default for Alpha complex. Add boolean exact version mechanism

3 files changed, 49 insertions, 34 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 9af85eac..13a8a909 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -114,9 +114,9 @@ if(PYTHONINTERP_FOUND)
       set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'nerve_gic', ")
     endif ()
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+      set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'alpha_complex', ")
       set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'subsampling', ")
       set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'tangential_complex', ")
-      set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'alpha_complex', ")
       set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'euclidean_witness_complex', ")
       set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'euclidean_strong_witness_complex', ")
     endif ()
@@ -162,10 +162,17 @@ if(PYTHONINTERP_FOUND)
           set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
           add_GUDHI_PYTHON_lib("${GMPXX_LIBRARIES}")
           set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
-        message("** Add gmpxx ${GMPXX_LIBRARIES_DIR}")
+          message("** Add gmpxx ${GMPXX_LIBRARIES_DIR}")
         endif(GMPXX_FOUND)
       endif(GMP_FOUND)
-    endif(CGAL_FOUND)
+      if(MPFR_FOUND)
+        add_gudhi_debug_info("MPFR_LIBRARIES = ${MPFR_LIBRARIES}")
+        set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_MPFR', ")
+        add_GUDHI_PYTHON_lib("${MPFR_LIBRARIES}")
+        set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${MPFR_LIBRARIES_DIR}', ")
+        message("** Add mpfr ${MPFR_LIBRARIES}")
+      endif(MPFR_FOUND)
+endif(CGAL_FOUND)
 
     # Specific for Mac
     if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
@@ -223,13 +230,14 @@ if(PYTHONINTERP_FOUND)
 
     # Test examples
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-      # Bottleneck and Alpha
-      add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
-               -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
-
+      if (MPFR_FOUND)
+        # Bottleneck and Alpha
+        add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+                 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
+      endif(MPFR_FOUND)
       if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
         # Tangential
         add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
@@ -300,22 +308,23 @@ if(PYTHONINTERP_FOUND)
     endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
 
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-      # Alpha
-      add_test(NAME alpha_complex_from_points_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
-
-      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
-        add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
-               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
-      endif()
-
-      add_gudhi_py_test(test_alpha_complex)
-
+      if (MPFR_FOUND)
+        # Alpha
+        add_test(NAME alpha_complex_from_points_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
+  
+        if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+          add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+        endif()
+  
+        add_gudhi_py_test(test_alpha_complex)
+      endif(MPFR_FOUND)
     endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
 
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index 8f2c98d5..abac6e7b 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -28,7 +28,7 @@ cdef extern from "Alpha_complex_interface.h" namespace "Gudhi":
         # bool from_file is a workaround for cython to find the correct signature
         Alpha_complex_interface(string off_file, bool from_file)
         vector[double] get_point(int vertex)
-        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, bool exact_version)
 
 # AlphaComplex python interface
 cdef class AlphaComplex:
@@ -66,7 +66,7 @@ cdef class AlphaComplex:
         """
 
     # The real cython constructor
-    def __cinit__(self, points=None, off_file=''):
+    def __cinit__(self, points = None, off_file = ''):
         if off_file:
             if os.path.isfile(off_file):
                 self.thisptr = new Alpha_complex_interface(str.encode(off_file), True)
@@ -99,17 +99,22 @@ cdef class AlphaComplex:
         cdef vector[double] point = self.thisptr.get_point(vertex)
         return point
 
-    def create_simplex_tree(self, max_alpha_square=float('inf')):
+    def create_simplex_tree(self, max_alpha_square = float('inf'),
+                            exact_version = False):
         """
         :param max_alpha_square: The maximum alpha square threshold the
             simplices shall not exceed. Default is set to infinity, and
             there is very little point using anything else since it does
             not save time.
         :type max_alpha_square: float
+        :param exact_version: Exact computation version. Default is false
+            which means Safe version is used.
+        :type exact_version: bool
         :returns: A simplex tree created from the Delaunay Triangulation.
         :rtype: SimplexTree
         """
         stree = SimplexTree()
         cdef intptr_t stree_int_ptr=stree.thisptr
-        self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr, max_alpha_square)
+        self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
+                                         max_alpha_square, exact_version)
         return stree
diff --git a/src/python/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h
index 96353cc4..a7621f2b 100644
--- a/src/python/include/Alpha_complex_interface.h
+++ b/src/python/include/Alpha_complex_interface.h
@@ -13,6 +13,7 @@
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Alpha_complex.h>
+#include <CGAL/Epeck_d.h>
 #include <CGAL/Epick_d.h>
 
 #include <boost/range/adaptor/transformed.hpp>
@@ -28,7 +29,7 @@ namespace Gudhi {
 namespace alpha_complex {
 
 class Alpha_complex_interface {
-  using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+  using Dynamic_kernel = CGAL::Epeck_d< CGAL::Dynamic_dimension_tag >;
   using Point_d = Dynamic_kernel::Point_d;
 
  public:
@@ -51,7 +52,7 @@ class Alpha_complex_interface {
     std::vector<double> vd;
     try {
       Point_d const& ph = alpha_complex_->get_point(vh);
-      for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
+      for (auto coord = ph.cartesian_begin(); coord != ph.cartesian_end(); coord++)
         vd.push_back(CGAL::to_double(*coord));
     } catch (std::out_of_range const&) {
       // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown
@@ -59,8 +60,8 @@ class Alpha_complex_interface {
     return vd;
   }
 
-  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square) {
-    alpha_complex_->create_complex(*simplex_tree, max_alpha_square);
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, bool exact_version) {
+    alpha_complex_->create_complex(*simplex_tree, max_alpha_square, exact_version);
     simplex_tree->initialize_filtration();
   }