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-rw-r--r--src/cmake/modules/FindMPFR.cmake51
-rw-r--r--src/cmake/modules/GUDHI_third_party_libraries.cmake2
-rw-r--r--src/python/CMakeLists.txt61
-rw-r--r--src/python/gudhi/alpha_complex.pyx13
-rw-r--r--src/python/include/Alpha_complex_interface.h9
5 files changed, 102 insertions, 34 deletions
diff --git a/src/cmake/modules/FindMPFR.cmake b/src/cmake/modules/FindMPFR.cmake
new file mode 100644
index 00000000..6c963272
--- /dev/null
+++ b/src/cmake/modules/FindMPFR.cmake
@@ -0,0 +1,51 @@
+# Try to find the MPFR libraries
+# MPFR_FOUND - system has MPFR lib
+# MPFR_INCLUDE_DIR - the MPFR include directory
+# MPFR_LIBRARIES_DIR - Directory where the MPFR libraries are located
+# MPFR_LIBRARIES - the MPFR libraries
+
+# TODO: support MacOSX
+
+include(FindPackageHandleStandardArgs)
+
+if(MPFR_INCLUDE_DIR)
+ set(MPFR_in_cache TRUE)
+else()
+ set(MPFR_in_cache FALSE)
+endif()
+if(NOT MPFR_LIBRARIES)
+ set(MPFR_in_cache FALSE)
+endif()
+
+# Is it already configured?
+if (MPFR_in_cache)
+ set(MPFR_FOUND TRUE)
+else()
+ find_path(MPFR_INCLUDE_DIR
+ NAMES mpfr.h
+ HINTS ENV MPFR_INC_DIR
+ ENV MPFR_DIR
+ ${CGAL_INSTALLATION_PACKAGE_DIR}/auxiliary/gmp/include
+ PATH_SUFFIXES include
+ DOC "The directory containing the MPFR header files"
+ )
+
+ find_library(MPFR_LIBRARIES NAMES mpfr libmpfr-4 libmpfr-1
+ HINTS ENV MPFR_LIB_DIR
+ ENV MPFR_DIR
+ ${CGAL_INSTALLATION_PACKAGE_DIR}/auxiliary/gmp/lib
+ PATH_SUFFIXES lib
+ DOC "Path to the MPFR library"
+ )
+
+ if ( MPFR_LIBRARIES )
+ get_filename_component(MPFR_LIBRARIES_DIR ${MPFR_LIBRARIES} PATH CACHE )
+ endif()
+
+ # Attempt to load a user-defined configuration for MPFR if couldn't be found
+ if ( NOT MPFR_INCLUDE_DIR OR NOT MPFR_LIBRARIES_DIR )
+ include( MPFRConfig OPTIONAL )
+ endif()
+
+ find_package_handle_standard_args(MPFR "DEFAULT_MSG" MPFR_LIBRARIES MPFR_INCLUDE_DIR)
+endif()
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 24a34150..d8c7a428 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -6,6 +6,8 @@ if(NOT Boost_FOUND)
message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
endif(NOT Boost_FOUND)
+find_package(MPFR)
+
find_package(GMP)
if(GMP_FOUND)
INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
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();
}
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-27 14:44:12 +0000