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-rw-r--r--src/python/CMakeLists.txt17
-rw-r--r--src/python/gudhi/alpha_complex.pyx13
-rw-r--r--src/python/include/Alpha_complex_interface.h9
-rwxr-xr-xsrc/python/test/test_alpha_complex.py35
4 files changed, 59 insertions, 15 deletions
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 9af85eac..1704f491 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")
@@ -229,7 +236,6 @@ if(PYTHONINTERP_FOUND)
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(MATPLOTLIB_FOUND AND NUMPY_FOUND)
# Tangential
add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
@@ -305,7 +311,6 @@ if(PYTHONINTERP_FOUND)
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}
@@ -313,9 +318,7 @@ if(PYTHONINTERP_FOUND)
${PYTHON_EXECUTABLE} "${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 (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..bfb9783a 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: :code:`EXACT` computation version if set.
+ Default is false which means :code:`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();
}
diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py
index 24f8bf53..ab84daaa 100755
--- a/src/python/test/test_alpha_complex.py
+++ b/src/python/test/test_alpha_complex.py
@@ -1,4 +1,8 @@
from gudhi import AlphaComplex, SimplexTree
+import math
+import numpy as np
+import itertools
+import pytest
""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
@@ -88,3 +92,34 @@ def test_filtered_alpha():
]
assert simplex_tree.get_star([0]) == [([0], 0.0), ([0, 1], 0.25), ([0, 2], 0.25)]
assert simplex_tree.get_cofaces([0], 1) == [([0, 1], 0.25), ([0, 2], 0.25)]
+
+def alpha_persistence_comparison(exact_version):
+ #generate periodic signal
+ time = np.arange(0, 10, 1)
+ signal = [math.sin(x) for x in time]
+ delta = math.pi
+ delayed = [math.sin(x + delta) for x in time]
+
+ #construct embedding
+ embedding1 = [[signal[i], -signal[i]] for i in range(len(time))]
+ embedding2 = [[signal[i], delayed[i]] for i in range(len(time))]
+
+ #build alpha complex and simplex tree
+ alpha_complex1 = AlphaComplex(points=embedding1)
+ simplex_tree1 = alpha_complex1.create_simplex_tree(exact_version = exact_version)
+
+ alpha_complex2 = AlphaComplex(points=embedding2)
+ simplex_tree2 = alpha_complex2.create_simplex_tree(exact_version = exact_version)
+
+ diag1 = simplex_tree1.persistence()
+ diag2 = simplex_tree2.persistence()
+
+ for (first_p, second_p) in itertools.zip_longest(diag1, diag2):
+ assert first_p[0] == pytest.approx(second_p[0])
+ assert first_p[1] == pytest.approx(second_p[1])
+
+def test_exact_alpha_version():
+ alpha_persistence_comparison(exact_version = True)
+
+def test_safe_alpha_version():
+ alpha_persistence_comparison(exact_version = False)
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-19 22:18:10 +0000