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-rw-r--r--src/Contraction/example/CMakeLists.txt6
-rw-r--r--src/Persistent_cohomology/example/CMakeLists.txt41
-rw-r--r--src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h16
-rw-r--r--src/Persistent_cohomology/test/CMakeLists.txt16
-rw-r--r--src/cmake/modules/FindTBB.cmake12
-rw-r--r--src/common/doc/main_page.h8
6 files changed, 48 insertions, 51 deletions
diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt
index b8384cb3..4c09a0a7 100644
--- a/src/Contraction/example/CMakeLists.txt
+++ b/src/Contraction/example/CMakeLists.txt
@@ -9,5 +9,7 @@ target_link_libraries(RipsContraction ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBR
target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})
-add_test(RipsContraction.sphere.0.2 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/sphere3D_2646.off 0.2)
-add_test(RipsContraction.S0310000 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off 0.3)
+add_test(RipsContraction.tore3D.0.2 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 0.2)
+# TODO(DS) : These tests are too long under Windows
+#add_test(RipsContraction.sphere.0.2 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/sphere3D_2646.off 0.2)
+#add_test(RipsContraction.S0310000 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off 0.3)
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index a0af11c1..5fb4ba12 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -35,28 +35,34 @@ add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips
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}")
+if(GMP_FOUND)
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_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 (TBB_FOUND)
- target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
- target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES})
- endif()
+ if(GMPXX_FOUND)
+ message("GMPXX_LIBRARIES = ${GMPXX_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_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 (TBB_FOUND)
+ target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
+ target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES})
+ endif(TBB_FOUND)
add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100)
+ endif(GMPXX_FOUND)
+else()
+ # message(WARNING "GMP not found.")
+endif(GMP_FOUND)
if(CGAL_FOUND)
add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
- target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
+ target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
if (TBB_FOUND)
target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
- endif()
+ endif(TBB_FOUND)
add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45)
@@ -72,28 +78,27 @@ if(GMPXX_FOUND AND GMP_FOUND)
target_link_libraries(alpha_complex_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp)
- target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
+ target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
add_executable(custom_persistence_sort custom_persistence_sort.cpp)
- target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
+ target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
if (TBB_FOUND)
target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES})
target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES})
- endif()
+ endif(TBB_FOUND)
add_test(alpha_complex_persistence_2_0_45 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -m 0.45 -p 2)
add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off ${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt 2 0)
add_test(custom_persistence_sort ${CMAKE_CURRENT_BINARY_DIR}/custom_persistence_sort)
else()
message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
- endif()
+ endif(EIGEN3_FOUND)
else()
message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
endif ()
else()
# message(WARNING "CGAL not found.")
- endif()
+ endif(CGAL_FOUND)
-endif()
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index efa9a367..a7d1e463 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -594,7 +594,7 @@ class Persistent_cohomology {
}
/** @brief Returns Betti numbers.
- * @return A vector of persistent Betti numbers.
+ * @return A vector of Betti numbers.
*/
std::vector<int> betti_numbers() const {
// Init Betti numbers vector with zeros until Simplicial complex dimension
@@ -632,7 +632,7 @@ class Persistent_cohomology {
/** @brief Returns the persistent Betti numbers.
* @param[in] from The persistence birth limit to be added in the number \f$(persistent birth \leq from)\f$.
- * @param[in] to The persistence death limit to be added in the number \f$(persistent death > from)\f$.
+ * @param[in] to The persistence death limit to be added in the number \f$(persistent death > to)\f$.
* @return A vector of persistent Betti numbers.
*/
std::vector<int> persistent_betti_numbers(Filtration_value from, Filtration_value to) const {
@@ -641,7 +641,10 @@ class Persistent_cohomology {
for (auto pair : persistent_pairs_) {
// Count persistence intervals that covers the given interval
- if (cpx_->filtration(get<0>(pair)) <= from && cpx_->filtration(get<1>(pair)) > to) {
+ // null_simplex test : if the function is called with to=+infinity, we still get something useful. And it will
+ // still work if we change the complex filtration function to reject null simplices.
+ if (cpx_->filtration(get<0>(pair)) <= from &&
+ (get<1>(pair) == cpx_->null_simplex() || cpx_->filtration(get<1>(pair)) > to)) {
// Increment corresponding betti number
betti_numbers[cpx_->dimension(get<0>(pair))] += 1;
}
@@ -652,7 +655,7 @@ class Persistent_cohomology {
/** @brief Returns the persistent Betti number of the dimension passed by parameter.
* @param[in] dimension The Betti number dimension to get.
* @param[in] from The persistence birth limit to be added in the number \f$(persistent birth \leq from)\f$.
- * @param[in] to The persistence death limit to be added in the number \f$(persistent death > from)\f$.
+ * @param[in] to The persistence death limit to be added in the number \f$(persistent death > to)\f$.
* @return Persistent Betti number of the given dimension
*/
int persistent_betti_number(int dimension, Filtration_value from, Filtration_value to) const {
@@ -660,7 +663,10 @@ class Persistent_cohomology {
for (auto pair : persistent_pairs_) {
// Count persistence intervals that covers the given interval
- if (cpx_->filtration(get<0>(pair)) <= from && cpx_->filtration(get<1>(pair)) > to) {
+ // null_simplex test : if the function is called with to=+infinity, we still get something useful. And it will
+ // still work if we change the complex filtration function to reject null simplices.
+ if (cpx_->filtration(get<0>(pair)) <= from &&
+ (get<1>(pair) == cpx_->null_simplex() || cpx_->filtration(get<1>(pair)) > to)) {
if (cpx_->dimension(get<0>(pair)) == dimension) {
// Increment betti number found
++betti_number;
diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt
index 31a86a2d..a21f39c4 100644
--- a/src/Persistent_cohomology/test/CMakeLists.txt
+++ b/src/Persistent_cohomology/test/CMakeLists.txt
@@ -4,11 +4,11 @@ project(Persistent_cohomology_tests)
if (GCOVR_PATH)
# for gcovr to make coverage reports - Corbera Jenkins plugin
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
+endif(GCOVR_PATH)
if (GPROF_PATH)
# for gprof to make coverage reports - Jenkins
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
+endif(GPROF_PATH)
add_executable ( PersistentCohomologyUT persistent_cohomology_unit_test.cpp )
target_link_libraries(PersistentCohomologyUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
@@ -17,7 +17,7 @@ target_link_libraries(BettiNumbersUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_F
if (TBB_FOUND)
target_link_libraries(PersistentCohomologyUT ${TBB_LIBRARIES})
target_link_libraries(BettiNumbersUT ${TBB_LIBRARIES})
-endif()
+endif(TBB_FOUND)
# Unitary tests
add_test(NAME PersistentCohomologyUT
@@ -33,10 +33,10 @@ add_test(NAME BettiNumbersUT
if(GMPXX_FOUND AND GMP_FOUND)
add_executable ( PersistentCohomologyMultiFieldUT persistent_cohomology_unit_test_multi_field.cpp )
-target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
-if (TBB_FOUND)
- target_link_libraries(PersistentCohomologyMultiFieldUT ${TBB_LIBRARIES})
-endif()
+ target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+ if (TBB_FOUND)
+ target_link_libraries(PersistentCohomologyMultiFieldUT ${TBB_LIBRARIES})
+ endif(TBB_FOUND)
# Unitary tests
add_test(NAME PersistentCohomologyMultiFieldUT
@@ -45,5 +45,5 @@ endif()
# XML format for Jenkins xUnit plugin
--log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/PersistentCohomologyMultiFieldUT.xml --log_level=test_suite --report_level=no)
-endif()
+endif(GMPXX_FOUND AND GMP_FOUND)
diff --git a/src/cmake/modules/FindTBB.cmake b/src/cmake/modules/FindTBB.cmake
index a29c6d9c..13f4d929 100644
--- a/src/cmake/modules/FindTBB.cmake
+++ b/src/cmake/modules/FindTBB.cmake
@@ -107,11 +107,7 @@ if (WIN32)
endif(MSVC12)
#note there was no MSVC13
if(MSVC14)
- if(RUNNING_CGAL_AUTO_TEST)
- set (TBB_FOUND "NO")
- return()#binaries for TBB not publicly available when CGAL-4.7 is published
- endif(RUNNING_CGAL_AUTO_TEST)
- message(STATUS "[Warning] FindTBB.cmake: TBB 4.4 (latest available when CGAL-4.7 is published) does not provide support for MSVC 2015.")
+ set(_TBB_COMPILER "vc14")
endif(MSVC14)
# Todo: add other Windows compilers such as ICL.
set(_TBB_ARCHITECTURE ${TBB_ARCHITECTURE})
@@ -218,11 +214,7 @@ macro(TBB_CORRECT_LIB_DIR var_name)
string(REPLACE em64t "${_TBB_ARCHITECTURE}" ${var_name} ${${var_name}})
# endif (NOT "${_TBB_ARCHITECTURE}" STREQUAL "em64t")
string(REPLACE ia32 "${_TBB_ARCHITECTURE}" ${var_name} ${${var_name}})
- string(REPLACE vc7.1 "${_TBB_COMPILER}" ${var_name} ${${var_name}})
- string(REPLACE vc8 "${_TBB_COMPILER}" ${var_name} ${${var_name}})
- string(REPLACE vc9 "${_TBB_COMPILER}" ${var_name} ${${var_name}})
- string(REPLACE vc10 "${_TBB_COMPILER}" ${var_name} ${${var_name}})
- string(REPLACE vc11 "${_TBB_COMPILER}" ${var_name} ${${var_name}})
+ string(REGEX REPLACE "vc[0-9]+(\.[0-9]+)?" "${_TBB_COMPILER}" ${var_name} ${${var_name}})
endmacro(TBB_CORRECT_LIB_DIR var_content)
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 20ffbc2a..2391e147 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -168,14 +168,10 @@
*
* The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic
* Library</a> (GMP) and will not be built if GMP is not installed:
- * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_shapes_persistence.cpp</a>
* \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
* Persistent_cohomology/performance_rips_persistence.cpp</a>
* \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
* Persistent_cohomology/rips_multifield_persistence.cpp</a>
- * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
- * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
*
* Having GMP version 4.2 or higher installed is recommended.
*
@@ -191,10 +187,6 @@
* Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
* \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
* Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
- * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_off.cpp</a>
- * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_points.cpp</a>
*
* The following example requires CGAL version &ge; 4.6:
* \li <a href="_witness_complex_2witness_complex_sphere_8cpp-example.html">
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-02 20:55:12 +0000