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-rw-r--r--src/Bottleneck_distance/example/CMakeLists.txt4
-rw-r--r--src/Bottleneck_distance/example/bottleneck_read_file_example.cpp36
-rw-r--r--src/Spatial_searching/doc/Intro_spatial_searching.h2
-rw-r--r--src/Spatial_searching/example/example_spatial_searching.cpp8
-rw-r--r--src/Spatial_searching/include/gudhi/Kd_tree_search.h61
-rw-r--r--src/Spatial_searching/test/test_Kd_tree_search.cpp8
-rw-r--r--src/common/doc/file_formats.h54
-rw-r--r--src/common/include/gudhi/reader_utils.h78
-rw-r--r--src/cython/CMakeLists.txt103
9 files changed, 265 insertions, 89 deletions
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index 9a37f02e..dc1da31c 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -19,6 +19,10 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
"${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
+ add_test(NAME Bottleneck_read_file_example
+ COMMAND $<TARGET_FILE:bottleneck_read_file_example>
+ "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers")
+
install(TARGETS bottleneck_read_file_example DESTINATION bin)
install(TARGETS bottleneck_basic_example DESTINATION bin)
install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index bde05825..238d99ad 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -20,9 +20,8 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-#define CGAL_HAS_THREADS
-
#include <gudhi/Bottleneck.h>
+#include <gudhi/reader_utils.h>
#include <iostream>
#include <vector>
#include <utility> // for pair
@@ -30,43 +29,22 @@
#include <sstream>
#include <string>
-std::vector< std::pair<double, double> > read_diagram_from_file(const char* filename) {
- std::ifstream in;
- in.open(filename);
- std::vector< std::pair<double, double> > result;
- if (!in.is_open()) {
- std::cerr << "File : " << filename << " do not exist. The program will now terminate \n";
- throw "File do not exist \n";
- }
-
- std::string line;
- while (!in.eof()) {
- getline(in, line);
- if (line.length() != 0) {
- std::stringstream lineSS;
- lineSS << line;
- double beginn, endd;
- lineSS >> beginn;
- lineSS >> endd;
- result.push_back(std::make_pair(beginn, endd));
- }
- }
- in.close();
- return result;
-} // read_diagram_from_file
-
int main(int argc, char** argv) {
if (argc < 3) {
std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
"should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
" distance (set by default to zero). The program will now terminate \n";
+ return -1;
}
- std::vector< std::pair< double, double > > diag1 = read_diagram_from_file(argv[1]);
- std::vector< std::pair< double, double > > diag2 = read_diagram_from_file(argv[2]);
+ std::vector<std::pair<double, double>> diag1 = read_persistence_intervals_in_dimension(argv[1]);
+ std::vector<std::pair<double, double>> diag2 = read_persistence_intervals_in_dimension(argv[2]);
+
double tolerance = 0.;
if (argc == 4) {
tolerance = atof(argv[3]);
}
double b = Gudhi::persistence_diagram::bottleneck_distance(diag1, diag2, tolerance);
std::cout << "The distance between the diagrams is : " << b << ". The tolerance is : " << tolerance << std::endl;
+
+ return 0;
}
diff --git a/src/Spatial_searching/doc/Intro_spatial_searching.h b/src/Spatial_searching/doc/Intro_spatial_searching.h
index 23705378..9a3c1b65 100644
--- a/src/Spatial_searching/doc/Intro_spatial_searching.h
+++ b/src/Spatial_searching/doc/Intro_spatial_searching.h
@@ -46,7 +46,7 @@ namespace spatial_searching {
*
* \section spatial_searching_examples Example
*
- * This example generates 500 random points, then performs queries for nearest and farthest points using different methods.
+ * This example generates 500 random points, then performs radius search, and queries for nearest and farthest points using different methods.
*
* \include Spatial_searching/example_spatial_searching.cpp
*
diff --git a/src/Spatial_searching/example/example_spatial_searching.cpp b/src/Spatial_searching/example/example_spatial_searching.cpp
index 14b324ae..9e6a8f32 100644
--- a/src/Spatial_searching/example/example_spatial_searching.cpp
+++ b/src/Spatial_searching/example/example_spatial_searching.cpp
@@ -48,5 +48,13 @@ int main(void) {
for (auto ifs_iterator = ifn_range.begin(); ifs_iterator->first != 0; ++ifs_iterator)
std::cout << ifs_iterator->first << " (sq. dist. = " << ifs_iterator->second << ")\n";
+ // Radius search
+ std::cout << "Radius search:\n";
+ std::vector<std::size_t> rs_result;
+ points_ds.radius_search(points[45], 0.5, std::back_inserter(rs_result));
+ K k;
+ for (auto const& p_idx : rs_result)
+ std::cout << p_idx << " (sq. dist. = " << k.squared_distance_d_object()(points[p_idx], points[45]) << ")\n";
+
return 0;
}
diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
index 6728d56e..f13a98f7 100644
--- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h
+++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
@@ -27,6 +27,7 @@
#include <CGAL/Orthogonal_incremental_neighbor_search.h>
#include <CGAL/Search_traits.h>
#include <CGAL/Search_traits_adapter.h>
+#include <CGAL/Fuzzy_sphere.h>
#include <CGAL/property_map.h>
#include <boost/property_map/property_map.hpp>
@@ -87,6 +88,10 @@ class Kd_tree_search {
std::ptrdiff_t,
Point_property_map,
Traits_base> STraits;
+ typedef CGAL::Distance_adapter<
+ std::ptrdiff_t,
+ Point_property_map,
+ CGAL::Euclidean_distance<Traits_base> > Orthogonal_distance;
typedef CGAL::Orthogonal_k_neighbor_search<STraits> K_neighbor_search;
typedef typename K_neighbor_search::Tree Tree;
@@ -104,6 +109,7 @@ class Kd_tree_search {
/// of a point P and `second` is the squared distance between P and the query point.
typedef Incremental_neighbor_search INS_range;
+ typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere;
/// \brief Constructor
/// @param[in] points Const reference to the point range. This range
/// is not copied, so it should not be destroyed or modified afterwards.
@@ -164,9 +170,9 @@ class Kd_tree_search {
/// @param[in] k Number of nearest points to search.
/// @param[in] sorted Indicates if the computed sequence of k-nearest neighbors needs to be sorted.
/// @param[in] eps Approximation factor.
- /// @return A range containing the k-nearest neighbors.
- KNS_range query_k_nearest_neighbors(const
- Point &p,
+ /// @return A range (whose `value_type` is `std::size_t`) containing the k-nearest neighbors.
+ KNS_range query_k_nearest_neighbors(
+ Point const& p,
unsigned int k,
bool sorted = true,
FT eps = FT(0)) const {
@@ -179,8 +185,7 @@ class Kd_tree_search {
k,
eps,
true,
- CGAL::Distance_adapter<std::ptrdiff_t, Point_property_map, CGAL::Euclidean_distance<Traits_base> >(
- std::begin(m_points)), sorted);
+ Orthogonal_distance(std::begin(m_points)), sorted);
return search;
}
@@ -188,10 +193,11 @@ class Kd_tree_search {
/// \brief Search incrementally for the nearest neighbors from a query point.
/// @param[in] p The query point.
/// @param[in] eps Approximation factor.
- /// @return A range containing the neighbors sorted by their distance to p.
+ /// @return A range (whose `value_type` is `std::size_t`) containing the
+ /// neighbors sorted by their distance to p.
/// All the neighbors are not computed by this function, but they will be
/// computed incrementally when the iterator on the range is incremented.
- INS_range query_incremental_nearest_neighbors(const Point &p, FT eps = FT(0)) const {
+ INS_range query_incremental_nearest_neighbors(Point const& p, FT eps = FT(0)) const {
// Initialize the search structure, and search all N points
// Note that we need to pass the Distance explicitly since it needs to
// know the property map
@@ -200,8 +206,7 @@ class Kd_tree_search {
p,
eps,
true,
- CGAL::Distance_adapter<std::ptrdiff_t, Point_property_map, CGAL::Euclidean_distance<Traits_base> >(
- std::begin(m_points)) );
+ Orthogonal_distance(std::begin(m_points)) );
return search;
}
@@ -211,9 +216,9 @@ class Kd_tree_search {
/// @param[in] k Number of farthest points to search.
/// @param[in] sorted Indicates if the computed sequence of k-farthest neighbors needs to be sorted.
/// @param[in] eps Approximation factor.
- /// @return A range containing the k-farthest neighbors.
- KNS_range query_k_farthest_neighbors(const
- Point &p,
+ /// @return A range (whose `value_type` is `std::size_t`) containing the k-farthest neighbors.
+ KNS_range query_k_farthest_neighbors(
+ Point const& p,
unsigned int k,
bool sorted = true,
FT eps = FT(0)) const {
@@ -226,8 +231,7 @@ class Kd_tree_search {
k,
eps,
false,
- CGAL::Distance_adapter<std::ptrdiff_t, Point_property_map, CGAL::Euclidean_distance<Traits_base> >(
- std::begin(m_points)), sorted);
+ Orthogonal_distance(std::begin(m_points)), sorted);
return search;
}
@@ -235,10 +239,11 @@ class Kd_tree_search {
/// \brief Search incrementally for the farthest neighbors from a query point.
/// @param[in] p The query point.
/// @param[in] eps Approximation factor.
- /// @return A range containing the neighbors sorted by their distance to p.
+ /// @return A range (whose `value_type` is `std::size_t`)
+ /// containing the neighbors sorted by their distance to p.
/// All the neighbors are not computed by this function, but they will be
/// computed incrementally when the iterator on the range is incremented.
- INS_range query_incremental_farthest_neighbors(const Point &p, FT eps = FT(0)) const {
+ INS_range query_incremental_farthest_neighbors(Point const& p, FT eps = FT(0)) const {
// Initialize the search structure, and search all N points
// Note that we need to pass the Distance explicitly since it needs to
// know the property map
@@ -247,12 +252,32 @@ class Kd_tree_search {
p,
eps,
false,
- CGAL::Distance_adapter<std::ptrdiff_t, Point_property_map, CGAL::Euclidean_distance<Traits_base> >(
- std::begin(m_points)) );
+ Orthogonal_distance(std::begin(m_points)) );
return search;
}
+ /// \brief Search for all the neighbors in a ball.
+ /// @param[in] p The query point.
+ /// @param[in] radius The search radius
+ /// @param[out] it The points that lie inside the sphere of center `p` and radius `radius`.
+ /// Note: `it` is used this way: `*it++ = each_point`.
+ /// @param[in] eps Approximation factor.
+ template <typename OutputIterator>
+ void radius_search(
+ Point const& p,
+ FT radius,
+ OutputIterator it,
+ FT eps = FT(0)) const {
+
+ m_tree.search(it, Fuzzy_sphere(p, radius, eps, m_tree.traits()));
+ }
+
+ int tree_depth() const
+ {
+ return m_tree.root()->depth();
+ }
+
private:
Point_range const& m_points;
Tree m_tree;
diff --git a/src/Spatial_searching/test/test_Kd_tree_search.cpp b/src/Spatial_searching/test/test_Kd_tree_search.cpp
index 0ef22023..f79114bc 100644
--- a/src/Spatial_searching/test/test_Kd_tree_search.cpp
+++ b/src/Spatial_searching/test/test_Kd_tree_search.cpp
@@ -109,4 +109,12 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) {
// Same result for KFN and IFN?
BOOST_CHECK(kfn_result == ifn_result);
+
+ // Test radius search
+ Point rs_q(rd.get_double(-1., 1), rd.get_double(-1., 1), rd.get_double(-1., 1), rd.get_double(-1., 1));
+ std::vector<std::size_t> rs_result;
+ points_ds.radius_search(rs_q, 0.5, std::back_inserter(rs_result));
+ K k;
+ for (auto const& p_idx : rs_result)
+ BOOST_CHECK(k.squared_distance_d_object()(points[p_idx], rs_q) <= 0.5);
}
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
new file mode 100644
index 00000000..c145b271
--- /dev/null
+++ b/src/common/doc/file_formats.h
@@ -0,0 +1,54 @@
+/* This file is part of the Gudhi Library. The Gudhi library
+* (Geometric Understanding in Higher Dimensions) is a generic C++
+* library for computational topology.
+*
+* Author(s): Clément Jamin
+*
+* Copyright (C) 2017 INRIA
+*
+* This program is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program. If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef DOC_COMMON_FILE_FORMAT_H_
+#define DOC_COMMON_FILE_FORMAT_H_
+
+namespace Gudhi {
+
+/*! \page fileformats File formats
+
+ \tableofcontents
+
+ \section FileFormatsPers Persistence Diagram
+
+ Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
+ Lines starting with `#` are ignored (comments).<br>
+ Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
+ \code{.unparsed}
+ [[field] dimension] birth death
+ \endcode
+
+ Here is a simple sample file:
+ \code{.unparsed}
+ # Beautiful persistence diagram
+ 2 2.7 3.7
+ 2 9.6 14.
+ 3 34.2 34.974
+ 4 3. inf
+ \endcode
+
+ Other sample files can be found in the `data/persistence_diagram` folder.
+*/
+} // namespace Gudhi
+
+#endif // DOC_COMMON_FILE_FORMAT_H_
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 97a87edd..f1684d78 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -2,7 +2,7 @@
* (Geometric Understanding in Higher Dimensions) is a generic C++
* library for computational topology.
*
- * Author(s): Clement Maria, Pawel Dlotko
+ * Author(s): Clement Maria, Pawel Dlotko, Clement Jamin
*
* Copyright (C) 2014 INRIA
*
@@ -24,7 +24,9 @@
#define READER_UTILS_H_
#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Debug_utils.h>
+#include <boost/function_output_iterator.hpp>
#include <boost/graph/adjacency_list.hpp>
#include <iostream>
@@ -92,7 +94,10 @@ template< typename Graph_t, typename Filtration_value, typename Vertex_handle >
Graph_t read_graph(std::string file_name) {
std::ifstream in_(file_name.c_str(), std::ios::in);
if (!in_.is_open()) {
- std::cerr << "Unable to open file " << file_name << std::endl;
+ std::string error_str("read_graph - Unable to open file ");
+ error_str.append(file_name);
+ std::cerr << error_str << std::endl;
+ throw std::invalid_argument(error_str);
}
typedef std::pair< Vertex_handle, Vertex_handle > Edge_t;
@@ -295,4 +300,73 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
return result;
} // read_lower_triangular_matrix_from_csv_file
+/**
+Reads a file containing persistence intervals.
+Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
+The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);`
+where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+Note: the function does not check that birth <= death.
+**/
+template <typename OutputIterator>
+void read_persistence_intervals_and_dimension(std::string const& filename, OutputIterator out) {
+
+ std::ifstream in(filename);
+ if (!in.is_open()) {
+ std::string error_str("read_persistence_intervals_and_dimension - Unable to open file ");
+ error_str.append(filename);
+ std::cerr << error_str << std::endl;
+ throw std::invalid_argument(error_str);
+ }
+
+ while (!in.eof()) {
+ std::string line;
+ getline(in, line);
+ if (line.length() != 0 && line[0] != '#') {
+ double numbers[4];
+ int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
+ if (n >= 2) {
+ //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
+ int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+ *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
+ }
+ }
+ }
+} // read_persistence_diagram_from_file
+
+/**
+Reads a file containing persistence intervals.
+Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
+The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>`
+where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+Note: the function does not check that birth <= death.
+**/
+inline std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) {
+
+ std::map<int, std::vector<std::pair<double, double>>> ret;
+ read_persistence_intervals_and_dimension(
+ filename,
+ boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
+ return ret;
+} // read_persistence_diagram_from_file
+
+
+/**
+Reads a file containing persistence intervals.
+Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
+If `only_this_dim` = -1, dimension is ignored and all lines are returned.
+If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim`
+(or where dimension is not specified) are returned.
+The return value is an `std::vector<std::pair<birth, death>>`
+where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+Note: the function does not check that birth <= death.
+**/
+inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
+
+ std::vector<std::pair<double, double>> ret;
+ read_persistence_intervals_and_dimension(
+ filename,
+ boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
+ return ret;
+} // read_persistence_diagram_from_file
+
#endif // READER_UTILS_H_
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 7586188c..5c98b09a 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -22,7 +22,6 @@ if(CYTHON_FOUND)
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
- # TODO: Something more clever could be done.
# This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h
# CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac).
# The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h
@@ -31,10 +30,27 @@ if(CYTHON_FOUND)
# ( _MSC_VER >= 1900 )
# #define CGAL_CAN_USE_CXX11_THREAD_LOCAL
# #endif
- if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+ set(CGAL_CAN_USE_CXX11_THREAD_LOCAL "
+ int main() {
+ #ifndef __has_feature
+ #define __has_feature(x) 0 // Compatibility with non-clang compilers.
+ #endif
+ #if __has_feature(cxx_thread_local) || \
+ ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \
+ ( _MSC_VER >= 1900 )
+ bool has_feature_thread_local = true;
+ #else
+ // Explicit error of compilation for CMake test purpose - has_feature_thread_local is not defined
+ #endif
+ bool result = has_feature_thread_local;
+ } ")
+ check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
+
+ if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
add_gudhi_cython_lib(${Boost_THREAD_LIBRARY})
set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
endif()
+
# Gudhi and CGAL compilation option
if(MSVC)
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ")
@@ -135,6 +151,8 @@ if(CYTHON_FOUND)
else(CGAL_HEADER_ONLY)
add_gudhi_cython_lib(${CGAL_LIBRARIES})
set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
+ add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY})
+ set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
endif(CGAL_HEADER_ONLY)
# GMP and GMPXX are not required, but if present, CGAL will link with them.
if(GMP_FOUND)
@@ -199,39 +217,52 @@ if(CYTHON_FOUND)
PATTERN "*.pyd")
# Test examples
- add_test(NAME alpha_complex_from_points_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_from_points_example.py")
- set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-
- add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
- set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-
- add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
- -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
- set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-
- add_test(NAME bottleneck_basic_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/bottleneck_basic_example.py")
- set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+ if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+ add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+ -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
+ set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME bottleneck_basic_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/bottleneck_basic_example.py")
+ set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+ set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+ set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+ set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+ endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
- add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
- set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+ if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+ add_test(NAME alpha_complex_from_points_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_from_points_example.py")
+ set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+ set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+ endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
- add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
- set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+ if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+ endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -267,12 +298,6 @@ if(CYTHON_FOUND)
COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/simplex_tree_example.py)
set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
- add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
- set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-
add_test(NAME witness_complex_from_nearest_landmark_table_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/witness_complex_from_nearest_landmark_table.py)
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-28 22:42:19 +0000