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-rw-r--r--src/Cech_complex/doc/Intro_cech_complex.h2
-rw-r--r--src/Doxyfile.in2
-rw-r--r--src/Rips_complex/utilities/ripscomplex.md1
-rw-r--r--src/Rips_complex/utilities/sparse_rips_persistence.cpp15
-rw-r--r--src/cmake/modules/GUDHI_compilation_flags.cmake2
-rw-r--r--src/common/doc/installation.h2
-rw-r--r--src/common/include/gudhi/Unitary_tests_utils.h1
-rw-r--r--src/python/CMakeLists.txt2
-rw-r--r--src/python/doc/installation.rst4
-rw-r--r--src/python/include/Alpha_complex_interface.h11
10 files changed, 28 insertions, 14 deletions
diff --git a/src/Cech_complex/doc/Intro_cech_complex.h b/src/Cech_complex/doc/Intro_cech_complex.h
index 90086de7..80c88dc6 100644
--- a/src/Cech_complex/doc/Intro_cech_complex.h
+++ b/src/Cech_complex/doc/Intro_cech_complex.h
@@ -24,7 +24,7 @@ namespace cech_complex {
* \section cechdefinition Čech complex definition
*
* Čech complex
- * <a target="_blank" href="https://en.wikipedia.org/wiki/%C4%8Cech_cohomology">(Wikipedia)</a> is a
+ * <a target="_blank" href="https://en.wikipedia.org/wiki/%C4%8Cech_complex">(Wikipedia)</a> is a
* <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a> constructed
* from a proximity graph. The set of all simplices is filtered by the radius of their minimal enclosing ball.
*
diff --git a/src/Doxyfile.in b/src/Doxyfile.in
index 57775498..ec551882 100644
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -765,7 +765,7 @@ INPUT_ENCODING = UTF-8
# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
# *.qsf, *.as and *.js.
-FILE_PATTERNS =
+#FILE_PATTERNS =
# The RECURSIVE tag can be used to specify whether or not subdirectories should
# be searched for input files as well.
diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md
index 03838085..61f31e3c 100644
--- a/src/Rips_complex/utilities/ripscomplex.md
+++ b/src/Rips_complex/utilities/ripscomplex.md
@@ -99,6 +99,7 @@ where `dim` is the dimension of the homological feature, `birth` and `death` are
* `-h [ --help ]` Produce help message
* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.
+* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction.
* `-e [ --approximation ]` (default = .5) Epsilon, where the sparse Rips complex is a (1+epsilon)/(1-epsilon)-approximation of the Rips complex.
* `-d [ --cpx-dimension ]` (default = INT_MAX) Maximal dimension of the Rips complex we want to compute.
* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.
diff --git a/src/Rips_complex/utilities/sparse_rips_persistence.cpp b/src/Rips_complex/utilities/sparse_rips_persistence.cpp
index 1a86eafe..cefd8a67 100644
--- a/src/Rips_complex/utilities/sparse_rips_persistence.cpp
+++ b/src/Rips_complex/utilities/sparse_rips_persistence.cpp
@@ -28,21 +28,24 @@ using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomolog
using Point = std::vector<double>;
using Points_off_reader = Gudhi::Points_off_reader<Point>;
-void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, double& epsilon,
+void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag,
+ Filtration_value& threshold, double& epsilon,
int& dim_max, int& p, Filtration_value& min_persistence);
int main(int argc, char* argv[]) {
std::string off_file_points;
std::string filediag;
+ Filtration_value threshold;
double epsilon;
int dim_max;
int p;
Filtration_value min_persistence;
- program_options(argc, argv, off_file_points, filediag, epsilon, dim_max, p, min_persistence);
+ program_options(argc, argv, off_file_points, filediag, threshold, epsilon, dim_max, p, min_persistence);
Points_off_reader off_reader(off_file_points);
- Sparse_rips sparse_rips(off_reader.get_point_cloud(), Gudhi::Euclidean_distance(), epsilon);
+ Sparse_rips sparse_rips(off_reader.get_point_cloud(), Gudhi::Euclidean_distance(), epsilon,
+ -std::numeric_limits<Filtration_value>::infinity(), threshold);
// Construct the Rips complex in a Simplex Tree
Simplex_tree simplex_tree;
@@ -73,7 +76,8 @@ int main(int argc, char* argv[]) {
return 0;
}
-void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, double& epsilon,
+void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag,
+ Filtration_value& threshold, double& epsilon,
int& dim_max, int& p, Filtration_value& min_persistence) {
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
@@ -84,6 +88,9 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std::
visible.add_options()("help,h", "produce help message")(
"output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
"Name of file in which the persistence diagram is written. Default print in std::cout")(
+ "max-edge-length,r",
+ po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+ "Maximal length of an edge for the Rips complex construction.")(
"approximation,e", po::value<double>(&epsilon)->default_value(.5),
"Epsilon, where the sparse Rips complex is a (1+epsilon)-approximation of the Rips complex.")(
"cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
diff --git a/src/cmake/modules/GUDHI_compilation_flags.cmake b/src/cmake/modules/GUDHI_compilation_flags.cmake
index 86cd531b..6cd2614d 100644
--- a/src/cmake/modules/GUDHI_compilation_flags.cmake
+++ b/src/cmake/modules/GUDHI_compilation_flags.cmake
@@ -38,7 +38,7 @@ function(can_cgal_use_cxx11_thread_local)
check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
endfunction()
-set (CMAKE_CXX_STANDARD 11)
+set (CMAKE_CXX_STANDARD 14)
enable_testing()
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index 54f86573..2e64bef8 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -5,7 +5,7 @@
* Examples of GUDHI headers inclusion can be found in \ref utilities.
*
* \section compiling Compiling
- * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> &ge; 1.56.0
+ * The library uses c++14 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> &ge; 1.56.0
* and <a target="_blank" href="https://www.cmake.org/">CMake</a> &ge; 3.1.
* It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
*
diff --git a/src/common/include/gudhi/Unitary_tests_utils.h b/src/common/include/gudhi/Unitary_tests_utils.h
index 4ad4dae8..7d039304 100644
--- a/src/common/include/gudhi/Unitary_tests_utils.h
+++ b/src/common/include/gudhi/Unitary_tests_utils.h
@@ -14,6 +14,7 @@
#include <iostream>
#include <limits> // for std::numeric_limits<>
+#include <cmath> // for std::fabs
template<typename FloatingType >
void GUDHI_TEST_FLOAT_EQUALITY_CHECK(FloatingType a, FloatingType b,
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 07931d10..1b1684e1 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -77,7 +77,7 @@ if(PYTHONINTERP_FOUND)
if(MSVC)
set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ")
else(MSVC)
- set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ")
+ set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-std=c++14', ")
endif(MSVC)
if(CMAKE_COMPILER_IS_GNUCXX)
set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst
index 3711ca8e..7699a5bb 100644
--- a/src/python/doc/installation.rst
+++ b/src/python/doc/installation.rst
@@ -8,11 +8,11 @@ Installation
Conda
*****
The easiest way to install the Python version of GUDHI is using
-`conda <https://gudhi.inria.fr/licensing/>`_.
+`conda <https://gudhi.inria.fr/conda/>`_.
Compiling
*********
-The library uses c++11 and requires `Boost <https://www.boost.org/>`_ ≥ 1.56.0,
+The library uses c++14 and requires `Boost <https://www.boost.org/>`_ ≥ 1.56.0,
`CMake <https://www.cmake.org/>`_ ≥ 3.1 to generate makefiles,
`NumPy <http://numpy.org>`_ and `Cython <https://www.cython.org/>`_ to compile
the GUDHI Python module.
diff --git a/src/python/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h
index b3553d32..96353cc4 100644
--- a/src/python/include/Alpha_complex_interface.h
+++ b/src/python/include/Alpha_complex_interface.h
@@ -15,6 +15,8 @@
#include <gudhi/Alpha_complex.h>
#include <CGAL/Epick_d.h>
+#include <boost/range/adaptor/transformed.hpp>
+
#include "Simplex_tree_interface.h"
#include <iostream>
@@ -31,7 +33,10 @@ class Alpha_complex_interface {
public:
Alpha_complex_interface(const std::vector<std::vector<double>>& points) {
- alpha_complex_ = new Alpha_complex<Dynamic_kernel>(points);
+ auto mkpt = [](std::vector<double> const& vec){
+ return Point_d(vec.size(), vec.begin(), vec.end());
+ };
+ alpha_complex_ = new Alpha_complex<Dynamic_kernel>(boost::adaptors::transform(points, mkpt));
}
Alpha_complex_interface(const std::string& off_file_name, bool from_file = true) {
@@ -45,9 +50,9 @@ class Alpha_complex_interface {
std::vector<double> get_point(int vh) {
std::vector<double> vd;
try {
- Point_d ph = alpha_complex_->get_point(vh);
+ Point_d const& ph = alpha_complex_->get_point(vh);
for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
- vd.push_back(*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
}
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-28 01:22:50 +0000