diff options
author | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2020-11-18 08:03:56 +0100 |
---|---|---|
committer | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2020-11-18 08:03:56 +0100 |
commit | 8b7a25482dfd9c38825e022d5f95135f0aade738 (patch) | |
tree | e986157f9921aa261a58c8d812f2802cab248310 | |
parent | d33eaa80b7c337fde11bb5db60df79fbc81fb483 (diff) | |
parent | ad5d38986542715e0a0518537afaadcda71d9c49 (diff) |
merge master and resolve conflicts
80 files changed, 1597 insertions, 662 deletions
diff --git a/.circleci/config.yml b/.circleci/config.yml index b04efd52..285a66a5 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -8,11 +8,11 @@ jobs: - run: name: Build and test examples command: | - mkdir build; - cd build; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF ..; - make all; - ctest --output-on-failure; + mkdir build + cd build + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF .. + make all + ctest --output-on-failure tests: docker: @@ -22,11 +22,11 @@ jobs: - run: name: Build and test unitary tests command: | - mkdir build; - cd build; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF ..; - make all; - ctest --output-on-failure; + mkdir build + cd build + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF .. + make all + ctest --output-on-failure utils: docker: @@ -36,11 +36,11 @@ jobs: - run: name: Build and test utilities command: | - mkdir build; - cd build; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=OFF ..; - make all; - ctest --output-on-failure; + mkdir build + cd build + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=OFF .. + make all + ctest --output-on-failure python: docker: @@ -52,24 +52,26 @@ jobs: command: | git submodule init git submodule update - mkdir build; - cd build; - cmake -DUSER_VERSION_DIR=version ..; - make user_version; - cd version; - mkdir build; - cd build; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..; - cd python; - python3 setup.py build_ext --inplace; - make sphinx; - cp -R sphinx /tmp/sphinx; - python3 setup.py install; - python3 setup.py clean --all; - ctest -j 2 --output-on-failure; - + mkdir build + cd build + cmake -DUSER_VERSION_DIR=version .. + make user_version + cd version + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 . + cd python + python3 setup.py build_ext --inplace + make sphinx + cp -R sphinx /tmp/sphinx + python3 setup.py install + python3 setup.py clean --all + python3 -B -m pytest test/*.py --cov-report html --cov=gudhi + cp -R htmlcov /tmp/htmlcov - store_artifacts: path: /tmp/sphinx + destination: sphinx + - store_artifacts: + path: /tmp/htmlcov + destination: htmlcov doxygen: docker: @@ -81,16 +83,17 @@ jobs: command: | git submodule init git submodule update - mkdir build; - cd build; - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF -DUSER_VERSION_DIR=version ..; - make doxygen 2>&1 | tee dox.log; - grep warning dox.log; - cp dox.log version/doc/html/; - cp -R version/doc/html /tmp/doxygen; + mkdir build + cd build + cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF -DUSER_VERSION_DIR=version .. + make doxygen 2>&1 | tee dox.log + grep warning dox.log + cp dox.log version/doc/html/ + cp -R version/doc/html /tmp/doxygen - store_artifacts: path: /tmp/doxygen + destination: doxygen workflows: version: 2 diff --git a/.github/next_release.md b/.github/next_release.md index cd2376eb..190f8408 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -1,13 +1,13 @@ We are pleased to announce the release 3.4.0 of the GUDHI library. -As a major new feature, the GUDHI library now offers ... +As a major new feature, the GUDHI library now offers dD weighted alpha complex, ... We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.4.0.tar.gz). Below is a list of changes made since GUDHI 3.3.0: -- [Module](link) - - ... +- [Alpha complex](https://gudhi.inria.fr/doc/latest/group__alpha__complex.html) + - the C++ weighted version for alpha complex is now available in dimension D. - [Module](link) - ... diff --git a/.github/test-requirements.txt b/.github/test-requirements.txt index 98f1007e..688a2a11 100644 --- a/.github/test-requirements.txt +++ b/.github/test-requirements.txt @@ -1,4 +1,5 @@ pytest +pytest-cov sphinx sphinxcontrib-bibtex sphinx-paramlinks @@ -7,6 +8,7 @@ scipy scikit-learn POT tensorflow +tensorflow-addons torch<1.5 pykeops hnswlib diff --git a/CMakeLists.txt b/CMakeLists.txt index 8b82036b..4257a025 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required(VERSION 3.1) +cmake_minimum_required(VERSION 3.5) project(GUDHIdev) diff --git a/Dockerfile_for_circleci_image b/Dockerfile_for_circleci_image index 464097e7..ec1b8ff8 100644 --- a/Dockerfile_for_circleci_image +++ b/Dockerfile_for_circleci_image @@ -23,6 +23,9 @@ ENV LANG en_US.UTF-8 ENV LANGUAGE en_US:en ENV LC_ALL en_US.UTF-8 +# Update again +RUN apt-get update + # Required for Gudhi compilation RUN apt-get install -y make \ git \ @@ -38,7 +41,6 @@ RUN apt-get install -y make \ libgmp3-dev \ libmpfr-dev \ libtbb-dev \ - libcgal-dev \ locales \ python3 \ python3-pip \ @@ -48,6 +50,15 @@ RUN apt-get install -y make \ pkg-config \ curl +RUN curl -LO "https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz" \ + && tar xf CGAL-5.1.tar.xz \ + && mkdir build \ + && cd build \ + && cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \ + && make install \ + && cd .. \ + && rm -rf build CGAL-5.1 + ADD .github/build-requirements.txt / ADD .github/test-requirements.txt / diff --git a/Dockerfile_for_pip b/Dockerfile_for_pip index 8f60e37c..98668a04 100644 --- a/Dockerfile_for_pip +++ b/Dockerfile_for_pip @@ -14,23 +14,24 @@ RUN mkdir -p /opt/cmake \ && sh cmake-3.16.2-Linux-x86_64.sh --skip-license --prefix=/opt/cmake \ && rm -f cmake-3.16.2-Linux-x86_64.sh -RUN git clone -b boost-1.73.0 --depth 1 https://github.com/boostorg/boost.git \ - && cd boost \ - && git submodule update --init \ - && ./bootstrap.sh --with-libraries=filesystem,program_options,system,thread,test \ - && ./b2 headers \ - && ./b2 install \ +# yum install boost-devel installs boost 1.53 and copy is the only way to install headers only boost +RUN wget https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.gz \ + && tar xf boost_1_73_0.tar.gz \ + && cd boost_1_73_0 \ + && ./bootstrap.sh \ + && ls \ + && cp -r boost /usr/local/include/ \ && cd .. \ && rm -rf boost -RUN wget https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-5.0.2/CGAL-5.0.2.tar.xz \ - && tar xf CGAL-5.0.2.tar.xz \ +RUN wget https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz \ + && tar xf CGAL-5.1.tar.xz \ && mkdir build \ && cd build \ - && /opt/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.0.2/ \ + && /opt/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \ && make install \ && cd .. \ - && rm -rf build CGAL-5.0.2 + && rm -rf build CGAL-5.1 ADD .github/build-requirements.txt / diff --git a/Dockerfile_gudhi_installation b/Dockerfile_gudhi_installation index 92430fce..ebd21f8d 100644 --- a/Dockerfile_gudhi_installation +++ b/Dockerfile_gudhi_installation @@ -23,6 +23,9 @@ ENV LANG en_US.UTF-8 ENV LANGUAGE en_US:en ENV LC_ALL en_US.UTF-8 +# Update again +RUN apt-get update + # Required for Gudhi compilation RUN apt-get install -y make \ g++ \ @@ -47,6 +50,15 @@ RUN apt-get install -y make \ pkg-config \ curl +RUN curl -LO "https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz" \ + && tar xf CGAL-5.1.tar.xz \ + && mkdir build \ + && cd build \ + && cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \ + && make install \ + && cd .. \ + && rm -rf build CGAL-5.1 + RUN pip3 install \ numpy \ matplotlib \ diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 60da7169..c068b268 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -22,6 +22,18 @@ namespace alpha_complex { * * @{ * +<div class="toc"> +Table of Contents +<ul> +<li class="level1"><a href="#definition">Definition</a></li> +<li class="level1"><a href="#pointsexample">Example from points</a></li> +<li class="level1"><a href="#createcomplexalgorithm">Create complex algorithm</a></li> +<li class="level1"><a href="#weightedversion">Weighted specific version</a></li> +<li class="level1"><a href="#offexample">Example from OFF file</a></li> +<li class="level1"><a href="#weighted3dexample">3d specific version</a></li> +</ul> +</div> + * \section definition Definition * * Alpha_complex is a <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a> @@ -62,7 +74,7 @@ namespace alpha_complex { * [10^12,10^12+10^6]. Using `CGAL::Epick_d` makes the computations slightly faster, and the combinatorics are still * exact, but the computation of filtration values can exceptionally be arbitrarily bad. In all cases, we still * guarantee that the output is a valid filtration (faces have a filtration value no larger than their cofaces). - * - For performances reasons, it is advised to use `Alpha_complex` with \ref cgal ≥ 5.0.0. + * - For performances reasons, it is advised to use \ref eigen ≥ 3.3.5 and \ref cgal ≥ 5.2.0. * * \section pointsexample Example from points * @@ -146,6 +158,30 @@ namespace alpha_complex { * `SimplicialComplexForAlpha::prune_above_filtration()`). * In the following example, the value is given by the user as argument of the program. * + * \section weightedversion Weighted specific version + * <b>Requires:</b> \ref eigen ≥ 3.1.0 and \ref cgal ≥ 5.1.0. + * + * A weighted version for Alpha complex is available (cf. Alpha_complex). It is like a usual Alpha complex, but based + * on a <a href="https://doc.cgal.org/latest/Triangulation/index.html#title20">CGAL regular triangulation</a> instead + * of Delaunay. + * + * This example builds the CGAL weighted alpha shapes from a small molecule, and initializes the alpha complex with + * it. This example is taken from <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title13">CGAL 3d + * weighted alpha shapes</a>. + * + * Then, it is asked to display information about the alpha complex. + * + * \include Alpha_complex/Weighted_alpha_complex_from_points.cpp + * + * When launching: + * + * \code $> ./Weighted_alpha_complex_example_from_points + * \endcode + * + * the program output is: + * + * \include Alpha_complex/weightedalpha3dfrompoints_for_doc.txt + * * * \section offexample Example from OFF file * @@ -166,7 +202,7 @@ namespace alpha_complex { * \include Alpha_complex/alphaoffreader_for_doc_32.txt * * - * \section weighted3dexample 3d specific example + * \section weighted3dexample 3d specific version * * A specific module for Alpha complex is available in 3d (cf. Alpha_complex_3d) and allows to construct standard, * weighted, periodic or weighted and periodic versions of alpha complexes. Alpha values computation can be @@ -181,14 +217,7 @@ namespace alpha_complex { * * \include Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * - * When launching: - * - * \code $> ./Alpha_complex_example_weighted_3d_from_points - * \endcode - * - * the program output is: - * - * \include Alpha_complex/weightedalpha3dfrompoints_for_doc.txt + * The results will be the same as in \ref weightedversion . * */ /** @} */ // end defgroup alpha_complex diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 2eecd50c..1fc2330a 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -25,7 +25,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Alpha_complex_example_fast_from_off_32 COMMAND $<TARGET_FILE:Alpha_complex_example_fast_from_off> "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt") -if (DIFF_PATH) + if (DIFF_PATH) # Do not forget to copy test results files in current binary dir file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) @@ -43,8 +43,10 @@ if (DIFF_PATH) add_test(Alpha_complex_example_fast_from_off_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) set_tests_properties(Alpha_complex_example_fast_from_off_32_diff_files PROPERTIES DEPENDS Alpha_complex_example_fast_from_off_32) -endif() + endif() +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +if (NOT CGAL_VERSION VERSION_LESS 4.11.0) add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp ) target_link_libraries(Alpha_complex_example_weighted_3d_from_points ${CGAL_LIBRARY}) if (TBB_FOUND) @@ -61,4 +63,13 @@ endif() add_test(NAME Alpha_complex_example_3d_from_points COMMAND $<TARGET_FILE:Alpha_complex_example_3d_from_points>) -endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +endif(NOT CGAL_VERSION VERSION_LESS 4.11.0) + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) + add_executable ( Weighted_alpha_complex_example_from_points Weighted_alpha_complex_from_points.cpp ) + target_link_libraries(Weighted_alpha_complex_example_from_points ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Weighted_alpha_complex_example_from_points ${TBB_LIBRARIES}) + endif() + add_test(NAME Weighted_alpha_complex_example_from_points COMMAND $<TARGET_FILE:Weighted_alpha_complex_example_from_points>) +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index c044194e..ee12d418 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -7,7 +7,7 @@ #include <vector> #include <limits> // for numeric limits -// Complexity = FAST, weighted = true, periodic = false +// Complexity = SAFE, weighted = true, periodic = false using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, true, false>; using Bare_point = Weighted_alpha_complex_3d::Bare_point_3; @@ -18,11 +18,11 @@ int main(int argc, char **argv) { // Init of a list of points and weights from a small molecule // ---------------------------------------------------------------------------- std::vector<Weighted_point> weighted_points; - weighted_points.push_back(Weighted_point(Bare_point(1, -1, -1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(-1, 1, -1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(-1, -1, 1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(1, 1, 1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(2, 2, 2), 1.)); + weighted_points.emplace_back(Bare_point(1, -1, -1), 4.); + weighted_points.emplace_back(Bare_point(-1, 1, -1), 4.); + weighted_points.emplace_back(Bare_point(-1, -1, 1), 4.); + weighted_points.emplace_back(Bare_point(1, 1, 1), 4.); + weighted_points.emplace_back(Bare_point(2, 2, 2), 1.); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points @@ -34,10 +34,10 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- - std::clog << "Alpha complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() + std::clog << "Weighted alpha complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; - std::clog << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + std::clog << "Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; for (auto f_simplex : simplex.filtration_simplex_range()) { std::clog << " ( "; for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp new file mode 100644 index 00000000..d1f3e436 --- /dev/null +++ b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp @@ -0,0 +1,52 @@ +#include <gudhi/Alpha_complex.h> +// to construct a simplex_tree from alpha complex +#include <gudhi/Simplex_tree.h> + +#include <CGAL/Epeck_d.h> + +#include <iostream> +#include <vector> + +// Explicit dimension 2 Epeck_d kernel +using Kernel = CGAL::Epeck_d< CGAL::Dimension_tag<3> >; +using Bare_point = Kernel::Point_d; +using Weighted_point = Kernel::Weighted_point_d; +using Vector_of_points = std::vector<Weighted_point>; + +int main() { + // ---------------------------------------------------------------------------- + // Init of a list of points and weights from a small molecule + // ---------------------------------------------------------------------------- + Vector_of_points points; + points.emplace_back(Bare_point(1, -1, -1), 4.); + points.emplace_back(Bare_point(-1, 1, -1), 4.); + points.emplace_back(Bare_point(-1, -1, 1), 4.); + points.emplace_back(Bare_point(1, 1, 1), 4.); + points.emplace_back(Bare_point(2, 2, 2), 1.); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Gudhi::alpha_complex::Alpha_complex<Kernel, true> alpha_complex_from_weighted_points(points); + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_weighted_points.create_complex(simplex)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::clog << "Weighted alpha complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + std::clog << "Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + std::clog << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + std::clog << vertex << " "; + } + std::clog << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + std::clog << std::endl; + } + } + return 0; +} diff --git a/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt b/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt index 7a09998d..f0695f1a 100644 --- a/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt +++ b/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt @@ -1,5 +1,5 @@ -Alpha complex is of dimension 3 - 29 simplices - 5 vertices. -Iterator on alpha complex simplices in the filtration order, with [filtration value]: +Weighted alpha complex is of dimension 3 - 29 simplices - 5 vertices. +Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]: ( 0 ) -> [-4] ( 1 ) -> [-4] ( 2 ) -> [-4] diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index ba91998d..b315fa99 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -12,14 +12,17 @@ #ifndef ALPHA_COMPLEX_H_ #define ALPHA_COMPLEX_H_ +#include <gudhi/Alpha_complex/Alpha_kernel_d.h> #include <gudhi/Debug_utils.h> // to construct Alpha_complex from a OFF file of points #include <gudhi/Points_off_io.h> #include <stdlib.h> #include <math.h> // isnan, fmax +#include <memory> // for std::unique_ptr #include <CGAL/Delaunay_triangulation.h> +#include <CGAL/Regular_triangulation.h> // aka. Weighted Delaunay triangulation #include <CGAL/Epeck_d.h> // For EXACT or SAFE version #include <CGAL/Epick_d.h> // For FAST version #include <CGAL/Spatial_sort_traits_adapter_d.h> @@ -29,6 +32,10 @@ #include <Eigen/src/Core/util/Macros.h> // for EIGEN_VERSION_AT_LEAST +#include <boost/range/size.hpp> +#include <boost/range/combine.hpp> +#include <boost/range/adaptor/transformed.hpp> + #include <iostream> #include <vector> #include <string> @@ -91,49 +98,56 @@ template<typename D> struct Is_Epeck_D<CGAL::Epeck_d<D>> { static const bool val * guarantee that the output is a valid filtration (faces have a filtration value no larger than their cofaces). * - For performances reasons, it is advised to use `Alpha_complex` with \ref cgal ≥ 5.0.0. */ -template<class Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>> +template<class Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>, bool Weighted = false> class Alpha_complex { public: + /** \brief Geometric traits class that provides the geometric types and predicates needed by the triangulations.*/ + using Geom_traits = std::conditional_t<Weighted, CGAL::Regular_triangulation_traits_adapter<Kernel>, Kernel>; + // Add an int in TDS to save point index in the structure - typedef CGAL::Triangulation_data_structure<typename Kernel::Dimension, - CGAL::Triangulation_vertex<Kernel, std::ptrdiff_t>, - CGAL::Triangulation_full_cell<Kernel> > TDS; - /** \brief A Delaunay triangulation of a set of points in \f$ \mathbb{R}^D\f$.*/ - typedef CGAL::Delaunay_triangulation<Kernel, TDS> Delaunay_triangulation; - - /** \brief A point in Euclidean space.*/ - typedef typename Kernel::Point_d Point_d; - /** \brief Geometric traits class that provides the geometric types and predicates needed by Delaunay - * triangulations.*/ - typedef Kernel Geom_traits; + using TDS = CGAL::Triangulation_data_structure<typename Geom_traits::Dimension, + CGAL::Triangulation_vertex<Geom_traits, std::ptrdiff_t>, + CGAL::Triangulation_full_cell<Geom_traits> >; - private: - typedef typename Kernel::Compute_squared_radius_d Squared_Radius; - typedef typename Kernel::Side_of_bounded_sphere_d Is_Gabriel; - typedef typename Kernel::Point_dimension_d Point_Dimension; + /** \brief A (Weighted or not) Delaunay triangulation of a set of points in \f$ \mathbb{R}^D\f$.*/ + using Triangulation = std::conditional_t<Weighted, CGAL::Regular_triangulation<Kernel, TDS>, + CGAL::Delaunay_triangulation<Kernel, TDS>>; + + /** \brief CGAL kernel container for computations in function of the weighted or not characteristics.*/ + using A_kernel_d = Alpha_kernel_d<Kernel, Weighted>; + + // Numeric type of coordinates in the kernel + using FT = typename A_kernel_d::FT; + /** \brief Sphere is a std::pair<Kernel::Point_d, Kernel::FT> (aka. circurmcenter and squared radius). + * If Weighted, Sphere is a Kernel::Weighted_point_d (aka. circurmcenter and the weight value is the squared radius). + */ + using Sphere = typename A_kernel_d::Sphere; + + /** \brief A point, or a weighted point in Euclidean space.*/ + using Point_d = typename Geom_traits::Point_d; + + private: // Vertex_iterator type from CGAL. - typedef typename Delaunay_triangulation::Vertex_iterator CGAL_vertex_iterator; + using CGAL_vertex_iterator = typename Triangulation::Vertex_iterator; // size_type type from CGAL. - typedef typename Delaunay_triangulation::size_type size_type; + using size_type = typename Triangulation::size_type; // Structure to switch from simplex tree vertex handle to CGAL vertex iterator. - typedef typename std::vector< CGAL_vertex_iterator > Vector_vertex_iterator; - - // Numeric type of coordinates in the kernel - typedef typename Kernel::FT FT; + using Vector_vertex_iterator = std::vector< CGAL_vertex_iterator >; private: /** \brief Vertex iterator vector to switch from simplex tree vertex handle to CGAL vertex iterator. * Vertex handles are inserted sequentially, starting at 0.*/ Vector_vertex_iterator vertex_handle_to_iterator_; /** \brief Pointer on the CGAL Delaunay triangulation.*/ - Delaunay_triangulation* triangulation_; + std::unique_ptr<Triangulation> triangulation_; /** \brief Kernel for triangulation_ functions access.*/ - Kernel kernel_; + A_kernel_d kernel_; + /** \brief Cache for geometric constructions: circumcenter and squared radius of a simplex.*/ - std::vector<std::pair<Point_d, FT>> cache_, old_cache_; + std::vector<Sphere> cache_, old_cache_; public: /** \brief Alpha_complex constructor from an OFF file name. @@ -145,8 +159,7 @@ class Alpha_complex { * * @param[in] off_file_name OFF file [path and] name. */ - Alpha_complex(const std::string& off_file_name) - : triangulation_(nullptr) { + Alpha_complex(const std::string& off_file_name) { Gudhi::Points_off_reader<Point_d> off_reader(off_file_name); if (!off_reader.is_valid()) { std::cerr << "Alpha_complex - Unable to read file " << off_file_name << "\n"; @@ -158,23 +171,40 @@ class Alpha_complex { /** \brief Alpha_complex constructor from a list of points. * - * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * The vertices may be not contiguous as some points may be discarded in the triangulation (duplicate points, + * weighted hidden point, ...). * - * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d + * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d or Kernel::Weighted_point_d. * - * The type InputPointRange must be a range for which std::begin and - * std::end return input iterators on a Kernel::Point_d. + * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a + * Kernel::Point_d or Kernel::Weighted_point_d. */ template<typename InputPointRange > - Alpha_complex(const InputPointRange& points) - : triangulation_(nullptr) { + Alpha_complex(const InputPointRange& points) { init_from_range(points); } - /** \brief Alpha_complex destructor deletes the Delaunay triangulation. + /** \brief Alpha_complex constructor from a list of points and weights. + * + * The vertices may be not contiguous as some points may be discarded in the triangulation (duplicate points, + * weighted hidden point, ...). + * + * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d. + * + * @param[in] weights Range of points weights. Weights must be in Kernel::FT. + * + * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a + * Kernel::Point_d. */ - ~Alpha_complex() { - delete triangulation_; + template <typename InputPointRange, typename WeightRange> + Alpha_complex(const InputPointRange& points, WeightRange weights) { + static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex"); + // FIXME: this test is only valid if we have a forward range + GUDHI_CHECK(boost::size(weights) == boost::size(points), + std::invalid_argument("Points number in range different from weights range number")); + auto weighted_points = boost::range::combine(points, weights) + | boost::adaptors::transformed([](auto const&t){return Point_d(boost::get<0>(t), boost::get<1>(t));}); + init_from_range(weighted_points); } // Forbid copy/move constructor/assignment operator @@ -202,15 +232,17 @@ class Alpha_complex { << std::endl; #endif +#if CGAL_VERSION_NR < 1050101000 + // Make compilation fail if weighted and CGAL < 5.1 + static_assert(!Weighted, "Weighted Alpha_complex is only available for CGAL >= 5.1"); +#endif + auto first = std::begin(points); auto last = std::end(points); if (first != last) { - // point_dimension function initialization - Point_Dimension point_dimension = kernel_.point_dimension_d_object(); - - // Delaunay triangulation is point dimension. - triangulation_ = new Delaunay_triangulation(point_dimension(*first)); + // Delaunay triangulation init with point dimension. + triangulation_ = std::make_unique<Triangulation>(kernel_.get_dimension(*first)); std::vector<Point_d> point_cloud(first, last); @@ -218,18 +250,20 @@ class Alpha_complex { std::vector<std::ptrdiff_t> indices(boost::counting_iterator<std::ptrdiff_t>(0), boost::counting_iterator<std::ptrdiff_t>(point_cloud.size())); - typedef boost::iterator_property_map<typename std::vector<Point_d>::iterator, - CGAL::Identity_property_map<std::ptrdiff_t>> Point_property_map; - typedef CGAL::Spatial_sort_traits_adapter_d<Kernel, Point_property_map> Search_traits_d; + using Point_property_map = boost::iterator_property_map<typename std::vector<Point_d>::iterator, + CGAL::Identity_property_map<std::ptrdiff_t>>; + using Search_traits_d = CGAL::Spatial_sort_traits_adapter_d<Geom_traits, Point_property_map>; CGAL::spatial_sort(indices.begin(), indices.end(), Search_traits_d(std::begin(point_cloud))); - typename Delaunay_triangulation::Full_cell_handle hint; + typename Triangulation::Full_cell_handle hint; for (auto index : indices) { - typename Delaunay_triangulation::Vertex_handle pos = triangulation_->insert(point_cloud[index], hint); - // Save index value as data to retrieve it after insertion - pos->data() = index; - hint = pos->full_cell(); + typename Triangulation::Vertex_handle pos = triangulation_->insert(point_cloud[index], hint); + if (pos != nullptr) { + // Save index value as data to retrieve it after insertion + pos->data() = index; + hint = pos->full_cell(); + } } // -------------------------------------------------------------------------------------------- // structure to retrieve CGAL points from vertex handle - one vertex handle per point. @@ -270,9 +304,7 @@ class Alpha_complex { v.clear(); for (auto vertex : cplx.simplex_vertex_range(s)) v.push_back(get_point_(vertex)); - Point_d c = kernel_.construct_circumcenter_d_object()(v.cbegin(), v.cend()); - FT r = kernel_.squared_distance_d_object()(c, v[0]); - cache_.emplace_back(std::move(c), std::move(r)); + cache_.emplace_back(kernel_.get_sphere(v.cbegin(), v.cend())); } return cache_[k]; } @@ -282,13 +314,13 @@ class Alpha_complex { auto radius(SimplicialComplexForAlpha& cplx, typename SimplicialComplexForAlpha::Simplex_handle s) { auto k = cplx.key(s); if(k!=cplx.null_key()) - return old_cache_[k].second; + return kernel_.get_squared_radius(old_cache_[k]); // Using a transform_range is slower, currently. thread_local std::vector<Point_d> v; v.clear(); for (auto vertex : cplx.simplex_vertex_range(s)) v.push_back(get_point_(vertex)); - return kernel_.compute_squared_radius_d_object()(v.cbegin(), v.cend()); + return kernel_.get_squared_radius(v.cbegin(), v.cend()); } public: @@ -322,9 +354,9 @@ class Alpha_complex { bool exact = false, bool default_filtration_value = false) { // From SimplicialComplexForAlpha type required to insert into a simplicial complex (with or without subfaces). - typedef typename SimplicialComplexForAlpha::Vertex_handle Vertex_handle; - typedef typename SimplicialComplexForAlpha::Simplex_handle Simplex_handle; - typedef std::vector<Vertex_handle> Vector_vertex; + using Vertex_handle = typename SimplicialComplexForAlpha::Vertex_handle; + using Simplex_handle = typename SimplicialComplexForAlpha::Simplex_handle; + using Vector_vertex = std::vector<Vertex_handle>; if (triangulation_ == nullptr) { std::cerr << "Alpha_complex cannot create_complex from a NULL triangulation\n"; @@ -368,6 +400,7 @@ class Alpha_complex { // -------------------------------------------------------------------------------------------- if (!default_filtration_value) { + CGAL::NT_converter<FT, Filtration_value> cgal_converter; // -------------------------------------------------------------------------------------------- // ### For i : d -> 0 for (int decr_dim = triangulation_->maximal_dimension(); decr_dim >= 0; decr_dim--) { @@ -378,14 +411,13 @@ class Alpha_complex { // ### If filt(Sigma) is NaN : filt(Sigma) = alpha(Sigma) if (std::isnan(complex.filtration(f_simplex))) { Filtration_value alpha_complex_filtration = 0.0; - // No need to compute squared_radius on a single point - alpha is 0.0 - if (f_simplex_dim > 0) { + // No need to compute squared_radius on a non-weighted single point - alpha is 0.0 + if (Weighted || f_simplex_dim > 0) { auto const& sqrad = radius(complex, f_simplex); #if CGAL_VERSION_NR >= 1050000000 if(exact) CGAL::exact(sqrad); #endif - CGAL::NT_converter<FT, Filtration_value> cv; - alpha_complex_filtration = cv(sqrad); + alpha_complex_filtration = cgal_converter(sqrad); } complex.assign_filtration(f_simplex, alpha_complex_filtration); #ifdef DEBUG_TRACES @@ -393,7 +425,7 @@ class Alpha_complex { #endif // DEBUG_TRACES } // No need to propagate further, unweighted points all have value 0 - if (decr_dim > 1) + if (decr_dim > !Weighted) propagate_alpha_filtration(complex, f_simplex); } } @@ -416,8 +448,8 @@ class Alpha_complex { template <typename SimplicialComplexForAlpha, typename Simplex_handle> void propagate_alpha_filtration(SimplicialComplexForAlpha& complex, Simplex_handle f_simplex) { // From SimplicialComplexForAlpha type required to assign filtration values. - typedef typename SimplicialComplexForAlpha::Filtration_value Filtration_value; - typedef typename SimplicialComplexForAlpha::Vertex_handle Vertex_handle; + using Filtration_value = typename SimplicialComplexForAlpha::Filtration_value; + using Vertex_handle = typename SimplicialComplexForAlpha::Vertex_handle; // ### Foreach Tau face of Sigma for (auto f_boundary : complex.boundary_simplex_range(f_simplex)) { @@ -450,7 +482,7 @@ class Alpha_complex { while(shortiter != enditer && *longiter == *shortiter) { ++longiter; ++shortiter; } Vertex_handle extra = *longiter; auto const& cache=get_cache(complex, f_boundary); - bool is_gab = kernel_.squared_distance_d_object()(cache.first, get_point_(extra)) >= cache.second; + bool is_gab = kernel_.is_gabriel(cache, get_point_(extra)); #ifdef DEBUG_TRACES std::clog << " | Tau is_gabriel(Sigma)=" << is_gab << " - vertexForGabriel=" << extra << std::endl; #endif // DEBUG_TRACES diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h new file mode 100644 index 00000000..28d6d7a9 --- /dev/null +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -0,0 +1,141 @@ +/* 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. + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2020 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#ifndef ALPHA_COMPLEX_ALPHA_KERNEL_D_H_ +#define ALPHA_COMPLEX_ALPHA_KERNEL_D_H_ + +#include <CGAL/version.h> // for CGAL_VERSION_NR + +#include <Eigen/Core> // for EIGEN_VERSION_AT_LEAST + +#include <utility> // for std::make_pair + +// Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10 +#if CGAL_VERSION_NR < 1041101000 +# error Alpha_complex is only available for CGAL >= 4.11 +#endif + +#if !EIGEN_VERSION_AT_LEAST(3,1,0) +# error Alpha_complex is only available for Eigen3 >= 3.1.0 installed with CGAL +#endif + +namespace Gudhi { + +namespace alpha_complex { + +/** + * \class Alpha_kernel_d + * \brief Alpha complex kernel container. + * + * \details + * The Alpha complex kernel container stores CGAL Kernel and dispatch basics computations in function of the weighted + * or not version of the Alpha complex. + */ +template < typename Kernel, bool Weighted = false > +class Alpha_kernel_d { +}; + +// Unweighted Kernel_d version +template < typename Kernel > +class Alpha_kernel_d<Kernel, false> { + private: + // Kernel for functions access. + Kernel kernel_; + public: + // Fake type for compilation to succeed (cf. std::conditional in Alpha_complex.h) + using Weighted_point_d = void; + using Point_d = typename Kernel::Point_d; + // Numeric type of coordinates in the kernel + using FT = typename Kernel::FT; + // Sphere is a pair of point and squared radius. + using Sphere = typename std::pair<Point_d, FT>; + + int get_dimension(const Point_d& p0) const { + return kernel_.point_dimension_d_object()(p0); + } + + template<class PointIterator> + Sphere get_sphere(PointIterator begin, PointIterator end) const { + Point_d c = kernel_.construct_circumcenter_d_object()(begin, end); + FT r = kernel_.squared_distance_d_object()(c, *begin); + return std::make_pair(std::move(c), std::move(r)); + } + + template<class PointIterator> + FT get_squared_radius(PointIterator begin, PointIterator end) const { + return kernel_.compute_squared_radius_d_object()(begin, end); + } + + FT get_squared_radius(const Sphere& sph) const { + return sph.second; + } + + bool is_gabriel(const Sphere& circumcenter, const Point_d& point) { + return kernel_.squared_distance_d_object()(circumcenter.first, point) >= circumcenter.second; + } +}; + +// Weighted Kernel_d version +template < typename Kernel > +class Alpha_kernel_d<Kernel, true> { + private: + // Kernel for functions access. + Kernel kernel_; + + public: + // Fake type for compilation to succeed (cf. std::conditional in Alpha_complex.h) + using Point_d = void; + using Weighted_point_d = typename Kernel::Weighted_point_d; + using Bare_point_d = typename Kernel::Point_d; + // Numeric type of coordinates in the kernel + using FT = typename Kernel::FT; + // Sphere is a weighted point (point + weight [= squared radius]). + using Sphere = Weighted_point_d; + + int get_dimension(const Weighted_point_d& p0) const { + return kernel_.point_dimension_d_object()(p0.point()); + } + + template<class PointIterator> + Sphere get_sphere(PointIterator begin, PointIterator end) const { + // power_center_d_object has been renamed between CGAL 5.1 and 5.2 +#if CGAL_VERSION_NR < 1050200000 + return kernel_.power_center_d_object()(begin, end); +#else + return kernel_.construct_power_sphere_d_object()(begin, end); +#endif + } + + template<class PointIterator> + FT get_squared_radius(PointIterator begin, PointIterator end) const { + return kernel_.compute_squared_radius_smallest_orthogonal_sphere_d_object()(begin, end); + } + + FT get_squared_radius(const Sphere& sph) const { + return sph.weight(); + } + + bool is_gabriel(const Sphere& circumcenter, const Weighted_point_d& point) { + // power_center_d_object has been renamed between CGAL 5.1 and 5.2 +#if CGAL_VERSION_NR < 1050200000 + return kernel_.power_distance_d_object()(circumcenter, point) >= 0; +#else + return kernel_.compute_power_product_d_object()(circumcenter, point) >= 0; +#endif + } +}; + +} // namespace alpha_complex + +namespace alphacomplex = alpha_complex; + +} // namespace Gudhi + +#endif // ALPHA_COMPLEX_ALPHA_KERNEL_D_H_
\ No newline at end of file diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index f56e12d0..4e5fc933 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -38,8 +38,6 @@ #include <CGAL/iterator.h> #include <CGAL/version.h> // for CGAL_VERSION_NR -#include <Eigen/src/Core/util/Macros.h> // for EIGEN_VERSION_AT_LEAST - #include <boost/container/static_vector.hpp> #include <iostream> @@ -56,10 +54,6 @@ # error Alpha_complex_3d is only available for CGAL >= 4.11 #endif -#if !EIGEN_VERSION_AT_LEAST(3,1,0) -# error Alpha_complex_3d is only available for Eigen3 >= 3.1.0 installed with CGAL -#endif - namespace Gudhi { namespace alpha_complex { @@ -160,8 +154,10 @@ class Alpha_complex_3d { using Kernel = CGAL::Periodic_3_regular_triangulation_traits_3<Predicates>; }; + public: using Kernel = typename Kernel_3<Predicates, Weighted, Periodic>::Kernel; + private: using TdsVb = typename std::conditional<Periodic, CGAL::Periodic_3_triangulation_ds_vertex_base_3<>, CGAL::Triangulation_ds_vertex_base_3<>>::type; diff --git a/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp new file mode 100644 index 00000000..6da4c084 --- /dev/null +++ b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp @@ -0,0 +1,109 @@ +/* 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. + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2020 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "alpha_kernel_d" +#include <boost/test/unit_test.hpp> +#include <boost/mpl/list.hpp> + +#include <CGAL/Epick_d.h> +#include <CGAL/Epeck_d.h> +#include <CGAL/NT_converter.h> + +#include <iostream> +#include <vector> +#include <utility> // for std::pair + +#include <gudhi/Alpha_complex/Alpha_kernel_d.h> +#include <gudhi/Unitary_tests_utils.h> + +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epeck_d< CGAL::Dynamic_dimension_tag > Exact_kernel_d; +// Use static dimension_tag for the user not to be able to set dimension +typedef CGAL::Epeck_d< CGAL::Dimension_tag<4> > Exact_kernel_s; +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Inexact_kernel_d; +// Use static dimension_tag for the user not to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Inexact_kernel_s; +// The triangulation uses the default instantiation of the TriangulationDataStructure template parameter + +typedef boost::mpl::list<Exact_kernel_d, Exact_kernel_s, Inexact_kernel_d, Inexact_kernel_s> list_of_kernel_variants; + +BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_dimension, TestedKernel, list_of_kernel_variants) { + // Test for a point (weighted or not) in 4d, that the dimension is 4. + + Gudhi::alpha_complex::Alpha_kernel_d<TestedKernel, false> kernel; + std::vector<double> p0 {0., 1., 2., 3.}; + typename TestedKernel::Point_d p0_d(p0.begin(), p0.end()); + + std::clog << "Dimension is " << kernel.get_dimension(p0_d) << std::endl; + BOOST_CHECK(kernel.get_dimension(p0_d) == 4); + + Gudhi::alpha_complex::Alpha_kernel_d<TestedKernel, true> w_kernel; + typename TestedKernel::Weighted_point_d w_p0_d(p0_d, 10.); + + std::clog << "Dimension is " << w_kernel.get_dimension(w_p0_d) << std::endl; + BOOST_CHECK(w_kernel.get_dimension(w_p0_d) == 4); +} + +BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_sphere, TestedKernel, list_of_kernel_variants) { + // Test with 5 points on a 3-sphere, that get_sphere returns the same center and squared radius + // for dD unweighted and for dD weighted with all weights at 0. + + using Unweighted_kernel = Gudhi::alpha_complex::Alpha_kernel_d<TestedKernel, false>; + // Sphere: (x-1)² + (y-1)² + z² + t² = 1 + // At least 5 points for a 3-sphere + std::vector<double> p0 {1., 0., 0., 0.}; + std::vector<double> p1 {0., 1., 0., 0.}; + std::vector<double> p2 {1., 1., 1., 0.}; + std::vector<double> p3 {1., 1., 0., 1.}; + std::vector<double> p4 {1., 1., -1., 0.}; + + using Point_d = typename Unweighted_kernel::Point_d; + std::vector<Point_d> unw_pts; + unw_pts.emplace_back(p0.begin(), p0.end()); + unw_pts.emplace_back(p1.begin(), p1.end()); + unw_pts.emplace_back(p2.begin(), p2.end()); + unw_pts.emplace_back(p3.begin(), p3.end()); + unw_pts.emplace_back(p4.begin(), p4.end()); + + Unweighted_kernel kernel; + auto unw_sphere = kernel.get_sphere(unw_pts.cbegin(), unw_pts.cend()); + + std::clog << "Center is " << unw_sphere.first << " - squared radius is " << unw_sphere.second << std::endl; + + using Weighted_kernel = Gudhi::alpha_complex::Alpha_kernel_d<TestedKernel, true>; + + using Weighted_point_d = typename Weighted_kernel::Weighted_point_d; + using Bare_point_d = typename Weighted_kernel::Bare_point_d; + std::vector<Weighted_point_d> w_pts; + w_pts.emplace_back(Bare_point_d(p0.begin(), p0.end()), 0.); + w_pts.emplace_back(Bare_point_d(p1.begin(), p1.end()), 0.); + w_pts.emplace_back(Bare_point_d(p2.begin(), p2.end()), 0.); + w_pts.emplace_back(Bare_point_d(p3.begin(), p3.end()), 0.); + w_pts.emplace_back(Bare_point_d(p4.begin(), p4.end()), 0.); + + Weighted_kernel w_kernel; + auto w_sphere = w_kernel.get_sphere(w_pts.cbegin(), w_pts.cend()); + + std::clog << "Center is " << w_sphere.point() << " - squared radius is " << w_sphere.weight() << std::endl; + + CGAL::NT_converter<typename Weighted_kernel::FT, double> cast_to_double; + // The results shall be the same with weights = 0. + GUDHI_TEST_FLOAT_EQUALITY_CHECK(cast_to_double(unw_sphere.second), cast_to_double(w_sphere.weight())); + BOOST_CHECK(unw_sphere.first == w_sphere.point()); + + auto unw_sq_rd = kernel.get_squared_radius(unw_pts.cbegin(), unw_pts.cend()); + std::clog << "Squared radius is " << unw_sq_rd << std::endl; + GUDHI_TEST_FLOAT_EQUALITY_CHECK(cast_to_double(unw_sphere.second), cast_to_double(unw_sq_rd)); + auto w_sq_rd = w_kernel.get_squared_radius(w_pts.cbegin(), w_pts.cend()); + std::clog << "Squared radius is " << w_sq_rd << std::endl; + GUDHI_TEST_FLOAT_EQUALITY_CHECK(cast_to_double(w_sphere.weight()), cast_to_double(w_sq_rd)); +} diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index fe4b23e4..db5d840f 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -18,6 +18,10 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) gudhi_add_boost_test(Alpha_complex_test_unit) gudhi_add_boost_test(Delaunay_complex_test_unit) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + +if (NOT CGAL_VERSION VERSION_LESS 4.11.0) + add_executable ( Alpha_complex_3d_test_unit Alpha_complex_3d_unit_test.cpp ) target_link_libraries(Alpha_complex_3d_test_unit ${CGAL_LIBRARY}) add_executable ( Weighted_alpha_complex_3d_test_unit Weighted_alpha_complex_3d_unit_test.cpp ) @@ -38,4 +42,21 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) gudhi_add_boost_test(Periodic_alpha_complex_3d_test_unit) gudhi_add_boost_test(Weighted_periodic_alpha_complex_3d_test_unit) -endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) + add_executable ( Alpha_kernel_d_test_unit Alpha_kernel_d_unit_test.cpp ) + target_link_libraries(Alpha_kernel_d_test_unit ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_kernel_d_test_unit ${TBB_LIBRARIES}) + endif() + gudhi_add_boost_test(Alpha_kernel_d_test_unit) + + add_executable ( Weighted_alpha_complex_test_unit Weighted_alpha_complex_unit_test.cpp ) + target_link_libraries(Weighted_alpha_complex_test_unit ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Weighted_alpha_complex_test_unit ${TBB_LIBRARIES}) + endif() + gudhi_add_boost_test(Weighted_alpha_complex_test_unit) + +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)
\ No newline at end of file diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp new file mode 100644 index 00000000..d267276c --- /dev/null +++ b/src/Alpha_complex/test/Weighted_alpha_complex_unit_test.cpp @@ -0,0 +1,229 @@ +/* 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. + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2020 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "weighted_alpha_complex" +#include <boost/test/unit_test.hpp> +#include <boost/mpl/list.hpp> + +#include <CGAL/Epick_d.h> +#include <CGAL/Epeck_d.h> + +#include <cmath> // float comparison +#include <vector> +#include <random> +#include <array> +#include <cmath> // for std::fabs + +#include <gudhi/Alpha_complex.h> +#include <gudhi/Alpha_complex_3d.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Unitary_tests_utils.h> + +using list_of_exact_kernel_variants = boost::mpl::list<CGAL::Epeck_d< CGAL::Dynamic_dimension_tag >, + CGAL::Epeck_d< CGAL::Dimension_tag<4> > + > ; + +BOOST_AUTO_TEST_CASE_TEMPLATE(Zero_weighted_alpha_complex, Kernel, list_of_exact_kernel_variants) { + // Check that in exact mode for static dimension 4 the code for dD unweighted and for dD weighted with all weights + // 0 give exactly the same simplex tree (simplices and filtration values). + + // Random points construction + using Point_d = typename Kernel::Point_d; + std::vector<Point_d> points; + std::uniform_real_distribution<double> rd_pts(-10., 10.); + std::random_device rand_dev; + std::mt19937 rand_engine(rand_dev()); + for (int idx = 0; idx < 20; idx++) { + std::vector<double> point {rd_pts(rand_engine), rd_pts(rand_engine), rd_pts(rand_engine), rd_pts(rand_engine)}; + points.emplace_back(point.begin(), point.end()); + } + + // Alpha complex from points + Gudhi::alpha_complex::Alpha_complex<Kernel, false> alpha_complex_from_points(points); + Gudhi::Simplex_tree<> simplex; + Gudhi::Simplex_tree<>::Filtration_value infty = std::numeric_limits<Gudhi::Simplex_tree<>::Filtration_value>::infinity(); + BOOST_CHECK(alpha_complex_from_points.create_complex(simplex, infty, true)); + std::clog << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" + << std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + std::clog << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + std::clog << vertex << " "; + } + std::clog << ") -> " << "[" << simplex.filtration(f_simplex) << "] " << std::endl; + } + + // Alpha complex from zero weighted points + std::vector<typename Kernel::FT> weights(20, 0.); + Gudhi::alpha_complex::Alpha_complex<Kernel, true> alpha_complex_from_zero_weighted_points(points, weights); + Gudhi::Simplex_tree<> zw_simplex; + BOOST_CHECK(alpha_complex_from_zero_weighted_points.create_complex(zw_simplex, infty, true)); + + std::clog << "Iterator on zero weighted alpha complex simplices in the filtration order, with [filtration value]:" + << std::endl; + for (auto f_simplex : zw_simplex.filtration_simplex_range()) { + std::clog << " ( "; + for (auto vertex : zw_simplex.simplex_vertex_range(f_simplex)) { + std::clog << vertex << " "; + } + std::clog << ") -> " << "[" << zw_simplex.filtration(f_simplex) << "] " << std::endl; + } + + BOOST_CHECK(zw_simplex == simplex); +} + +template <typename Point_d> +bool cgal_3d_point_sort (Point_d a,Point_d b) { + if (a[0] != b[0]) + return a[0] < b[0]; + if (a[1] != b[1]) + return a[1] < b[1]; + return a[2] < b[2]; +} + +BOOST_AUTO_TEST_CASE(Weighted_alpha_complex_3d_comparison) { + // check that for random weighted 3d points in safe mode the 3D and dD codes give the same result with some tolerance + + // Random points construction + using Kernel_dD = CGAL::Epeck_d< CGAL::Dimension_tag<3> >; + using Bare_point_d = typename Kernel_dD::Point_d; + using Weighted_point_d = typename Kernel_dD::Weighted_point_d; + std::vector<Weighted_point_d> w_points_d; + + using Exact_weighted_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, true, false>; + using Bare_point_3 = typename Exact_weighted_alpha_complex_3d::Bare_point_3; + using Weighted_point_3 = typename Exact_weighted_alpha_complex_3d::Weighted_point_3; + std::vector<Weighted_point_3> w_points_3; + + std::uniform_real_distribution<double> rd_pts(-10., 10.); + std::uniform_real_distribution<double> rd_wghts(-0.5, 0.5); + std::random_device rand_dev; + std::mt19937 rand_engine(rand_dev()); + for (int idx = 0; idx < 20; idx++) { + std::vector<double> point {rd_pts(rand_engine), rd_pts(rand_engine), rd_pts(rand_engine)}; + double weight = rd_wghts(rand_engine); + w_points_d.emplace_back(Bare_point_d(point.begin(), point.end()), weight); + w_points_3.emplace_back(Bare_point_3(point[0], point[1], point[2]), weight); + } + + // Structures necessary for comparison + using Points = std::vector<std::array<double,3>>; + using Points_and_filtrations = std::map<Points, double>; + Points_and_filtrations pts_fltr_dD; + Points_and_filtrations pts_fltr_3d; + + // Weighted alpha complex for dD version + Gudhi::alpha_complex::Alpha_complex<Kernel_dD, true> alpha_complex_dD_from_weighted_points(w_points_d); + Gudhi::Simplex_tree<> w_simplex_d; + BOOST_CHECK(alpha_complex_dD_from_weighted_points.create_complex(w_simplex_d)); + + std::clog << "Iterator on weighted alpha complex dD simplices in the filtration order, with [filtration value]:" + << std::endl; + for (auto f_simplex : w_simplex_d.filtration_simplex_range()) { + Points points; + for (auto vertex : w_simplex_d.simplex_vertex_range(f_simplex)) { + CGAL::NT_converter<Kernel_dD::RT, double> cgal_converter; + Bare_point_d pt = alpha_complex_dD_from_weighted_points.get_point(vertex).point(); + points.push_back({cgal_converter(pt[0]), cgal_converter(pt[1]), cgal_converter(pt[2])}); + } + std::clog << " ( "; + std::sort (points.begin(), points.end()); + for (auto point : points) { + std::clog << point[0] << " " << point[1] << " " << point[2] << " | "; + } + std::clog << ") -> " << "[" << w_simplex_d.filtration(f_simplex) << "] "; + std::clog << std::endl; + pts_fltr_dD[points] = w_simplex_d.filtration(f_simplex); + } + + // Weighted alpha complex for 3D version + Exact_weighted_alpha_complex_3d alpha_complex_3D_from_weighted_points(w_points_3); + Gudhi::Simplex_tree<> w_simplex_3; + BOOST_CHECK(alpha_complex_3D_from_weighted_points.create_complex(w_simplex_3)); + + std::clog << "Iterator on weighted alpha complex 3D simplices in the filtration order, with [filtration value]:" + << std::endl; + for (auto f_simplex : w_simplex_3.filtration_simplex_range()) { + Points points; + for (auto vertex : w_simplex_3.simplex_vertex_range(f_simplex)) { + Bare_point_3 pt = alpha_complex_3D_from_weighted_points.get_point(vertex).point(); + CGAL::NT_converter<Exact_weighted_alpha_complex_3d::Kernel::RT, double> cgal_converter; + points.push_back({cgal_converter(pt[0]), cgal_converter(pt[1]), cgal_converter(pt[2])}); + } + std::clog << " ( "; + std::sort (points.begin(), points.end()); + for (auto point : points) { + std::clog << point[0] << " " << point[1] << " " << point[2] << " | "; + } + std::clog << ") -> " << "[" << w_simplex_3.filtration(f_simplex) << "] " << std::endl; + pts_fltr_3d[points] = w_simplex_d.filtration(f_simplex); + } + + // Compares structures + auto d3_itr = pts_fltr_3d.begin(); + auto dD_itr = pts_fltr_dD.begin(); + for (; d3_itr != pts_fltr_3d.end() && dD_itr != pts_fltr_dD.end(); ++d3_itr) { + if (d3_itr->first != dD_itr->first) { + for(auto point : d3_itr->first) + std::clog << point[0] << " " << point[1] << " " << point[2] << " | "; + std::clog << " versus "; + for(auto point : dD_itr->first) + std::clog << point[0] << " " << point[1] << " " << point[2] << " | "; + std::clog << std::endl; + BOOST_CHECK(false); + } + // In safe mode, relative error is less than 1e-5 (can be changed with set_relative_precision_of_to_double) + if (std::fabs(d3_itr->second - dD_itr->second) > 1e-5 * (std::fabs(d3_itr->second) + std::fabs(dD_itr->second))) { + std::clog << d3_itr->second << " versus " << dD_itr->second << " diff " + << std::fabs(d3_itr->second - dD_itr->second) << std::endl; + BOOST_CHECK(false); + } + ++dD_itr; + } +} + +using list_of_1d_kernel_variants = boost::mpl::list<CGAL::Epeck_d< CGAL::Dynamic_dimension_tag >, + CGAL::Epeck_d< CGAL::Dimension_tag<1>>, + CGAL::Epick_d< CGAL::Dynamic_dimension_tag >, + CGAL::Epick_d< CGAL::Dimension_tag<1>> + >; + +BOOST_AUTO_TEST_CASE_TEMPLATE(Weighted_alpha_complex_non_visible_points, Kernel, list_of_1d_kernel_variants) { + // check that for 2 closed weighted 1-d points, one with a high weight to hide the second one with a small weight, + // that the point with a small weight has the same high filtration value than the edge formed by the 2 points + using Point_d = typename Kernel::Point_d; + std::vector<Point_d> points; + std::vector<double> p1 {0.}; + points.emplace_back(p1.begin(), p1.end()); + // closed enough points + std::vector<double> p2 {0.1}; + points.emplace_back(p2.begin(), p2.end()); + std::vector<typename Kernel::FT> weights {100., 0.01}; + + Gudhi::alpha_complex::Alpha_complex<Kernel, true> alpha_complex(points, weights); + Gudhi::Simplex_tree<> stree; + BOOST_CHECK(alpha_complex.create_complex(stree)); + + std::clog << "Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]:" + << std::endl; + for (auto f_simplex : stree.filtration_simplex_range()) { + std::clog << " ( "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + std::clog << vertex << " "; + } + std::clog << ") -> " << "[" << stree.filtration(f_simplex) << "] " << std::endl; + } + + BOOST_CHECK(stree.filtration(stree.find({0})) == -100.); + BOOST_CHECK(stree.filtration(stree.find({1})) == stree.filtration(stree.find({0, 1}))); + BOOST_CHECK(stree.filtration(stree.find({1})) > 100000); +}
\ No newline at end of file diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index 2ffbdde0..303bd0a6 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -1,78 +1,82 @@ project(Alpha_complex_utilities) -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) - target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} Boost::program_options) +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) + if (TARGET Boost::program_options) + add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) + target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} Boost::program_options) - if (TBB_FOUND) - target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - add_test(NAME Alpha_complex_utilities_safe_alpha_complex_persistence COMMAND $<TARGET_FILE:alpha_complex_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "safe.pers") - add_test(NAME Alpha_complex_utilities_fast_alpha_complex_persistence COMMAND $<TARGET_FILE:alpha_complex_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "fast.pers" "-f") - add_test(NAME Alpha_complex_utilities_exact_alpha_complex_persistence COMMAND $<TARGET_FILE:alpha_complex_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "exact.pers" "-e") - if (DIFF_PATH) - add_test(Alpha_complex_utilities_diff_exact_alpha_complex ${DIFF_PATH} - "exact.pers" "safe.pers") - set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex PROPERTIES DEPENDS - "Alpha_complex_utilities_exact_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence") - - add_test(Alpha_complex_utilities_diff_fast_alpha_complex ${DIFF_PATH} - "fast.pers" "safe.pers") - set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex PROPERTIES DEPENDS - "Alpha_complex_utilities_fast_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence") + if (TBB_FOUND) + target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + add_test(NAME Alpha_complex_utilities_safe_alpha_complex_persistence COMMAND $<TARGET_FILE:alpha_complex_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "safe.pers") + add_test(NAME Alpha_complex_utilities_fast_alpha_complex_persistence COMMAND $<TARGET_FILE:alpha_complex_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "fast.pers" "-f") + add_test(NAME Alpha_complex_utilities_exact_alpha_complex_persistence COMMAND $<TARGET_FILE:alpha_complex_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "exact.pers" "-e") + if (DIFF_PATH) + add_test(Alpha_complex_utilities_diff_exact_alpha_complex ${DIFF_PATH} + "exact.pers" "safe.pers") + set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex PROPERTIES DEPENDS + "Alpha_complex_utilities_exact_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence") - endif() - - install(TARGETS alpha_complex_persistence DESTINATION bin) + add_test(Alpha_complex_utilities_diff_fast_alpha_complex ${DIFF_PATH} + "fast.pers" "safe.pers") + set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex PROPERTIES DEPENDS + "Alpha_complex_utilities_fast_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence") + endif() - add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) - target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} Boost::program_options) - if (TBB_FOUND) - target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) + install(TARGETS alpha_complex_persistence DESTINATION bin) + endif() +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) - add_test(NAME Alpha_complex_utilities_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" - "-p" "2" "-m" "0.45" "-o" "safe_3d.pers") +if (NOT CGAL_VERSION VERSION_LESS 4.11.0) + if (TARGET Boost::program_options) + add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) + target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} Boost::program_options) + if (TBB_FOUND) + target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) - add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" - "-p" "2" "-m" "0.45" "-o" "exact_3d.pers" "-e") + add_test(NAME Alpha_complex_utilities_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "safe_3d.pers") - add_test(NAME Alpha_complex_utilities_fast_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" - "-p" "2" "-m" "0.45" "-o" "fast_3d.pers" "-f") + add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "exact_3d.pers" "-e") - if (DIFF_PATH) - add_test(Alpha_complex_utilities_diff_exact_alpha_complex_3d ${DIFF_PATH} - "exact_3d.pers" "safe_3d.pers") - set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex_3d PROPERTIES DEPENDS - "Alpha_complex_utilities_exact_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d") - add_test(Alpha_complex_utilities_diff_fast_alpha_complex_3d ${DIFF_PATH} - "fast_3d.pers" "safe_3d.pers") - set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex_3d PROPERTIES DEPENDS - "Alpha_complex_utilities_fast_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d") - endif() + add_test(NAME Alpha_complex_utilities_fast_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "fast_3d.pers" "-f") - add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" - "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" - "-p" "2" "-m" "0") + if (DIFF_PATH) + add_test(Alpha_complex_utilities_diff_exact_alpha_complex_3d ${DIFF_PATH} + "exact_3d.pers" "safe_3d.pers") + set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex_3d PROPERTIES DEPENDS + "Alpha_complex_utilities_exact_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d") + add_test(Alpha_complex_utilities_diff_fast_alpha_complex_3d ${DIFF_PATH} + "fast_3d.pers" "safe_3d.pers") + set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex_3d PROPERTIES DEPENDS + "Alpha_complex_utilities_fast_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d") + endif() - add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" - "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" - "-p" "2" "-m" "0") + add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" + "-p" "2" "-m" "0") - add_test(NAME Alpha_complex_utilities_weighted_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" - "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" - "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" - "-p" "2" "-m" "0" "-e") + add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" + "-p" "2" "-m" "0") - install(TARGETS alpha_complex_3d_persistence DESTINATION bin) - -endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + add_test(NAME Alpha_complex_utilities_weighted_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" + "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" + "-p" "2" "-m" "0" "-e") + + install(TARGETS alpha_complex_3d_persistence DESTINATION bin) + endif() +endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp index e17831d9..e86b34e2 100644 --- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp @@ -17,19 +17,82 @@ #include <gudhi/Persistent_cohomology.h> // to construct a simplex_tree from alpha complex #include <gudhi/Simplex_tree.h> +#include <gudhi/Points_off_io.h> #include <iostream> #include <string> #include <limits> // for numeric_limits +#include <vector> +#include <fstream> using Simplex_tree = Gudhi::Simplex_tree<>; using Filtration_value = Simplex_tree::Filtration_value; void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &fast, - std::string &output_file_diag, Filtration_value &alpha_square_max_value, + std::string &weight_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, Filtration_value &min_persistence); +template<class Point_d> +std::vector<Point_d> read_off(const std::string &off_file_points) { + Gudhi::Points_off_reader<Point_d> off_reader(off_file_points); + if (!off_reader.is_valid()) { + std::cerr << "Alpha_complex - Unable to read file " << off_file_points << "\n"; + exit(-1); // ----- >> + } + return off_reader.get_point_cloud(); +} + +std::vector<double> read_weight_file(const std::string &weight_file) { + std::vector<double> weights; + // Read weights information from file + std::ifstream weights_ifstr(weight_file); + if (weights_ifstr.good()) { + double weight = 0.0; + // Attempt read the weight in a double format, return false if it fails + while (weights_ifstr >> weight) { + weights.push_back(weight); + } + } else { + std::cerr << "Unable to read weights file " << weight_file << std::endl; + exit(-1); + } + return weights; +} + +template<class Kernel> +Simplex_tree create_simplex_tree(const std::string &off_file_points, const std::string &weight_file, + bool exact_version, Filtration_value alpha_square_max_value) { + Simplex_tree stree; + auto points = read_off<typename Kernel::Point_d>(off_file_points); + + if (weight_file != std::string()) { + std::vector<double> weights = read_weight_file(weight_file); + if (points.size() != weights.size()) { + std::cerr << "Alpha_complex - Inconsistency between number of points (" << points.size() + << ") and number of weights (" << weights.size() << ")" << "\n"; + exit(-1); // ----- >> + } + // Init of an alpha complex from an OFF file + Gudhi::alpha_complex::Alpha_complex<Kernel, true> alpha_complex_from_file(points, weights); + + if (!alpha_complex_from_file.create_complex(stree, alpha_square_max_value, exact_version)) { + std::cerr << "Alpha complex simplicial complex creation failed." << std::endl; + exit(-1); + } + } else { + // Init of an alpha complex from an OFF file + Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(points); + + if (!alpha_complex_from_file.create_complex(stree, alpha_square_max_value, exact_version)) { + std::cerr << "Alpha complex simplicial complex creation failed." << std::endl; + exit(-1); + } + } + return stree; +} + int main(int argc, char **argv) { + std::string weight_file; std::string off_file_points; std::string output_file_diag; bool exact_version = false; @@ -38,48 +101,34 @@ int main(int argc, char **argv) { int coeff_field_characteristic; Filtration_value min_persistence; - program_options(argc, argv, off_file_points, exact_version, fast_version, output_file_diag, alpha_square_max_value, - coeff_field_characteristic, min_persistence); + program_options(argc, argv, off_file_points, exact_version, fast_version, weight_file, output_file_diag, + alpha_square_max_value, coeff_field_characteristic, min_persistence); if ((exact_version) && (fast_version)) { std::cerr << "You cannot set the exact and the fast version." << std::endl; exit(-1); } - Simplex_tree simplex; + Simplex_tree stree; if (fast_version) { // WARNING : CGAL::Epick_d is fast but not safe (unlike CGAL::Epeck_d) // (i.e. when the points are on a grid) using Fast_kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; - - // Init of an alpha complex from an OFF file - Gudhi::alpha_complex::Alpha_complex<Fast_kernel> alpha_complex_from_file(off_file_points); - - if (!alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { - std::cerr << "Fast Alpha complex simplicial complex creation failed." << std::endl; - exit(-1); - } + stree = create_simplex_tree<Fast_kernel>(off_file_points, weight_file, exact_version, alpha_square_max_value); } else { using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>; - - // Init of an alpha complex from an OFF file - Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points); - - if (!alpha_complex_from_file.create_complex(simplex, alpha_square_max_value, exact_version)) { - std::cerr << "Alpha complex simplicial complex creation failed." << std::endl; - exit(-1); - } + stree = create_simplex_tree<Kernel>(off_file_points, weight_file, exact_version, alpha_square_max_value); } // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- - std::clog << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() - << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; + std::clog << "Simplicial complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() + << " simplices - " << stree.num_vertices() << " vertices." << std::endl; - std::clog << "Simplex_tree dim: " << simplex.dimension() << std::endl; + std::clog << "Simplex_tree dim: " << stree.dimension() << std::endl; // Compute the persistence diagram of the complex Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh( - simplex); + stree); // initializes the coefficient field for homology pcoh.init_coefficients(coeff_field_characteristic); @@ -98,7 +147,7 @@ int main(int argc, char **argv) { } void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &fast, - std::string &output_file_diag, Filtration_value &alpha_square_max_value, + std::string &weight_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, Filtration_value &min_persistence) { namespace po = boost::program_options; po::options_description hidden("Hidden options"); @@ -111,6 +160,8 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool "To activate exact version of Alpha complex (default is false, not available if fast is set)")( "fast,f", po::bool_switch(&fast), "To activate fast version of Alpha complex (default is false, not available if exact is set)")( + "weight-file,w", po::value<std::string>(&weight_file)->default_value(std::string()), + "Name of file containing a point weights. Format is one weight per line:\n W1\n ...\n Wn ")( "output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()), "Name of file in which the persistence diagram is written. Default print in std::clog")( "max-alpha-square-value,r", po::value<Filtration_value>(&alpha_square_max_value) diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md index 527598a9..0d3c6027 100644 --- a/src/Alpha_complex/utilities/alphacomplex.md +++ b/src/Alpha_complex/utilities/alphacomplex.md @@ -46,6 +46,9 @@ for the Alpha complex construction. coefficient field Z/pZ for computing homology.
* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature
to be recorded. Enter a negative value to see zero length intervals.
+* `-w [ --weight-file ]` is the path to the file containing the weights of the
+points (one value per line).
+Default version is not weighted.
* `-e [ --exact ]` for the exact computation version.
* `-f [ --fast ]` for the fast computation version.
@@ -58,6 +61,10 @@ to be recorded. Enter a negative value to see zero length intervals. N.B.:
* Filtration values are alpha square values.
+* Weights values are explained on CGAL
+[dD Triangulations](https://doc.cgal.org/latest/Triangulation/index.html)
+and
+[Regular triangulation](https://doc.cgal.org/latest/Triangulation/index.html#title20) documentation.
## alpha_complex_3d_persistence ##
diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt index dc659f2d..0ff290ef 100644 --- a/src/Bitmap_cubical_complex/example/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -6,5 +6,3 @@ if (TBB_FOUND) endif() add_test(NAME Bitmap_cubical_complex_example_random COMMAND $<TARGET_FILE:Random_bitmap_cubical_complex> "2" "100" "100") - -install(TARGETS Random_bitmap_cubical_complex DESTINATION bin) diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h index 18901469..8ac7ae23 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h @@ -83,7 +83,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c * The boundary elements are guaranteed to be returned so that the * incidence coefficients are alternating. */ - virtual std::vector<std::size_t> get_boundary_of_a_cell(std::size_t cell) const; + virtual std::vector<std::size_t> get_boundary_of_a_cell(std::size_t cell) const override; /** * A version of a function that return coboundary of a given cell for an object of @@ -93,7 +93,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c * To compute incidence between cells use compute_incidence_between_cells * procedure */ - virtual std::vector<std::size_t> get_coboundary_of_a_cell(std::size_t cell) const; + virtual std::vector<std::size_t> get_coboundary_of_a_cell(std::size_t cell) const override; /** * This procedure compute incidence numbers between cubes. For a cube \f$A\f$ of @@ -114,7 +114,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c * @exception std::logic_error In case when the cube \f$B\f$ is not n-1 * dimensional face of a cube \f$A\f$. **/ - virtual int compute_incidence_between_cells(std::size_t coface, std::size_t face) { + virtual int compute_incidence_between_cells(std::size_t coface, std::size_t face) const override { // first get the counters for coface and face: std::vector<unsigned> coface_counter = this->compute_counter_for_given_cell(coface); std::vector<unsigned> face_counter = this->compute_counter_for_given_cell(face); diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 9839c59d..d16ea6e5 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -12,14 +12,16 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) - target_link_libraries(alpha_rips_persistence_bottleneck_distance Boost::program_options) + if (TARGET Boost::program_options) + add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) + target_link_libraries(alpha_rips_persistence_bottleneck_distance Boost::program_options) - if (TBB_FOUND) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) - endif(TBB_FOUND) - - add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck - 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") + if (TBB_FOUND) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) + endif(TBB_FOUND) + + add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck + 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") + endif() endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index e466828a..c916898d 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -35,8 +35,12 @@ namespace persistence_diagram { inline double bottleneck_distance_approx(Persistence_graph& g, double e) { double b_lower_bound = 0.; - double b_upper_bound = g.diameter_bound(); - const double alpha = std::pow(g.size(), 1. / 5.); + double b_upper_bound = g.max_dist_to_diagonal(); + int siz = g.size(); + if (siz <= 1) + // The value of alpha would be wrong in this case + return b_upper_bound; + const double alpha = std::pow(siz, 1. / 5.); Graph_matching m(g); Graph_matching biggest_unperfect(g); while (b_upper_bound - b_lower_bound > 2 * e) { diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index e1e3522e..33f03b9c 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -45,14 +45,14 @@ class Persistence_graph { int corresponding_point_in_v(int u_point_index) const; /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ double distance(int u_point_index, int v_point_index) const; - /** \internal \brief Returns size = |U| = |V|. */ + /** \internal \brief Returns size = |U| + |V|. */ int size() const; /** \internal \brief Is there as many infinite points (alive components) in both diagrams ? */ double bottleneck_alive() const; /** \internal \brief Returns the O(n^2) sorted distances between the points. */ std::vector<double> sorted_distances() const; - /** \internal \brief Returns an upper bound for the diameter of the convex hull of all non infinite points */ - double diameter_bound() const; + /** \internal \brief Returns an upper bound for the bottleneck distance of the finite points. */ + double max_dist_to_diagonal() const; /** \internal \brief Returns the corresponding internal point */ Internal_point get_u_point(int u_point_index) const; /** \internal \brief Returns the corresponding internal point */ @@ -160,13 +160,13 @@ inline Internal_point Persistence_graph::get_v_point(int v_point_index) const { return Internal_point(m, m, v_point_index); } -inline double Persistence_graph::diameter_bound() const { +inline double Persistence_graph::max_dist_to_diagonal() const { double max = 0.; - for (auto it = u.cbegin(); it != u.cend(); it++) - max = (std::max)(max, it->y()); - for (auto it = v.cbegin(); it != v.cend(); it++) - max = (std::max)(max, it->y()); - return max; + for (auto& p : u) + max = (std::max)(max, p.y() - p.x()); + for (auto& p : v) + max = (std::max)(max, p.y() - p.x()); + return max / 2; } } // namespace persistence_diagram diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index 2c520045..44141baa 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -153,4 +153,9 @@ BOOST_AUTO_TEST_CASE(global) { BOOST_CHECK(bottleneck_distance(v1, v2, 0.) <= upper_bound / 100.); BOOST_CHECK(bottleneck_distance(v1, v2, upper_bound / 10000.) <= upper_bound / 100. + upper_bound / 10000.); BOOST_CHECK(std::abs(bottleneck_distance(v1, v2, 0.) - bottleneck_distance(v1, v2, upper_bound / 10000.)) <= upper_bound / 10000.); + + std::vector< std::pair<double, double> > empty; + std::vector< std::pair<double, double> > one = {{8, 10}}; + BOOST_CHECK(bottleneck_distance(empty, empty) == 0); + BOOST_CHECK(bottleneck_distance(empty, one) == 1); } diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 9e4d78ac..79ec42c1 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required(VERSION 3.1) +cmake_minimum_required(VERSION 3.5) project(GUDHI) @@ -50,6 +50,14 @@ include_directories(include) # Include module CMake subdirectories # GUDHI_SUB_DIRECTORIES is managed in CMAKE_MODULE_PATH/GUDHI_modules.cmake +if (WITH_GUDHI_PYTHON) + # specific for cython module + add_subdirectory(${GUDHI_PYTHON_PATH}) +else() + message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python") +endif() + foreach(GUDHI_MODULE ${GUDHI_MODULES}) foreach(GUDHI_SUB_DIRECTORY ${GUDHI_SUB_DIRECTORIES}) if(EXISTS ${CMAKE_SOURCE_DIR}/${GUDHI_SUB_DIRECTORY}/${GUDHI_MODULE}/CMakeLists.txt) @@ -60,14 +68,6 @@ endforeach() add_subdirectory(GudhUI) -if (WITH_GUDHI_PYTHON) - # specific for cython module - add_subdirectory(${GUDHI_PYTHON_PATH}) -else() - message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF") - set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python") -endif() - message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"") message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"") diff --git a/src/Cech_complex/benchmark/CMakeLists.txt b/src/Cech_complex/benchmark/CMakeLists.txt index c04bca53..bc54c0f3 100644 --- a/src/Cech_complex/benchmark/CMakeLists.txt +++ b/src/Cech_complex/benchmark/CMakeLists.txt @@ -1,12 +1,13 @@ -cmake_minimum_required(VERSION 2.6) project(Cech_complex_benchmark) # Do not forget to copy test files in current binary dir file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) -add_executable(cech_complex_benchmark cech_complex_benchmark.cpp) -target_link_libraries(cech_complex_benchmark Boost::filesystem) - -if (TBB_FOUND) - target_link_libraries(cech_complex_benchmark ${TBB_LIBRARIES}) -endif() +if(TARGET Boost::filesystem) + add_executable(cech_complex_benchmark cech_complex_benchmark.cpp) + target_link_libraries(cech_complex_benchmark Boost::filesystem) + + if (TBB_FOUND) + target_link_libraries(cech_complex_benchmark ${TBB_LIBRARIES}) + endif() +endif()
\ No newline at end of file diff --git a/src/Cech_complex/example/CMakeLists.txt b/src/Cech_complex/example/CMakeLists.txt index 98757988..1b08c7cb 100644 --- a/src/Cech_complex/example/CMakeLists.txt +++ b/src/Cech_complex/example/CMakeLists.txt @@ -1,13 +1,14 @@ -cmake_minimum_required(VERSION 2.6) project(Cech_complex_examples) -add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp ) -target_link_libraries(Cech_complex_example_step_by_step Boost::program_options) -if (TBB_FOUND) - target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES}) +if (TARGET Boost::program_options) + add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp ) + target_link_libraries(Cech_complex_example_step_by_step Boost::program_options) + if (TBB_FOUND) + target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES}) + endif() + add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:Cech_complex_example_step_by_step> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-d" "3") endif() -add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:Cech_complex_example_step_by_step> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-d" "3") add_executable ( Cech_complex_example_from_points cech_complex_example_from_points.cpp) if (TBB_FOUND) diff --git a/src/Cech_complex/test/CMakeLists.txt b/src/Cech_complex/test/CMakeLists.txt index db510af3..e6a2a18f 100644 --- a/src/Cech_complex/test/CMakeLists.txt +++ b/src/Cech_complex/test/CMakeLists.txt @@ -1,6 +1,3 @@ -cmake_minimum_required(VERSION 2.6) -project(Cech_complex_tests) - include(GUDHI_boost_test) add_executable ( Cech_complex_test_unit test_cech_complex.cpp ) diff --git a/src/Cech_complex/utilities/CMakeLists.txt b/src/Cech_complex/utilities/CMakeLists.txt index 253d7304..b183c8d8 100644 --- a/src/Cech_complex/utilities/CMakeLists.txt +++ b/src/Cech_complex/utilities/CMakeLists.txt @@ -1,14 +1,15 @@ -cmake_minimum_required(VERSION 2.6) project(Cech_complex_utilities) -add_executable(cech_persistence cech_persistence.cpp) -target_link_libraries(cech_persistence Boost::program_options) +if (TARGET Boost::program_options) + add_executable(cech_persistence cech_persistence.cpp) + target_link_libraries(cech_persistence Boost::program_options) -if (TBB_FOUND) - target_link_libraries(cech_persistence ${TBB_LIBRARIES}) -endif() + if (TBB_FOUND) + target_link_libraries(cech_persistence ${TBB_LIBRARIES}) + endif() -add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:cech_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") + add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:cech_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") -install(TARGETS cech_persistence DESTINATION bin) + install(TARGETS cech_persistence DESTINATION bin) +endif()
\ No newline at end of file diff --git a/src/Collapse/example/CMakeLists.txt b/src/Collapse/example/CMakeLists.txt index ba0e75e3..4456a844 100644 --- a/src/Collapse/example/CMakeLists.txt +++ b/src/Collapse/example/CMakeLists.txt @@ -1,23 +1,28 @@ project(Edge_collapse_examples) -# Point cloud -add_executable ( Edge_collapse_example_basic edge_collapse_basic_example.cpp ) -if (TBB_FOUND) - target_link_libraries(Edge_collapse_example_basic ${TBB_LIBRARIES}) -endif() +if (NOT EIGEN3_VERSION VERSION_LESS 3.1.0) -add_test(NAME Edge_collapse_example_basic COMMAND $<TARGET_FILE:Edge_collapse_example_basic>) + # Point cloud + add_executable ( Edge_collapse_example_basic edge_collapse_basic_example.cpp ) + + if (TBB_FOUND) + target_link_libraries(Edge_collapse_example_basic ${TBB_LIBRARIES}) + endif() + + add_test(NAME Edge_collapse_example_basic COMMAND $<TARGET_FILE:Edge_collapse_example_basic>) + + # Point cloud + add_executable ( Edge_collapse_conserve_persistence edge_collapse_conserve_persistence.cpp ) + + if (TBB_FOUND) + target_link_libraries(Edge_collapse_conserve_persistence ${TBB_LIBRARIES}) + endif() + + add_test(NAME Edge_collapse_conserve_persistence_1 COMMAND $<TARGET_FILE:Edge_collapse_conserve_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "0.2") + + add_test(NAME Edge_collapse_conserve_persistence_2 COMMAND $<TARGET_FILE:Edge_collapse_conserve_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "1.8") -# Point cloud -add_executable ( Edge_collapse_conserve_persistence edge_collapse_conserve_persistence.cpp ) - -if (TBB_FOUND) - target_link_libraries(Edge_collapse_conserve_persistence ${TBB_LIBRARIES}) -endif() - -add_test(NAME Edge_collapse_conserve_persistence_1 COMMAND $<TARGET_FILE:Edge_collapse_conserve_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "0.2") - -add_test(NAME Edge_collapse_conserve_persistence_2 COMMAND $<TARGET_FILE:Edge_collapse_conserve_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "1.8") +endif()
\ No newline at end of file diff --git a/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h b/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h index b6b7f7c1..713c6608 100644 --- a/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h +++ b/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h @@ -18,6 +18,7 @@ #include <boost/iterator/iterator_facade.hpp> #include <Eigen/Sparse> +#include <Eigen/src/Core/util/Macros.h> // for EIGEN_VERSION_AT_LEAST #ifdef GUDHI_USE_TBB #include <tbb/parallel_sort.h> @@ -34,6 +35,11 @@ #include <iterator> // for std::inserter #include <type_traits> // for std::decay +// Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10 +#if !EIGEN_VERSION_AT_LEAST(3,1,0) +# error Edge Collapse is only available for Eigen3 >= 3.1.0 +#endif + namespace Gudhi { namespace collapse { diff --git a/src/Collapse/test/CMakeLists.txt b/src/Collapse/test/CMakeLists.txt index c7eafb46..c04199e2 100644 --- a/src/Collapse/test/CMakeLists.txt +++ b/src/Collapse/test/CMakeLists.txt @@ -1,9 +1,13 @@ project(Collapse_tests) -include(GUDHI_boost_test) +if (NOT EIGEN3_VERSION VERSION_LESS 3.1.0) -add_executable ( Collapse_test_unit collapse_unit_test.cpp ) -if (TBB_FOUND) - target_link_libraries(Collapse_test_unit ${TBB_LIBRARIES}) -endif() -gudhi_add_boost_test(Collapse_test_unit) + include(GUDHI_boost_test) + + add_executable ( Collapse_test_unit collapse_unit_test.cpp ) + if (TBB_FOUND) + target_link_libraries(Collapse_test_unit ${TBB_LIBRARIES}) + endif() + gudhi_add_boost_test(Collapse_test_unit) + +endif()
\ No newline at end of file diff --git a/src/Collapse/utilities/CMakeLists.txt b/src/Collapse/utilities/CMakeLists.txt index c742144b..bce99e90 100644 --- a/src/Collapse/utilities/CMakeLists.txt +++ b/src/Collapse/utilities/CMakeLists.txt @@ -1,33 +1,37 @@ project(Collapse_utilities) -# From a point cloud -add_executable ( point_cloud_edge_collapse_rips_persistence point_cloud_edge_collapse_rips_persistence.cpp ) -target_link_libraries(point_cloud_edge_collapse_rips_persistence Boost::program_options) +if (NOT EIGEN3_VERSION VERSION_LESS 3.1.0) + if (TARGET Boost::program_options) + # From a point cloud + add_executable ( point_cloud_edge_collapse_rips_persistence point_cloud_edge_collapse_rips_persistence.cpp ) + target_link_libraries(point_cloud_edge_collapse_rips_persistence Boost::program_options) + + if (TBB_FOUND) + target_link_libraries(point_cloud_edge_collapse_rips_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Edge_collapse_utilities_point_cloud_rips_persistence COMMAND $<TARGET_FILE:point_cloud_edge_collapse_rips_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "off_results.pers") + + install(TARGETS point_cloud_edge_collapse_rips_persistence DESTINATION bin) + + # From a distance matrix + add_executable ( distance_matrix_edge_collapse_rips_persistence distance_matrix_edge_collapse_rips_persistence.cpp ) + target_link_libraries(distance_matrix_edge_collapse_rips_persistence Boost::program_options) + + if (TBB_FOUND) + target_link_libraries(distance_matrix_edge_collapse_rips_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Edge_collapse_utilities_distance_matrix_rips_persistence COMMAND $<TARGET_FILE:distance_matrix_edge_collapse_rips_persistence> + "${CMAKE_SOURCE_DIR}/data/distance_matrix/tore3D_1307_distance_matrix.csv" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "csv_results.pers") + + install(TARGETS distance_matrix_edge_collapse_rips_persistence DESTINATION bin) + + if (DIFF_PATH) + add_test(Edge_collapse_utilities_diff_persistence ${DIFF_PATH} + "off_results.pers" "csv_results.pers") + set_tests_properties(Edge_collapse_utilities_diff_persistence PROPERTIES DEPENDS + "Edge_collapse_utilities_point_cloud_rips_persistence;Edge_collapse_utilities_distance_matrix_rips_persistence") + endif() + endif() -if (TBB_FOUND) - target_link_libraries(point_cloud_edge_collapse_rips_persistence ${TBB_LIBRARIES}) -endif() -add_test(NAME Edge_collapse_utilities_point_cloud_rips_persistence COMMAND $<TARGET_FILE:point_cloud_edge_collapse_rips_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "off_results.pers") - -install(TARGETS point_cloud_edge_collapse_rips_persistence DESTINATION bin) - -# From a distance matrix -add_executable ( distance_matrix_edge_collapse_rips_persistence distance_matrix_edge_collapse_rips_persistence.cpp ) -target_link_libraries(distance_matrix_edge_collapse_rips_persistence Boost::program_options) - -if (TBB_FOUND) - target_link_libraries(distance_matrix_edge_collapse_rips_persistence ${TBB_LIBRARIES}) -endif() -add_test(NAME Edge_collapse_utilities_distance_matrix_rips_persistence COMMAND $<TARGET_FILE:distance_matrix_edge_collapse_rips_persistence> - "${CMAKE_SOURCE_DIR}/data/distance_matrix/tore3D_1307_distance_matrix.csv" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "csv_results.pers") - -install(TARGETS distance_matrix_edge_collapse_rips_persistence DESTINATION bin) - -if (DIFF_PATH) - add_test(Edge_collapse_utilities_diff_persistence ${DIFF_PATH} - "off_results.pers" "csv_results.pers") - set_tests_properties(Edge_collapse_utilities_diff_persistence PROPERTIES DEPENDS - "Edge_collapse_utilities_point_cloud_rips_persistence;Edge_collapse_utilities_distance_matrix_rips_persistence") - -endif() +endif()
\ No newline at end of file diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt index 1667472f..4b0f4677 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -22,7 +22,4 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") - install(TARGETS CoordGIC DESTINATION bin) - install(TARGETS FuncGIC DESTINATION bin) - endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt index a7c6ef39..997f85dc 100644 --- a/src/Persistence_representations/example/CMakeLists.txt +++ b/src/Persistence_representations/example/CMakeLists.txt @@ -3,30 +3,24 @@ project(Persistence_representations_example) add_executable ( Persistence_representations_example_landscape_on_grid persistence_landscape_on_grid.cpp ) add_test(NAME Persistence_representations_example_landscape_on_grid COMMAND $<TARGET_FILE:Persistence_representations_example_landscape_on_grid>) -install(TARGETS Persistence_representations_example_landscape_on_grid DESTINATION bin) add_executable ( Persistence_representations_example_landscape persistence_landscape.cpp ) add_test(NAME Persistence_representations_example_landscape COMMAND $<TARGET_FILE:Persistence_representations_example_landscape>) -install(TARGETS Persistence_representations_example_landscape DESTINATION bin) add_executable ( Persistence_representations_example_intervals persistence_intervals.cpp ) add_test(NAME Persistence_representations_example_intervals COMMAND $<TARGET_FILE:Persistence_representations_example_intervals> "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers") -install(TARGETS Persistence_representations_example_intervals DESTINATION bin) add_executable ( Persistence_representations_example_vectors persistence_vectors.cpp ) add_test(NAME Persistence_representations_example_vectors COMMAND $<TARGET_FILE:Persistence_representations_example_vectors>) -install(TARGETS Persistence_representations_example_vectors DESTINATION bin) add_executable ( Persistence_representations_example_heat_maps persistence_heat_maps.cpp ) add_test(NAME Persistence_representations_example_heat_maps COMMAND $<TARGET_FILE:Persistence_representations_example_heat_maps>) -install(TARGETS Persistence_representations_example_heat_maps DESTINATION bin) add_executable ( Sliced_Wasserstein sliced_wasserstein.cpp ) add_test(NAME Sliced_Wasserstein COMMAND $<TARGET_FILE:Sliced_Wasserstein>) -install(TARGETS Sliced_Wasserstein DESTINATION bin) diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt index f38cc543..ad8dc84b 100644 --- a/src/Persistent_cohomology/benchmark/CMakeLists.txt +++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt @@ -2,11 +2,13 @@ project(Persistent_cohomology_benchmark) if(GMP_FOUND) if(GMPXX_FOUND) - add_executable ( performance_rips_persistence EXCLUDE_FROM_ALL performance_rips_persistence.cpp ) - target_link_libraries(performance_rips_persistence Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) - if (TBB_FOUND) - target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - file(COPY "${CMAKE_SOURCE_DIR}/data/points/Kl.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + if (TARGET Boost::program_options) + add_executable ( performance_rips_persistence EXCLUDE_FROM_ALL performance_rips_persistence.cpp ) + target_link_libraries(performance_rips_persistence Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + if (TBB_FOUND) + target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + file(COPY "${CMAKE_SOURCE_DIR}/data/points/Kl.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + endif() endif(GMPXX_FOUND) endif(GMP_FOUND) diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 4c08cd68..c68c6524 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -1,46 +1,53 @@ project(Persistent_cohomology_examples) add_executable(plain_homology plain_homology.cpp) +if (TBB_FOUND) + target_link_libraries(plain_homology ${TBB_LIBRARIES}) +endif() +add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $<TARGET_FILE:plain_homology>) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) - -add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) -target_link_libraries(rips_persistence_step_by_step Boost::program_options) - -add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp) -target_link_libraries(rips_persistence_via_boundary_matrix Boost::program_options) - -add_executable(persistence_from_file persistence_from_file.cpp) -target_link_libraries(persistence_from_file Boost::program_options) - if (TBB_FOUND) - target_link_libraries(plain_homology ${TBB_LIBRARIES}) target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES}) - target_link_libraries(rips_persistence_step_by_step ${TBB_LIBRARIES}) - target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES}) - target_link_libraries(persistence_from_file ${TBB_LIBRARIES}) endif() - -add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $<TARGET_FILE:plain_homology>) add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $<TARGET_FILE:persistence_from_simple_simplex_tree> "1" "0") -add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence_step_by_step> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") -add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $<TARGET_FILE:rips_persistence_via_boundary_matrix> - "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") -add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $<TARGET_FILE:persistence_from_file> - "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0") -add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $<TARGET_FILE:persistence_from_file> - "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") -install(TARGETS plain_homology DESTINATION bin) -install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin) -install(TARGETS rips_persistence_step_by_step DESTINATION bin) -install(TARGETS rips_persistence_via_boundary_matrix DESTINATION bin) -install(TARGETS persistence_from_file DESTINATION bin) +if(TARGET Boost::program_options) + add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) + target_link_libraries(rips_persistence_step_by_step Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_persistence_step_by_step ${TBB_LIBRARIES}) + endif() + add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence_step_by_step> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") +endif() + +if(TARGET Boost::program_options) + add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp) + target_link_libraries(rips_persistence_via_boundary_matrix Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES}) + endif() + add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $<TARGET_FILE:rips_persistence_via_boundary_matrix> + "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") +endif() + +if(TARGET Boost::program_options) + add_executable(persistence_from_file persistence_from_file.cpp) + target_link_libraries(persistence_from_file Boost::program_options) + if (TBB_FOUND) + target_link_libraries(persistence_from_file ${TBB_LIBRARIES}) + endif() + add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $<TARGET_FILE:persistence_from_file> + "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0") + add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $<TARGET_FILE:persistence_from_file> + "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") +endif() if(GMP_FOUND) - if(GMPXX_FOUND) + if(GMPXX_FOUND) + if(TARGET Boost::program_options) add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) target_link_libraries(rips_multifield_persistence Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) @@ -49,20 +56,15 @@ if(GMP_FOUND) endif(TBB_FOUND) add_test(NAME Persistent_cohomology_example_multifield_2_71 COMMAND $<TARGET_FILE:rips_multifield_persistence> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "2" "-q" "71") - install(TARGETS rips_multifield_persistence DESTINATION bin) - endif(GMPXX_FOUND) + endif() + endif(GMPXX_FOUND) endif(GMP_FOUND) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - add_executable(custom_persistence_sort custom_persistence_sort.cpp) target_link_libraries(custom_persistence_sort ${CGAL_LIBRARY}) - if (TBB_FOUND) target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(NAME Persistent_cohomology_example_custom_persistence_sort COMMAND $<TARGET_FILE:custom_persistence_sort>) - - install(TARGETS custom_persistence_sort DESTINATION bin) - endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index 244a93ec..206f4c11 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -72,8 +72,3 @@ if (DIFF_PATH) endif() -install(TARGETS Rips_complex_example_from_off DESTINATION bin) -install(TARGETS Rips_complex_example_one_skeleton_from_points DESTINATION bin) -install(TARGETS Rips_complex_example_one_skeleton_from_distance_matrix DESTINATION bin) -install(TARGETS Rips_complex_example_from_csv_distance_matrix DESTINATION bin) -install(TARGETS Rips_complex_example_one_skeleton_rips_from_correlation_matrix DESTINATION bin) diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt index d2448d7b..d8c8e0b8 100644 --- a/src/Rips_complex/utilities/CMakeLists.txt +++ b/src/Rips_complex/utilities/CMakeLists.txt @@ -1,34 +1,45 @@ project(Rips_complex_utilities) -add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) -target_link_libraries(rips_distance_matrix_persistence Boost::program_options) - -add_executable(rips_persistence rips_persistence.cpp) -target_link_libraries(rips_persistence Boost::program_options) - -add_executable(rips_correlation_matrix_persistence rips_correlation_matrix_persistence.cpp) -target_link_libraries(rips_correlation_matrix_persistence Boost::system Boost::program_options) - -add_executable(sparse_rips_persistence sparse_rips_persistence.cpp) -target_link_libraries(sparse_rips_persistence Boost::program_options) +if(TARGET Boost::program_options) + add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) + target_link_libraries(rips_distance_matrix_persistence Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence> + "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") + install(TARGETS rips_distance_matrix_persistence DESTINATION bin) +endif() -if (TBB_FOUND) - target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) - target_link_libraries(rips_persistence ${TBB_LIBRARIES}) - target_link_libraries(rips_correlation_matrix_persistence ${TBB_LIBRARIES}) - target_link_libraries(sparse_rips_persistence ${TBB_LIBRARIES}) +if(TARGET Boost::program_options) + add_executable(rips_persistence rips_persistence.cpp) + target_link_libraries(rips_persistence Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Rips_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") + install(TARGETS rips_persistence DESTINATION bin) endif() -add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence> - "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") -add_test(NAME Rips_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") -add_test(NAME Rips_complex_utility_from_rips_correlation_matrix COMMAND $<TARGET_FILE:rips_correlation_matrix_persistence> - "${CMAKE_SOURCE_DIR}/data/correlation_matrix/lower_triangular_correlation_matrix.csv" "-c" "0.3" "-d" "3" "-p" "3" "-m" "0") -add_test(NAME Sparse_rips_complex_utility_on_tore_3D COMMAND $<TARGET_FILE:sparse_rips_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-e" "0.5" "-m" "0.2" "-d" "3" "-p" "2") +if(TARGET Boost::program_options) + add_executable(rips_correlation_matrix_persistence rips_correlation_matrix_persistence.cpp) + target_link_libraries(rips_correlation_matrix_persistence Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_correlation_matrix_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Rips_complex_utility_from_rips_correlation_matrix COMMAND $<TARGET_FILE:rips_correlation_matrix_persistence> + "${CMAKE_SOURCE_DIR}/data/correlation_matrix/lower_triangular_correlation_matrix.csv" "-c" "0.3" "-d" "3" "-p" "3" "-m" "0") + install(TARGETS rips_correlation_matrix_persistence DESTINATION bin) +endif() -install(TARGETS rips_distance_matrix_persistence DESTINATION bin) -install(TARGETS rips_persistence DESTINATION bin) -install(TARGETS rips_correlation_matrix_persistence DESTINATION bin) -install(TARGETS sparse_rips_persistence DESTINATION bin) +if(TARGET Boost::program_options) + add_executable(sparse_rips_persistence sparse_rips_persistence.cpp) + target_link_libraries(sparse_rips_persistence Boost::program_options) + if (TBB_FOUND) + target_link_libraries(sparse_rips_persistence ${TBB_LIBRARIES}) + endif() + add_test(NAME Sparse_rips_complex_utility_on_tore_3D COMMAND $<TARGET_FILE:sparse_rips_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-e" "0.5" "-m" "0.2" "-d" "3" "-p" "2") + install(TARGETS sparse_rips_persistence DESTINATION bin) +endif() diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index a0aabee2..73b2c6f9 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -34,13 +34,15 @@ if(GMP_FOUND AND NOT CGAL_VERSION VERSION_LESS 4.11.0) endif() if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - add_executable ( Simplex_tree_example_cech_complex_cgal_mini_sphere_3d cech_complex_cgal_mini_sphere_3d.cpp ) - target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d Boost::program_options ${CGAL_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${TBB_LIBRARIES}) + if(TARGET Boost::program_options) + add_executable ( Simplex_tree_example_cech_complex_cgal_mini_sphere_3d cech_complex_cgal_mini_sphere_3d.cpp ) + target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d Boost::program_options ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${TBB_LIBRARIES}) + endif() + add_test(NAME Simplex_tree_example_cech_complex_cgal_mini_sphere_3d COMMAND $<TARGET_FILE:Simplex_tree_example_cech_complex_cgal_mini_sphere_3d> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" -r 0.3 -d 3) endif() - add_test(NAME Simplex_tree_example_cech_complex_cgal_mini_sphere_3d COMMAND $<TARGET_FILE:Simplex_tree_example_cech_complex_cgal_mini_sphere_3d> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" -r 0.3 -d 3) endif () add_executable ( Simplex_tree_example_graph_expansion_with_blocker graph_expansion_with_blocker.cpp ) diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 889dbd00..85d6c3b0 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1667,6 +1667,37 @@ class Simplex_tree { return sh; // None of its faces has the same filtration. } + public: + /** \brief This function resets the filtration value of all the simplices of dimension at least min_dim. Resets all + * the Simplex_tree when `min_dim = 0`. + * `reset_filtration` may break the filtration property with `min_dim > 0`, and it is the user's responsibility to + * make it a valid filtration (using a large enough `filt_value`, or calling `make_filtration_non_decreasing` + * afterwards for instance). + * @param[in] filt_value The new filtration value. + * @param[in] min_dim The minimal dimension. Default value is 0. + */ + void reset_filtration(Filtration_value filt_value, int min_dim = 0) { + rec_reset_filtration(&root_, filt_value, min_dim); + clear_filtration(); // Drop the cache. + } + + private: + /** \brief Recursively resets filtration value when minimal depth <= 0. + * @param[in] sib Siblings to be parsed. + * @param[in] filt_value The new filtration value. + * @param[in] min_depth The minimal depth. + */ + void rec_reset_filtration(Siblings * sib, Filtration_value filt_value, int min_depth) { + for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) { + if (min_depth <= 0) { + sh->second.assign_filtration(filt_value); + } + if (has_children(sh)) { + rec_reset_filtration(sh->second.children(), filt_value, min_depth - 1); + } + } + } + private: Vertex_handle null_vertex_; /** \brief Total number of simplices in the complex, without the empty simplex.*/ diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h index 9007b6bd..ee64a277 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h @@ -85,6 +85,12 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< typedef typename SimplexTree::Vertex_handle Vertex_handle; typedef typename SimplexTree::Siblings Siblings; + // For cython purpose only. The object it initializes should be overwritten ASAP and never used before it is overwritten. + Simplex_tree_boundary_simplex_iterator() + : sib_(nullptr), + st_(nullptr) { + } + // any end() iterator explicit Simplex_tree_boundary_simplex_iterator(SimplexTree * st) : last_(st->null_vertex()), diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index 9b5fa8fe..bdd41d34 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -940,3 +940,54 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(generators, typeST, list_of_tested_variants) { BOOST_CHECK(st.edge_with_same_filtration(st.find({1,5}))==st.find({1,5})); } } + +BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_reset_filtration, typeST, list_of_tested_variants) { + std::clog << "********************************************************************" << std::endl; + std::clog << "TEST RESET FILTRATION" << std::endl; + typeST st; + + st.insert_simplex_and_subfaces({2, 1, 0}, 3.); + st.insert_simplex_and_subfaces({3, 0}, 2.); + st.insert_simplex_and_subfaces({3, 4, 5}, 3.); + st.insert_simplex_and_subfaces({0, 1, 6, 7}, 4.); + + /* Inserted simplex: */ + /* 1 6 */ + /* o---o */ + /* /X\7/ */ + /* o---o---o---o */ + /* 2 0 3\X/4 */ + /* o */ + /* 5 */ + + for (auto f_simplex : st.skeleton_simplex_range(3)) { + std::clog << "vertex = ("; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::clog << vertex << ","; + } + std::clog << ") - filtration = " << st.filtration(f_simplex); + std::clog << " - dimension = " << st.dimension(f_simplex) << std::endl; + // Guaranteed by construction + BOOST_CHECK(st.filtration(f_simplex) >= 2.); + } + + // dimension until 5 even if simplex tree is of dimension 3 to test the limits + for(int dimension = 5; dimension >= 0; dimension --) { + std::clog << "### reset_filtration - dimension = " << dimension << "\n"; + st.reset_filtration(0., dimension); + for (auto f_simplex : st.skeleton_simplex_range(3)) { + std::clog << "vertex = ("; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::clog << vertex << ","; + } + std::clog << ") - filtration = " << st.filtration(f_simplex); + std::clog << " - dimension = " << st.dimension(f_simplex) << std::endl; + if (st.dimension(f_simplex) < dimension) + BOOST_CHECK(st.filtration(f_simplex) >= 2.); + else + BOOST_CHECK(st.filtration(f_simplex) == 0.); + } + } + +} + diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt index 0e5d2f11..456612df 100644 --- a/src/Skeleton_blocker/example/CMakeLists.txt +++ b/src/Skeleton_blocker/example/CMakeLists.txt @@ -7,7 +7,3 @@ add_executable(Skeleton_blocker_example_link Skeleton_blocker_link.cpp) add_test(NAME Skeleton_blocker_example_from_simplices COMMAND $<TARGET_FILE:Skeleton_blocker_example_from_simplices>) add_test(NAME Skeleton_blocker_example_iteration COMMAND $<TARGET_FILE:Skeleton_blocker_example_iteration>) add_test(NAME Skeleton_blocker_example_link COMMAND $<TARGET_FILE:Skeleton_blocker_example_link>) - -install(TARGETS Skeleton_blocker_example_from_simplices DESTINATION bin) -install(TARGETS Skeleton_blocker_example_iteration DESTINATION bin) -install(TARGETS Skeleton_blocker_example_link DESTINATION bin) diff --git a/src/Spatial_searching/example/CMakeLists.txt b/src/Spatial_searching/example/CMakeLists.txt index eeb3e85f..308afa00 100644 --- a/src/Spatial_searching/example/CMakeLists.txt +++ b/src/Spatial_searching/example/CMakeLists.txt @@ -5,5 +5,4 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) target_link_libraries(Spatial_searching_example_spatial_searching ${CGAL_LIBRARY}) add_test(NAME Spatial_searching_example_spatial_searching COMMAND $<TARGET_FILE:Spatial_searching_example_spatial_searching>) - install(TARGETS Spatial_searching_example_spatial_searching DESTINATION bin) endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt index 28aab103..dfac055c 100644 --- a/src/Subsampling/example/CMakeLists.txt +++ b/src/Subsampling/example/CMakeLists.txt @@ -14,9 +14,4 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Subsampling_example_sparsify_point_set COMMAND $<TARGET_FILE:Subsampling_example_sparsify_point_set>) - install(TARGETS Subsampling_example_pick_n_random_points DESTINATION bin) - install(TARGETS Subsampling_example_choose_n_farthest_points DESTINATION bin) - install(TARGETS Subsampling_example_custom_kernel DESTINATION bin) - install(TARGETS Subsampling_example_sparsify_point_set DESTINATION bin) - endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h index 66421a69..b70af8a0 100644 --- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h +++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h @@ -48,7 +48,8 @@ enum : std::size_t { * \tparam PointOutputIterator Output iterator whose value type is Kernel::Point_d. * \tparam DistanceOutputIterator Output iterator for distances. * \details It chooses `final_size` points from a random access range - * `input_pts` and outputs them in the output iterator `output_it`. It also + * `input_pts` (or the number of distinct points if `final_size` is larger) + * and outputs them in the output iterator `output_it`. It also * outputs the distance from each of those points to the set of previous * points in `dist_it`. * @param[in] k A kernel object. @@ -99,7 +100,7 @@ void choose_n_farthest_points(Kernel const &k, *dist_it++ = dist_to_L[curr_max_w]; std::size_t i = 0; for (auto&& p : input_pts) { - double curr_dist = sqdist(p, *(std::begin(input_pts) + curr_max_w)); + double curr_dist = sqdist(p, input_pts[curr_max_w]); if (curr_dist < dist_to_L[i]) dist_to_L[i] = curr_dist; ++i; @@ -111,6 +112,8 @@ void choose_n_farthest_points(Kernel const &k, curr_max_dist = dist_to_L[i]; curr_max_w = i; } + // If all that remains are duplicates of points already taken, stop. + if (curr_max_dist == 0) break; } } diff --git a/src/Subsampling/test/test_choose_n_farthest_points.cpp b/src/Subsampling/test/test_choose_n_farthest_points.cpp index 5c4bd4cb..b318d58e 100644 --- a/src/Subsampling/test/test_choose_n_farthest_points.cpp +++ b/src/Subsampling/test/test_choose_n_farthest_points.cpp @@ -39,7 +39,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point, Kernel, list_of_tested for (FT k = 0; k < 5; k += 1.0) for (FT l = 0; l < 5; l += 1.0) { std::vector<FT> point({i, j, k, l}); - points.push_back(Point_d(point.begin(), point.end())); + points.emplace_back(point.begin(), point.end()); } landmarks.clear(); @@ -75,7 +75,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point_limits, Kernel, list_of landmarks.clear(); distances.clear(); std::vector<FT> point({0.0, 0.0, 0.0, 0.0}); - points.push_back(Point_d(point.begin(), point.end())); + points.emplace_back(point.begin(), point.end()); // Choose -1 farthest points in a one point cloud Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 1 && distances.size() == 1); @@ -92,8 +92,16 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point_limits, Kernel, list_of landmarks.clear(); distances.clear(); std::vector<FT> point2({1.0, 0.0, 0.0, 0.0}); - points.push_back(Point_d(point2.begin(), point2.end())); - // Choose all farthest points in a one point cloud + points.emplace_back(point2.begin(), point2.end()); + // Choose all farthest points among 2 points + Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); + BOOST_CHECK(landmarks.size() == 2 && distances.size() == 2); + BOOST_CHECK(distances[0] == std::numeric_limits<FT>::infinity()); + BOOST_CHECK(distances[1] == 1); + landmarks.clear(); distances.clear(); + + // Ignore duplicated points + points.emplace_back(point.begin(), point.end()); Gudhi::subsampling::choose_n_farthest_points(k, points, -1, -1, std::back_inserter(landmarks), std::back_inserter(distances)); BOOST_CHECK(landmarks.size() == 2 && distances.size() == 2); BOOST_CHECK(distances[0] == std::numeric_limits<FT>::infinity()); diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index cb1486a4..b66b5f39 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -15,6 +15,4 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Tangential_complex_example_with_perturb COMMAND $<TARGET_FILE:Tangential_complex_example_with_perturb>) - install(TARGETS Tangential_complex_example_basic DESTINATION bin) - install(TARGETS Tangential_complex_example_with_perturb DESTINATION bin) endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index 2659798e..5e9736ed 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -7,8 +7,6 @@ endif() add_test(NAME Witness_complex_example_nearest_landmark_table COMMAND $<TARGET_FILE:Witness_complex_example_nearest_landmark_table>) -install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin) - # CGAL and Eigen3 are required for Euclidean version of Witness if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) @@ -33,10 +31,5 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Witness_complex_example_strong_off_test_torus COMMAND $<TARGET_FILE:Witness_complex_example_strong_off> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") - - install(TARGETS Witness_complex_example_off DESTINATION bin) - install(TARGETS Witness_complex_example_sphere DESTINATION bin) - install(TARGETS Witness_complex_example_strong_off DESTINATION bin) - endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt index d986d2d1..60fea0b4 100644 --- a/src/Witness_complex/utilities/CMakeLists.txt +++ b/src/Witness_complex/utilities/CMakeLists.txt @@ -2,26 +2,26 @@ project(Witness_complex_utilities) # CGAL and Eigen3 are required for Euclidean version of Witness if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - - add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp ) - target_link_libraries(Witness_complex_strong_witness_persistence Boost::program_options) + if(TARGET Boost::program_options) + add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp ) + target_link_libraries(Witness_complex_strong_witness_persistence Boost::program_options) - add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp ) - target_link_libraries(Witness_complex_weak_witness_persistence Boost::program_options) + add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp ) + target_link_libraries(Witness_complex_weak_witness_persistence Boost::program_options) - if (TBB_FOUND) - target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES}) - target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES}) - endif() - - add_test(NAME Witness_complex_strong_test_torus_persistence - COMMAND $<TARGET_FILE:Witness_complex_strong_witness_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") - add_test(NAME Witness_complex_weak_test_torus_persistence - COMMAND $<TARGET_FILE:Witness_complex_weak_witness_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + if (TBB_FOUND) + target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES}) + target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES}) + endif() - install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin) - install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin) + add_test(NAME Witness_complex_strong_test_torus_persistence + COMMAND $<TARGET_FILE:Witness_complex_strong_witness_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + add_test(NAME Witness_complex_weak_test_torus_persistence + COMMAND $<TARGET_FILE:Witness_complex_weak_witness_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin) + endif() endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/cmake/modules/GUDHI_modules.cmake b/src/cmake/modules/GUDHI_modules.cmake index aab1dd08..ccaf1ac5 100644 --- a/src/cmake/modules/GUDHI_modules.cmake +++ b/src/cmake/modules/GUDHI_modules.cmake @@ -30,7 +30,12 @@ if (WITH_GUDHI_EXAMPLE) set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};example") endif() if (WITH_GUDHI_TEST) - set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};test") + # All tests are using boost tests + if(TARGET Boost::unit_test_framework) + set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};test") + else() + message("++ WITH_GUDHI_TEST but no TARGET Boost::unit_test_framework") + endif() endif() if (WITH_GUDHI_UTILITIES) set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};utilities") diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index a56a2756..9dadac4f 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -1,42 +1,11 @@ # This files manage third party libraries required by GUDHI -find_package(Boost 1.56.0 REQUIRED COMPONENTS system filesystem unit_test_framework program_options thread) +find_package(Boost 1.56.0 QUIET OPTIONAL_COMPONENTS filesystem unit_test_framework program_options) -if(NOT Boost_FOUND) +# Boost_FOUND is not reliable +if(NOT Boost_VERSION) message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.") -endif(NOT Boost_FOUND) - -# cf. https://cliutils.gitlab.io/modern-cmake/chapters/packages/Boost.html -# This is needed if your Boost version is newer than your CMake version -# or if you have an old version of CMake (<3.5) -if(NOT TARGET Boost::program_options) - add_library(Boost::program_options IMPORTED INTERFACE) - set_property(TARGET Boost::program_options PROPERTY - INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) - set_property(TARGET Boost::program_options PROPERTY - INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) -endif() -if(NOT TARGET Boost::filesystem) - add_library(Boost::filesystem IMPORTED INTERFACE) - set_property(TARGET Boost::filesystem PROPERTY - INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) - set_property(TARGET Boost::filesystem PROPERTY - INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) -endif() -if(NOT TARGET Boost::unit_test_framework) - add_library(Boost::unit_test_framework IMPORTED INTERFACE) - set_property(TARGET Boost::unit_test_framework PROPERTY - INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) - set_property(TARGET Boost::unit_test_framework PROPERTY - INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) -endif() -if(NOT TARGET Boost::system) - add_library(Boost::system IMPORTED INTERFACE) - set_property(TARGET Boost::system PROPERTY - INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) - set_property(TARGET Boost::system PROPERTY - INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) -endif() +endif(NOT Boost_VERSION) find_package(GMP) if(GMP_FOUND) @@ -186,6 +155,7 @@ if( PYTHONINTERP_FOUND ) find_python_module("pykeops") find_python_module("eagerpy") find_python_module_no_version("hnswlib") + find_python_module("tensorflow") endif() if(NOT GUDHI_PYTHON_PATH) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index ce2c5448..9df1c2f0 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -6,7 +6,7 @@ * * \section compiling Compiling * The library uses c++14 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> ≥ 1.56.0 - * and <a target="_blank" href="https://www.cmake.org/">CMake</a> ≥ 3.1. + * and <a target="_blank" href="https://www.cmake.org/">CMake</a> ≥ 3.5. * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. * * \subsection utilities Utilities and examples @@ -14,13 +14,13 @@ \verbatim cd /path-to-gudhi/ mkdir build cd build/ -cmake .. +cmake -DCMAKE_BUILD_TYPE=Release .. make \endverbatim * By default, examples are disabled. You can activate their compilation with - * <a href="https://cmake.org/cmake/help/v3.0/manual/ccmake.1.html">ccmake</a> (on Linux and Mac OSX), - * <a href="https://cmake.org/cmake/help/v3.0/manual/cmake-gui.1.html">cmake-gui</a> (on Windows) or by modifying the + * <a href="https://cmake.org/cmake/help/latest/manual/ccmake.1.html">ccmake</a> (on Linux and Mac OSX), + * <a href="https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html">cmake-gui</a> (on Windows) or by modifying the * cmake command as follows : -\verbatim cmake -DWITH_GUDHI_EXAMPLE=ON .. +\verbatim cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=ON .. make \endverbatim * A list of utilities and examples is available <a href="examples.html">here</a>. * @@ -28,7 +28,7 @@ make \endverbatim * To install the library (headers and activated utilities), run the following command in a terminal: * \verbatim make install \endverbatim * This action may require to be in the sudoer or administrator of the machine in function of the operating system and - * of <a href="https://cmake.org/cmake/help/v3.0/variable/CMAKE_INSTALL_PREFIX.html">CMAKE_INSTALL_PREFIX</a>. + * of <a href="https://cmake.org/cmake/help/latest/variable/CMAKE_INSTALL_PREFIX.html">CMAKE_INSTALL_PREFIX</a>. * * \subsection testsuites Test suites * To test your build, run the following command in a terminal: @@ -66,9 +66,9 @@ make doxygen * Some GUDHI modules (cf. \ref main_page "modules list"), and few examples require CGAL, a C++ library that provides * easy access to efficient and reliable geometric algorithms. * - * \note There is no need to install CGAL, you can just <CODE>cmake . && make</CODE> CGAL (or even - * <CODE>cmake -DCGAL_HEADER_ONLY=ON .</CODE>), thereafter you will be able to compile - * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE> + * \note There is no need to install CGAL, you can just <CODE>cmake -DCMAKE_BUILD_TYPE=Release . && make</CODE> CGAL + * (or even <CODE>cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_HEADER_ONLY=ON .</CODE>), thereafter you will be able to + * compile GUDHI by calling <CODE>cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE> * * The procedure to install this library according to * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 4f26481e..56b6876c 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -103,6 +103,9 @@ if(PYTHONINTERP_FOUND) if(EAGERPY_FOUND) add_gudhi_debug_info("EagerPy version ${EAGERPY_VERSION}") endif() + if(TENSORFLOW_FOUND) + add_gudhi_debug_info("TensorFlow version ${TENSORFLOW_VERSION}") + endif() set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ") set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") @@ -342,29 +345,27 @@ 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 - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" - --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) - - add_gudhi_py_test(test_tangential_complex) - - # Witness complex AND Subsampling - add_test(NAME euclidean_strong_witness_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/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) - - add_test(NAME euclidean_witness_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/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) - endif() + # Tangential + add_test(NAME tangential_complex_plain_homology_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/tangential_complex_plain_homology_from_off_file_example.py" + --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) + + add_gudhi_py_test(test_tangential_complex) + + # Witness complex + add_test(NAME euclidean_strong_witness_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/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) + + add_test(NAME euclidean_witness_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/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) # Subsampling add_gudhi_py_test(test_subsampling) @@ -419,13 +420,11 @@ 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} - 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_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) add_gudhi_py_test(test_alpha_complex) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) @@ -442,30 +441,26 @@ if(PYTHONINTERP_FOUND) ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) - if(NUMPY_FOUND) - add_test(NAME random_cubical_complex_persistence_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/random_cubical_complex_persistence_example.py" - 10 10 10) - endif() + add_test(NAME random_cubical_complex_persistence_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/random_cubical_complex_persistence_example.py" + 10 10 10) add_gudhi_py_test(test_cubical_complex) # Rips - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_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/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) + add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_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/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) - add_test(NAME rips_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/rips_complex_diagram_persistence_from_off_file_example.py - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) - endif() + add_test(NAME rips_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/rips_complex_diagram_persistence_from_off_file_example.py + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) add_test(NAME rips_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} @@ -496,11 +491,17 @@ if(PYTHONINTERP_FOUND) # Wasserstein if(OT_FOUND AND PYBIND11_FOUND) - if(TORCH_FOUND AND EAGERPY_FOUND) + # EagerPy dependency because of enable_autodiff=True + if(EAGERPY_FOUND) add_gudhi_py_test(test_wasserstein_distance) endif() add_gudhi_py_test(test_wasserstein_barycenter) endif() + if(OT_FOUND) + if(TORCH_FOUND AND TENSORFLOW_FOUND AND EAGERPY_FOUND) + add_gudhi_py_test(test_wasserstein_with_tensors) + endif() + endif() # Representations if(SKLEARN_FOUND AND MATPLOTLIB_FOUND) diff --git a/src/python/doc/bottleneck_distance_user.rst b/src/python/doc/bottleneck_distance_user.rst index 6c6e08d9..7baa76cc 100644 --- a/src/python/doc/bottleneck_distance_user.rst +++ b/src/python/doc/bottleneck_distance_user.rst @@ -47,7 +47,7 @@ The following example explains how the distance is computed: :figclass: align-center The point (0, 13) is at distance 6.5 from the diagonal and more - specifically from the point (6.5, 6.5) + specifically from the point (6.5, 6.5). Basic example @@ -72,6 +72,6 @@ The output is: .. testoutput:: - Bottleneck distance approximation = 0.81 + Bottleneck distance approximation = 0.72 Bottleneck distance value = 0.75 diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 78e1af73..66efe45a 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -40,7 +40,7 @@ different, and in particular the `python/` subdirectory is actually `src/python/ there. The library uses c++14 and requires `Boost <https://www.boost.org/>`_ :math:`\geq` 1.56.0, -`CMake <https://www.cmake.org/>`_ :math:`\geq` 3.1 to generate makefiles, +`CMake <https://www.cmake.org/>`_ :math:`\geq` 3.5 to generate makefiles, `NumPy <http://numpy.org>`_, `Cython <https://www.cython.org/>`_ and `pybind11 <https://github.com/pybind/pybind11>`_ to compile the GUDHI Python module. @@ -65,7 +65,7 @@ one can build the GUDHI Python module, by running the following commands in a te cd /path-to-gudhi/ mkdir build cd build/ - cmake .. + cmake -DCMAKE_BUILD_TYPE=Release .. cd python make @@ -394,6 +394,11 @@ mathematics, science, and engineering. :class:`~gudhi.point_cloud.knn.KNearestNeighbors` can use the Python package `SciPy <http://scipy.org>`_ as a backend if explicitly requested. +TensorFlow +---------- + +`TensorFlow <https://www.tensorflow.org>`_ is currently only used in some automatic differentiation tests. + Bug reports and contributions ***************************** diff --git a/src/python/doc/rips_complex_sum.inc b/src/python/doc/rips_complex_sum.inc index c123ea2a..2cb24990 100644 --- a/src/python/doc/rips_complex_sum.inc +++ b/src/python/doc/rips_complex_sum.inc @@ -1,14 +1,14 @@ .. table:: :widths: 30 40 30 - +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------+ - | .. figure:: | The Vietoris-Rips complex is a simplicial complex built as the | :Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse | - | ../../doc/Rips_complex/rips_complex_representation.png | clique-complex of a proximity graph. | | - | :figclass: align-center | | :Since: GUDHI 2.0.0 | - | | We also provide sparse approximations, to speed-up the computation | | - | | of persistent homology, and weighted versions, which are more robust | :License: MIT | - | | to outliers. | | - | | | | - +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------+ - | * :doc:`rips_complex_user` | * :doc:`rips_complex_ref` | - +----------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------+ + +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------------------+ + | .. figure:: | The Vietoris-Rips complex is a simplicial complex built as the | :Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse, Yuichi Ike | + | ../../doc/Rips_complex/rips_complex_representation.png | clique-complex of a proximity graph. | | + | :figclass: align-center | | :Since: GUDHI 2.0.0 | + | | We also provide sparse approximations, to speed-up the computation | | + | | of persistent homology, and weighted versions, which are more robust | :License: MIT | + | | to outliers. | | + | | | | + +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------------------+ + | * :doc:`rips_complex_user` | * :doc:`rips_complex_ref` | + +----------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/python/doc/rips_complex_user.rst b/src/python/doc/rips_complex_user.rst index 6048cc4e..27d218d4 100644 --- a/src/python/doc/rips_complex_user.rst +++ b/src/python/doc/rips_complex_user.rst @@ -7,9 +7,9 @@ Rips complex user manual Definition ---------- -==================================================================== ================================ ====================== -:Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse :Since: GUDHI 2.0.0 :License: GPL v3 -==================================================================== ================================ ====================== +================================================================================ ================================ ====================== +:Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse, Yuichi Ike :Since: GUDHI 2.0.0 :License: GPL v3 +================================================================================ ================================ ====================== +-------------------------------------------+----------------------------------------------------------------------+ | :doc:`rips_complex_user` | :doc:`rips_complex_ref` | diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py index 727af4fa..1e0273b3 100755 --- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -65,6 +64,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index e1e572df..4e97cfe3 100755 --- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -82,6 +81,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index 58cb2bb5..29076c74 100755 --- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -79,6 +78,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index 499171df..ee3290c6 100755 --- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse -import matplotlib.pyplot as plot import errno import os import gudhi @@ -75,6 +74,7 @@ if is_file_perseus(args.file): print("betti_numbers()=") print(periodic_cubical_complex.betti_numbers()) if args.no_barcode == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_barcode(diag) plot.show() else: diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index 1acb187c..ea2eb7e1 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -2,7 +2,6 @@ import sys import argparse -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -84,5 +83,6 @@ invert_diag = [ ] if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(invert_diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 79ccca96..236d085d 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -60,5 +59,6 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py index 6f992508..e80233a9 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -70,6 +69,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py index 85bade4a..a4b4e9f5 100755 --- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -62,6 +61,7 @@ with open(args.file, "r") as f: print(st.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/gudhi/representations/vector_methods.py b/src/python/gudhi/representations/vector_methods.py index 5ca127f6..cdcb1fde 100644 --- a/src/python/gudhi/representations/vector_methods.py +++ b/src/python/gudhi/representations/vector_methods.py @@ -323,22 +323,15 @@ class BettiCurve(BaseEstimator, TransformerMixin): Returns: numpy array with shape (number of diagrams) x (**resolution**): output Betti curves. """ - num_diag, Xfit = len(X), [] + Xfit = [] x_values = np.linspace(self.sample_range[0], self.sample_range[1], self.resolution) step_x = x_values[1] - x_values[0] - for i in range(num_diag): - - diagram, num_pts_in_diag = X[i], X[i].shape[0] - + for diagram in X: + diagram_int = np.clip(np.ceil((diagram[:,:2] - self.sample_range[0]) / step_x), 0, self.resolution).astype(int) bc = np.zeros(self.resolution) - for j in range(num_pts_in_diag): - [px,py] = diagram[j,:2] - min_idx = np.clip(np.ceil((px - self.sample_range[0]) / step_x).astype(int), 0, self.resolution) - max_idx = np.clip(np.ceil((py - self.sample_range[0]) / step_x).astype(int), 0, self.resolution) - for k in range(min_idx, max_idx): - bc[k] += 1 - + for interval in diagram_int: + bc[interval[0]:interval[1]] += 1 Xfit.append(np.reshape(bc,[1,-1])) Xfit = np.concatenate(Xfit, 0) diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 75e94e0b..3c4cbed3 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -36,6 +36,12 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": Simplex_tree_skeleton_iterator operator++() nogil bint operator!=(Simplex_tree_skeleton_iterator) nogil + cdef cppclass Simplex_tree_boundary_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Boundary_simplex_iterator": + Simplex_tree_boundary_iterator() nogil + Simplex_tree_simplex_handle& operator*() nogil + Simplex_tree_boundary_iterator operator++() nogil + bint operator!=(Simplex_tree_boundary_iterator) nogil + cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>": Simplex_tree() nogil @@ -58,6 +64,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": void compute_extended_filtration() nogil vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(vector[pair[int, pair[double, double]]] dgm, double min_persistence) nogil Simplex_tree_interface_full_featured* collapse_edges(int nb_collapse_iteration) nogil + void reset_filtration(double filtration, int dimension) nogil # Iterators over Simplex tree pair[vector[int], double] get_simplex_and_filtration(Simplex_tree_simplex_handle f_simplex) nogil Simplex_tree_simplices_iterator get_simplices_iterator_begin() nogil @@ -66,6 +73,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_end() nogil Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension) nogil Simplex_tree_skeleton_iterator get_skeleton_iterator_end(int dimension) nogil + pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] get_boundary_iterators(vector[int] simplex) nogil except + cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>": diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 92645ffc..cdd2e87b 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -285,6 +285,22 @@ cdef class SimplexTree: ct.append((v, filtered_simplex.second)) return ct + def get_boundaries(self, simplex): + """This function returns a generator with the boundaries of a given N-simplex. + If you do not need the filtration values, the boundary can also be obtained as + :code:`itertools.combinations(simplex,len(simplex)-1)`. + + :param simplex: The N-simplex, represented by a list of vertex. + :type simplex: list of int. + :returns: The (simplices of the) boundary of a simplex + :rtype: generator with tuples(simplex, filtration) + """ + cdef pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] it = self.get_ptr().get_boundary_iterators(simplex) + + while it.first != it.second: + yield self.get_ptr().get_simplex_and_filtration(dereference(it.first)) + preincrement(it.first) + def remove_maximal_simplex(self, simplex): """This function removes a given maximal N-simplex from the simplicial complex. @@ -328,7 +344,7 @@ cdef class SimplexTree: return self.get_ptr().prune_above_filtration(filtration) def expansion(self, max_dim): - """Expands the Simplex_tree containing only its one skeleton + """Expands the simplex tree containing only its one skeleton until dimension max_dim. The expanded simplicial complex until dimension :math:`d` @@ -338,7 +354,7 @@ cdef class SimplexTree: The filtration value assigned to a simplex is the maximal filtration value of one of its edges. - The Simplex_tree must contain no simplex of dimension bigger than + The simplex tree must contain no simplex of dimension bigger than 1 when calling the method. :param max_dim: The maximal dimension. @@ -358,6 +374,20 @@ cdef class SimplexTree: """ return self.get_ptr().make_filtration_non_decreasing() + def reset_filtration(self, filtration, min_dim = 0): + """This function resets the filtration value of all the simplices of dimension at least min_dim. Resets all the + simplex tree when `min_dim = 0`. + `reset_filtration` may break the filtration property with `min_dim > 0`, and it is the user's responsibility to + make it a valid filtration (using a large enough `filt_value`, or calling `make_filtration_non_decreasing` + afterwards for instance). + + :param filtration: New threshold value. + :type filtration: float. + :param min_dim: The minimal dimension. Default value is 0. + :type min_dim: int. + """ + self.get_ptr().reset_filtration(filtration, min_dim) + def extend_filtration(self): """ Extend filtration for computing extended persistence. This function only uses the filtration values at the 0-dimensional simplices, and computes the extended persistence diagram induced by the lower-star filtration @@ -365,12 +395,12 @@ cdef class SimplexTree: .. note:: - Note that after calling this function, the filtration values are actually modified within the Simplex_tree. + Note that after calling this function, the filtration values are actually modified within the simplex tree. The function :func:`extended_persistence` retrieves the original values. .. note:: - Note that this code creates an extra vertex internally, so you should make sure that the Simplex_tree does + Note that this code creates an extra vertex internally, so you should make sure that the simplex tree does not contain a vertex with the largest possible value (i.e., 4294967295). This `notebook <https://github.com/GUDHI/TDA-tutorial/blob/master/Tuto-GUDHI-extended-persistence.ipynb>`_ diff --git a/src/python/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx index f77c6f75..b11d07e5 100644 --- a/src/python/gudhi/subsampling.pyx +++ b/src/python/gudhi/subsampling.pyx @@ -33,7 +33,7 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi The iteration starts with the landmark `starting point`. :param points: The input point set. - :type points: Iterable[Iterable[float]]. + :type points: Iterable[Iterable[float]] Or @@ -42,14 +42,15 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi And in both cases - :param nb_points: Number of points of the subsample. - :type nb_points: unsigned. + :param nb_points: Number of points of the subsample (the subsample may be \ + smaller if there are fewer than nb_points distinct input points) + :type nb_points: int :param starting_point: The iteration starts with the landmark `starting \ - point`,which is the index of the point to start with. If not set, this \ + point`, which is the index of the point to start with. If not set, this \ index is chosen randomly. - :type starting_point: unsigned. + :type starting_point: int :returns: The subsample point set. - :rtype: List[List[float]]. + :rtype: List[List[float]] """ if off_file: if os.path.isfile(off_file): @@ -76,7 +77,7 @@ def pick_n_random_points(points=None, off_file='', nb_points=0): """Subsample a point set by picking random vertices. :param points: The input point set. - :type points: Iterable[Iterable[float]]. + :type points: Iterable[Iterable[float]] Or @@ -86,7 +87,7 @@ def pick_n_random_points(points=None, off_file='', nb_points=0): And in both cases :param nb_points: Number of points of the subsample. - :type nb_points: unsigned. + :type nb_points: int :returns: The subsample point set. :rtype: List[List[float]] """ @@ -107,7 +108,7 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): between any two points is greater than or equal to min_squared_dist. :param points: The input point set. - :type points: Iterable[Iterable[float]]. + :type points: Iterable[Iterable[float]] Or @@ -118,7 +119,7 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): :param min_squared_dist: Minimum squared distance separating the output \ points. - :type min_squared_dist: float. + :type min_squared_dist: float :returns: The subsample point set. :rtype: List[List[float]] """ diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h index e288a8cf..baff3850 100644 --- a/src/python/include/Simplex_tree_interface.h +++ b/src/python/include/Simplex_tree_interface.h @@ -39,6 +39,7 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { using Skeleton_simplex_iterator = typename Base::Skeleton_simplex_iterator; using Complex_simplex_iterator = typename Base::Complex_simplex_iterator; using Extended_filtration_data = typename Base::Extended_filtration_data; + using Boundary_simplex_iterator = typename Base::Boundary_simplex_iterator; public: @@ -219,6 +220,15 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { // this specific case works because the range is just a pair of iterators - won't work if range was a vector return Base::skeleton_simplex_range(dimension).end(); } + + std::pair<Boundary_simplex_iterator, Boundary_simplex_iterator> get_boundary_iterators(const Simplex& simplex) { + auto bd_sh = Base::find(simplex); + if (bd_sh == Base::null_simplex()) + throw std::runtime_error("simplex not found - cannot find boundaries"); + // this specific case works because the range is just a pair of iterators - won't work if range was a vector + auto boundary_srange = Base::boundary_simplex_range(bd_sh); + return std::make_pair(boundary_srange.begin(), boundary_srange.end()); + } }; } // namespace Gudhi diff --git a/src/python/test/test_bottleneck_distance.py b/src/python/test/test_bottleneck_distance.py index 6915bea8..07fcc9cc 100755 --- a/src/python/test/test_bottleneck_distance.py +++ b/src/python/test/test_bottleneck_distance.py @@ -25,3 +25,15 @@ def test_basic_bottleneck(): assert gudhi.bottleneck_distance(diag1, diag2, 0.1) == pytest.approx(0.75, abs=0.1) assert gudhi.hera.bottleneck_distance(diag1, diag2, 0) == 0.75 assert gudhi.hera.bottleneck_distance(diag1, diag2, 0.1) == pytest.approx(0.75, rel=0.1) + + import numpy as np + + # Translating both diagrams along the diagonal should not affect the distance, + # checks that negative numbers are not an issue + diag1 = np.array(diag1) - 100 + diag2 = np.array(diag2) - 100 + + assert gudhi.bottleneck_distance(diag1, diag2) == 0.75 + assert gudhi.bottleneck_distance(diag1, diag2, 0.1) == pytest.approx(0.75, abs=0.1) + assert gudhi.hera.bottleneck_distance(diag1, diag2, 0) == 0.75 + assert gudhi.hera.bottleneck_distance(diag1, diag2, 0.1) == pytest.approx(0.75, rel=0.1) diff --git a/src/python/test/test_representations.py b/src/python/test/test_representations.py index e5c211a0..43c914f3 100755 --- a/src/python/test/test_representations.py +++ b/src/python/test/test_representations.py @@ -39,11 +39,11 @@ def test_multiple(): d2 = BottleneckDistance(epsilon=0.00001).fit_transform(l1) d3 = pairwise_persistence_diagram_distances(l1, l1b, e=0.00001, n_jobs=4) assert d1 == pytest.approx(d2) - assert d3 == pytest.approx(d2, abs=1e-5) # Because of 0 entries (on the diagonal) + assert d3 == pytest.approx(d2, abs=1e-5) # Because of 0 entries (on the diagonal) d1 = pairwise_persistence_diagram_distances(l1, l2, metric="wasserstein", order=2, internal_p=2) d2 = WassersteinDistance(order=2, internal_p=2, n_jobs=4).fit(l2).transform(l1) print(d1.shape, d2.shape) - assert d1 == pytest.approx(d2, rel=.02) + assert d1 == pytest.approx(d2, rel=0.02) def test_dummy_atol(): @@ -53,8 +53,22 @@ def test_dummy_atol(): for weighting_method in ["cloud", "iidproba"]: for contrast in ["gaussian", "laplacian", "indicator"]: - atol_vectoriser = Atol(quantiser=KMeans(n_clusters=1, random_state=202006), weighting_method=weighting_method, contrast=contrast) + atol_vectoriser = Atol( + quantiser=KMeans(n_clusters=1, random_state=202006), + weighting_method=weighting_method, + contrast=contrast, + ) atol_vectoriser.fit([a, b, c]) atol_vectoriser(a) atol_vectoriser.transform(X=[a, b, c]) + +from gudhi.representations.vector_methods import BettiCurve + + +def test_infinity(): + a = np.array([[1.0, 8.0], [2.0, np.inf], [3.0, 4.0]]) + c = BettiCurve(20, [0.0, 10.0])(a) + assert c[1] == 0 + assert c[7] == 3 + assert c[9] == 2 diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 83be0602..3b23fa0b 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -356,5 +356,46 @@ def test_collapse_edges(): st.collapse_edges() assert st.num_simplices() == 9 assert st.find([1, 3]) == False - for simplex in st.get_skeleton(0): - assert simplex[1] == 1. + for simplex in st.get_skeleton(0): + assert simplex[1] == 1. + +def test_reset_filtration(): + st = SimplexTree() + + assert st.insert([0, 1, 2], 3.) == True + assert st.insert([0, 3], 2.) == True + assert st.insert([3, 4, 5], 3.) == True + assert st.insert([0, 1, 6, 7], 4.) == True + + # Guaranteed by construction + for simplex in st.get_simplices(): + assert st.filtration(simplex[0]) >= 2. + + # dimension until 5 even if simplex tree is of dimension 3 to test the limits + for dimension in range(5, -1, -1): + st.reset_filtration(0., dimension) + for simplex in st.get_skeleton(3): + print(simplex) + if len(simplex[0]) < (dimension) + 1: + assert st.filtration(simplex[0]) >= 2. + else: + assert st.filtration(simplex[0]) == 0. + +def test_boundaries_iterator(): + st = SimplexTree() + + assert st.insert([0, 1, 2, 3], filtration=1.0) == True + assert st.insert([1, 2, 3, 4], filtration=2.0) == True + + assert list(st.get_boundaries([1, 2, 3])) == [([1, 2], 1.0), ([1, 3], 1.0), ([2, 3], 1.0)] + assert list(st.get_boundaries([2, 3, 4])) == [([2, 3], 1.0), ([2, 4], 2.0), ([3, 4], 2.0)] + assert list(st.get_boundaries([2])) == [] + + with pytest.raises(RuntimeError): + list(st.get_boundaries([])) + + with pytest.raises(RuntimeError): + list(st.get_boundaries([0, 4])) # (0, 4) does not exist + + with pytest.raises(RuntimeError): + list(st.get_boundaries([6])) # (6) does not exist diff --git a/src/python/test/test_wasserstein_distance.py b/src/python/test/test_wasserstein_distance.py index 90d26809..e3b521d6 100755 --- a/src/python/test/test_wasserstein_distance.py +++ b/src/python/test/test_wasserstein_distance.py @@ -97,27 +97,3 @@ def test_wasserstein_distance_pot(): def test_wasserstein_distance_hera(): _basic_wasserstein(hera_wrap(delta=1e-12), 1e-12, test_matching=False) _basic_wasserstein(hera_wrap(delta=.1), .1, test_matching=False) - -def test_wasserstein_distance_grad(): - import torch - - diag1 = torch.tensor([[2.7, 3.7], [9.6, 14.0], [34.2, 34.974]], requires_grad=True) - diag2 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True) - diag3 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True) - assert diag1.grad is None and diag2.grad is None and diag3.grad is None - dist12 = pot(diag1, diag2, internal_p=2, order=2, enable_autodiff=True) - dist30 = pot(diag3, torch.tensor([]), internal_p=2, order=2, enable_autodiff=True) - dist12.backward() - dist30.backward() - assert not torch.isnan(diag1.grad).any() and not torch.isnan(diag2.grad).any() and not torch.isnan(diag3.grad).any() - diag4 = torch.tensor([[0., 10.]], requires_grad=True) - diag5 = torch.tensor([[1., 11.], [3., 4.]], requires_grad=True) - dist45 = pot(diag4, diag5, internal_p=1, order=1, enable_autodiff=True) - assert dist45 == 3. - dist45.backward() - assert np.array_equal(diag4.grad, [[-1., -1.]]) - assert np.array_equal(diag5.grad, [[1., 1.], [-1., 1.]]) - diag6 = torch.tensor([[5., 10.]], requires_grad=True) - pot(diag6, diag6, internal_p=2, order=2, enable_autodiff=True).backward() - # https://github.com/jonasrauber/eagerpy/issues/6 - # assert np.array_equal(diag6.grad, [[0., 0.]]) diff --git a/src/python/test/test_wasserstein_with_tensors.py b/src/python/test/test_wasserstein_with_tensors.py new file mode 100755 index 00000000..e3f1411a --- /dev/null +++ b/src/python/test/test_wasserstein_with_tensors.py @@ -0,0 +1,47 @@ +""" 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. + Author(s): Mathieu Carriere + + Copyright (C) 2020 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +from gudhi.wasserstein import wasserstein_distance as pot +import numpy as np +import torch +import tensorflow as tf + +def test_wasserstein_distance_grad(): + diag1 = torch.tensor([[2.7, 3.7], [9.6, 14.0], [34.2, 34.974]], requires_grad=True) + diag2 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True) + diag3 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True) + assert diag1.grad is None and diag2.grad is None and diag3.grad is None + dist12 = pot(diag1, diag2, internal_p=2, order=2, enable_autodiff=True) + dist30 = pot(diag3, torch.tensor([]), internal_p=2, order=2, enable_autodiff=True) + dist12.backward() + dist30.backward() + assert not torch.isnan(diag1.grad).any() and not torch.isnan(diag2.grad).any() and not torch.isnan(diag3.grad).any() + diag4 = torch.tensor([[0., 10.]], requires_grad=True) + diag5 = torch.tensor([[1., 11.], [3., 4.]], requires_grad=True) + dist45 = pot(diag4, diag5, internal_p=1, order=1, enable_autodiff=True) + assert dist45 == 3. + dist45.backward() + assert np.array_equal(diag4.grad, [[-1., -1.]]) + assert np.array_equal(diag5.grad, [[1., 1.], [-1., 1.]]) + diag6 = torch.tensor([[5., 10.]], requires_grad=True) + pot(diag6, diag6, internal_p=2, order=2, enable_autodiff=True).backward() + # https://github.com/jonasrauber/eagerpy/issues/6 + # assert np.array_equal(diag6.grad, [[0., 0.]]) + +def test_wasserstein_distance_grad_tensorflow(): + with tf.GradientTape() as tape: + diag4 = tf.convert_to_tensor(tf.Variable(initial_value=np.array([[0., 10.]]), trainable=True)) + diag5 = tf.convert_to_tensor(tf.Variable(initial_value=np.array([[1., 11.], [3., 4.]]), trainable=True)) + dist45 = pot(diag4, diag5, internal_p=1, order=1, enable_autodiff=True) + assert dist45 == 3. + + grads = tape.gradient(dist45, [diag4, diag5]) + assert np.array_equal(grads[0].values, [[-1., -1.]]) + assert np.array_equal(grads[1].values, [[1., 1.], [-1., 1.]])
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