diff options
| author | mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-06-27 01:03:45 +0000 |
|---|---|---|
| committer | mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-06-27 01:03:45 +0000 |
| commit | d221f79cfb7d84941d791835e52fa4a596269cc6 (patch) | |
| tree | cde0df00ef5e7ec21c6a9e123e5d35bd7f5968f3 | |
| parent | 0741c3eabbfece1c73ac76aa44adbe2904b6124d (diff) | |
| parent | 5645e9fcbe5730462b2befb8685d3bb6857279be (diff) | |
merged trunk
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/kernels@3644 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 2be9ba6b6a381e677081a751e7d8f8c1d79385b0
168 files changed, 5473 insertions, 612 deletions
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt index 5e71f7eb..6811d7e1 100644 --- a/CMakeGUDHIVersion.txt +++ b/CMakeGUDHIVersion.txt @@ -1,5 +1,5 @@ set (GUDHI_MAJOR_VERSION 2) -set (GUDHI_MINOR_VERSION 1) +set (GUDHI_MINOR_VERSION 2) set (GUDHI_PATCH_VERSION 0) set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION}) diff --git a/CMakeLists.txt b/CMakeLists.txt index b28dcbf2..54f56a25 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,35 +1,20 @@ -cmake_minimum_required(VERSION 2.6) +cmake_minimum_required(VERSION 3.1) + project(GUDHIdev) include(CMakeGUDHIVersion.txt) list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/") -enable_testing() - -# This variable is used by Cython CMakeLists.txt to know its path +# This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path set(GUDHI_CYTHON_PATH "src/cython") -# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH -include(GUDHI_third_party_libraries) - -if(MSVC) - # Turn off some VC++ warnings - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") -else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic") -endif() -if(CMAKE_BUILD_TYPE MATCHES Debug) - message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}") -else() - message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}") -endif() +# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH +include(GUDHI_third_party_libraries NO_POLICY_SCOPE) -if (DEBUG_TRACES) - # For programs to be more verbose - message(STATUS "DEBUG_TRACES are activated") - add_definitions(-DDEBUG_TRACES) -endif() +include(GUDHI_compilation_flags) +# Only for dev version +add_cxx_compiler_flag("-pedantic") # Add your new module in the list, order is not important include(GUDHI_modules) @@ -39,6 +24,7 @@ add_gudhi_module(Alpha_complex) add_gudhi_module(Bitmap_cubical_complex) add_gudhi_module(Bottleneck_distance) add_gudhi_module(Contraction) +add_gudhi_module(Cech_complex) add_gudhi_module(Hasse_complex) add_gudhi_module(Persistence_representations) add_gudhi_module(Persistent_cohomology) diff --git a/data/persistence_diagram/rips_on_tore3D_1307.pers b/data/persistence_diagram/rips_on_tore3D_1307.pers new file mode 100644 index 00000000..f1bd600b --- /dev/null +++ b/data/persistence_diagram/rips_on_tore3D_1307.pers @@ -0,0 +1,2044 @@ +2 0.138335 inf +1 0.104347 inf +1 0.0983494 inf +0 0 inf +0 0 0.122545 +0 0 0.121171 +0 0 0.120964 +0 0 0.12057 +0 0 0.12047 +0 0 0.120414 +0 0 0.119758 +0 0 0.119091 +0 0 0.118893 +0 0 0.118874 +0 0 0.118398 +0 0 0.118204 +0 0 0.118102 +0 0 0.118095 +0 0 0.117908 +0 0 0.117806 +0 0 0.117768 +0 0 0.117751 +0 0 0.117407 +0 0 0.117253 +0 0 0.116946 +0 0 0.116892 +0 0 0.116706 +0 0 0.116528 +0 0 0.116232 +0 0 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+1 0.0965111 0.0968328 +1 0.0997832 0.100102 +1 0.116346 0.11663 +1 0.125517 0.125757 +1 0.125432 0.125671 +1 0.111594 0.111803 +1 0.10228 0.102465 +1 0.110192 0.110371 +1 0.0993469 0.0995118 +1 0.104171 0.104324 +1 0.0807541 0.0808958 +1 0.10346 0.103585 +1 0.127331 0.127396 +1 0.0945151 0.0945558 +1 0.104771 0.104801 +1 0.103878 0.103908 +1 0.11169 0.111695 diff --git a/scripts/metagen.sh b/scripts/metagen.sh new file mode 100755 index 00000000..4483d24e --- /dev/null +++ b/scripts/metagen.sh @@ -0,0 +1,15 @@ +#!/bin/bash +sep="_" +for geom in "sphere" "klein" "torus" +do + for number in 10 100 1000 + do + for dim in {3..5} + do + echo "./off_file_from_shape_generator on $geom $geom$sep$number$sep$dim.off $number $dim" + ./off_file_from_shape_generator on $geom $geom$sep$number$sep$dim.off $number $dim + done + done +done + +#./off_file_from_shape_generator in|on sphere|cube off_file_name points_number[integer > 0] dimension[integer > 1] radius[double > 0.0 | default = 1.0] diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index db298ea6..7a375c9f 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -57,9 +57,13 @@ namespace alpha_complex { * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a> * \cite cgal:s-gkd-15b from CGAL as template parameter. * - * \remark When the simplicial complex is constructed with an infinite value of alpha, the complex is a Delaunay + * \remark + * - When the simplicial complex is constructed with an infinite value of alpha, the complex is a Delaunay * complex. - * + * - For people only interested in the topology of the \ref alpha_complex (for instance persistence), + * \ref alpha_complex is equivalent to the \ref cech_complex and much smaller if you do not bound the radii. + * \ref cech_complex can still make sense in higher dimension precisely because you can bound the radii. + * * \section pointsexample Example from points * * This example builds the Delaunay triangulation from the given points in a 2D static kernel, and creates a @@ -89,63 +93,29 @@ namespace alpha_complex { * \image html "alpha_complex_doc.png" "Simplicial complex structure construction example" * * \subsection filtrationcomputation Filtration value computation algorithm - * - * - * - * <ul> - * <li style="list-style-type: none;">\f$ \textbf{for } i : dimension \rightarrow 0 \textbf{ do} \f$ - * <ul> - * <li style="list-style-type: none;">\f$\textbf{for all } \sigma of dimension i \f$ - * <ul> - * <li style="list-style-type: none;">\f$\textbf{if } filtration( \sigma ) is NaN \textbf{ then} \f$ - * <ul> - * <li style="list-style-type: none;">\f$ filtration( \sigma ) = \alpha^2( \sigma ) \f$ - * </li> - * </ul> - * </li> - * <li style="list-style-type: none;">\f$\textbf{end if}\f$ - * </li> - * <li style="list-style-type: none;">\f$\textbf{for all } \tau face of \sigma \textbf{ do} \f$ - * // propagate alpha filtration value - * <ul> - * <li style="list-style-type: none;">\f$\textbf{if } filtration( \tau ) is not NaN \textbf{ then} \f$ - * <ul> - * <li style="list-style-type: none;">\f$ filtration( \tau ) = min ( filtration( \tau ), filtration( \sigma ) ) \f$ - * </li> - * </ul> - * </li> - * <li style="list-style-type: none;">\f$\textbf{else}\f$ - * <ul> - * <li style="list-style-type: none;">\f$\textbf{if } \tau is not Gabriel for \sigma \textbf{ then} \f$ - * <ul> - * <li style="list-style-type: none;">\f$ filtration( \tau ) = filtration( \sigma ) \f$ - * </li> - * </ul> - * </li> - * <li style="list-style-type: none;">\f$\textbf{end if}\f$ - * </li> - * </ul> - * </li> - * <li style="list-style-type: none;">\f$\textbf{end if}\f$ - * </li> - * </ul> - * </li> - * <li style="list-style-type: none;">\f$\textbf{end for}\f$ - * </li> - * </ul> - * </li> - * <li style="list-style-type: none;">\f$\textbf{end for}\f$ - * </li> - * </ul> - * </li> - * <li style="list-style-type: none;">\f$\textbf{end for}\f$ - * </li> - * <li style="list-style-type: none;">\f$make\_filtration\_non\_decreasing()\f$ - * </li> - * <li style="list-style-type: none;">\f$prune\_above\_filtration()\f$ - * </li> - * </ul> - * + * <br> + * \f$ + * \textbf{for } \text{i : dimension } \rightarrow 0 \textbf{ do}\\ + * \quad \textbf{for all } \sigma \text{ of dimension i}\\ + * \quad\quad \textbf{if } \text{filtration(} \sigma ) \text{ is NaN} \textbf{ then}\\ + * \quad\quad\quad \text{filtration(} \sigma ) = \alpha^2( \sigma )\\ + * \quad\quad \textbf{end if}\\ + * \quad\quad \textbf{for all } \tau \text{ face of } \sigma \textbf{ do}\quad\quad + * \textit{// propagate alpha filtration value}\\ + * \quad\quad\quad \textbf{if } \text{filtration(} \tau ) \text{ is not NaN} \textbf{ then}\\ + * \quad\quad\quad\quad \text{filtration(} \tau \text{) = min( filtration(} \tau \text{), filtration(} \sigma + * \text{) )}\\ + * \quad\quad\quad \textbf{else}\\ + * \quad\quad\quad\quad \textbf{if } \textbf{if } \tau \text{ is not Gabriel for } \sigma \textbf{ then}\\ + * \quad\quad\quad\quad\quad \text{filtration(} \tau \text{) = filtration(} \sigma \text{)}\\ + * \quad\quad\quad\quad \textbf{end if}\\ + * \quad\quad\quad \textbf{end if}\\ + * \quad\quad \textbf{end for}\\ + * \quad \textbf{end for}\\ + * \textbf{end for}\\ + * \text{make_filtration_non_decreasing()}\\ + * \text{prune_above_filtration()}\\ + * \f$ * * \subsubsection dimension2 Dimension 2 * diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 5bf553e9..2fc62452 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Alpha_complex_examples) # need CGAL 4.7 diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index 9e0b3b3c..9255d3db 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Alpha_complex_tests) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index a2dfac20..7ace6064 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Alpha_complex_utilities) if(CGAL_FOUND) diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index efa20db9..8cda0b70 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -35,6 +35,8 @@ #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Delaunay_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> +#include <CGAL/Alpha_shape_cell_base_3.h> +#include <CGAL/Alpha_shape_vertex_base_3.h> #include <CGAL/iterator.h> #include <fstream> diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp index 54c074c4..cbe003ff 100644 --- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp @@ -30,6 +30,8 @@ #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Delaunay_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> +#include <CGAL/Alpha_shape_cell_base_3.h> +#include <CGAL/Alpha_shape_vertex_base_3.h> #include <CGAL/iterator.h> #include <fstream> diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp index 7c6e1583..11010701 100644 --- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -32,6 +32,8 @@ #include <CGAL/Periodic_3_Delaunay_triangulation_traits_3.h> #include <CGAL/Periodic_3_Delaunay_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> +#include <CGAL/Alpha_shape_cell_base_3.h> +#include <CGAL/Alpha_shape_vertex_base_3.h> #include <CGAL/iterator.h> #include <fstream> diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp index 54483819..cdeeabfc 100644 --- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp @@ -31,6 +31,8 @@ #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Regular_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> +#include <CGAL/Alpha_shape_cell_base_3.h> +#include <CGAL/Alpha_shape_vertex_base_3.h> #include <CGAL/iterator.h> // For CGAL < 4.11 diff --git a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp index f03f29a7..d030c88c 100644 --- a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp @@ -31,6 +31,8 @@ #include <CGAL/Periodic_3_regular_triangulation_traits_3.h> #include <CGAL/Periodic_3_regular_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> +#include <CGAL/Alpha_shape_cell_base_3.h> +#include <CGAL/Alpha_shape_vertex_base_3.h> #include <CGAL/iterator.h> #include <fstream> diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt index 99304aa4..dc659f2d 100644 --- a/src/Bitmap_cubical_complex/example/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bitmap_cubical_complex_examples) add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp ) diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h index 47e71f8a..9b74e267 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h @@ -492,7 +492,7 @@ class Bitmap_cubical_complex_base { this->multipliers.push_back(multiplier); multiplier *= 2 * sizes[i] + 1; } - this->data = std::vector<T>(multiplier, std::numeric_limits<T>::max()); + this->data = std::vector<T>(multiplier, std::numeric_limits<T>::infinity()); this->total_number_of_cells = multiplier; } @@ -562,7 +562,7 @@ void Bitmap_cubical_complex_base<T>::put_data_to_bins(T diameter_of_bin) { template <typename T> std::pair<T, T> Bitmap_cubical_complex_base<T>::min_max_filtration() { - std::pair<T, T> min_max(std::numeric_limits<T>::max(), std::numeric_limits<T>::min()); + std::pair<T, T> min_max(std::numeric_limits<T>::infinity(), -std::numeric_limits<T>::infinity()); for (std::size_t i = 0; i != this->data.size(); ++i) { if (this->data[i] < min_max.first) min_max.first = this->data[i]; if (this->data[i] > min_max.second) min_max.second = this->data[i]; 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 97070cda..8c35f590 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 @@ -177,7 +177,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c } } // std::reverse( this->sizes.begin() , this->sizes.end() ); - this->data = std::vector<T>(multiplier, std::numeric_limits<T>::max()); + this->data = std::vector<T>(multiplier, std::numeric_limits<T>::infinity()); this->total_number_of_cells = multiplier; } Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& sizes); diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt index 02b026f2..8b43632a 100644 --- a/src/Bitmap_cubical_complex/test/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bitmap_cubical_complex_tests) include(GUDHI_test_coverage) diff --git a/src/Bitmap_cubical_complex/utilities/CMakeLists.txt b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt index 676a730a..416db67f 100644 --- a/src/Bitmap_cubical_complex/utilities/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bitmap_cubical_complex_utilities) add_executable ( cubical_complex_persistence cubical_complex_persistence.cpp ) diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt index 20a4e47b..3105a1d5 100644 --- a/src/Bottleneck_distance/benchmark/CMakeLists.txt +++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_benchmark) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 6095d6eb..c6f10127 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_examples) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 41f8b16a..b0fc3949 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -30,6 +30,7 @@ #include <limits> // for numeric_limits #include <cmath> +#include <cfloat> // FLT_EVAL_METHOD namespace Gudhi { @@ -43,6 +44,13 @@ double bottleneck_distance_approx(Persistence_graph& g, double e) { Graph_matching biggest_unperfect(g); while (b_upper_bound - b_lower_bound > 2 * e) { double step = b_lower_bound + (b_upper_bound - b_lower_bound) / alpha; +#if !defined FLT_EVAL_METHOD || FLT_EVAL_METHOD < 0 || FLT_EVAL_METHOD > 1 + // On platforms where double computation is done with excess precision, + // we force it to its true precision so the following test is reliable. + volatile double drop_excess_precision = step; + step = drop_excess_precision; + // Alternative: step = CGAL::IA_force_to_double(step); +#endif if (step <= b_lower_bound || step >= b_upper_bound) // Avoid precision problem break; m.set_r(step); diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index 2676b82c..bb739280 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_tests) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/utilities/CMakeLists.txt b/src/Bottleneck_distance/utilities/CMakeLists.txt index d19e3b1c..2f35885c 100644 --- a/src/Bottleneck_distance/utilities/CMakeLists.txt +++ b/src/Bottleneck_distance/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_utilities) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 0ae26081..37178492 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,12 +1,19 @@ -cmake_minimum_required(VERSION 2.6) -project(GUDHI) +cmake_minimum_required(VERSION 3.1) -include("CMakeGUDHIVersion.txt") +project(GUDHI) -enable_testing() +include(CMakeGUDHIVersion.txt) list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/") +# This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path +set(GUDHI_CYTHON_PATH "cython") + +# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH +include(GUDHI_third_party_libraries NO_POLICY_SCOPE) + +include(GUDHI_compilation_flags) + # Add your new module in the list, order is not important include(GUDHI_modules) @@ -14,6 +21,7 @@ add_gudhi_module(common) add_gudhi_module(Alpha_complex) add_gudhi_module(Bitmap_cubical_complex) add_gudhi_module(Bottleneck_distance) +add_gudhi_module(Cech_complex) add_gudhi_module(Contraction) add_gudhi_module(Hasse_complex) add_gudhi_module(Persistence_representations) @@ -34,30 +42,6 @@ message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"") set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR}) include(GUDHI_doxygen_target) -# This variable is used by Cython CMakeLists.txt to know its path -set(GUDHI_CYTHON_PATH "cython") -# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH -include(GUDHI_third_party_libraries) - -if(MSVC) - # Turn off some VC++ warnings - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") -else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic") -endif() - -if(CMAKE_BUILD_TYPE MATCHES Debug) - message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}") -else() - message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}") -endif() - -if (DEBUG_TRACES) - message(STATUS "DEBUG_TRACES are activated") - # For programs to be more verbose - add_definitions(-DDEBUG_TRACES) -endif() - #--------------------------------------------------------------------------------------- # Gudhi compilation part include_directories(include) diff --git a/src/Cech_complex/benchmark/CMakeLists.txt b/src/Cech_complex/benchmark/CMakeLists.txt new file mode 100644 index 00000000..b7697764 --- /dev/null +++ b/src/Cech_complex/benchmark/CMakeLists.txt @@ -0,0 +1,12 @@ +cmake_minimum_required(VERSION 2.6) +project(Cech_complex_benchmark) + +# Do not forget to copy test files in current binary dir +file(COPY "${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_SYSTEM_LIBRARY} ${Boost_FILESYSTEM_LIBRARY}) + +if (TBB_FOUND) + target_link_libraries(cech_complex_benchmark ${TBB_LIBRARIES}) +endif() diff --git a/src/Cech_complex/benchmark/cech_complex_benchmark.cpp b/src/Cech_complex/benchmark/cech_complex_benchmark.cpp new file mode 100644 index 00000000..86314930 --- /dev/null +++ b/src/Cech_complex/benchmark/cech_complex_benchmark.cpp @@ -0,0 +1,144 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2018 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Points_off_io.h> +#include <gudhi/distance_functions.h> +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Clock.h> +#include <gudhi/Rips_complex.h> +#include <gudhi/Cech_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Miniball.hpp> + +#include "boost/filesystem.hpp" // includes all needed Boost.Filesystem declarations + +#include <string> +#include <vector> + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; +using Point = std::vector<Filtration_value>; +using Point_cloud = std::vector<Point>; +using Points_off_reader = Gudhi::Points_off_reader<Point>; +using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>; +using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; +using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>; + +class Minimal_enclosing_ball_radius { + public: + // boost::range_value is not SFINAE-friendly so we cannot use it in the return type + template <typename Point> + typename std::iterator_traits<typename boost::range_iterator<Point>::type>::value_type operator()( + const Point& p1, const Point& p2) const { + // Type def + using Point_cloud = std::vector<Point>; + using Point_iterator = typename Point_cloud::const_iterator; + using Coordinate_iterator = typename Point::const_iterator; + using Min_sphere = + typename Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>; + + Point_cloud point_cloud; + point_cloud.push_back(p1); + point_cloud.push_back(p2); + + GUDHI_CHECK((p1.end() - p1.begin()) != (p2.end() - p2.begin()), "inconsistent point dimensions"); + Min_sphere min_sphere(p1.end() - p1.begin(), point_cloud.begin(), point_cloud.end()); + + return std::sqrt(min_sphere.squared_radius()); + } +}; + +int main(int argc, char* argv[]) { + std::string off_file_points = "tore3D_1307.off"; + Filtration_value threshold = 1e20; + + // Extract the points from the file filepoints + Points_off_reader off_reader(off_file_points); + + Gudhi::Clock euclidean_clock("Gudhi::Euclidean_distance"); + // Compute the proximity graph of the points + Proximity_graph euclidean_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>( + off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); + + std::cout << euclidean_clock << std::endl; + + Gudhi::Clock miniball_clock("Minimal_enclosing_ball_radius"); + // Compute the proximity graph of the points + Proximity_graph miniball_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>( + off_reader.get_point_cloud(), threshold, Minimal_enclosing_ball_radius()); + std::cout << miniball_clock << std::endl; + + Gudhi::Clock common_miniball_clock("Gudhi::Minimal_enclosing_ball_radius()"); + // Compute the proximity graph of the points + Proximity_graph common_miniball_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>( + off_reader.get_point_cloud(), threshold, Gudhi::Minimal_enclosing_ball_radius()); + std::cout << common_miniball_clock << std::endl; + + boost::filesystem::path full_path(boost::filesystem::current_path()); + std::cout << "Current path is : " << full_path << std::endl; + + std::cout << "File name;Radius;Rips time;Cech time; Ratio Rips/Cech time;Rips nb simplices;Cech nb simplices;" + << std::endl; + boost::filesystem::directory_iterator end_itr; // default construction yields past-the-end + for (boost::filesystem::directory_iterator itr(boost::filesystem::current_path()); itr != end_itr; ++itr) { + if (!boost::filesystem::is_directory(itr->status())) { + if (itr->path().extension() == ".off") // see below + { + Points_off_reader off_reader(itr->path().string()); + Point p0 = off_reader.get_point_cloud()[0]; + + for (Filtration_value radius = 0.1; radius < 0.4; radius += 0.1) { + std::cout << itr->path().stem() << ";"; + std::cout << radius << ";"; + Gudhi::Clock rips_clock("Rips computation"); + Rips_complex rips_complex_from_points(off_reader.get_point_cloud(), radius, + Gudhi::Minimal_enclosing_ball_radius()); + Simplex_tree rips_stree; + rips_complex_from_points.create_complex(rips_stree, p0.size() - 1); + // ------------------------------------------ + // Display information about the Rips complex + // ------------------------------------------ + double rips_sec = rips_clock.num_seconds(); + std::cout << rips_sec << ";"; + + Gudhi::Clock cech_clock("Cech computation"); + Cech_complex cech_complex_from_points(off_reader.get_point_cloud(), radius); + Simplex_tree cech_stree; + cech_complex_from_points.create_complex(cech_stree, p0.size() - 1); + // ------------------------------------------ + // Display information about the Cech complex + // ------------------------------------------ + double cech_sec = cech_clock.num_seconds(); + std::cout << cech_sec << ";"; + std::cout << cech_sec / rips_sec << ";"; + + assert(rips_stree.num_simplices() >= cech_stree.num_simplices()); + std::cout << rips_stree.num_simplices() << ";"; + std::cout << cech_stree.num_simplices() << ";" << std::endl; + } + } + } + } + + return 0; +} diff --git a/src/Cech_complex/concept/SimplicialComplexForCech.h b/src/Cech_complex/concept/SimplicialComplexForCech.h new file mode 100644 index 00000000..89231eec --- /dev/null +++ b/src/Cech_complex/concept/SimplicialComplexForCech.h @@ -0,0 +1,66 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2018 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef CONCEPT_CECH_COMPLEX_SIMPLICIAL_COMPLEX_FOR_CECH_H_ +#define CONCEPT_CECH_COMPLEX_SIMPLICIAL_COMPLEX_FOR_CECH_H_ + +namespace Gudhi { + +namespace cech_complex { + +/** \brief The concept SimplicialComplexForCech describes the requirements for a type to implement a simplicial + * complex, that can be created from a `Cech_complex`. + */ +struct SimplicialComplexForCech { + /** Handle to specify a simplex. */ + typedef unspecified Simplex_handle; + /** Handle to specify a vertex. Must be a non-negative integer. */ + typedef unspecified Vertex_handle; + /** Handle to specify the simplex filtration value. */ + typedef unspecified Filtration_value; + + /** Assigns the 'simplex' with the given 'filtration' value. */ + int assign_filtration(Simplex_handle simplex, Filtration_value filtration); + + /** \brief Returns a range over vertices of a given + * simplex. */ + Simplex_vertex_range simplex_vertex_range(Simplex_handle const & simplex); + + /** \brief Inserts a given `Gudhi::ProximityGraph` in the simplicial complex. */ + template<class ProximityGraph> + void insert_graph(const ProximityGraph& proximity_graph); + + /** \brief Expands the simplicial complex containing only its one skeleton until a given maximal dimension. + * expansion can be blocked by the blocker oracle. */ + template< typename Blocker > + void expansion_with_blockers(int max_dim, Blocker block_simplex); + + /** Returns the number of vertices in the simplicial complex. */ + std::size_t num_vertices(); + +}; + +} // namespace alpha_complex + +} // namespace Gudhi + +#endif // CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_H_ diff --git a/src/Cech_complex/doc/COPYRIGHT b/src/Cech_complex/doc/COPYRIGHT new file mode 100644 index 00000000..5f1d97cc --- /dev/null +++ b/src/Cech_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Vincent Rouvreau + +Copyright (C) 2015 Inria + +This program is free software: you can redistribute it and/or modify it under +the terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +This program is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +this program. If not, see <http://www.gnu.org/licenses/>. diff --git a/src/Cech_complex/doc/Intro_cech_complex.h b/src/Cech_complex/doc/Intro_cech_complex.h new file mode 100644 index 00000000..4483bcb9 --- /dev/null +++ b/src/Cech_complex/doc/Intro_cech_complex.h @@ -0,0 +1,114 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2018 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef DOC_CECH_COMPLEX_INTRO_CECH_COMPLEX_H_ +#define DOC_CECH_COMPLEX_INTRO_CECH_COMPLEX_H_ + +namespace Gudhi { + +namespace cech_complex { + +/** \defgroup cech_complex Čech complex + * + * \author Vincent Rouvreau + * + * @{ + * + * \section cechdefinition Čech complex definition + * + * Čech complex + * <a target="_blank" href="https://en.wikipedia.org/wiki/%C4%8Cech_cohomology">(Wikipedia)</a> is a + * <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a> constructed + * from a proximity graph. The set of all simplices is filtered by the radius of their minimal enclosing ball. + * + * The input shall be a point cloud in an Euclidean space. + * + * \remark For people only interested in the topology of the \ref cech_complex (for instance persistence), + * \ref alpha_complex is equivalent to the \ref cech_complex and much smaller if you do not bound the radii. + * \ref cech_complex can still make sense in higher dimension precisely because you can bound the radii. + * + * \subsection cechalgorithm Algorithm + * + * Cech_complex first builds a proximity graph from a point cloud. + * The filtration value of each edge of the `Gudhi::Proximity_graph` is computed from + * `Gudhi::Minimal_enclosing_ball_radius` function. + * + * All edges that have a filtration value strictly greater than a user given maximal radius value, \f$max\_radius\f$, + * are not inserted into the complex. + * + * Vertex name correspond to the index of the point in the given range (aka. the point cloud). + * + * \image html "cech_one_skeleton.png" "Čech complex proximity graph representation" + * + * When creating a simplicial complex from this proximity graph, Cech_complex inserts the proximity graph into the + * simplicial complex data structure, and then expands the simplicial complex when required. + * + * On this example, as edges \f$(x,y)\f$, \f$(y,z)\f$ and \f$(z,y)\f$ are in the complex, the minimal ball radius + * containing the points \f$(x,y,z)\f$ is computed. + * + * \f$(x,y,z)\f$ is inserted to the simplicial complex with the filtration value set with + * \f$mini\_ball\_radius(x,y,z))\f$ iff \f$mini\_ball\_radius(x,y,z)) \leq max\_radius\f$. + * + * And so on for higher dimensions. + * + * \image html "cech_complex_representation.png" "Čech complex expansion" + * + * The minimal ball radius computation is insured by + * <a target="_blank" href="https://people.inf.ethz.ch/gaertner/subdir/software/miniball.html"> + * the miniball software (V3.0)</a> - Smallest Enclosing Balls of Points - and distributed with GUDHI. + * Please refer to + * <a target="_blank" href="https://people.inf.ethz.ch/gaertner/subdir/texts/own_work/esa99_final.pdf"> + * the miniball software design description</a> for more information about this computation. + * + * This radius computation is the reason why the Cech_complex is taking much more time to be computed than the + * \ref rips_complex but it offers more topological guarantees. + * + * If the Cech_complex interfaces are not detailed enough for your need, please refer to + * <a href="_cech_complex_2cech_complex_step_by_step_8cpp-example.html"> + * cech_complex_step_by_step.cpp</a> example, where the graph construction over the Simplex_tree is more detailed. + * + * \subsection cechpointscloudexample Example from a point cloud + * + * This example builds the proximity graph from the given points, and maximal radius values. + * Then it creates a `Simplex_tree` with it. + * + * Then, it is asked to display information about the simplicial complex. + * + * \include Cech_complex/cech_complex_example_from_points.cpp + * + * When launching (maximal enclosing ball radius is 1., is expanded until dimension 2): + * + * \code $> ./Cech_complex_example_from_points + * \endcode + * + * the program output is: + * + * \include Cech_complex/cech_complex_example_from_points_for_doc.txt + * + */ +/** @} */ // end defgroup cech_complex + +} // namespace cech_complex + +} // namespace Gudhi + +#endif // DOC_CECH_COMPLEX_INTRO_CECH_COMPLEX_H_ diff --git a/src/Cech_complex/doc/cech_complex_representation.ipe b/src/Cech_complex/doc/cech_complex_representation.ipe new file mode 100644 index 00000000..377745a3 --- /dev/null +++ b/src/Cech_complex/doc/cech_complex_representation.ipe @@ -0,0 +1,330 @@ +<?xml version="1.0"?> +<!DOCTYPE ipe SYSTEM "ipe.dtd"> +<ipe version="70107" creator="Ipe 7.1.10"> +<info created="D:20150603143945" modified="D:20180305162524"/> +<ipestyle name="basic"> +<symbol name="arrow/arc(spx)"> +<path 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Binary files differnew file mode 100644 index 00000000..cc636616 --- /dev/null +++ b/src/Cech_complex/doc/cech_one_skeleton.png diff --git a/src/Cech_complex/example/CMakeLists.txt b/src/Cech_complex/example/CMakeLists.txt new file mode 100644 index 00000000..ab391215 --- /dev/null +++ b/src/Cech_complex/example/CMakeLists.txt @@ -0,0 +1,16 @@ +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_LIBRARY}) +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") + +add_executable ( Cech_complex_example_from_points cech_complex_example_from_points.cpp) +if (TBB_FOUND) + target_link_libraries(Cech_complex_example_from_points ${TBB_LIBRARIES}) +endif() +add_test(NAME Cech_complex_example_from_points COMMAND $<TARGET_FILE:Cech_complex_example_from_points>) diff --git a/src/Cech_complex/example/cech_complex_example_from_points.cpp b/src/Cech_complex/example/cech_complex_example_from_points.cpp new file mode 100644 index 00000000..3cc5a4df --- /dev/null +++ b/src/Cech_complex/example/cech_complex_example_from_points.cpp @@ -0,0 +1,54 @@ +#include <gudhi/Cech_complex.h> +#include <gudhi/Simplex_tree.h> + +#include <iostream> +#include <string> +#include <vector> +#include <array> + +int main() { + // Type definitions + using Point_cloud = std::vector<std::array<double, 2>>; + using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; + using Filtration_value = Simplex_tree::Filtration_value; + using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>; + + Point_cloud points; + points.push_back({1., 0.}); // 0 + points.push_back({0., 1.}); // 1 + points.push_back({2., 1.}); // 2 + points.push_back({3., 2.}); // 3 + points.push_back({0., 3.}); // 4 + points.push_back({3. + std::sqrt(3.), 3.}); // 5 + points.push_back({1., 4.}); // 6 + points.push_back({3., 4.}); // 7 + points.push_back({2., 4. + std::sqrt(3.)}); // 8 + points.push_back({0., 4.}); // 9 + points.push_back({-0.5, 2.}); // 10 + + // ---------------------------------------------------------------------------- + // Init of a Cech complex from points + // ---------------------------------------------------------------------------- + Filtration_value max_radius = 1.; + Cech_complex cech_complex_from_points(points, max_radius); + + Simplex_tree stree; + cech_complex_from_points.create_complex(stree, 2); + // ---------------------------------------------------------------------------- + // Display information about the one skeleton Cech complex + // ---------------------------------------------------------------------------- + std::cout << "Cech complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - " + << stree.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : stree.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " + << "[" << stree.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + return 0; +} diff --git a/src/Cech_complex/example/cech_complex_example_from_points_for_doc.txt b/src/Cech_complex/example/cech_complex_example_from_points_for_doc.txt new file mode 100644 index 00000000..be0afc76 --- /dev/null +++ b/src/Cech_complex/example/cech_complex_example_from_points_for_doc.txt @@ -0,0 +1,31 @@ +Iterator on Cech complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 7 ) -> [0] + ( 8 ) -> [0] + ( 9 ) -> [0] + ( 10 ) -> [0] + ( 9 4 ) -> [0.5] + ( 9 6 ) -> [0.5] + ( 10 1 ) -> [0.559017] + ( 10 4 ) -> [0.559017] + ( 1 0 ) -> [0.707107] + ( 2 0 ) -> [0.707107] + ( 3 2 ) -> [0.707107] + ( 6 4 ) -> [0.707107] + ( 9 6 4 ) -> [0.707107] + ( 2 1 ) -> [1] + ( 2 1 0 ) -> [1] + ( 4 1 ) -> [1] + ( 5 3 ) -> [1] + ( 7 3 ) -> [1] + ( 7 5 ) -> [1] + ( 7 6 ) -> [1] + ( 8 6 ) -> [1] + ( 8 7 ) -> [1] + ( 10 4 1 ) -> [1] diff --git a/src/Cech_complex/example/cech_complex_step_by_step.cpp b/src/Cech_complex/example/cech_complex_step_by_step.cpp new file mode 100644 index 00000000..d2dc8b65 --- /dev/null +++ b/src/Cech_complex/example/cech_complex_step_by_step.cpp @@ -0,0 +1,166 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2018 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Points_off_io.h> + +#include <gudhi/Miniball.hpp> + +#include <boost/program_options.hpp> + +#include <string> +#include <vector> +#include <limits> // infinity +#include <utility> // for pair +#include <map> + +// ---------------------------------------------------------------------------- +// rips_persistence_step_by_step is an example of each step that is required to +// build a Rips over a Simplex_tree. Please refer to rips_persistence to see +// how to do the same thing with the Rips_complex wrapper for less detailed +// steps. +// ---------------------------------------------------------------------------- + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree<>; +using Simplex_handle = Simplex_tree::Simplex_handle; +using Filtration_value = Simplex_tree::Filtration_value; +using Point = std::vector<double>; +using Points_off_reader = Gudhi::Points_off_reader<Point>; +using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>; + +class Cech_blocker { + private: + using Point_cloud = std::vector<Point>; + using Point_iterator = Point_cloud::const_iterator; + using Coordinate_iterator = Point::const_iterator; + using Min_sphere = Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>; + + public: + bool operator()(Simplex_handle sh) { + std::vector<Point> points; + for (auto vertex : simplex_tree_.simplex_vertex_range(sh)) { + points.push_back(point_cloud_[vertex]); +#ifdef DEBUG_TRACES + std::cout << "#(" << vertex << ")#"; +#endif // DEBUG_TRACES + } + Filtration_value radius = Gudhi::Minimal_enclosing_ball_radius()(points); +#ifdef DEBUG_TRACES + std::cout << "radius = " << radius << " - " << (radius > max_radius_) << std::endl; +#endif // DEBUG_TRACES + simplex_tree_.assign_filtration(sh, radius); + return (radius > max_radius_); + } + Cech_blocker(Simplex_tree& simplex_tree, Filtration_value max_radius, const std::vector<Point>& point_cloud) + : simplex_tree_(simplex_tree), max_radius_(max_radius), point_cloud_(point_cloud) { + dimension_ = point_cloud_[0].size(); + } + + private: + Simplex_tree simplex_tree_; + Filtration_value max_radius_; + std::vector<Point> point_cloud_; + int dimension_; +}; + +void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max); + +int main(int argc, char* argv[]) { + std::string off_file_points; + Filtration_value max_radius; + int dim_max; + + program_options(argc, argv, off_file_points, max_radius, dim_max); + + // Extract the points from the file filepoints + Points_off_reader off_reader(off_file_points); + + // Compute the proximity graph of the points + Proximity_graph prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(off_reader.get_point_cloud(), max_radius, + Gudhi::Minimal_enclosing_ball_radius()); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree st; + // insert the proximity graph in the simplex tree + st.insert_graph(prox_graph); + // expand the graph until dimension dim_max + st.expansion_with_blockers(dim_max, Cech_blocker(st, max_radius, off_reader.get_point_cloud())); + + std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << st.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + st.initialize_filtration(); + +#if DEBUG_TRACES + std::cout << "********************************************************************\n"; + std::cout << "* The complex contains " << st.num_simplices() << " simplices - dimension=" << st.dimension() << "\n"; + std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << " " + << "[" << st.filtration(f_simplex) << "] "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << static_cast<int>(vertex) << " "; + } + std::cout << std::endl; + } +#endif // DEBUG_TRACES + + return 0; +} + +void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()("input-file", po::value<std::string>(&off_file_points), + "Name of an OFF file containing a point set.\n"); + + po::options_description visible("Allowed options", 100); + visible.add_options()("help,h", "produce help message")( + "max-radius,r", + po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()), + "Maximal length of an edge for the Rips complex construction.")( + "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute."); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Construct a Cech complex defined on a set of input points.\n \n"; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Cech_complex/include/gudhi/Cech_complex.h b/src/Cech_complex/include/gudhi/Cech_complex.h new file mode 100644 index 00000000..f9b8a269 --- /dev/null +++ b/src/Cech_complex/include/gudhi/Cech_complex.h @@ -0,0 +1,130 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2018 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef CECH_COMPLEX_H_ +#define CECH_COMPLEX_H_ + +#include <gudhi/distance_functions.h> // for Gudhi::Minimal_enclosing_ball_radius +#include <gudhi/graph_simplicial_complex.h> // for Gudhi::Proximity_graph +#include <gudhi/Debug_utils.h> // for GUDHI_CHECK +#include <gudhi/Cech_complex_blocker.h> // for Gudhi::cech_complex::Cech_blocker + +#include <iostream> +#include <stdexcept> // for exception management +#include <vector> + +namespace Gudhi { + +namespace cech_complex { + +/** + * \class Cech_complex + * \brief Cech complex data structure. + * + * \ingroup cech_complex + * + * \details + * The data structure is a proximity graph, containing edges when the edge length is less or equal + * to a given max_radius. Edge length is computed from `Gudhi::Minimal_enclosing_ball_radius` distance function. + * + * \tparam SimplicialComplexForProximityGraph furnishes `Vertex_handle` and `Filtration_value` type definition required + * by `Gudhi::Proximity_graph`. + * + * \tparam ForwardPointRange must be a range for which `std::begin()` and `std::end()` methods return input + * iterators on a point. `std::begin()` and `std::end()` methods are also required for a point. + */ +template <typename SimplicialComplexForProximityGraph, typename ForwardPointRange> +class Cech_complex { + private: + // Required by compute_proximity_graph + using Vertex_handle = typename SimplicialComplexForProximityGraph::Vertex_handle; + using Filtration_value = typename SimplicialComplexForProximityGraph::Filtration_value; + using Proximity_graph = Gudhi::Proximity_graph<SimplicialComplexForProximityGraph>; + + // Retrieve Coordinate type from ForwardPointRange + using Point_from_range_iterator = typename boost::range_const_iterator<ForwardPointRange>::type; + using Point_from_range = typename std::iterator_traits<Point_from_range_iterator>::value_type; + using Coordinate_iterator = typename boost::range_const_iterator<Point_from_range>::type; + using Coordinate = typename std::iterator_traits<Coordinate_iterator>::value_type; + + public: + // Point and Point_cloud type definition + using Point = std::vector<Coordinate>; + using Point_cloud = std::vector<Point>; + + public: + /** \brief Cech_complex constructor from a list of points. + * + * @param[in] points Range of points. + * @param[in] max_radius Maximal radius value. + * + * \tparam ForwardPointRange must be a range of Point. Point must be a range of <b>copyable</b> Cartesian coordinates. + * + */ + Cech_complex(const ForwardPointRange& points, Filtration_value max_radius) : max_radius_(max_radius) { + // Point cloud deep copy + point_cloud_.reserve(boost::size(points)); + for (auto&& point : points) point_cloud_.emplace_back(std::begin(point), std::end(point)); + + cech_skeleton_graph_ = Gudhi::compute_proximity_graph<SimplicialComplexForProximityGraph>( + point_cloud_, max_radius_, Gudhi::Minimal_enclosing_ball_radius()); + } + + /** \brief Initializes the simplicial complex from the proximity graph and expands it until a given maximal + * dimension, using the Cech blocker oracle. + * + * @param[in] complex SimplicialComplexForCech to be created. + * @param[in] dim_max graph expansion until this given maximal dimension. + * @exception std::invalid_argument In debug mode, if `complex.num_vertices()` does not return 0. + * + */ + template <typename SimplicialComplexForCechComplex> + void create_complex(SimplicialComplexForCechComplex& complex, int dim_max) { + GUDHI_CHECK(complex.num_vertices() == 0, + std::invalid_argument("Cech_complex::create_complex - simplicial complex is not empty")); + + // insert the proximity graph in the simplicial complex + complex.insert_graph(cech_skeleton_graph_); + // expand the graph until dimension dim_max + complex.expansion_with_blockers(dim_max, + Cech_blocker<SimplicialComplexForCechComplex, Cech_complex>(&complex, this)); + } + + /** @return max_radius value given at construction. */ + Filtration_value max_radius() const { return max_radius_; } + + /** @param[in] vertex Point position in the range. + * @return The point. + */ + const Point& get_point(Vertex_handle vertex) const { return point_cloud_[vertex]; } + + private: + Proximity_graph cech_skeleton_graph_; + Filtration_value max_radius_; + Point_cloud point_cloud_; +}; + +} // namespace cech_complex + +} // namespace Gudhi + +#endif // CECH_COMPLEX_H_ diff --git a/src/Cech_complex/include/gudhi/Cech_complex_blocker.h b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h new file mode 100644 index 00000000..b0d347b1 --- /dev/null +++ b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h @@ -0,0 +1,91 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2018 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef CECH_COMPLEX_BLOCKER_H_ +#define CECH_COMPLEX_BLOCKER_H_ + +#include <gudhi/distance_functions.h> // for Gudhi::Minimal_enclosing_ball_radius + +#include <iostream> +#include <vector> +#include <cmath> // for std::sqrt + +namespace Gudhi { + +namespace cech_complex { + +/** \internal + * \class Cech_blocker + * \brief Čech complex blocker. + * + * \ingroup cech_complex + * + * \details + * Čech blocker is an oracle constructed from a Cech_complex and a simplicial complex. + * + * \tparam SimplicialComplexForProximityGraph furnishes `Simplex_handle` and `Filtration_value` type definition, + * `simplex_vertex_range(Simplex_handle sh)`and `assign_filtration(Simplex_handle sh, Filtration_value filt)` methods. + * + * \tparam Chech_complex is required by the blocker. + */ +template <typename SimplicialComplexForCech, typename Cech_complex> +class Cech_blocker { + private: + using Point_cloud = typename Cech_complex::Point_cloud; + + using Simplex_handle = typename SimplicialComplexForCech::Simplex_handle; + using Filtration_value = typename SimplicialComplexForCech::Filtration_value; + + public: + /** \internal \brief Čech complex blocker operator() - the oracle - assigns the filtration value from the simplex + * radius and returns if the simplex expansion must be blocked. + * \param[in] sh The Simplex_handle. + * \return true if the simplex radius is greater than the Cech_complex max_radius*/ + bool operator()(Simplex_handle sh) { + Point_cloud points; + for (auto vertex : sc_ptr_->simplex_vertex_range(sh)) { + points.push_back(cc_ptr_->get_point(vertex)); +#ifdef DEBUG_TRACES + std::cout << "#(" << vertex << ")#"; +#endif // DEBUG_TRACES + } + Filtration_value radius = Gudhi::Minimal_enclosing_ball_radius()(points); +#ifdef DEBUG_TRACES + if (radius > cc_ptr_->max_radius()) std::cout << "radius > max_radius => expansion is blocked\n"; +#endif // DEBUG_TRACES + sc_ptr_->assign_filtration(sh, radius); + return (radius > cc_ptr_->max_radius()); + } + + /** \internal \brief Čech complex blocker constructor. */ + Cech_blocker(SimplicialComplexForCech* sc_ptr, Cech_complex* cc_ptr) : sc_ptr_(sc_ptr), cc_ptr_(cc_ptr) {} + + private: + SimplicialComplexForCech* sc_ptr_; + Cech_complex* cc_ptr_; +}; + +} // namespace cech_complex + +} // namespace Gudhi + +#endif // CECH_COMPLEX_BLOCKER_H_ diff --git a/src/Cech_complex/include/gudhi/Miniball.COPYRIGHT b/src/Cech_complex/include/gudhi/Miniball.COPYRIGHT new file mode 100644 index 00000000..dbe4c553 --- /dev/null +++ b/src/Cech_complex/include/gudhi/Miniball.COPYRIGHT @@ -0,0 +1,4 @@ +The miniball software is available under the GNU General Public License (GPLv3 - https://www.gnu.org/copyleft/gpl.html). +If your intended use is not compliant with this license, please buy a commercial license (EUR 500 - https://people.inf.ethz.ch/gaertner/subdir/software/miniball/license.html). +You need a license if the software that you develop using Miniball V3.0 is not open source. + diff --git a/src/Cech_complex/include/gudhi/Miniball.README b/src/Cech_complex/include/gudhi/Miniball.README new file mode 100644 index 00000000..033d8953 --- /dev/null +++ b/src/Cech_complex/include/gudhi/Miniball.README @@ -0,0 +1,26 @@ +https://people.inf.ethz.ch/gaertner/subdir/software/miniball.html + +Smallest Enclosing Balls of Points - Fast and Robust in C++. +(high-quality software for smallest enclosing balls of balls is available in the computational geometry algorithms library CGAL) + + +This is the miniball software (V3.0) for computing smallest enclosing balls of points in arbitrary dimensions. It consists of a C++ header file Miniball.hpp (around 500 lines of code) and two example programs miniball_example.cpp and miniball_example_containers.cpp that demonstrate the usage. The first example stores the coordinates of the input points in a two-dimensional array, the second example uses a list of vectors to show how generic containers can be used. + +Credits: Aditya Gupta and Alexandros Konstantinakis-Karmis have significantly contributed to this version of the software. + +Changes - https://people.inf.ethz.ch/gaertner/subdir/software/miniball/changes.txt - from previous versions. + +The theory - https://people.inf.ethz.ch/gaertner/subdir/texts/own_work/esa99_final.pdf - behind the miniball software (Proc. 7th Annual European Symposium on Algorithms (ESA), Lecture Notes in Computer Science 1643, Springer-Verlag, pp.325-338, 1999). + +Main Features: + + Very fast in low dimensions. 1 million points in 5-space are processed within 0.05 seconds on any recent machine. + + High numerical stability. Almost all input degeneracies (cospherical points, multiple points, points very close together) are routinely handled. + + Easily integrates into your code. You can freely choose the coordinate type of your points and the container to store the points. If you still need to adapt the code, the header is small and readable and contains documentation for all major methods. + + +Changes done for the GUDHI version of MiniBall: + - Add include guard + - Move Miniball namespace inside a new Gudhi namespace diff --git a/src/Cech_complex/include/gudhi/Miniball.hpp b/src/Cech_complex/include/gudhi/Miniball.hpp new file mode 100644 index 00000000..ce6cbb5b --- /dev/null +++ b/src/Cech_complex/include/gudhi/Miniball.hpp @@ -0,0 +1,523 @@ +// Copright (C) 1999-2013, Bernd Gaertner +// $Rev: 3581 $ +// +// This program is free software: you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation, either version 3 of the License, or +// (at your option) any later version. + +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. + +// You should have received a copy of the GNU General Public License +// along with this program. If not, see <http://www.gnu.org/licenses/>. +// +// Contact: +// -------- +// Bernd Gaertner +// Institute of Theoretical Computer Science +// ETH Zuerich +// CAB G31.1 +// CH-8092 Zuerich, Switzerland +// http://www.inf.ethz.ch/personal/gaertner + +#ifndef MINIBALL_HPP_ +#define MINIBALL_HPP_ + +#include <cassert> +#include <algorithm> +#include <list> +#include <ctime> +#include <limits> + +namespace Gudhi { + +namespace Miniball { + + // Global Functions + // ================ + template <typename NT> + inline NT mb_sqr (NT r) {return r*r;} + + // Functors + // ======== + + // functor to map a point iterator to the corresponding coordinate iterator; + // generic version for points whose coordinate containers have begin() + template < typename Pit_, typename Cit_ > + struct CoordAccessor { + typedef Pit_ Pit; + typedef Cit_ Cit; + inline Cit operator() (Pit it) const { return (*it).begin(); } + }; + + // partial specialization for points whose coordinate containers are arrays + template < typename Pit_, typename Cit_ > + struct CoordAccessor<Pit_, Cit_*> { + typedef Pit_ Pit; + typedef Cit_* Cit; + inline Cit operator() (Pit it) const { return *it; } + }; + + // Class Declaration + // ================= + + template <typename CoordAccessor> + class Miniball { + private: + // types + // The iterator type to go through the input points + typedef typename CoordAccessor::Pit Pit; + // The iterator type to go through the coordinates of a single point. + typedef typename CoordAccessor::Cit Cit; + // The coordinate type + typedef typename std::iterator_traits<Cit>::value_type NT; + // The iterator to go through the support points + typedef typename std::list<Pit>::iterator Sit; + + // data members... + const int d; // dimension + Pit points_begin; + Pit points_end; + CoordAccessor coord_accessor; + double time; + const NT nt0; // NT(0) + + //...for the algorithms + std::list<Pit> L; + Sit support_end; + int fsize; // number of forced points + int ssize; // number of support points + + // ...for the ball updates + NT* current_c; + NT current_sqr_r; + NT** c; + NT* sqr_r; + + // helper arrays + NT* q0; + NT* z; + NT* f; + NT** v; + NT** a; + + public: + // The iterator type to go through the support points + typedef typename std::list<Pit>::const_iterator SupportPointIterator; + + // PRE: [begin, end) is a nonempty range + // POST: computes the smallest enclosing ball of the points in the range + // [begin, end); the functor a maps a point iterator to an iterator + // through the d coordinates of the point + Miniball (int d_, Pit begin, Pit end, CoordAccessor ca = CoordAccessor()); + + // POST: returns a pointer to the first element of an array that holds + // the d coordinates of the center of the computed ball + const NT* center () const; + + // POST: returns the squared radius of the computed ball + NT squared_radius () const; + + // POST: returns the number of support points of the computed ball; + // the support points form a minimal set with the same smallest + // enclosing ball as the input set; in particular, the support + // points are on the boundary of the computed ball, and their + // number is at most d+1 + int nr_support_points () const; + + // POST: returns an iterator to the first support point + SupportPointIterator support_points_begin () const; + + // POST: returns a past-the-end iterator for the range of support points + SupportPointIterator support_points_end () const; + + // POST: returns the maximum excess of any input point w.r.t. the computed + // ball, divided by the squared radius of the computed ball. The + // excess of a point is the difference between its squared distance + // from the center and the squared radius; Ideally, the return value + // is 0. subopt is set to the absolute value of the most negative + // coefficient in the affine combination of the support points that + // yields the center. Ideally, this is a convex combination, and there + // is no negative coefficient in which case subopt is set to 0. + NT relative_error (NT& subopt) const; + + // POST: return true if the relative error is at most tol, and the + // suboptimality is 0; the default tolerance is 10 times the + // coordinate type's machine epsilon + bool is_valid (NT tol = NT(10) * std::numeric_limits<NT>::epsilon()) const; + + // POST: returns the time in seconds taken by the constructor call for + // computing the smallest enclosing ball + double get_time() const; + + // POST: deletes dynamically allocated arrays + ~Miniball(); + + private: + void mtf_mb (Sit n); + void mtf_move_to_front (Sit j); + void pivot_mb (Pit n); + void pivot_move_to_front (Pit j); + NT excess (Pit pit) const; + void pop (); + bool push (Pit pit); + NT suboptimality () const; + void create_arrays(); + void delete_arrays(); + }; + + // Class Definition + // ================ + template <typename CoordAccessor> + Miniball<CoordAccessor>::Miniball (int d_, Pit begin, Pit end, + CoordAccessor ca) + : d (d_), + points_begin (begin), + points_end (end), + coord_accessor (ca), + time (clock()), + nt0 (NT(0)), + L(), + support_end (L.begin()), + fsize(0), + ssize(0), + current_c (NULL), + current_sqr_r (NT(-1)), + c (NULL), + sqr_r (NULL), + q0 (NULL), + z (NULL), + f (NULL), + v (NULL), + a (NULL) + { + assert (points_begin != points_end); + create_arrays(); + + // set initial center + for (int j=0; j<d; ++j) c[0][j] = nt0; + current_c = c[0]; + + // compute miniball + pivot_mb (points_end); + + // update time + time = (clock() - time) / CLOCKS_PER_SEC; + } + + template <typename CoordAccessor> + Miniball<CoordAccessor>::~Miniball() + { + delete_arrays(); + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::create_arrays() + { + c = new NT*[d+1]; + v = new NT*[d+1]; + a = new NT*[d+1]; + for (int i=0; i<d+1; ++i) { + c[i] = new NT[d]; + v[i] = new NT[d]; + a[i] = new NT[d]; + } + sqr_r = new NT[d+1]; + q0 = new NT[d]; + z = new NT[d+1]; + f = new NT[d+1]; + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::delete_arrays() + { + delete[] f; + delete[] z; + delete[] q0; + delete[] sqr_r; + for (int i=0; i<d+1; ++i) { + delete[] a[i]; + delete[] v[i]; + delete[] c[i]; + } + delete[] a; + delete[] v; + delete[] c; + } + + template <typename CoordAccessor> + const typename Miniball<CoordAccessor>::NT* + Miniball<CoordAccessor>::center () const + { + return current_c; + } + + template <typename CoordAccessor> + typename Miniball<CoordAccessor>::NT + Miniball<CoordAccessor>::squared_radius () const + { + return current_sqr_r; + } + + template <typename CoordAccessor> + int Miniball<CoordAccessor>::nr_support_points () const + { + assert (ssize < d+2); + return ssize; + } + + template <typename CoordAccessor> + typename Miniball<CoordAccessor>::SupportPointIterator + Miniball<CoordAccessor>::support_points_begin () const + { + return L.begin(); + } + + template <typename CoordAccessor> + typename Miniball<CoordAccessor>::SupportPointIterator + Miniball<CoordAccessor>::support_points_end () const + { + return support_end; + } + + template <typename CoordAccessor> + typename Miniball<CoordAccessor>::NT + Miniball<CoordAccessor>::relative_error (NT& subopt) const + { + NT e, max_e = nt0; + // compute maximum absolute excess of support points + for (SupportPointIterator it = support_points_begin(); + it != support_points_end(); ++it) { + e = excess (*it); + if (e < nt0) e = -e; + if (e > max_e) { + max_e = e; + } + } + // compute maximum excess of any point + for (Pit i = points_begin; i != points_end; ++i) + if ((e = excess (i)) > max_e) + max_e = e; + + subopt = suboptimality(); + assert (current_sqr_r > nt0 || max_e == nt0); + return (current_sqr_r == nt0 ? nt0 : max_e / current_sqr_r); + } + + template <typename CoordAccessor> + bool Miniball<CoordAccessor>::is_valid (NT tol) const + { + NT suboptimality; + return ( (relative_error (suboptimality) <= tol) && (suboptimality == 0) ); + } + + template <typename CoordAccessor> + double Miniball<CoordAccessor>::get_time() const + { + return time; + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::mtf_mb (Sit n) + { + // Algorithm 1: mtf_mb (L_{n-1}, B), where L_{n-1} = [L.begin, n) + // B: the set of forced points, defining the current ball + // S: the superset of support points computed by the algorithm + // -------------------------------------------------------------- + // from B. Gaertner, Fast and Robust Smallest Enclosing Balls, ESA 1999, + // http://www.inf.ethz.ch/personal/gaertner/texts/own_work/esa99_final.pdf + + // PRE: B = S + assert (fsize == ssize); + + support_end = L.begin(); + if ((fsize) == d+1) return; + + // incremental construction + for (Sit i = L.begin(); i != n;) + { + // INV: (support_end - L.begin() == |S|-|B|) + assert (std::distance (L.begin(), support_end) == ssize - fsize); + + Sit j = i++; + if (excess(*j) > nt0) + if (push(*j)) { // B := B + p_i + mtf_mb (j); // mtf_mb (L_{i-1}, B + p_i) + pop(); // B := B - p_i + mtf_move_to_front(j); + } + } + // POST: the range [L.begin(), support_end) stores the set S\B + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::mtf_move_to_front (Sit j) + { + if (support_end == j) + support_end++; + L.splice (L.begin(), L, j); + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::pivot_mb (Pit n) + { + // Algorithm 2: pivot_mb (L_{n-1}), where L_{n-1} = [L.begin, n) + // -------------------------------------------------------------- + // from B. Gaertner, Fast and Robust Smallest Enclosing Balls, ESA 1999, + // http://www.inf.ethz.ch/personal/gaertner/texts/own_work/esa99_final.pdf + NT old_sqr_r; + const NT* c; + Pit pivot, k; + NT e, max_e, sqr_r; + Cit p; + do { + old_sqr_r = current_sqr_r; + sqr_r = current_sqr_r; + + pivot = points_begin; + max_e = nt0; + for (k = points_begin; k != n; ++k) { + p = coord_accessor(k); + e = -sqr_r; + c = current_c; + for (int j=0; j<d; ++j) + e += mb_sqr<NT>(*p++-*c++); + if (e > max_e) { + max_e = e; + pivot = k; + } + } + + if (max_e > nt0) { + // check if the pivot is already contained in the support set + if (std::find(L.begin(), support_end, pivot) == support_end) { + assert (fsize == 0); + if (push (pivot)) { + mtf_mb(support_end); + pop(); + pivot_move_to_front(pivot); + } + } + } + } while (old_sqr_r < current_sqr_r); + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::pivot_move_to_front (Pit j) + { + L.push_front(j); + if (std::distance(L.begin(), support_end) == d+2) + support_end--; + } + + template <typename CoordAccessor> + inline typename Miniball<CoordAccessor>::NT + Miniball<CoordAccessor>::excess (Pit pit) const + { + Cit p = coord_accessor(pit); + NT e = -current_sqr_r; + NT* c = current_c; + for (int k=0; k<d; ++k){ + e += mb_sqr<NT>(*p++-*c++); + } + return e; + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::pop () + { + --fsize; + } + + template <typename CoordAccessor> + bool Miniball<CoordAccessor>::push (Pit pit) + { + int i, j; + NT eps = mb_sqr<NT>(std::numeric_limits<NT>::epsilon()); + + Cit cit = coord_accessor(pit); + Cit p = cit; + + if (fsize==0) { + for (i=0; i<d; ++i) + q0[i] = *p++; + for (i=0; i<d; ++i) + c[0][i] = q0[i]; + sqr_r[0] = nt0; + } + else { + // set v_fsize to Q_fsize + for (i=0; i<d; ++i) + //v[fsize][i] = p[i]-q0[i]; + v[fsize][i] = *p++-q0[i]; + + // compute the a_{fsize,i}, i< fsize + for (i=1; i<fsize; ++i) { + a[fsize][i] = nt0; + for (j=0; j<d; ++j) + a[fsize][i] += v[i][j] * v[fsize][j]; + a[fsize][i]*=(2/z[i]); + } + + // update v_fsize to Q_fsize-\bar{Q}_fsize + for (i=1; i<fsize; ++i) { + for (j=0; j<d; ++j) + v[fsize][j] -= a[fsize][i]*v[i][j]; + } + + // compute z_fsize + z[fsize]=nt0; + for (j=0; j<d; ++j) + z[fsize] += mb_sqr<NT>(v[fsize][j]); + z[fsize]*=2; + + // reject push if z_fsize too small + if (z[fsize]<eps*current_sqr_r) { + return false; + } + + // update c, sqr_r + p=cit; + NT e = -sqr_r[fsize-1]; + for (i=0; i<d; ++i) + e += mb_sqr<NT>(*p++-c[fsize-1][i]); + f[fsize]=e/z[fsize]; + + for (i=0; i<d; ++i) + c[fsize][i] = c[fsize-1][i]+f[fsize]*v[fsize][i]; + sqr_r[fsize] = sqr_r[fsize-1] + e*f[fsize]/2; + } + current_c = c[fsize]; + current_sqr_r = sqr_r[fsize]; + ssize = ++fsize; + return true; + } + + template <typename CoordAccessor> + typename Miniball<CoordAccessor>::NT + Miniball<CoordAccessor>::suboptimality () const + { + NT* l = new NT[d+1]; + NT min_l = nt0; + l[0] = NT(1); + for (int i=ssize-1; i>0; --i) { + l[i] = f[i]; + for (int k=ssize-1; k>i; --k) + l[i]-=a[k][i]*l[k]; + if (l[i] < min_l) min_l = l[i]; + l[0] -= l[i]; + } + if (l[0] < min_l) min_l = l[0]; + delete[] l; + if (min_l < nt0) + return -min_l; + return nt0; + } +} // namespace Miniball + +} // namespace Gudhi + +#endif // MINIBALL_HPP_ diff --git a/src/Cech_complex/test/CMakeLists.txt b/src/Cech_complex/test/CMakeLists.txt new file mode 100644 index 00000000..8db51173 --- /dev/null +++ b/src/Cech_complex/test/CMakeLists.txt @@ -0,0 +1,15 @@ +cmake_minimum_required(VERSION 2.6) +project(Cech_complex_tests) + +include(GUDHI_test_coverage) + +add_executable ( Cech_complex_test_unit test_cech_complex.cpp ) +target_link_libraries(Cech_complex_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Cech_complex_test_unit ${TBB_LIBRARIES}) +endif() + +# Do not forget to copy test files in current binary dir +file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + +gudhi_add_coverage_test(Cech_complex_test_unit) diff --git a/src/Cech_complex/test/README b/src/Cech_complex/test/README new file mode 100644 index 00000000..adf704f7 --- /dev/null +++ b/src/Cech_complex/test/README @@ -0,0 +1,12 @@ +To compile: +*********** + +cmake . +make + +To launch with details: +*********************** + +./Cech_complex_test_unit --report_level=detailed --log_level=all + + ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Cech_complex/test/test_cech_complex.cpp b/src/Cech_complex/test/test_cech_complex.cpp new file mode 100644 index 00000000..9039169c --- /dev/null +++ b/src/Cech_complex/test/test_cech_complex.cpp @@ -0,0 +1,264 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2018 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "cech_complex" +#include <boost/test/unit_test.hpp> + +#include <cmath> // float comparison +#include <limits> +#include <string> +#include <vector> +#include <algorithm> // std::max + +#include <gudhi/Cech_complex.h> +// to construct Cech_complex from a OFF file of points +#include <gudhi/Points_off_io.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Unitary_tests_utils.h> +#include <gudhi/Miniball.hpp> + +// Type definitions +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; +using Point = std::vector<Filtration_value>; +using Point_cloud = std::vector<Point>; +using Points_off_reader = Gudhi::Points_off_reader<Point>; +using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>; + +using Point_iterator = Point_cloud::const_iterator; +using Coordinate_iterator = Point::const_iterator; +using Min_sphere = Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>; + +BOOST_AUTO_TEST_CASE(Cech_complex_for_documentation) { + // ---------------------------------------------------------------------------- + // + // Init of a Cech complex from a point cloud + // + // ---------------------------------------------------------------------------- + Point_cloud points; + points.push_back({1., 0.}); // 0 + points.push_back({0., 1.}); // 1 + points.push_back({2., 1.}); // 2 + points.push_back({3., 2.}); // 3 + points.push_back({0., 3.}); // 4 + points.push_back({3. + std::sqrt(3.), 3.}); // 5 + points.push_back({1., 4.}); // 6 + points.push_back({3., 4.}); // 7 + points.push_back({2., 4. + std::sqrt(3.)}); // 8 + points.push_back({0., 4.}); // 9 + points.push_back({-0.5, 2.}); // 10 + + Filtration_value max_radius = 1.0; + std::cout << "========== NUMBER OF POINTS = " << points.size() << " - Cech max_radius = " << max_radius + << "==========" << std::endl; + + Cech_complex cech_complex_for_doc(points, max_radius); + + GUDHI_TEST_FLOAT_EQUALITY_CHECK(cech_complex_for_doc.max_radius(), max_radius); + std::size_t i = 0; + for (; i < points.size(); i++) { + BOOST_CHECK(points[i] == cech_complex_for_doc.get_point(i)); + } + + const int DIMENSION_1 = 1; + Simplex_tree st; + cech_complex_for_doc.create_complex(st, DIMENSION_1); + std::cout << "st.dimension()=" << st.dimension() << std::endl; + BOOST_CHECK(st.dimension() == DIMENSION_1); + + const int NUMBER_OF_VERTICES = 11; + std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl; + BOOST_CHECK(st.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl; + BOOST_CHECK(st.num_simplices() == 27); + + // Check filtration values of vertices is 0.0 + for (auto f_simplex : st.skeleton_simplex_range(0)) { + BOOST_CHECK(st.filtration(f_simplex) == 0.0); + } + + // Check filtration values of edges + for (auto f_simplex : st.skeleton_simplex_range(DIMENSION_1)) { + if (DIMENSION_1 == st.dimension(f_simplex)) { + std::vector<Point> vp; + std::cout << "vertex = ("; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << ","; + vp.push_back(points.at(vertex)); + } + std::cout << ") - distance =" << Gudhi::Minimal_enclosing_ball_radius()(vp.at(0), vp.at(1)) + << " - filtration =" << st.filtration(f_simplex) << std::endl; + BOOST_CHECK(vp.size() == 2); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), + Gudhi::Minimal_enclosing_ball_radius()(vp.at(0), vp.at(1))); + } + } + + const int DIMENSION_2 = 2; + +#ifdef GUDHI_DEBUG + BOOST_CHECK_THROW(cech_complex_for_doc.create_complex(st, DIMENSION_2), std::invalid_argument); +#endif + + Simplex_tree st2; + cech_complex_for_doc.create_complex(st2, DIMENSION_2); + std::cout << "st2.dimension()=" << st2.dimension() << std::endl; + BOOST_CHECK(st2.dimension() == DIMENSION_2); + + std::cout << "st2.num_vertices()=" << st2.num_vertices() << std::endl; + BOOST_CHECK(st2.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st2.num_simplices()=" << st2.num_simplices() << std::endl; + BOOST_CHECK(st2.num_simplices() == 30); + + Point_cloud points012; + for (std::size_t vertex = 0; vertex <= 2; vertex++) { + points012.push_back(cech_complex_for_doc.get_point(vertex)); + } + std::size_t dimension = points[0].end() - points[0].begin(); + Min_sphere ms012(dimension, points012.begin(), points012.end()); + + Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2})); + std::cout << "f012= " << f012 << " | ms012_radius= " << std::sqrt(ms012.squared_radius()) << std::endl; + + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::sqrt(ms012.squared_radius())); + + Point_cloud points1410; + points1410.push_back(cech_complex_for_doc.get_point(1)); + points1410.push_back(cech_complex_for_doc.get_point(4)); + points1410.push_back(cech_complex_for_doc.get_point(10)); + Min_sphere ms1410(dimension, points1410.begin(), points1410.end()); + + Simplex_tree::Filtration_value f1410 = st2.filtration(st2.find({1, 4, 10})); + std::cout << "f1410= " << f1410 << " | ms1410_radius= " << std::sqrt(ms1410.squared_radius()) << std::endl; + + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f1410, std::sqrt(ms1410.squared_radius())); + + Point_cloud points469; + points469.push_back(cech_complex_for_doc.get_point(4)); + points469.push_back(cech_complex_for_doc.get_point(6)); + points469.push_back(cech_complex_for_doc.get_point(9)); + Min_sphere ms469(dimension, points469.begin(), points469.end()); + + Simplex_tree::Filtration_value f469 = st2.filtration(st2.find({4, 6, 9})); + std::cout << "f469= " << f469 << " | ms469_radius= " << std::sqrt(ms469.squared_radius()) << std::endl; + + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f469, std::sqrt(ms469.squared_radius())); + + BOOST_CHECK((st2.find({6, 7, 8}) == st2.null_simplex())); + BOOST_CHECK((st2.find({3, 5, 7}) == st2.null_simplex())); +} + +BOOST_AUTO_TEST_CASE(Cech_complex_from_points) { + // ---------------------------------------------------------------------------- + // Init of a list of points + // ---------------------------------------------------------------------------- + Point_cloud points; + std::vector<double> coords = {0.0, 0.0, 0.0, 1.0}; + points.push_back(Point(coords.begin(), coords.end())); + coords = {0.0, 0.0, 1.0, 0.0}; + points.push_back(Point(coords.begin(), coords.end())); + coords = {0.0, 1.0, 0.0, 0.0}; + points.push_back(Point(coords.begin(), coords.end())); + coords = {1.0, 0.0, 0.0, 0.0}; + points.push_back(Point(coords.begin(), coords.end())); + + // ---------------------------------------------------------------------------- + // Init of a Cech complex from the list of points + // ---------------------------------------------------------------------------- + Cech_complex cech_complex_from_points(points, 2.0); + + std::cout << "========== cech_complex_from_points ==========" << std::endl; + Simplex_tree st; + const int DIMENSION = 3; + cech_complex_from_points.create_complex(st, DIMENSION); + + // Another way to check num_simplices + std::cout << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl; + int num_simplices = 0; + for (auto f_simplex : st.filtration_simplex_range()) { + num_simplices++; + std::cout << " ( "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " + << "[" << st.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + BOOST_CHECK(num_simplices == 15); + std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl; + BOOST_CHECK(st.num_simplices() == 15); + + std::cout << "st.dimension()=" << st.dimension() << std::endl; + BOOST_CHECK(st.dimension() == DIMENSION); + std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl; + BOOST_CHECK(st.num_vertices() == 4); + + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl; + switch (st.dimension(f_simplex)) { + case 0: + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.0); + break; + case 1: + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.707107, .00001); + break; + case 2: + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.816497, .00001); + break; + case 3: + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.866025, .00001); + break; + default: + BOOST_CHECK(false); // Shall not happen + break; + } + } +} + +#ifdef GUDHI_DEBUG +BOOST_AUTO_TEST_CASE(Cech_create_complex_throw) { + // ---------------------------------------------------------------------------- + // + // Init of a Cech complex from a OFF file + // + // ---------------------------------------------------------------------------- + std::string off_file_name("alphacomplexdoc.off"); + double max_radius = 12.0; + std::cout << "========== OFF FILE NAME = " << off_file_name << " - Cech max_radius=" << max_radius + << "==========" << std::endl; + + Gudhi::Points_off_reader<Point> off_reader(off_file_name); + Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius); + + Simplex_tree stree; + std::vector<int> simplex = {0, 1, 2}; + stree.insert_simplex_and_subfaces(simplex); + std::cout << "Check exception throw in debug mode" << std::endl; + // throw excpt because stree is not empty + BOOST_CHECK_THROW(cech_complex_from_file.create_complex(stree, 1), std::invalid_argument); +} +#endif diff --git a/src/Cech_complex/utilities/CMakeLists.txt b/src/Cech_complex/utilities/CMakeLists.txt new file mode 100644 index 00000000..30b99729 --- /dev/null +++ b/src/Cech_complex/utilities/CMakeLists.txt @@ -0,0 +1,14 @@ +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_LIBRARY}) + +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") + +install(TARGETS cech_persistence DESTINATION bin) diff --git a/src/Cech_complex/utilities/cech_persistence.cpp b/src/Cech_complex/utilities/cech_persistence.cpp new file mode 100644 index 00000000..abd9dbcd --- /dev/null +++ b/src/Cech_complex/utilities/cech_persistence.cpp @@ -0,0 +1,136 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2018 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Cech_complex.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Points_off_io.h> + +#include <boost/program_options.hpp> + +#include <string> +#include <vector> +#include <limits> // infinity + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = Simplex_tree::Filtration_value; +using Point = std::vector<double>; +using Point_cloud = std::vector<Point>; +using Points_off_reader = Gudhi::Points_off_reader<Point>; +using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; + +void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, + Filtration_value& max_radius, int& dim_max, int& p, Filtration_value& min_persistence); + +int main(int argc, char* argv[]) { + std::string off_file_points; + std::string filediag; + Filtration_value max_radius; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, filediag, max_radius, dim_max, p, min_persistence); + + Points_off_reader off_reader(off_file_points); + Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius); + + // Construct the Cech complex in a Simplex Tree + Simplex_tree simplex_tree; + + cech_complex_from_file.create_complex(simplex_tree, dim_max); + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + +void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, + Filtration_value& max_radius, int& dim_max, int& p, Filtration_value& min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()("input-file", po::value<std::string>(&off_file_points), + "Name of an OFF file containing a point set.\n"); + + po::options_description visible("Allowed options", 100); + visible.add_options()("help,h", "produce help message")( + "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout")( + "max-radius,r", + po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()), + "Maximal length of an edge for the Cech complex construction.")( + "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Cech complex we want to compute.")( + "field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "min-persistence,m", po::value<Filtration_value>(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " + "intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Cech complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Cech_complex/utilities/cechcomplex.md b/src/Cech_complex/utilities/cechcomplex.md new file mode 100644 index 00000000..f7817dbb --- /dev/null +++ b/src/Cech_complex/utilities/cechcomplex.md @@ -0,0 +1,38 @@ + + +# Čech complex # + +## cech_persistence ## +This program computes the persistent homology with coefficient field *Z/pZ* of +a Čech complex defined on a set of input points, using Euclidean distance. The +output diagram contains one bar per line, written with the convention: + +`p dim birth death` + +where `dim` is the dimension of the homological feature, `birth` and `death` +are respectively the birth and death of the feature, and `p` is the +characteristic of the field *Z/pZ* used for homology coefficients (`p` must be +a prime number). + +**Usage** + +`cech_persistence [options] <OFF input file>` + +**Allowed options** + +* `-h [ --help ]` Produce help message +* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. +* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Čech complex construction. +* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Čech complex we want to compute. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the 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. + +Beware: this program may use a lot of RAM and take a lot of time if `max-edge-length` is set to a large value. + +**Example 1 with Z/2Z coefficients** + +`cech_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2` + +**Example 2 with Z/3Z coefficients** + +`cech_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3` diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt index a92d1685..582b7ab8 100644 --- a/src/Contraction/example/CMakeLists.txt +++ b/src/Contraction/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Contraction_examples) add_executable(RipsContraction Rips_contraction.cpp) diff --git a/src/Doxyfile b/src/Doxyfile index 2348b290..da753c04 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -38,7 +38,7 @@ PROJECT_NAME = "GUDHI" # could be handy for archiving the generated documentation or if some version # control system is used. -PROJECT_NUMBER = "2.1.0" +PROJECT_NUMBER = "2.2.0" # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer a @@ -843,7 +843,8 @@ EXAMPLE_RECURSIVE = NO IMAGE_PATH = doc/Skeleton_blocker/ \ doc/Alpha_complex/ \ doc/common/ \ - doc/Contraction/ \ + doc/Cech_complex/ \ + doc/Contraction/ \ doc/Simplex_tree/ \ doc/Persistent_cohomology/ \ doc/Witness_complex/ \ diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt index 2503a03e..b357b8f7 100644 --- a/src/GudhUI/CMakeLists.txt +++ b/src/GudhUI/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.8) project(GudhUI) # Need to find OpenGL first as find_package(Qt5) tries to #include"GL/gl.h" on some platforms @@ -38,4 +37,4 @@ if (OPENGL_FOUND) install(TARGETS GudhUI DESTINATION bin) endif() -endif(OPENGL_FOUND)
\ No newline at end of file +endif(OPENGL_FOUND) diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt index 542c6af4..fdecf86e 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Nerve_GIC_examples) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) @@ -17,11 +16,11 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC> - "tore3D_1307.off" "0") + "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC> - "lucky_cat.off" - "lucky_cat_PCA1") + "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" + "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") install(TARGETS CoordGIC DESTINATION bin) install(TARGETS FuncGIC DESTINATION bin) diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index aa6478e5..7aa95210 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -148,10 +148,20 @@ class Cover_complex { for (boost::tie(ei, ei_end) = boost::edges(G); ei != ei_end; ++ei) boost::remove_edge(*ei, G); } + // Thread local is not available on XCode version < V.8 + // If not available, random engine is a class member. +#ifndef GUDHI_CAN_USE_CXX11_THREAD_LOCAL + std::default_random_engine re; +#endif // GUDHI_CAN_USE_CXX11_THREAD_LOCAL + // Find random number in [0,1]. double GetUniform() { + // Thread local is not available on XCode version < V.8 + // If available, random engine is defined for each thread. +#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL thread_local std::default_random_engine re; - thread_local std::uniform_real_distribution<double> Dist(0, 1); +#endif // GUDHI_CAN_USE_CXX11_THREAD_LOCAL + std::uniform_real_distribution<double> Dist(0, 1); return Dist(re); } @@ -415,7 +425,6 @@ class Cover_complex { double set_graph_from_automatic_rips(Distance distance, int N = 100) { int m = floor(n / std::exp((1 + rate_power) * std::log(std::log(n) / std::log(rate_constant)))); m = std::min(m, n - 1); - std::vector<int> samples(m); double delta = 0; if (verbose) std::cout << n << " points in R^" << data_dimension << std::endl; @@ -423,8 +432,12 @@ class Cover_complex { if (distances.size() == 0) compute_pairwise_distances(distance); - #ifdef GUDHI_USE_TBB - tbb::parallel_for(0, N, [&](int i){ + // This cannot be parallelized if thread_local is not defined + // thread_local is not defined for XCode < v.8 + #if defined(GUDHI_USE_TBB) && defined(GUDHI_CAN_USE_CXX11_THREAD_LOCAL) + tbb::mutex deltamutex; + tbb::parallel_for(0, N, [&](int i){ + std::vector<int> samples(m); SampleWithoutReplacement(n, m, samples); double hausdorff_dist = 0; for (int j = 0; j < n; j++) { @@ -432,10 +445,13 @@ class Cover_complex { for (int k = 1; k < m; k++) mj = std::min(mj, distances[j][samples[k]]); hausdorff_dist = std::max(hausdorff_dist, mj); } + deltamutex.lock(); delta += hausdorff_dist / N; + deltamutex.unlock(); }); #else for (int i = 0; i < N; i++) { + std::vector<int> samples(m); SampleWithoutReplacement(n, m, samples); double hausdorff_dist = 0; for (int j = 0; j < n; j++) { @@ -717,6 +733,7 @@ class Cover_complex { #ifdef GUDHI_USE_TBB if (verbose) std::cout << "Computing connected components (parallelized)..." << std::endl; + tbb::mutex covermutex, idmutex; tbb::parallel_for(0, res, [&](int i){ // Compute connected components Graph G = one_skeleton.create_subgraph(); @@ -735,16 +752,20 @@ class Cover_complex { int identifier = ((i + component[j])*(i + component[j]) + 3 * i + component[j]) / 2; // Update covers + covermutex.lock(); cover[preimages[i][j]].push_back(identifier); cover_back[identifier].push_back(preimages[i][j]); cover_fct[identifier] = i; cover_std[identifier] = funcstd[i]; cover_color[identifier].second += func_color[preimages[i][j]]; cover_color[identifier].first += 1; + covermutex.unlock(); } // Maximal dimension is total number of connected components + idmutex.lock(); id += max + 1; + idmutex.unlock(); }); #else if (verbose) std::cout << "Computing connected components..." << std::endl; diff --git a/src/Nerve_GIC/test/CMakeLists.txt b/src/Nerve_GIC/test/CMakeLists.txt index c35cdff7..99263ea0 100644 --- a/src/Nerve_GIC/test/CMakeLists.txt +++ b/src/Nerve_GIC/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Graph_induced_complex_tests) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt index 7a838a8c..215f9dfd 100644 --- a/src/Nerve_GIC/utilities/CMakeLists.txt +++ b/src/Nerve_GIC/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Nerve_GIC_examples) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt index d236c3a6..a7c6ef39 100644 --- a/src/Persistence_representations/example/CMakeLists.txt +++ b/src/Persistence_representations/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_example) add_executable ( Persistence_representations_example_landscape_on_grid persistence_landscape_on_grid.cpp ) diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape.h b/src/Persistence_representations/include/gudhi/Persistence_landscape.h index 4381a55b..9cab0166 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_landscape.h +++ b/src/Persistence_representations/include/gudhi/Persistence_landscape.h @@ -734,7 +734,7 @@ double Persistence_landscape::compute_integral_of_landscape(double p) const { double Persistence_landscape::compute_value_at_a_given_point(unsigned level, double x) const { bool compute_value_at_a_given_pointDbg = false; // in such a case lambda_level = 0. - if (level > this->land.size()) return 0; + if (level >= this->land.size()) return 0; // we know that the points in this->land[level] are ordered according to x coordinate. Therefore, we can find the // point by using bisection: @@ -1235,40 +1235,43 @@ double compute_inner_product(const Persistence_landscape& l1, const Persistence_ std::cerr << "Computing inner product for a level : " << level << std::endl; getchar(); } - if (l1.land[level].size() * l2.land[level].size() == 0) continue; + auto&& l1_land_level = l1.land[level]; + auto&& l2_land_level = l2.land[level]; + + if (l1_land_level.size() * l2_land_level.size() == 0) continue; // endpoints of the interval on which we will compute the inner product of two locally linear functions: double x1 = -std::numeric_limits<int>::max(); double x2; - if (l1.land[level][1].first < l2.land[level][1].first) { - x2 = l1.land[level][1].first; + if (l1_land_level[1].first < l2_land_level[1].first) { + x2 = l1_land_level[1].first; } else { - x2 = l2.land[level][1].first; + x2 = l2_land_level[1].first; } // iterators for the landscapes l1 and l2 size_t l1It = 0; size_t l2It = 0; - while ((l1It < l1.land[level].size() - 1) && (l2It < l2.land[level].size() - 1)) { + while ((l1It < l1_land_level.size() - 1) && (l2It < l2_land_level.size() - 1)) { // compute the value of a inner product on a interval [x1,x2] double a, b, c, d; - if (l1.land[level][l1It + 1].first != l1.land[level][l1It].first) { - a = (l1.land[level][l1It + 1].second - l1.land[level][l1It].second) / - (l1.land[level][l1It + 1].first - l1.land[level][l1It].first); + if (l1_land_level[l1It + 1].first != l1_land_level[l1It].first) { + a = (l1_land_level[l1It + 1].second - l1_land_level[l1It].second) / + (l1_land_level[l1It + 1].first - l1_land_level[l1It].first); } else { a = 0; } - b = l1.land[level][l1It].second - a * l1.land[level][l1It].first; - if (l2.land[level][l2It + 1].first != l2.land[level][l2It].first) { - c = (l2.land[level][l2It + 1].second - l2.land[level][l2It].second) / - (l2.land[level][l2It + 1].first - l2.land[level][l2It].first); + b = l1_land_level[l1It].second - a * l1_land_level[l1It].first; + if (l2_land_level[l2It + 1].first != l2_land_level[l2It].first) { + c = (l2_land_level[l2It + 1].second - l2_land_level[l2It].second) / + (l2_land_level[l2It + 1].first - l2_land_level[l2It].first); } else { c = 0; } - d = l2.land[level][l2It].second - c * l2.land[level][l2It].first; + d = l2_land_level[l2It].second - c * l2_land_level[l2It].first; double contributionFromThisPart = (a * c * x2 * x2 * x2 / 3 + (a * d + b * c) * x2 * x2 / 2 + b * d * x2) - (a * c * x1 * x1 * x1 / 3 + (a * d + b * c) * x1 * x1 / 2 + b * d * x1); @@ -1276,10 +1279,10 @@ double compute_inner_product(const Persistence_landscape& l1, const Persistence_ result += contributionFromThisPart; if (dbg) { - std::cerr << "[l1.land[level][l1It].first,l1.land[level][l1It+1].first] : " << l1.land[level][l1It].first - << " , " << l1.land[level][l1It + 1].first << std::endl; - std::cerr << "[l2.land[level][l2It].first,l2.land[level][l2It+1].first] : " << l2.land[level][l2It].first - << " , " << l2.land[level][l2It + 1].first << std::endl; + std::cerr << "[l1_land_level[l1It].first,l1_land_level[l1It+1].first] : " << l1_land_level[l1It].first + << " , " << l1_land_level[l1It + 1].first << std::endl; + std::cerr << "[l2_land_level[l2It].first,l2_land_level[l2It+1].first] : " << l2_land_level[l2It].first + << " , " << l2_land_level[l2It + 1].first << std::endl; std::cerr << "a : " << a << ", b : " << b << " , c: " << c << ", d : " << d << std::endl; std::cerr << "x1 : " << x1 << " , x2 : " << x2 << std::endl; std::cerr << "contributionFromThisPart : " << contributionFromThisPart << std::endl; @@ -1288,14 +1291,14 @@ double compute_inner_product(const Persistence_landscape& l1, const Persistence_ } // we have two intervals in which functions are constant: - // [l1.land[level][l1It].first , l1.land[level][l1It+1].first] + // [l1_land_level[l1It].first , l1_land_level[l1It+1].first] // and - // [l2.land[level][l2It].first , l2.land[level][l2It+1].first] + // [l2_land_level[l2It].first , l2_land_level[l2It+1].first] // We also have an interval [x1,x2]. Since the intervals in the landscapes cover the whole R, then it is clear // that x2 - // is either l1.land[level][l1It+1].first of l2.land[level][l2It+1].first or both. Lets test it. - if (x2 == l1.land[level][l1It + 1].first) { - if (x2 == l2.land[level][l2It + 1].first) { + // is either l1_land_level[l1It+1].first of l2_land_level[l2It+1].first or both. Lets test it. + if (x2 == l1_land_level[l1It + 1].first) { + if (x2 == l2_land_level[l2It + 1].first) { // in this case, we increment both: ++l2It; if (dbg) { @@ -1314,12 +1317,16 @@ double compute_inner_product(const Persistence_landscape& l1, const Persistence_ std::cerr << "Incrementing second \n"; } } + + if ( l1It + 1 >= l1_land_level.size() )break; + if ( l2It + 1 >= l2_land_level.size() )break; + // Now, we shift x1 and x2: x1 = x2; - if (l1.land[level][l1It + 1].first < l2.land[level][l2It + 1].first) { - x2 = l1.land[level][l1It + 1].first; + if (l1_land_level[l1It + 1].first < l2_land_level[l2It + 1].first) { + x2 = l1_land_level[l1It + 1].first; } else { - x2 = l2.land[level][l2It + 1].first; + x2 = l2_land_level[l2It + 1].first; } } } diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h index e0fc7107..4a2b9d68 100644 --- a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h +++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h @@ -57,7 +57,7 @@ std::vector<std::pair<double, double> > read_persistence_intervals_in_one_dimens std::string line; std::vector<std::pair<double, double> > barcode_initial = - read_persistence_intervals_in_dimension(filename, (int)dimension); + read_persistence_intervals_in_dimension(filename, static_cast<int>(dimension)); std::vector<std::pair<double, double> > final_barcode; final_barcode.reserve(barcode_initial.size()); @@ -92,8 +92,8 @@ std::vector<std::pair<double, double> > read_persistence_intervals_in_one_dimens if ((barcode_initial[i].second == std::numeric_limits<double>::infinity()) && (what_to_substitute_for_infinite_bar != -1)) { - if (barcode_initial[i].first < what_to_substitute_for_infinite_bar) // if only birth < death. - { + if (barcode_initial[i].first < what_to_substitute_for_infinite_bar) { + // if only birth < death. final_barcode.push_back( std::pair<double, double>(barcode_initial[i].first, what_to_substitute_for_infinite_bar)); } diff --git a/src/Persistence_representations/test/CMakeLists.txt b/src/Persistence_representations/test/CMakeLists.txt index ca1713c3..fb650485 100644 --- a/src/Persistence_representations/test/CMakeLists.txt +++ b/src/Persistence_representations/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_test) include(GUDHI_test_coverage) diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt index 386e9fa5..89ef232f 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_heat_maps_utilities) add_persistence_representation_creation_utility(create_pssk "10" "-1" "-1" "4" "-1") diff --git a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt index 875ff45e..649b72cb 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_intervals_utilities) diff --git a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt index d7087ed8..6b24d032 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_landscapes_utilities) add_persistence_representation_creation_utility(create_landscapes "-1") diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt index c5ea4bbf..36f3196b 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_lanscapes_on_grid_utilities) # Need to set grid min and max for further average, distance and scalar_product diff --git a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt index a401c955..bc982094 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_vectors_utilities) add_persistence_representation_creation_utility(create_persistence_vectors "-1") diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt index 8b135ba1..2bb3b0c7 100644 --- a/src/Persistent_cohomology/benchmark/CMakeLists.txt +++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt @@ -1,6 +1,4 @@ -cmake_minimum_required(VERSION 2.6) project(Persistent_cohomology_benchmark) - if(GMP_FOUND) if(GMPXX_FOUND) diff --git a/src/Persistent_cohomology/concept/FilteredComplex.h b/src/Persistent_cohomology/concept/FilteredComplex.h index 178503c9..62b9002f 100644 --- a/src/Persistent_cohomology/concept/FilteredComplex.h +++ b/src/Persistent_cohomology/concept/FilteredComplex.h @@ -29,10 +29,6 @@ struct FilteredComplex { /** Handle to specify a simplex. */ typedef unspecified Simplex_handle; -/** \brief Key associated to each simplex. - * - * Must be an integer type. */ - typedef unspecified Simplex_key; /** \brief Type for the value of the filtration function. * * Must be comparable with <. */ @@ -58,20 +54,10 @@ struct FilteredComplex * filtration function on the complex. */ Filtration_value filtration(Simplex_handle sh); -/** \brief Returns a key that is different from the keys associated - * to the simplices. */ - Simplex_key null_key (); -/** \brief Returns the key associated to a simplex. - * - * This is never called on null_simplex(). */ - Simplex_key key ( Simplex_handle sh ); /** \brief Returns the simplex that has index idx in the filtration. * * This is only called on valid indices. */ Simplex_handle simplex ( size_t idx ); -/** \brief Assign a key to a simplex. */ - void assign_key(Simplex_handle sh, Simplex_key key); - /** \brief Iterator on the simplices belonging to the * boundary of a simplex. * @@ -115,6 +101,26 @@ typedef unspecified Filtration_simplex_range; * .begin() and .end() return type Filtration_simplex_iterator.*/ Filtration_simplex_range filtration_simplex_range(); +/** \name Map interface + * Conceptually a `std::unordered_map<Simplex_handle,std::size_t>`. + * @{ */ +/** \brief Data stored for each simplex. + * + * Must be an integer type. */ + typedef unspecified Simplex_key; +/** \brief Returns a constant dummy number that is either negative, + * or at least as large as `num_simplices()`. Suggested value: -1. */ + Simplex_key null_key (); +/** \brief Returns the number stored for a simplex by `assign_key`. + * + * This is never called on null_simplex(). */ + Simplex_key key ( Simplex_handle sh ); +/** \brief Store a number for a simplex, which can later be retrieved with `key(sh)`. + * + * This is never called on null_simplex(). */ + void assign_key(Simplex_handle sh, Simplex_key n); +/** @} */ + /* \brief Iterator over the simplices of the complex, * in an arbitrary order. diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 18e2913b..0f731519 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistent_cohomology_examples) add_executable(plain_homology plain_homology.cpp) diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt index 45f53eb9..f8baf861 100644 --- a/src/Persistent_cohomology/test/CMakeLists.txt +++ b/src/Persistent_cohomology/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistent_cohomology_tests) include(GUDHI_test_coverage) diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index af86636b..e7772bdb 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Rips_complex_examples) # Point cloud diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp index 1343f24d..05bacb9f 100644 --- a/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp +++ b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp @@ -15,11 +15,11 @@ int main() { using Distance_matrix = std::vector<std::vector<Filtration_value>>; // User defined correlation matrix is: - // |1 0.06 0.23 0.01 0.89| - // |0.06 1 0.74 0.01 0.61| - // |0.23 0.74 1 0.72 0.03| - // |0.01 0.01 0.72 1 0.7 | - // |0.89 0.61 0.03 0.7 1 | + // |1 0.06 0.23 0.01 0.89| + // |0.06 1 0.74 0.01 0.61| + // |0.23 0.74 1 0.72 0.03| + // |0.01 0.01 0.72 1 0.7 | + // |0.89 0.61 0.03 0.7 1 | Distance_matrix correlations; correlations.push_back({}); diff --git a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h index 19a44b28..4dcc08ed 100644 --- a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h +++ b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h @@ -54,7 +54,7 @@ namespace rips_complex { template <typename Filtration_value> class Sparse_rips_complex { private: - // TODO: use a different graph where we know we can safely insert in parallel. + // TODO(MG): use a different graph where we know we can safely insert in parallel. typedef typename boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<vertex_filtration_t, Filtration_value>, boost::property<edge_filtration_t, Filtration_value>> @@ -140,7 +140,7 @@ class Sparse_rips_complex { put(vertex_filtration_t(), graph_, v, 0); } - // TODO: + // TODO(MG): // - make it parallel // - only test near-enough neighbors for (int i = 0; i < n; ++i) diff --git a/src/Rips_complex/test/CMakeLists.txt b/src/Rips_complex/test/CMakeLists.txt index 3da9c90d..745d953c 100644 --- a/src/Rips_complex/test/CMakeLists.txt +++ b/src/Rips_complex/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Rips_complex_tests) include(GUDHI_test_coverage) diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt index deb73ff0..4b565628 100644 --- a/src/Rips_complex/utilities/CMakeLists.txt +++ b/src/Rips_complex/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Rips_complex_utilities) add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) diff --git a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp index d4671b45..c78677d2 100644 --- a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp +++ b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp @@ -31,6 +31,7 @@ #include <string> #include <vector> #include <limits> // infinity +#include <algorithm> // for sort // Types definition using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index b33b2d05..857e8518 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Simplex_tree_examples) add_executable ( Simplex_tree_example_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp ) diff --git a/src/Simplex_tree/example/graph_expansion_with_blocker.cpp b/src/Simplex_tree/example/graph_expansion_with_blocker.cpp index f675e353..f39de31f 100644 --- a/src/Simplex_tree/example/graph_expansion_with_blocker.cpp +++ b/src/Simplex_tree/example/graph_expansion_with_blocker.cpp @@ -29,33 +29,33 @@ using Simplex_handle = Simplex_tree::Simplex_handle; int main(int argc, char* const argv[]) { // Construct the Simplex Tree with a 1-skeleton graph example - Simplex_tree simplexTree; + Simplex_tree stree; - simplexTree.insert_simplex({0, 1}, 0.); - simplexTree.insert_simplex({0, 2}, 1.); - simplexTree.insert_simplex({0, 3}, 2.); - simplexTree.insert_simplex({1, 2}, 3.); - simplexTree.insert_simplex({1, 3}, 4.); - simplexTree.insert_simplex({2, 3}, 5.); - simplexTree.insert_simplex({2, 4}, 6.); - simplexTree.insert_simplex({3, 6}, 7.); - simplexTree.insert_simplex({4, 5}, 8.); - simplexTree.insert_simplex({4, 6}, 9.); - simplexTree.insert_simplex({5, 6}, 10.); - simplexTree.insert_simplex({6}, 10.); + stree.insert_simplex({0, 1}, 0.); + stree.insert_simplex({0, 2}, 1.); + stree.insert_simplex({0, 3}, 2.); + stree.insert_simplex({1, 2}, 3.); + stree.insert_simplex({1, 3}, 4.); + stree.insert_simplex({2, 3}, 5.); + stree.insert_simplex({2, 4}, 6.); + stree.insert_simplex({3, 6}, 7.); + stree.insert_simplex({4, 5}, 8.); + stree.insert_simplex({4, 6}, 9.); + stree.insert_simplex({5, 6}, 10.); + stree.insert_simplex({6}, 10.); - simplexTree.expansion_with_blockers(3, [&](Simplex_handle sh) { + stree.expansion_with_blockers(3, [&](Simplex_handle sh) { bool result = false; std::cout << "Blocker on ["; // User can loop on the vertices from the given simplex_handle i.e. - for (auto vertex : simplexTree.simplex_vertex_range(sh)) { + for (auto vertex : stree.simplex_vertex_range(sh)) { // We block the expansion, if the vertex '6' is in the given list of vertices if (vertex == 6) result = true; std::cout << vertex << ", "; } - std::cout << "] ( " << simplexTree.filtration(sh); + std::cout << "] ( " << stree.filtration(sh); // User can re-assign a new filtration value directly in the blocker (default is the maximal value of boudaries) - simplexTree.assign_filtration(sh, simplexTree.filtration(sh) + 1.); + stree.assign_filtration(sh, stree.filtration(sh) + 1.); std::cout << " + 1. ) = " << result << std::endl; @@ -63,13 +63,13 @@ int main(int argc, char* const argv[]) { }); std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices"; - std::cout << " - dimension " << simplexTree.dimension() << "\n"; + std::cout << "* The complex contains " << stree.num_simplices() << " simplices"; + std::cout << " - dimension " << stree.dimension() << "\n"; std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; - for (auto f_simplex : simplexTree.filtration_simplex_range()) { + for (auto f_simplex : stree.filtration_simplex_range()) { std::cout << " " - << "[" << simplexTree.filtration(f_simplex) << "] "; - for (auto vertex : simplexTree.simplex_vertex_range(f_simplex)) std::cout << "(" << vertex << ")"; + << "[" << stree.filtration(f_simplex) << "] "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) std::cout << "(" << vertex << ")"; std::cout << std::endl; } diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 5d4ea30c..ee96d5a2 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -689,7 +689,11 @@ class Simplex_tree { return { null_simplex(), true }; // ----->> // Copy before sorting - thread_local std::vector<Vertex_handle> copy; + // Thread local is not available on XCode version < V.8 - It will slow down computation +#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL + thread_local +#endif // GUDHI_CAN_USE_CXX11_THREAD_LOCAL + std::vector<Vertex_handle> copy; copy.clear(); copy.insert(copy.end(), first, last); std::sort(std::begin(copy), std::end(copy)); @@ -1238,9 +1242,8 @@ class Simplex_tree { } public: - /** \brief Browse the simplex tree to ensure the filtration is not decreasing. - * The simplex tree is browsed starting from the root until the leaf, and the filtration values are set with their - * parent value (increased), in case the values are decreasing. + /** \brief This function ensures that each simplex has a higher filtration value than its faces by increasing the + * filtration values. * @return The filtration modification information. * \post Some simplex tree functions require the filtration to be valid. `make_filtration_non_decreasing()` * function is not launching `initialize_filtration()` but returns the filtration modification information. If the 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 335bac1e..02c8bb64 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 @@ -101,7 +101,9 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< // any end() iterator explicit Simplex_tree_boundary_simplex_iterator(SimplexTree * st) - : sib_(nullptr), + : last_(st->null_vertex()), + next_(st->null_vertex()), + sib_(nullptr), sh_(st->null_simplex()), st_(st) { } @@ -109,7 +111,9 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< template<class SimplexHandle> Simplex_tree_boundary_simplex_iterator(SimplexTree * st, SimplexHandle sh) : last_(sh->first), + next_(st->null_vertex()), sib_(nullptr), + sh_(st->null_simplex()), st_(st) { // Only check once at the beginning instead of for every increment, as this is expensive. if (SimplexTree::Options::contiguous_vertices) @@ -123,9 +127,7 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< sh_ = sib_->members_.begin()+next_; else sh_ = sib_->find(next_); - } else { - sh_ = st->null_simplex(); - } // vertex: == end() + } } private: diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt index 8684ad2a..c63d8532 100644 --- a/src/Simplex_tree/test/CMakeLists.txt +++ b/src/Simplex_tree/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Simplex_tree_tests) include(GUDHI_test_coverage) diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt index de70f089..0e5d2f11 100644 --- a/src/Skeleton_blocker/example/CMakeLists.txt +++ b/src/Skeleton_blocker/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Skeleton_blocker_examples) add_executable(Skeleton_blocker_example_from_simplices Skeleton_blocker_from_simplices.cpp) diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt index 4a363294..19c65871 100644 --- a/src/Skeleton_blocker/test/CMakeLists.txt +++ b/src/Skeleton_blocker/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Skeleton_blocker_tests) include(GUDHI_test_coverage) diff --git a/src/Spatial_searching/example/CMakeLists.txt b/src/Spatial_searching/example/CMakeLists.txt index 4cf3d863..0f799987 100644 --- a/src/Spatial_searching/example/CMakeLists.txt +++ b/src/Spatial_searching/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Spatial_searching_examples) if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Spatial_searching/test/CMakeLists.txt b/src/Spatial_searching/test/CMakeLists.txt index b9da7b4e..b60ab1e3 100644 --- a/src/Spatial_searching/test/CMakeLists.txt +++ b/src/Spatial_searching/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Spatial_searching_tests) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt index 34400b1e..f26d107f 100644 --- a/src/Subsampling/example/CMakeLists.txt +++ b/src/Subsampling/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Subsampling_examples) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Subsampling/test/CMakeLists.txt b/src/Subsampling/test/CMakeLists.txt index dbf97db3..924f0925 100644 --- a/src/Subsampling/test/CMakeLists.txt +++ b/src/Subsampling/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Subsampling_tests) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt index 8729e394..f136ab27 100644 --- a/src/Tangential_complex/benchmark/CMakeLists.txt +++ b/src/Tangential_complex/benchmark/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Tangential_complex_benchmark) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index 16d1339d..af0dac51 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Tangential_complex_examples) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index d8356520..9d8fdcd3 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -1100,7 +1100,10 @@ class Tangential_complex { // of the sphere "star sphere" centered at "center_vertex" // and which contains all the // circumspheres of the star of "center_vertex" - boost::optional<FT> squared_star_sphere_radius_plus_margin; + boost::optional<FT> squared_star_sphere_radius_plus_margin = boost::make_optional(false, FT()); + // This is the strange way boost is recommending to get rid of "may be used uninitialized in this function". + // Former code was : + // boost::optional<FT> squared_star_sphere_radius_plus_margin; // Insert points until we find a point which is outside "star sphere" for (auto nn_it = ins_range.begin(); diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt index 1948c8f6..902f19af 100644 --- a/src/Tangential_complex/test/CMakeLists.txt +++ b/src/Tangential_complex/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Tangential_complex_tests) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index a8231392..3d838c0d 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Witness_complex_examples) add_executable ( Witness_complex_example_nearest_landmark_table example_nearest_landmark_table.cpp ) diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h index 81566824..4b755daa 100644 --- a/src/Witness_complex/example/generators.h +++ b/src/Witness_complex/example/generators.h @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_ -#define EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_ +#ifndef GENERATORS_H_ +#define GENERATORS_H_ #include <CGAL/Epick_d.h> #include <CGAL/point_generators_d.h> @@ -163,4 +163,4 @@ void generate_points_torus(Point_Vector& W, int nbP, int dim) { } } -#endif // EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_ +#endif // GENERATORS_H_ diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt index 0b523eaf..58ac60c5 100644 --- a/src/Witness_complex/test/CMakeLists.txt +++ b/src/Witness_complex/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Witness_complex_tests) include(GUDHI_test_coverage) diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt index 125a41ff..ce5e29f2 100644 --- a/src/Witness_complex/utilities/CMakeLists.txt +++ b/src/Witness_complex/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Witness_complex_utilities) # CGAL and Eigen3 are required for Euclidean version of Witness diff --git a/src/cmake/modules/GUDHI_compilation_flags.cmake b/src/cmake/modules/GUDHI_compilation_flags.cmake new file mode 100644 index 00000000..a01d6e13 --- /dev/null +++ b/src/cmake/modules/GUDHI_compilation_flags.cmake @@ -0,0 +1,72 @@ +# This files manage compilation flags required by GUDHI + +include(TestCXXAcceptsFlag) +include(CheckCXXSourceCompiles) + +# add a compiler flag only if it is accepted +macro(add_cxx_compiler_flag _flag) + string(REPLACE "-" "_" _flag_var ${_flag}) + check_cxx_accepts_flag("${_flag}" CXX_COMPILER_${_flag_var}_OK) + if(CXX_COMPILER_${_flag_var}_OK) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_flag}") + endif() +endmacro() + +function(can_cgal_use_cxx11_thread_local) + # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h + # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac). + # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h + # #if __has_feature(cxx_thread_local) || \ + # ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ + # ( _MSC_VER >= 1900 ) + # #define CGAL_CAN_USE_CXX11_THREAD_LOCAL + # #endif + set(CGAL_CAN_USE_CXX11_THREAD_LOCAL " + int main() { + #ifndef __has_feature + #define __has_feature(x) 0 // Compatibility with non-clang compilers. + #endif + #if __has_feature(cxx_thread_local) || \ + ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ + ( _MSC_VER >= 1900 ) + bool has_feature_thread_local = true; + #else + // Explicit error of compilation for CMake test purpose - has_feature_thread_local is not defined + #endif + bool result = has_feature_thread_local; + } ") + check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) +endfunction() + +set (CMAKE_CXX_STANDARD 11) + +enable_testing() + +if(MSVC) + # Turn off some VC++ warnings + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") +endif() + +add_cxx_compiler_flag("-Wall") + +if (DEBUG_TRACES) + # For programs to be more verbose + message(STATUS "DEBUG_TRACES are activated") + add_definitions(-DDEBUG_TRACES) +endif() + +set(GUDHI_CAN_USE_CXX11_THREAD_LOCAL " + int main() { + thread_local int result = 0; + return result; + } ") +check_cxx_source_compiles("${GUDHI_CAN_USE_CXX11_THREAD_LOCAL}" GUDHI_CAN_USE_CXX11_THREAD_LOCAL_RESULT) +if (GUDHI_CAN_USE_CXX11_THREAD_LOCAL_RESULT) + add_definitions(-DGUDHI_CAN_USE_CXX11_THREAD_LOCAL) +endif() + +if(CMAKE_BUILD_TYPE MATCHES Debug) + message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}") +else() + message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}") +endif() diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index a008dd0a..7433f2f3 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -54,12 +54,12 @@ if(CGAL_FOUND) endforeach(CGAL_INCLUDE_DIR ${CGAL_INCLUDE_DIRS}) endif(NOT CGAL_VERSION VERSION_GREATER 4.9.0) - if (NOT CGAL_VERSION VERSION_GREATER 4.11.0) + if (CGAL_VERSION VERSION_LESS 4.11.0) # For dev version include_directories(BEFORE "src/common/include/gudhi_patches") # For user version include_directories(BEFORE "include/gudhi_patches") - endif (NOT CGAL_VERSION VERSION_GREATER 4.11.0) + endif () endif() endif() diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake index 4abc2574..1205966a 100644 --- a/src/cmake/modules/GUDHI_user_version_target.cmake +++ b/src/cmake/modules/GUDHI_user_version_target.cmake @@ -48,10 +48,10 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI) set(GUDHI_DIRECTORIES "doc;example;concept;utilities") - if (NOT CGAL_VERSION VERSION_GREATER 4.11.0) - set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches") + if (CGAL_VERSION VERSION_LESS 4.11.0) + set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/Miniball;include/gudhi_patches") else () - set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi") + set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/Miniball") endif () foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST}) diff --git a/src/common/doc/header.html b/src/common/doc/header.html index 2f54e68d..c12d2816 100644 --- a/src/common/doc/header.html +++ b/src/common/doc/header.html @@ -9,7 +9,7 @@ <!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME--> <!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME--> <!-- GUDHI website css for header BEGIN --> -<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" /> +<link rel="stylesheet" type="text/css" href="https://gudhi.inria.fr/assets/css/styles_feeling_responsive.css" /> <!-- GUDHI website css for header END --> <link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/> <script type="text/javascript" src="$relpath^jquery.js"></script> @@ -24,60 +24,61 @@ $extrastylesheet <!-- GUDHI website header BEGIN --> <div id="navigation" class="sticky"> - <nav class="top-bar" role="navigation" data-topbar> - <ul class="title-area"> - <li class="name"> - <h1 class="show-for-small-only"><a href="http://gudhi.gforge.inria.fr" class="icon-tree"> GUDHI C++ library</a></h1> - </li> - <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone --> - <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li> - </ul> - <section class="top-bar-section"> - <ul class="right"> - <li class="divider"></li> - <li><a href="http://gudhi.gforge.inria.fr/contact/">Contact</a></li> - </ul> - <ul class="left"> - <li><a href="http://gudhi.gforge.inria.fr/"> <img src="http://gudhi.gforge.inria.fr/assets/img/home.png" alt=" GUDHI"> GUDHI </a></li> - <li class="divider"></li> - <li class="has-dropdown"> - <a href="#">Project</a> - <ul class="dropdown"> - <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li> - <li><a href="http://gudhi.gforge.inria.fr/keepintouch/">Keep in touch</a></li> - <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li> - <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li> - <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li> - </ul> - </li> - <li class="divider"></li> - <li class="has-dropdown"> - <a href="#">Download</a> - <ul class="dropdown"> - <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li> - <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li> - <li><a href="https://gforge.inria.fr/frs/download.php/file/37365/2018-02-01-16-59-31_GUDHI_2.1.0_OSX_UTILS.tar.gz" target="_blank">Utils for Mac OSx</a></li> - <li><a href="https://gforge.inria.fr/frs/download.php/file/37366/2018-01-31-09-25-53_GUDHI_2.1.0_WIN64_UTILS.zip" target="_blank">Utils for Win x64</a></li> - </ul> - </li> - <li class="divider"></li> - <li class="has-dropdown"> - <a href="#">Documentation</a> - <ul class="dropdown"> - <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li> - <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li> - <li><a href="http://gudhi.gforge.inria.fr/python/latest/">Python documentation</a></li> - <li><a href="http://gudhi.gforge.inria.fr/python/latest/installation.html">Python installation manual</a></li> - <li><a href="http://gudhi.gforge.inria.fr/utils/">Utilities</a></li> - <li><a href="http://bertrand.michel.perso.math.cnrs.fr/Enseignements/TDA-Gudhi-Python.html" target="_blank">Tutorial</a></li> - </ul> - </li> - <li class="divider"></li> - <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li> - <li class="divider"></li> - </ul> - </section> - </nav> + <nav class="top-bar" role="navigation" data-topbar> + <ul class="title-area"> + <li class="name"> + <h1 class="show-for-small-only"><a href="" class="icon-tree"> GUDHI C++ library</a></h1> + </li> + <!-- Remove the class "menu-icon" to get rid of menu icon. 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It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. + * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> ≥ 1.48.0 + * and <a target="_blank" href="https://www.cmake.org/">CMake</a> ≥ 3.1. + * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. * * \subsection demos Demos and examples * To build the demos and examples, run the following commands in a terminal: diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index b3e9ea03..db1e80ce 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -42,6 +42,22 @@ </td> </tr> </table> + \subsection CechComplexDataStructure Čech complex + \image html "cech_complex_representation.png" "Čech complex representation" +<table border="0"> + <tr> + <td width="25%"> + <b>Author:</b> Vincent Rouvreau<br> + <b>Introduced in:</b> GUDHI 2.2.0<br> + <b>Copyright:</b> GPL v3<br> + </td> + <td width="75%"> + The Čech complex is a simplicial complex constructed from a proximity graph.<br> + The set of all simplices is filtered by the radius of their minimal enclosing ball.<br> + <b>User manual:</b> \ref cech_complex - <b>Reference manual:</b> Gudhi::cech_complex::Cech_complex + </td> + </tr> +</table> \subsection CubicalComplexDataStructure Cubical complex \image html "Cubical_complex_representation.png" "Cubical complex representation" <table border="0"> @@ -57,12 +73,13 @@ <b>User manual:</b> \ref cubical_complex - <b>Reference manual:</b> Gudhi::cubical_complex::Bitmap_cubical_complex </td> </tr> +</table> \subsection RipsComplexDataStructure Rips complex \image html "rips_complex_representation.png" "Rips complex representation" <table border="0"> <tr> <td width="25%"> - <b>Author:</b> Clément Maria, Pawel Dlotko, Vincent Rouvreau<br> + <b>Author:</b> Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse<br> <b>Introduced in:</b> GUDHI 2.0.0<br> <b>Copyright:</b> GPL v3<br> </td> @@ -75,7 +92,6 @@ </td> </tr> </table> -</table> \subsection SimplexTreeDataStructure Simplex tree \image html "Simplex_tree_representation.png" "Simplex tree representation" <table border="0"> diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt index 1273c699..04015cdc 100644 --- a/src/common/example/CMakeLists.txt +++ b/src/common/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Common_examples) add_executable ( vector_double_off_reader example_vector_double_points_off_reader.cpp ) diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h index 024f0568..05a1e145 100644 --- a/src/common/include/gudhi/Off_reader.h +++ b/src/common/include/gudhi/Off_reader.h @@ -137,7 +137,7 @@ class Off_reader { if (!std::ifstream::sentry(stream_)) return false; std::getline(stream_, uncomment_line); } while (uncomment_line[0] == '#'); - return (bool)stream_; + return static_cast<bool>(stream_); } template<typename OffVisitor> diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index f7baed6f..5ef12f2e 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -25,7 +25,10 @@ #include <gudhi/Debug_utils.h> +#include <gudhi/Miniball.hpp> + #include <boost/range/metafunctions.hpp> +#include <boost/range/size.hpp> #include <cmath> // for std::sqrt #include <type_traits> // for std::decay @@ -68,6 +71,53 @@ class Euclidean_distance { } }; +/** @brief Compute the radius of the minimal enclosing ball between Points given by a range of coordinates. + * The points are assumed to have the same dimension. */ +class Minimal_enclosing_ball_radius { + public: + /** \brief Minimal_enclosing_ball_radius from two points. + * + * @param[in] point_1 First point. + * @param[in] point_2 second point. + * @return The minimal enclosing ball radius for the two points (aka. Euclidean distance / 2.). + * + * \tparam Point must be a range of Cartesian coordinates. + * + */ + template< typename Point > + typename std::iterator_traits<typename boost::range_iterator<Point>::type>::value_type + operator()(const Point& point_1, const Point& point_2) const { + return Euclidean_distance()(point_1, point_2) / 2.; + } + /** \brief Minimal_enclosing_ball_radius from a point cloud. + * + * @param[in] point_cloud The points. + * @return The minimal enclosing ball radius for the points. + * + * \tparam Point_cloud must be a range of points with Cartesian coordinates. + * Point_cloud is a range over a range of Coordinate. + * + */ + template< typename Point_cloud, + typename Point_iterator = typename boost::range_const_iterator<Point_cloud>::type, + typename Point = typename std::iterator_traits<Point_iterator>::value_type, + typename Coordinate_iterator = typename boost::range_const_iterator<Point>::type, + typename Coordinate = typename std::iterator_traits<Coordinate_iterator>::value_type> + Coordinate + operator()(const Point_cloud& point_cloud) const { + using Min_sphere = Miniball::Miniball<Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>; + + Min_sphere ms(boost::size(*point_cloud.begin()), point_cloud.begin(), point_cloud.end()); +#ifdef DEBUG_TRACES + std::cout << "Minimal_enclosing_ball_radius = " << std::sqrt(ms.squared_radius()) << " | nb points = " + << boost::size(point_cloud) << " | dimension = " + << boost::size(*point_cloud.begin()) << std::endl; +#endif // DEBUG_TRACES + + return std::sqrt(ms.squared_radius()); + } +}; + } // namespace Gudhi #endif // DISTANCE_FUNCTIONS_H_ diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index 6ab7b0b4..49fe56cc 100644 --- a/src/common/include/gudhi/graph_simplicial_complex.h +++ b/src/common/include/gudhi/graph_simplicial_complex.h @@ -42,6 +42,12 @@ struct vertex_filtration_t { typedef boost::vertex_property_tag kind; }; +/** \brief Proximity_graph contains the vertices and edges with their filtration values in order to store the result + * of `Gudhi::compute_proximity_graph` function. + * + * \tparam SimplicialComplexForProximityGraph furnishes `Filtration_value` type definition. + * + */ template <typename SimplicialComplexForProximityGraph> using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS , boost::property < vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value > diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h index 1f8f2cd8..f8107c8b 100644 --- a/src/common/include/gudhi/random_point_generators.h +++ b/src/common/include/gudhi/random_point_generators.h @@ -190,7 +190,8 @@ template <typename Kernel, typename OutputIterator> static void generate_uniform_points_on_torus_d(const Kernel &k, int dim, std::size_t num_slices, OutputIterator out, double radius_noise_percentage = 0., - std::vector<typename Kernel::FT> current_point = std::vector<typename Kernel::FT>()) { + std::vector<typename Kernel::FT> current_point = + std::vector<typename Kernel::FT>()) { CGAL::Random rng; int point_size = static_cast<int>(current_point.size()); if (point_size == 2 * dim) { diff --git a/src/common/include/gudhi/writing_persistence_to_file.h b/src/common/include/gudhi/writing_persistence_to_file.h index 4c5ce918..34448576 100644 --- a/src/common/include/gudhi/writing_persistence_to_file.h +++ b/src/common/include/gudhi/writing_persistence_to_file.h @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef WRITING_PERSISTENCE_TO_FILE_H -#define WRITING_PERSISTENCE_TO_FILE_H +#ifndef WRITING_PERSISTENCE_TO_FILE_H_ +#define WRITING_PERSISTENCE_TO_FILE_H_ #include <iostream> #include <string> @@ -112,6 +112,6 @@ void write_persistence_intervals_to_stream(const Persistence_interval_range& int } } -} +} // namespace Gudhi -#endif // WRITING_PERSISTENCE_TO_FILE_H +#endif // WRITING_PERSISTENCE_TO_FILE_H_ diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt index de3e765a..0b49fa1e 100644 --- a/src/common/test/CMakeLists.txt +++ b/src/common/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Common_tests) include(GUDHI_test_coverage) diff --git a/src/common/utilities/CMakeLists.txt b/src/common/utilities/CMakeLists.txt index b3e4b436..7f1d1cd7 100644 --- a/src/common/utilities/CMakeLists.txt +++ b/src/common/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(off_file_from_shape_generator) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index b19cc550..17d440ee 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -1,8 +1,5 @@ -cmake_minimum_required(VERSION 2.8) project(Cython) -include(CheckCXXSourceCompiles) - function( add_gudhi_cython_lib THE_LIB ) if(EXISTS ${THE_LIB}) get_filename_component(THE_LIB_FILE_NAME ${THE_LIB} NAME_WE) @@ -72,40 +69,16 @@ if(CYTHON_FOUND) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) if(CGAL_FOUND) - # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h - # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac). - # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h - # #if __has_feature(cxx_thread_local) || \ - # ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ - # ( _MSC_VER >= 1900 ) - # #define CGAL_CAN_USE_CXX11_THREAD_LOCAL - # #endif - set(CGAL_CAN_USE_CXX11_THREAD_LOCAL " - int main() { - #ifndef __has_feature - #define __has_feature(x) 0 // Compatibility with non-clang compilers. - #endif - #if __has_feature(cxx_thread_local) || \ - ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ - ( _MSC_VER >= 1900 ) - bool has_feature_thread_local = true; - #else - // Explicit error of compilation for CMake test purpose - has_feature_thread_local is not defined - #endif - bool result = has_feature_thread_local; - } ") - check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) - + can_cgal_use_cxx11_thread_local() if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) add_gudhi_cython_lib(${Boost_THREAD_LIBRARY}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") endif() - # Add CGAL compilation args if(CGAL_HEADER_ONLY) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") else(CGAL_HEADER_ONLY) - add_gudhi_cython_lib(${CGAL_LIBRARIES}) + add_gudhi_cython_lib(${CGAL_LIBRARY}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") # If CGAL is not header only, CGAL library may link with boost system, add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY}) @@ -183,7 +156,7 @@ if(CYTHON_FOUND) 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 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) + --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) add_gudhi_py_test(test_tangential_complex) diff --git a/src/cython/cython/cubical_complex.pyx b/src/cython/cython/cubical_complex.pyx index a98a3ec3..e94cd539 100644 --- a/src/cython/cython/cubical_complex.pyx +++ b/src/cython/cython/cubical_complex.pyx @@ -104,22 +104,21 @@ cdef class CubicalComplex: return self.pcohptr != NULL def num_simplices(self): - """This function returns the number of simplices of the simplicial - complex. + """This function returns the number of all cubes in the complex. - :returns: int -- the simplicial complex number of simplices. + :returns: int -- the number of all cubes in the complex. """ return self.thisptr.num_simplices() def dimension(self): - """This function returns the dimension of the simplicial complex. + """This function returns the dimension of the complex. - :returns: int -- the simplicial complex dimension. + :returns: int -- the complex dimension. """ return self.thisptr.dimension() def persistence(self, homology_coeff_field=11, min_persistence=0): - """This function returns the persistence of the simplicial complex. + """This function returns the persistence of the complex. :param homology_coeff_field: The homology coefficient field. Must be a prime number @@ -130,7 +129,7 @@ cdef class CubicalComplex: Sets min_persistence to -1.0 to see all values. :type min_persistence: float. :returns: list of pairs(dimension, pair(birth, death)) -- the - persistence of the simplicial complex. + persistence of the complex. """ if self.pcohptr != NULL: del self.pcohptr @@ -142,12 +141,15 @@ cdef class CubicalComplex: return persistence_result def betti_numbers(self): - """This function returns the Betti numbers of the simplicial complex. + """This function returns the Betti numbers of the complex. :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]). :note: betti_numbers function requires persistence function to be launched first. + + :note: betti_numbers function always returns [1, 0, 0, ...] as infinity + filtration cubes are not removed from the complex. """ cdef vector[int] bn_result if self.pcohptr != NULL: @@ -155,8 +157,7 @@ cdef class CubicalComplex: return bn_result def persistent_betti_numbers(self, from_value, to_value): - """This function returns the persistent Betti numbers of the - simplicial complex. + """This function returns the persistent Betti numbers of the complex. :param from_value: The persistence birth limit to be added in the numbers (persistent birth <= from_value). @@ -177,8 +178,8 @@ cdef class CubicalComplex: return pbn_result def persistence_intervals_in_dimension(self, dimension): - """This function returns the persistence intervals of the simplicial - complex in a specific dimension. + """This function returns the persistence intervals of the complex in a + specific dimension. :param dimension: The specific dimension. :type from_value: int. diff --git a/src/cython/cython/periodic_cubical_complex.pyx b/src/cython/cython/periodic_cubical_complex.pyx index c25b83e9..e626950b 100644 --- a/src/cython/cython/periodic_cubical_complex.pyx +++ b/src/cython/cython/periodic_cubical_complex.pyx @@ -106,22 +106,21 @@ cdef class PeriodicCubicalComplex: return self.pcohptr != NULL def num_simplices(self): - """This function returns the number of simplices of the simplicial - complex. + """This function returns the number of all cubes in the complex. - :returns: int -- the simplicial complex number of simplices. + :returns: int -- the number of all cubes in the complex. """ return self.thisptr.num_simplices() def dimension(self): - """This function returns the dimension of the simplicial complex. + """This function returns the dimension of the complex. - :returns: int -- the simplicial complex dimension. + :returns: int -- the complex dimension. """ return self.thisptr.dimension() def persistence(self, homology_coeff_field=11, min_persistence=0): - """This function returns the persistence of the simplicial complex. + """This function returns the persistence of the complex. :param homology_coeff_field: The homology coefficient field. Must be a prime number @@ -132,7 +131,7 @@ cdef class PeriodicCubicalComplex: Sets min_persistence to -1.0 to see all values. :type min_persistence: float. :returns: list of pairs(dimension, pair(birth, death)) -- the - persistence of the simplicial complex. + persistence of the complex. """ if self.pcohptr != NULL: del self.pcohptr @@ -144,12 +143,15 @@ cdef class PeriodicCubicalComplex: return persistence_result def betti_numbers(self): - """This function returns the Betti numbers of the simplicial complex. + """This function returns the Betti numbers of the complex. :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]). :note: betti_numbers function requires persistence function to be launched first. + + :note: betti_numbers function always returns [1, 0, 0, ...] as infinity + filtration cubes are not removed from the complex. """ cdef vector[int] bn_result if self.pcohptr != NULL: @@ -157,8 +159,7 @@ cdef class PeriodicCubicalComplex: return bn_result def persistent_betti_numbers(self, from_value, to_value): - """This function returns the persistent Betti numbers of the - simplicial complex. + """This function returns the persistent Betti numbers of the complex. :param from_value: The persistence birth limit to be added in the numbers (persistent birth <= from_value). @@ -179,8 +180,8 @@ cdef class PeriodicCubicalComplex: return pbn_result def persistence_intervals_in_dimension(self, dimension): - """This function returns the persistence intervals of the simplicial - complex in a specific dimension. + """This function returns the persistence intervals of the complex in a + specific dimension. :param dimension: The specific dimension. :type from_value: int. diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index e2405e96..216ab8d6 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -1,4 +1,5 @@ import matplotlib.pyplot as plt +import matplotlib.patches as mpatches import numpy as np import os @@ -28,13 +29,13 @@ __author__ = "Vincent Rouvreau, Bertrand Michel" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" -def __min_birth_max_death(persistence, band_boot=0.): +def __min_birth_max_death(persistence, band=0.): """This function returns (min_birth, max_death) from the persistence. :param persistence: The persistence to plot. :type persistence: list of tuples(dimension, tuple(birth, death)). - :param band_boot: bootstrap band - :type band_boot: float. + :param band: band + :type band: float. :returns: (float, float) -- (min_birth, max_death). """ # Look for minimum birth date and maximum death date for plot optimisation @@ -48,8 +49,8 @@ def __min_birth_max_death(persistence, band_boot=0.): max_death = float(interval[1][0]) if float(interval[1][0]) < min_birth: min_birth = float(interval[1][0]) - if band_boot > 0.: - max_death += band_boot + if band > 0.: + max_death += band return (min_birth, max_death) """ @@ -59,37 +60,27 @@ palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00', '#000000', '#880000', '#008800', '#000088', '#888800', '#880088', '#008888'] -def show_palette_values(alpha=0.6): - """This function shows palette color values in function of the dimension. +def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, + max_barcodes=1000, inf_delta=0.1, legend=False): + """This function plots the persistence bar code from persistence values list + or from a :doc:`persistence file <fileformats>`. - :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6). - :type alpha: float. - :returns: plot the dimension palette values. - """ - colors = [] - for color in palette: - colors.append(color) - - y_pos = np.arange(len(palette)) - - plt.barh(y_pos, y_pos + 1, align='center', alpha=alpha, color=colors) - plt.ylabel('Dimension') - plt.title('Dimension palette values') - return plt - -def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=0): - """This function plots the persistence bar code. - - :param persistence: The persistence to plot. + :param persistence: Persistence values list. :type persistence: list of tuples(dimension, tuple(birth, death)). - :param persistence_file: A persistence file style name (reset persistence if both are set). + :param persistence_file: A :doc:`persistence file <fileformats>` style name + (reset persistence if both are set). :type persistence_file: string - :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6). + :param alpha: barcode transparency value (0.0 transparent through 1.0 opaque - default is 0.6). :type alpha: float. - :param max_barcodes: number of maximal barcodes to be displayed + :param max_barcodes: number of maximal barcodes to be displayed. + Set it to 0 to see all, Default value is 1000. (persistence will be sorted by life time if max_barcodes is set) :type max_barcodes: int. - :returns: plot -- An horizontal bar plot of persistence. + :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta). + A reasonable value is between 0.05 and 0.5 - default is 0.1. + :type inf_delta: float. + :returns: A matplotlib object containing horizontal bar plot of persistence + (launch `show()` method on it to display it). """ if persistence_file is not '': if os.path.isfile(persistence_file): @@ -107,9 +98,11 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max # Sort by life time, then takes only the max_plots elements persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_barcodes] + persistence = sorted(persistence, key=lambda birth: birth[1][0]) + (min_birth, max_death) = __min_birth_max_death(persistence) ind = 0 - delta = ((max_death - min_birth) / 10.0) + delta = ((max_death - min_birth) * inf_delta) # Replace infinity values with max_death + delta for bar code to be more # readable infinity = max_death + delta @@ -120,33 +113,49 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max # Finite death case plt.barh(ind, (interval[1][1] - interval[1][0]), height=0.8, left = interval[1][0], alpha=alpha, - color = palette[interval[0]]) + color = palette[interval[0]], + linewidth=0) else: # Infinite death case for diagram to be nicer plt.barh(ind, (infinity - interval[1][0]), height=0.8, left = interval[1][0], alpha=alpha, - color = palette[interval[0]]) + color = palette[interval[0]], + linewidth=0) ind = ind + 1 + if legend: + dimensions = list(set(item[0] for item in persistence)) + plt.legend(handles=[mpatches.Patch(color=palette[dim], + label=str(dim)) for dim in dimensions], + loc='lower right') plt.title('Persistence barcode') # Ends plot on infinity value and starts a little bit before min_birth plt.axis([axis_start, infinity, 0, ind]) return plt -def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band_boot=0., max_plots=0): - """This function plots the persistence diagram with an optional confidence band. +def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, + band=0., max_plots=1000, inf_delta=0.1, legend=False): + """This function plots the persistence diagram from persistence values list + or from a :doc:`persistence file <fileformats>`. - :param persistence: The persistence to plot. + :param persistence: Persistence values list. :type persistence: list of tuples(dimension, tuple(birth, death)). - :param persistence_file: A persistence file style name (reset persistence if both are set). + :param persistence_file: A :doc:`persistence file <fileformats>` style name + (reset persistence if both are set). :type persistence_file: string - :param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity line (default is 0.6). + :param alpha: plot transparency value (0.0 transparent through 1.0 opaque - default is 0.6). :type alpha: float. - :param band_boot: bootstrap band (not displayed if :math:`\leq` 0.) - :type band_boot: float. + :param band: band (not displayed if :math:`\leq` 0. - default is 0.) + :type band: float. :param max_plots: number of maximal plots to be displayed + Set it to 0 to see all, Default value is 1000. + (persistence will be sorted by life time if max_plots is set) :type max_plots: int. - :returns: plot -- A diagram plot of persistence. + :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta). + A reasonable value is between 0.05 and 0.5 - default is 0.1. + :type inf_delta: float. + :returns: A matplotlib object containing diagram plot of persistence + (launch `show()` method on it to display it). """ if persistence_file is not '': if os.path.isfile(persistence_file): @@ -164,9 +173,9 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban # Sort by life time, then takes only the max_plots elements persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots] - (min_birth, max_death) = __min_birth_max_death(persistence, band_boot) + (min_birth, max_death) = __min_birth_max_death(persistence, band) ind = 0 - delta = ((max_death - min_birth) / 10.0) + delta = ((max_death - min_birth) * inf_delta) # Replace infinity values with max_death + delta for diagram to be more # readable infinity = max_death + delta @@ -179,8 +188,8 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban plt.plot(x, [infinity] * len(x), linewidth=1.0, color='k', alpha=alpha) plt.text(axis_start, infinity, r'$\infty$', color='k', alpha=alpha) # bootstrap band - if band_boot > 0.: - plt.fill_between(x, x, x+band_boot, alpha=alpha, facecolor='red') + if band > 0.: + plt.fill_between(x, x, x+band, alpha=alpha, facecolor='red') # Draw points in loop for interval in reversed(persistence): @@ -194,6 +203,10 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban color = palette[interval[0]]) ind = ind + 1 + if legend: + dimensions = list(set(item[0] for item in persistence)) + plt.legend(handles=[mpatches.Patch(color=palette[dim], label=str(dim)) for dim in dimensions]) + plt.title('Persistence diagram') plt.xlabel('Birth') plt.ylabel('Death') diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx index 8abeb5f8..e302486b 100644 --- a/src/cython/cython/simplex_tree.pyx +++ b/src/cython/cython/simplex_tree.pyx @@ -55,6 +55,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": void expansion(int max_dim) void remove_maximal_simplex(vector[int] simplex) bool prune_above_filtration(double filtration) + bool make_filtration_non_decreasing() 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>>": @@ -64,6 +65,7 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": vector[int] persistent_betti_numbers(double from_value, double to_value) vector[pair[double,double]] intervals_in_dimension(int dimension) void write_output_diagram(string diagram_file_name) + vector[pair[vector[int], vector[int]]] persistence_pairs() # SimplexTree python interface cdef class SimplexTree: @@ -399,6 +401,26 @@ cdef class SimplexTree: """ self.thisptr.expansion(max_dim) + def make_filtration_non_decreasing(self): + """This function ensures that each simplex has a higher filtration + value than its faces by increasing the filtration values. + + :returns: The filtration modification information. + :rtype: bint + + + .. note:: + + Some simplex tree functions require the filtration to be valid. + make_filtration_non_decreasing function is not launching + :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>` + but returns the filtration modification + information. If the complex has changed , please call + :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>` + to recompute it. + """ + return self.thisptr.make_filtration_non_decreasing() + def persistence(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False): """This function returns the persistence of the simplicial complex. @@ -486,6 +508,25 @@ cdef class SimplexTree: " to be launched first.") return intervals_result + def persistence_pairs(self): + """This function returns the persistence pairs of the simplicial + complex. + + :returns: The persistence intervals. + :rtype: list of pair of list of int + + :note: intervals_in_dim function requires + :func:`persistence()<gudhi.SimplexTree.persistence>` + function to be launched first. + """ + cdef vector[pair[vector[int],vector[int]]] persistence_pairs_result + if self.pcohptr != NULL: + persistence_pairs_result = self.pcohptr.persistence_pairs() + else: + print("persistence_pairs function requires persistence function" + " to be launched first.") + return persistence_pairs_result + def write_persistence_diagram(self, persistence_file=''): """This function writes the persistence intervals of the simplicial complex in a user given file name. diff --git a/src/cython/cython/tangential_complex.pyx b/src/cython/cython/tangential_complex.pyx index 10fa1468..4bb07076 100644 --- a/src/cython/cython/tangential_complex.pyx +++ b/src/cython/cython/tangential_complex.pyx @@ -33,9 +33,9 @@ __license__ = "GPL v3" cdef extern from "Tangential_complex_interface.h" namespace "Gudhi": cdef cppclass Tangential_complex_interface "Gudhi::tangential_complex::Tangential_complex_interface": - Tangential_complex_interface(vector[vector[double]] points) + Tangential_complex_interface(int intrisic_dim, vector[vector[double]] points) # bool from_file is a workaround for cython to find the correct signature - Tangential_complex_interface(string off_file, bool from_file) + Tangential_complex_interface(int intrisic_dim, string off_file, bool from_file) vector[double] get_point(unsigned vertex) unsigned number_of_vertices() unsigned number_of_simplices() @@ -54,9 +54,12 @@ cdef class TangentialComplex: cdef Tangential_complex_interface * thisptr # Fake constructor that does nothing but documenting the constructor - def __init__(self, points=None, off_file=''): + def __init__(self, intrisic_dim, points=None, off_file=''): """TangentialComplex constructor. + :param intrisic_dim: Intrinsic dimension of the manifold. + :type intrisic_dim: integer + :param points: A list of points in d-Dimension. :type points: list of list of double @@ -67,17 +70,17 @@ cdef class TangentialComplex: """ # The real cython constructor - def __cinit__(self, points=None, off_file=''): + def __cinit__(self, intrisic_dim, points=None, off_file=''): if off_file is not '': if os.path.isfile(off_file): - self.thisptr = new Tangential_complex_interface(str.encode(off_file), True) + self.thisptr = new Tangential_complex_interface(intrisic_dim, str.encode(off_file), True) else: print("file " + off_file + " not found.") else: if points is None: # Empty tangential construction points=[] - self.thisptr = new Tangential_complex_interface(points) + self.thisptr = new Tangential_complex_interface(intrisic_dim, points) def __dealloc__(self): diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html index c9356116..bc0e9658 100644 --- a/src/cython/doc/_templates/layout.html +++ b/src/cython/doc/_templates/layout.html @@ -56,6 +56,12 @@ </a></p> {%- endif %} {%- endblock %} + <h2><a href="index.html">GUDHI</a></h2> + <h2><a href="fileformats.html">File formats</a></h2> + <h2><a href="installation.html">GUDHI installation</a></h2> + <h2><a href="citation.html">Acknowledging the GUDHI library</a></h2> + <h2><a href="genindex.html">Index</a></h2> + <h2><a href="examples.html">Examples</a></h2> {%- if sidebars != None %} {#- new style sidebar: explicitly include/exclude templates #} {%- for sidebartemplate in sidebars %} @@ -64,13 +70,6 @@ {%- else %} {#- old style sidebars: using blocks -- should be deprecated #} {%- block sidebartoc %} -<h2><a href="index.html">GUDHI</a></h2> -<h2><a href="fileformats.html">File formats</a></h2> -<h2><a href="installation.html">GUDHI installation</a></h2> -<h2><a href="citation.html">Acknowledging the GUDHI library</a></h2> -<h2><a href="genindex.html">Index</a></h2> -<h2><a href="examples.html">Examples</a></h2> - {%- include "localtoc.html" %} {%- endblock %} {%- block sidebarrel %} @@ -108,7 +107,7 @@ {%- macro css() %} <!-- GUDHI website css for header BEGIN --> -<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" /> +<link rel="stylesheet" type="text/css" href="https://gudhi.inria.fr/assets/css/styles_feeling_responsive.css" /> <!-- GUDHI website css for header END --> <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" /> <link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css" /> @@ -166,60 +165,61 @@ <body role="document"> <!-- GUDHI website header BEGIN --> <div id="navigation" class="sticky"> - <nav class="top-bar" role="navigation" data-topbar> - <ul class="title-area"> - <li class="name"> - <h1 class="show-for-small-only"><a href="http://gudhi.gforge.inria.fr" class="icon-tree"> GUDHI C++ library</a></h1> - </li> - <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone --> - <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li> - </ul> - <section class="top-bar-section"> - <ul class="right"> - <li class="divider"></li> - <li><a href="http://gudhi.gforge.inria.fr/contact/">Contact</a></li> - </ul> - <ul class="left"> - <li><a href="http://gudhi.gforge.inria.fr/"> <img src="http://gudhi.gforge.inria.fr/assets/img/home.png" alt=" GUDHI"> GUDHI </a></li> - <li class="divider"></li> - <li class="has-dropdown"> - <a href="#">Project</a> - <ul class="dropdown"> - <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li> - <li><a href="http://gudhi.gforge.inria.fr/keepintouch/">Keep in touch</a></li> - <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li> - <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li> - <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li> - </ul> - </li> - <li class="divider"></li> - <li class="has-dropdown"> - <a href="#">Download</a> - <ul class="dropdown"> - <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li> - <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li> - <li><a href="https://gforge.inria.fr/frs/download.php/file/37365/2018-02-01-16-59-31_GUDHI_2.1.0_OSX_UTILS.tar.gz" target="_blank">Utils for Mac OSx</a></li> - <li><a href="https://gforge.inria.fr/frs/download.php/file/37366/2018-01-31-09-25-53_GUDHI_2.1.0_WIN64_UTILS.zip" target="_blank">Utils for Win x64</a></li> - </ul> - </li> - <li class="divider"></li> - <li class="has-dropdown"> - <a href="#">Documentation</a> - <ul class="dropdown"> - <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li> - <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li> - <li><a href="http://gudhi.gforge.inria.fr/python/latest/">Python documentation</a></li> - <li><a href="http://gudhi.gforge.inria.fr/python/latest/installation.html">Python installation manual</a></li> - <li><a href="http://gudhi.gforge.inria.fr/utils/">Utilities</a></li> - <li><a href="http://bertrand.michel.perso.math.cnrs.fr/Enseignements/TDA-Gudhi-Python.html" target="_blank">Tutorial</a></li> - </ul> - </li> - <li class="divider"></li> - <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li> - <li class="divider"></li> - </ul> - </section> - </nav> + <nav class="top-bar" role="navigation" data-topbar> + <ul class="title-area"> + <li class="name"> + <h1 class="show-for-small-only"><a href="" class="icon-tree"> GUDHI C++ library</a></h1> + </li> + <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone --> + <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li> + </ul> + <section class="top-bar-section"> + <ul class="right"> + <li class="divider"></li> + <li><a href="/contact/">Contact</a></li> + </ul> + <ul class="left"> + <li><a href="/"> <img src="/assets/img/home.png" alt=" GUDHI"> GUDHI </a></li> + <li class="divider"></li> + <li class="has-dropdown"> + <a href="#">Project</a> + <ul class="dropdown"> + <li><a href="/people/">People</a></li> + <li><a href="/keepintouch/">Keep in touch</a></li> + <li><a href="/partners/">Partners and Funding</a></li> + <li><a href="/relatedprojects/">Related projects</a></li> + <li><a href="/theyaretalkingaboutus/">They are talking about us</a></li> + </ul> + </li> + <li class="divider"></li> + <li class="has-dropdown"> + <a href="#">Download</a> + <ul class="dropdown"> + <li><a href="/licensing/">Licensing</a></li> + <li><a href="https://gforge.inria.fr/frs/download.php/latestzip/5253/library-latest.zip" target="_blank">Get the latest sources</a></li> + <li><a href="https://gforge.inria.fr/frs/download.php/latestzip/5280/utils_osx-latest.zip" target="_blank">Utils for Mac OSx</a></li> + <li><a href="https://gforge.inria.fr/frs/download.php/latestzip/5279/utils_win64-latest.zip" target="_blank">Utils for Win x64</a></li> + </ul> + </li> + <li class="divider"></li> + <li class="has-dropdown"> + <a href="#">Documentation</a> + <ul class="dropdown"> + <li><a href="/doc/latest/">C++ documentation</a></li> + <li><a href="/doc/latest/installation.html">C++ installation manual</a></li> + <li><a href="/python/latest/">Python documentation</a></li> + <li><a href="/python/latest/installation.html">Python installation manual</a></li> + <li><a href="/utils/">Utilities</a></li> + <li><a href="/tutorials/">Tutorials</a></li> + <li><a href="/dockerfile/">Dockerfile</a></li> + </ul> + </li> + <li class="divider"></li> + <li><a href="/interfaces/">Interfaces</a></li> + <li class="divider"></li> + </ul> + </section> + </nav> </div><!-- /#navigation --> <!-- GUDHI website header BEGIN --> diff --git a/src/cython/doc/alpha_complex_ref.rst b/src/cython/doc/alpha_complex_ref.rst index 6a122b09..7da79543 100644 --- a/src/cython/doc/alpha_complex_ref.rst +++ b/src/cython/doc/alpha_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================== Alpha complex reference manual ============================== diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.inc index 1680a712..1680a712 100644 --- a/src/cython/doc/alpha_complex_sum.rst +++ b/src/cython/doc/alpha_complex_sum.inc diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst index db7edd6f..d1e9c7cd 100644 --- a/src/cython/doc/alpha_complex_user.rst +++ b/src/cython/doc/alpha_complex_user.rst @@ -1,11 +1,15 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Alpha complex user manual ========================= Definition ---------- -.. include:: alpha_complex_sum.rst +.. include:: alpha_complex_sum.inc -Alpha_complex is constructing a :doc:`Simplex_tree <simplex_tree_sum>` using +Alpha_complex is constructing a :doc:`Simplex_tree <simplex_tree_ref>` using `Delaunay Triangulation <http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations>`_ :cite:`cgal:hdj-t-15b` from `CGAL <http://www.cgal.org/>`_ (the Computational Geometry Algorithms Library :cite:`cgal:eb-15b`). @@ -99,9 +103,9 @@ Filtration value computation algorithm **end for** **end for** **end for** - + make_filtration_non_decreasing() - + prune_above_filtration() Dimension 2 diff --git a/src/cython/doc/bottleneck_distance_sum.rst b/src/cython/doc/bottleneck_distance_sum.inc index 030fad9e..030fad9e 100644 --- a/src/cython/doc/bottleneck_distance_sum.rst +++ b/src/cython/doc/bottleneck_distance_sum.inc diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst index 7692dce2..605db022 100644 --- a/src/cython/doc/bottleneck_distance_user.rst +++ b/src/cython/doc/bottleneck_distance_user.rst @@ -1,9 +1,13 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Bottleneck distance user manual =============================== Definition ---------- -.. include:: bottleneck_distance_sum.rst +.. include:: bottleneck_distance_sum.inc Function -------- diff --git a/src/cython/doc/citation.rst b/src/cython/doc/citation.rst index f4fdf83b..117eb9dd 100644 --- a/src/cython/doc/citation.rst +++ b/src/cython/doc/citation.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Acknowledging the GUDHI library ############################### diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py index a13c9751..4a54d4fd 100755 --- a/src/cython/doc/conf.py +++ b/src/cython/doc/conf.py @@ -85,7 +85,7 @@ version = gudhi.__version__ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ['_build'] +exclude_patterns = ['_build', '*.inc'] # The reST default role (used for this markup: `text`) to use for all # documents. @@ -125,6 +125,7 @@ html_theme_options = { "sidebarbgcolor": "#A1ADCD", "sidebartextcolor": "black", "sidebarlinkcolor": "#334D5C", + "body_max_width": "1200px", } # Add any paths that contain custom themes here, relative to this directory. diff --git a/src/cython/doc/cubical_complex_ref.rst b/src/cython/doc/cubical_complex_ref.rst index 84aa4223..1fe9d5fb 100644 --- a/src/cython/doc/cubical_complex_ref.rst +++ b/src/cython/doc/cubical_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Cubical complex reference manual ################################ diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.inc index 280ad0e0..280ad0e0 100644 --- a/src/cython/doc/cubical_complex_sum.rst +++ b/src/cython/doc/cubical_complex_sum.inc diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index dd82ad93..320bd79b 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Cubical complex user manual =========================== Definition @@ -144,6 +148,7 @@ the program output is: .. testoutput:: Periodic cubical complex is of dimension 2 - 42 simplices. + Examples. --------- diff --git a/src/cython/doc/euclidean_strong_witness_complex_ref.rst b/src/cython/doc/euclidean_strong_witness_complex_ref.rst index bebf0f9a..1a602cd5 100644 --- a/src/cython/doc/euclidean_strong_witness_complex_ref.rst +++ b/src/cython/doc/euclidean_strong_witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ================================================= Euclidean strong witness complex reference manual ================================================= diff --git a/src/cython/doc/euclidean_witness_complex_ref.rst b/src/cython/doc/euclidean_witness_complex_ref.rst index 29b8806f..28daf965 100644 --- a/src/cython/doc/euclidean_witness_complex_ref.rst +++ b/src/cython/doc/euclidean_witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ========================================== Euclidean witness complex reference manual ========================================== diff --git a/src/cython/doc/examples.rst b/src/cython/doc/examples.rst index 1e596e18..d42f5a92 100644 --- a/src/cython/doc/examples.rst +++ b/src/cython/doc/examples.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Examples ######## diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst index 4f0b6f6d..ff20f26e 100644 --- a/src/cython/doc/fileformats.rst +++ b/src/cython/doc/fileformats.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + File formats ############ diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst index 3945d72a..4e444fb0 100644 --- a/src/cython/doc/index.rst +++ b/src/cython/doc/index.rst @@ -34,32 +34,32 @@ Data structures Alpha complex ============= -.. include:: alpha_complex_sum.rst +.. include:: alpha_complex_sum.inc Cubical complex =============== -.. include:: cubical_complex_sum.rst +.. include:: cubical_complex_sum.inc Rips complex ============ -.. include:: rips_complex_sum.rst +.. include:: rips_complex_sum.inc Simplex tree ============ -.. include:: simplex_tree_sum.rst +.. include:: simplex_tree_sum.inc Tangential complex ================== -.. include:: tangential_complex_sum.rst +.. include:: tangential_complex_sum.inc Witness complex =============== -.. include:: witness_complex_sum.rst +.. include:: witness_complex_sum.inc Toolbox @@ -68,17 +68,17 @@ Toolbox Bottleneck distance =================== -.. include:: bottleneck_distance_sum.rst +.. include:: bottleneck_distance_sum.inc Persistence cohomology ====================== -.. include:: persistent_cohomology_sum.rst +.. include:: persistent_cohomology_sum.inc Persistence graphical tools =========================== -.. include:: persistence_graphical_tools_sum.rst +.. include:: persistence_graphical_tools_sum.inc Bibliography ************ diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index c182f176..43ff85c5 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -1,12 +1,16 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Installation ############ Compiling ********* - -The library uses c++11 and requires `Boost <http://www.boost.org/>`_ with -version 1.48.0 or more recent. It is a multi-platform library and compiles on -Linux, Mac OSX and Visual Studio 2015. +The library uses c++11 and requires `Boost <https://www.boost.org/>`_ ≥ 1.48.0 +and `CMake <https://www.cmake.org/>`_ ≥ 3.1. +It is a multi-platform library and compiles on Linux, Mac OSX and Visual +Studio 2015. It also requires cmake to generate makefiles, and cython to compile the library. @@ -43,6 +47,9 @@ following command in a terminal: export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython' ctest -R py_test +If tests fail, please try to :code:`import gudhi` and check the errors. +The problem can come from a third-party library bad link or installation. + Documentation ============= diff --git a/src/cython/doc/periodic_cubical_complex_ref.rst b/src/cython/doc/periodic_cubical_complex_ref.rst index c6190a1b..4b831647 100644 --- a/src/cython/doc/periodic_cubical_complex_ref.rst +++ b/src/cython/doc/periodic_cubical_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Periodic cubical complex reference manual ######################################### diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst index 27c2f68a..a2c6bcef 100644 --- a/src/cython/doc/persistence_graphical_tools_ref.rst +++ b/src/cython/doc/persistence_graphical_tools_ref.rst @@ -1,8 +1,11 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================================ Persistence graphical tools reference manual ============================================ .. autofunction:: gudhi.__min_birth_max_death -.. autofunction:: gudhi.show_palette_values .. autofunction:: gudhi.plot_persistence_barcode .. autofunction:: gudhi.plot_persistence_diagram diff --git a/src/cython/doc/persistence_graphical_tools_sum.rst b/src/cython/doc/persistence_graphical_tools_sum.inc index d602daa7..d602daa7 100644 --- a/src/cython/doc/persistence_graphical_tools_sum.rst +++ b/src/cython/doc/persistence_graphical_tools_sum.inc diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index a5523d23..292915eb 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -1,49 +1,26 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Persistence graphical tools user manual ======================================= Definition ---------- -.. include:: persistence_graphical_tools_sum.rst - - -Show palette values -------------------- - -This function is useful to show the color palette values of dimension: - +.. include:: persistence_graphical_tools_sum.inc -.. testcode:: - - import gudhi - plt = gudhi.show_palette_values(alpha=1.0) - plt.show() - -.. plot:: - - import gudhi - plt = gudhi.show_palette_values(alpha=1.0) - plt.show() Show persistence as a barcode ----------------------------- This function can display the persistence result as a barcode: -.. testcode:: - - import gudhi - - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ - '/data/bitmap/3d_torus.txt') - diag = periodic_cc.persistence() - plt = gudhi.plot_persistence_barcode(diag) - plt.show() - .. plot:: + :include-source: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ - '/data/bitmap/3d_torus.txt') + perseus_file = gudhi.__root_source_dir__ + '/data/bitmap/3d_torus.txt' + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=perseus_file) diag = periodic_cc.persistence() print("diag = ", diag) plt = gudhi.plot_persistence_barcode(diag) @@ -54,24 +31,32 @@ Show persistence as a diagram This function can display the persistence result as a diagram: -.. testcode:: +.. plot:: + :include-source: import gudhi - - point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off') - rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2) - simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) - diag = simplex_tree.persistence() - plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) + + # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method + persistence_file=gudhi.__root_source_dir__ + \ + '/data/persistence_diagram/rips_on_tore3D_1307.pers' + plt = gudhi.plot_persistence_diagram(persistence_file=persistence_file, + legend=True) plt.show() +If you want more information on a specific dimension, for instance: + .. plot:: + :include-source: import gudhi - point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off') - rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2) - simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) - diag = simplex_tree.persistence() - plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) + persistence_file=gudhi.__root_source_dir__ + \ + '/data/persistence_diagram/rips_on_tore3D_1307.pers' + diag = \ + gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file=\ + persistence_file) + dim = 1 + # Display all points with some transparency + plt = gudhi.plot_persistence_diagram([(dim,interval) for interval in diag[dim]], + max_plots=0, alpha=0.1) plt.show() diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.inc index a26df1dc..a26df1dc 100644 --- a/src/cython/doc/persistent_cohomology_sum.rst +++ b/src/cython/doc/persistent_cohomology_sum.inc diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst index bf90c163..ce7fc685 100644 --- a/src/cython/doc/persistent_cohomology_user.rst +++ b/src/cython/doc/persistent_cohomology_user.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Persistent cohomology user manual ================================= Definition diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py deleted file mode 100755 index de33d506..00000000 --- a/src/cython/doc/pyplots/barcode_persistence.py +++ /dev/null @@ -1,7 +0,0 @@ -import gudhi - -periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ - '/data/bitmap/3d_torus.txt') -diag = periodic_cc.persistence() -plt = gudhi.plot_persistence_barcode(diag) -plt.show() diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py deleted file mode 100755 index ac20bf47..00000000 --- a/src/cython/doc/pyplots/diagram_persistence.py +++ /dev/null @@ -1,9 +0,0 @@ -import gudhi - -point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + \ - '/data/points/tore3D_1307.off') -rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2) -simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) -diag = simplex_tree.persistence() -plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) -plt.show() diff --git a/src/cython/doc/pyplots/show_palette_values.py b/src/cython/doc/pyplots/show_palette_values.py deleted file mode 100755 index fdf9645f..00000000 --- a/src/cython/doc/pyplots/show_palette_values.py +++ /dev/null @@ -1,3 +0,0 @@ -import gudhi -plt = gudhi.show_palette_values(alpha=1.0) -plt.show() diff --git a/src/cython/doc/reader_utils_ref.rst b/src/cython/doc/reader_utils_ref.rst index 9c1ea6fc..f3ecebad 100644 --- a/src/cython/doc/reader_utils_ref.rst +++ b/src/cython/doc/reader_utils_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================= Reader utils reference manual ============================= diff --git a/src/cython/doc/rips_complex_ref.rst b/src/cython/doc/rips_complex_ref.rst index b17dc4e0..22b5616c 100644 --- a/src/cython/doc/rips_complex_ref.rst +++ b/src/cython/doc/rips_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================= Rips complex reference manual ============================= diff --git a/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.inc index 5616bfa9..5616bfa9 100644 --- a/src/cython/doc/rips_complex_sum.rst +++ b/src/cython/doc/rips_complex_sum.inc diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index 7738aef0..a8c06cf9 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Rips complex user manual ========================= Definition @@ -243,7 +247,7 @@ the program output is: [3, 6] -> 11.00 Correlation matrix ---------------- +------------------ Example from a correlation matrix ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/src/cython/doc/simplex_tree_ref.rst b/src/cython/doc/simplex_tree_ref.rst index 6d196843..9eb8c199 100644 --- a/src/cython/doc/simplex_tree_ref.rst +++ b/src/cython/doc/simplex_tree_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================= Simplex tree reference manual ============================= diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.inc index fb0e54c1..fb0e54c1 100644 --- a/src/cython/doc/simplex_tree_sum.rst +++ b/src/cython/doc/simplex_tree_sum.inc diff --git a/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst index 4b1dde19..aebeb29f 100644 --- a/src/cython/doc/simplex_tree_user.rst +++ b/src/cython/doc/simplex_tree_user.rst @@ -1,9 +1,13 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Simplex tree user manual ======================== Definition ---------- -.. include:: simplex_tree_sum.rst +.. include:: simplex_tree_sum.inc A simplicial complex :math:`\mathbf{K}` on a set of vertices :math:`V = \{1, \cdots ,|V|\}` is a collection of simplices :math:`\{\sigma\}`, :math:`\sigma \subseteq V` such that diff --git a/src/cython/doc/strong_witness_complex_ref.rst b/src/cython/doc/strong_witness_complex_ref.rst index 4ed4fe46..d624d711 100644 --- a/src/cython/doc/strong_witness_complex_ref.rst +++ b/src/cython/doc/strong_witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ======================================= Strong witness complex reference manual ======================================= diff --git a/src/cython/doc/tangential_complex_ref.rst b/src/cython/doc/tangential_complex_ref.rst index 35589475..cdfda082 100644 --- a/src/cython/doc/tangential_complex_ref.rst +++ b/src/cython/doc/tangential_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + =================================== Tangential complex reference manual =================================== diff --git a/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.inc index 72b4d7ba..72b4d7ba 100644 --- a/src/cython/doc/tangential_complex_sum.rst +++ b/src/cython/doc/tangential_complex_sum.inc diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst index efa6d7ce..5ce69e86 100644 --- a/src/cython/doc/tangential_complex_user.rst +++ b/src/cython/doc/tangential_complex_user.rst @@ -1,6 +1,10 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Tangential complex user manual ============================== -.. include:: tangential_complex_sum.rst +.. include:: tangential_complex_sum.inc Definition ---------- @@ -122,8 +126,8 @@ This example builds the Tangential complex of point set read in an OFF file. .. testcode:: import gudhi - tc = gudhi.TangentialComplex(off_file=gudhi.__root_source_dir__ + \ - '/data/points/alphacomplexdoc.off') + tc = gudhi.TangentialComplex(intrisic_dim = 1, + off_file=gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off') result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \ ' simplices - ' + repr(tc.num_vertices()) + ' vertices.' print(result_str) @@ -169,7 +173,8 @@ simplices. .. testcode:: import gudhi - tc = gudhi.TangentialComplex(points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]]) + tc = gudhi.TangentialComplex(intrisic_dim = 1, + points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]]) result_str = 'Tangential contains ' + repr(tc.num_vertices()) + ' vertices.' print(result_str) diff --git a/src/cython/doc/todos.rst b/src/cython/doc/todos.rst index 78972a4c..ca274ced 100644 --- a/src/cython/doc/todos.rst +++ b/src/cython/doc/todos.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ========== To be done ========== diff --git a/src/cython/doc/witness_complex_ref.rst b/src/cython/doc/witness_complex_ref.rst index c78760cb..9987d3fd 100644 --- a/src/cython/doc/witness_complex_ref.rst +++ b/src/cython/doc/witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ================================ Witness complex reference manual ================================ diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.inc index a8a126a0..a8a126a0 100644 --- a/src/cython/doc/witness_complex_sum.rst +++ b/src/cython/doc/witness_complex_sum.inc diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst index 99be5185..40e94134 100644 --- a/src/cython/doc/witness_complex_user.rst +++ b/src/cython/doc/witness_complex_user.rst @@ -1,7 +1,11 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Witness complex user manual =========================== -.. include:: witness_complex_sum.rst +.. include:: witness_complex_sum.inc Definitions ----------- diff --git a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py index 27550025..4abe22d4 100755 --- a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -38,7 +38,7 @@ parser = argparse.ArgumentParser(description='AlphaComplex creation from ' 'points from the given OFF file.') parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-a", "--max_alpha_square", type=float, default=0.5) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -64,7 +64,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index 1c142d9a..3b29781f 100755 --- a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -40,7 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-a", "--max_alpha_square", type=float, required=True) parser.add_argument("-n", "--number_of_landmarks", type=int, required=True) parser.add_argument("-d", "--limit_dimension", type=int, required=True) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -71,7 +71,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index 216fcff2..db34962d 100755 --- a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -40,7 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-a", "--max_alpha_square", type=float, required=True) parser.add_argument("-n", "--number_of_landmarks", type=int, required=True) parser.add_argument("-d", "--limit_dimension", type=int, required=True) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -71,7 +71,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py index 9f37efc0..ac3d146c 100755 --- a/src/cython/example/gudhi_graphical_tools_example.py +++ b/src/cython/example/gudhi_graphical_tools_example.py @@ -29,11 +29,6 @@ __copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") -print("Show palette colors values for dimension") - -gudhi.show_palette_values() - -print("#####################################################################") print("Show barcode persistence example") persistence = [(2, (1.0, float('inf'))), (1, (1.4142135623730951, float('inf'))), @@ -50,5 +45,5 @@ pplot.show() print("#####################################################################") print("Show diagram persistence example with a confidence band") -pplot = gudhi.plot_persistence_diagram(persistence, band_boot=0.2) +pplot = gudhi.plot_persistence_diagram(persistence, band=0.2) pplot.show() diff --git a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index 4142fa99..0c9dfc43 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -40,7 +40,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from ' parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-c", "--min_edge_correlation", type=float, default=0.5) parser.add_argument("-d", "--max_dimension", type=int, default=1) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -80,5 +80,5 @@ print(simplex_tree.betti_numbers()) invert_diag = [(diag[pers][0],(1.-diag[pers][1][0], 1.-diag[pers][1][1])) for pers in range(len(diag))] if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(invert_diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(invert_diag, band=args.band) pplot.show() diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 01d1f38a..4d2ed577 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -39,7 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from ' parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-e", "--max_edge_length", type=float, default=0.5) parser.add_argument("-d", "--max_dimension", type=int, default=1) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -63,5 +63,5 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py index 865c66b6..d15d5eb0 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -39,7 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from ' parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-e", "--max_edge_length", type=float, default=0.5) parser.add_argument("-d", "--max_dimension", type=int, default=1) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -66,7 +66,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py index 680a8bf8..0f8f5e80 100755 --- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py @@ -33,11 +33,12 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from ' 'points read in a OFF file.', epilog='Example: ' 'example/tangential_complex_plain_homology_from_off_file_example.py ' - '-f ../data/points/tore3D_300.off' + '-f ../data/points/tore3D_300.off -i 3' '- Constructs a tangential complex with the ' 'points from the given OFF file') parser.add_argument("-f", "--file", type=str, required=True) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-i", "--intrisic_dim", type=int, required=True) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -48,7 +49,7 @@ with open(args.file, 'r') as f: print("#####################################################################") print("TangentialComplex creation from points read in a OFF file") - tc = gudhi.TangentialComplex(off_file=args.file) + tc = gudhi.TangentialComplex(intrisic_dim = args.intrisic_dim, off_file=args.file) st = tc.create_simplex_tree() message = "Number of simplices=" + repr(st.num_simplices()) @@ -60,7 +61,7 @@ with open(args.file, 'r') as f: print(st.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h index a86b1187..8cf71a4e 100644 --- a/src/cython/include/Persistent_cohomology_interface.h +++ b/src/cython/include/Persistent_cohomology_interface.h @@ -85,6 +85,32 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol return persistence; } + std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs() { + auto pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex, + persistent_cohomology::Field_Zp>::get_persistent_pairs(); + + std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs; + persistence_pairs.reserve(pairs.size()); + for (auto pair : pairs) { + std::vector<int> birth; + if (get<0>(pair) != stptr_->null_simplex()) { + for (auto vertex : stptr_->simplex_vertex_range(get<0>(pair))) { + birth.push_back(vertex); + } + } + + std::vector<int> death; + if (get<1>(pair) != stptr_->null_simplex()) { + for (auto vertex : stptr_->simplex_vertex_range(get<1>(pair))) { + death.push_back(vertex); + } + } + + persistence_pairs.push_back(std::make_pair(birth, death)); + } + return persistence_pairs; + } + private: // A copy FilteredComplex* stptr_; diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h index 2772460a..71418886 100644 --- a/src/cython/include/Tangential_complex_interface.h +++ b/src/cython/include/Tangential_complex_interface.h @@ -45,24 +45,19 @@ class Tangential_complex_interface { using TC = Tangential_complex<Dynamic_kernel, CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>; public: - Tangential_complex_interface(const std::vector<std::vector<double>>& points) { + Tangential_complex_interface(int intrisic_dim, const std::vector<std::vector<double>>& points) { Dynamic_kernel k; - unsigned intrisic_dim = 0; - if (points.size() > 0) - intrisic_dim = points[0].size() - 1; tangential_complex_ = new TC(points, intrisic_dim, k); tangential_complex_->compute_tangential_complex(); num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices(); } - Tangential_complex_interface(const std::string& off_file_name, bool from_file = true) { - Gudhi::Points_off_reader<Point_d> off_reader(off_file_name); + Tangential_complex_interface(int intrisic_dim, const std::string& off_file_name, bool from_file = true) { Dynamic_kernel k; - unsigned intrisic_dim = 0; + + Gudhi::Points_off_reader<Point_d> off_reader(off_file_name); std::vector<Point_d> points = off_reader.get_point_cloud(); - if (points.size() > 0) - intrisic_dim = points[0].size() - 1; tangential_complex_ = new TC(points, intrisic_dim, k); tangential_complex_->compute_tangential_complex(); diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in index b6ca4bcb..ee381a1b 100644 --- a/src/cython/setup.py.in +++ b/src/cython/setup.py.in @@ -46,4 +46,9 @@ setup( version='@GUDHI_VERSION@', url='http://gudhi.gforge.inria.fr/', ext_modules = cythonize(gudhi), + install_requires = [ + "matplotlib", + "numpy", + "cython", + ], ) diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py index 79d39aa8..92e591e9 100755 --- a/src/cython/test/test_cubical_complex.py +++ b/src/cython/test/test_cubical_complex.py @@ -72,6 +72,17 @@ def test_dimension_simple_constructor(): assert cub.betti_numbers() == [1, 0, 0] assert cub.persistent_betti_numbers(0, 1000) == [0, 0, 0] +def test_user_case_simple_constructor(): + cub = CubicalComplex(dimensions=[3, 3], + top_dimensional_cells = [float('inf'), 0.,0.,0.,1.,0.,0.,0.,0.]) + assert cub.__is_defined() == True + assert cub.__is_persistence_defined() == False + assert cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float('inf')))] + assert cub.__is_persistence_defined() == True + other_cub = CubicalComplex(dimensions=[3, 3], + top_dimensional_cells = [1000., 0.,0.,0.,1.,0.,0.,0.,0.]) + assert other_cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float('inf')))] + def test_dimension_file_constructor(): # Create test file test_file = open('CubicalOneSphere.txt', 'w') diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py index 029e7729..cb701c9a 100755 --- a/src/cython/test/test_simplex_tree.py +++ b/src/cython/test/test_simplex_tree.py @@ -161,3 +161,47 @@ def test_automatic_dimension(): assert st.upper_bound_dimension() == 2 assert st.dimension() == 1 assert st.upper_bound_dimension() == 1 + +def test_make_filtration_non_decreasing(): + st = SimplexTree() + assert st.__is_defined() == True + assert st.__is_persistence_defined() == False + + # Inserted simplex: + # 1 + # o + # /X\ + # o---o---o---o + # 2 0 3\X/4 + # o + # 5 + assert st.insert([2, 1, 0], filtration=2.0) == True + assert st.insert([3, 0], filtration=2.0) == True + assert st.insert([3, 4, 5], filtration=2.0) == True + + assert st.make_filtration_non_decreasing() == False + + # Because of non decreasing property of simplex tree, { 0 } , { 1 } and + # { 0, 1 } are going to be set from value 2.0 to 1.0 + st.insert([0, 1, 6, 7], filtration=1.0); + + assert st.make_filtration_non_decreasing() == False + + # Modify specific values to test make_filtration_non_decreasing + st.assign_filtration([0,1,6,7], 0.8); + st.assign_filtration([0,1,6], 0.9); + st.assign_filtration([0,6], 0.6); + st.assign_filtration([3,4,5], 1.2); + st.assign_filtration([3,4], 1.1); + st.assign_filtration([4,5], 1.99); + + assert st.make_filtration_non_decreasing() == True + + assert st.filtration([0,1,6,7]) == 1. + assert st.filtration([0,1,6]) == 1. + assert st.filtration([0,1]) == 1. + assert st.filtration([0]) == 1. + assert st.filtration([1]) == 1. + assert st.filtration([3,4,5]) == 2. + assert st.filtration([3,4]) == 2. + assert st.filtration([4,5]) == 2. diff --git a/src/cython/test/test_tangential_complex.py b/src/cython/test/test_tangential_complex.py index fe623c7b..5385a0d3 100755 --- a/src/cython/test/test_tangential_complex.py +++ b/src/cython/test/test_tangential_complex.py @@ -29,7 +29,7 @@ __license__ = "GPL v3" def test_tangential(): point_list = [[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]] - tc = TangentialComplex(points=point_list) + tc = TangentialComplex(intrisic_dim = 1, points=point_list) assert tc.__is_defined() == True assert tc.num_vertices() == 4 |
