diff options
| -rw-r--r-- | biblio/how_to_cite_gudhi.bib | 44 | ||||
| -rwxr-xr-x | scripts/generate_version.sh | 10 | ||||
| -rw-r--r-- | src/Alpha_complex/example/Alpha_complex_from_points.cpp | 5 | ||||
| -rw-r--r-- | src/Alpha_complex/include/gudhi/Alpha_complex.h | 33 | ||||
| -rw-r--r-- | src/Alpha_complex/test/Alpha_complex_unit_test.cpp | 3 | ||||
| -rw-r--r-- | src/CMakeLists.txt | 2 | ||||
| -rw-r--r-- | src/Contraction/include/gudhi/Edge_contraction.h | 4 | ||||
| -rw-r--r-- | src/Doxyfile | 18 | ||||
| -rw-r--r-- | src/Persistent_cohomology/example/CMakeLists.txt | 4 | ||||
| -rw-r--r-- | src/Persistent_cohomology/example/performance_rips_persistence.cpp | 81 | ||||
| -rw-r--r-- | src/Persistent_cohomology/example/plain_homology.cpp | 80 | ||||
| -rw-r--r-- | src/Simplex_tree/concept/SimplexTreeOptions.h | 6 | ||||
| -rw-r--r-- | src/Simplex_tree/include/gudhi/Simplex_tree.h | 16 | ||||
| -rw-r--r-- | src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h | 2 | ||||
| -rw-r--r-- | src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h | 4 | ||||
| -rw-r--r-- | src/common/doc/main_page.h | 186 | ||||
| -rw-r--r-- | src/common/test/dtoffrw_unit_test.cpp | 3 |
17 files changed, 363 insertions, 138 deletions
diff --git a/biblio/how_to_cite_gudhi.bib b/biblio/how_to_cite_gudhi.bib new file mode 100644 index 00000000..851dd5d9 --- /dev/null +++ b/biblio/how_to_cite_gudhi.bib @@ -0,0 +1,44 @@ +@book{gudhi:urm +, title = "{GUDHI} User and Reference Manual" +, author = "{The GUDHI Project}" +, publisher = "{GUDHI Editorial Board}" +, year = 2015 +, url = "http://gudhi.gforge.inria.fr/doc/latest/" +} + +@incollection{gudhi:FilteredComplexes +, author = "Cl\'ement Maria" +, title = "Filtered Complexes" +, publisher = "{GUDHI Editorial Board}" +, booktitle = "{GUDHI} User and Reference Manual" +, url = "http://gudhi.gforge.inria.fr/doc/latest/group__simplex__tree.html" +, year = 2015 +} + +@incollection{gudhi:PersistentCohomology +, author = "Cl\'ement Maria" +, title = "Persistent Cohomology" +, publisher = "{GUDHI Editorial Board}" +, booktitle = "{GUDHI} User and Reference Manual" +, url = "http://gudhi.gforge.inria.fr/doc/latest/group__persistent__cohomology.html" +, year = 2015 +} + +@incollection{gudhi:Contraction +, author = "David Salinas" +, title = "Contraction" +, publisher = "{GUDHI Editorial Board}" +, booktitle = "{GUDHI} User and Reference Manual" +, url = "http://gudhi.gforge.inria.fr/doc/latest/group__contr.html" +, year = 2015 +} + +@incollection{gudhi:Skeleton-Blocker +, author = "David Salinas" +, title = "Skeleton-Blocker" +, publisher = "{GUDHI Editorial Board}" +, booktitle = "{GUDHI} User and Reference Manual" +, url = "http://gudhi.gforge.inria.fr/doc/latest/group__skbl.html" +, year = 2015 +} + diff --git a/scripts/generate_version.sh b/scripts/generate_version.sh index 43a54c1c..323396dc 100755 --- a/scripts/generate_version.sh +++ b/scripts/generate_version.sh @@ -61,12 +61,13 @@ cp $ROOT_DIR/GUDHIVersion.cmake.in $VERSION_DIR PACKAGE_INC_DIR="/include" #PACKAGE_SRC_DIR="/source" PACKAGE_EX_DIR="/example" +PACKAGE_CONCEPT_DIR="/concept" PACKAGE_DOC_DIR="/doc" for package in `ls $ROOT_DIR/src/` do - echo $package - if [ -d "$ROOT_DIR/src/$package" ] + if [ -d "$ROOT_DIR/src/$package" ] && [ $package != "Bottleneck" ] then + echo $package if [ "$package" == "cmake" ] then # SPECIFIC FOR CMAKE MODULES @@ -91,6 +92,11 @@ do mkdir -p $VERSION_DIR$PACKAGE_EX_DIR/$package cp -R $ROOT_DIR/src/$package$PACKAGE_EX_DIR/* $VERSION_DIR$PACKAGE_EX_DIR/$package fi + if [ -d "$ROOT_DIR/src/$package$PACKAGE_CONCEPT_DIR" ] + then + mkdir -p $VERSION_DIR$PACKAGE_CONCEPT_DIR/$package + cp -R $ROOT_DIR/src/$package$PACKAGE_CONCEPT_DIR/* $VERSION_DIR$PACKAGE_CONCEPT_DIR/$package + fi if [ -d "$ROOT_DIR/src/$package$PACKAGE_DOC_DIR" ] then mkdir -p $VERSION_DIR$PACKAGE_DOC_DIR/$package diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp index b160d702..e2610dbd 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -1,8 +1,8 @@ -#include <stdio.h> #include <stdlib.h> #include <CGAL/Delaunay_triangulation.h> #include <CGAL/Epick_d.h> +#include <iostream> #include <string> #include <vector> @@ -33,8 +33,7 @@ int main(int argc, char **argv) { // Init of an alpha complex from the list of points // ---------------------------------------------------------------------------- double max_alpha_square_value = 1e10; - Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_points(3, points.size(), points.begin(), points.end(), - max_alpha_square_value); + Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_points(3, points, max_alpha_square_value); // ---------------------------------------------------------------------------- // Display information about the alpha complex diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index d8568be0..6b47ace7 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -27,7 +27,6 @@ #include <gudhi/graph_simplicial_complex.h> #include <gudhi/Simplex_tree.h> -#include <stdio.h> #include <stdlib.h> #include <math.h> // isnan, fmax @@ -107,7 +106,8 @@ class Alpha_complex : public Simplex_tree<> { * * @param[in] off_file_name OFF file [path and] name. */ - Alpha_complex(const std::string& off_file_name, Filtration_value max_alpha_square) + Alpha_complex(const std::string& off_file_name, + Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) : triangulation_(nullptr) { Gudhi::Delaunay_triangulation_off_reader<Delaunay_triangulation> off_reader(off_file_name); if (!off_reader.is_valid()) { @@ -123,7 +123,8 @@ class Alpha_complex : public Simplex_tree<> { * * @param[in] triangulation_ptr Pointer on a Delaunay triangulation. */ - Alpha_complex(Delaunay_triangulation* triangulation_ptr, Filtration_value max_alpha_square) + Alpha_complex(Delaunay_triangulation* triangulation_ptr, + Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) : triangulation_(triangulation_ptr) { set_filtration(max_alpha_square); init(); @@ -134,18 +135,22 @@ class Alpha_complex : public Simplex_tree<> { * the Alpha_complex. * * @param[in] dimension Dimension of points to be inserted. - * @param[in] size Number of points to be inserted. - * @param[in] firstPoint Iterator on the first point to be inserted. - * @param[in] last Point Iterator on the last point to be inserted. + * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a Kernel::Point_d. */ - template<typename ForwardIterator > - Alpha_complex(int dimension, size_type size, ForwardIterator firstPoint, ForwardIterator lastPoint, - Filtration_value max_alpha_square) + template<typename InputPointRange > + Alpha_complex(int dimension, const InputPointRange& points, + Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) : triangulation_(nullptr) { triangulation_ = new Delaunay_triangulation(dimension); - size_type inserted = triangulation_->insert(firstPoint, lastPoint); - if (inserted != size) { - std::cerr << "Alpha_complex - insertion failed " << inserted << " != " << size << std::endl; + auto first = std::begin(points); + auto last = std::end(points); + + size_type inserted = triangulation_->insert(first, last); + if (inserted != (last -first)) { + std::cerr << "Alpha_complex - insertion failed " << inserted << " != " << (last -first) << std::endl; exit(-1); // ----- >> } set_filtration(max_alpha_square); @@ -292,12 +297,12 @@ class Alpha_complex : public Simplex_tree<> { // ### Foreach Tau face of Sigma for (auto f_boundary : boundary_simplex_range(f_simplex)) { #ifdef DEBUG_TRACES - std::cout << " | --------------------------------------------------" << std::endl; + std::cout << " | --------------------------------------------------\n"; std::cout << " | Tau "; for (auto vertex : simplex_vertex_range(f_boundary)) { std::cout << vertex << " "; } - std::cout << "is a face of Sigma" << std::endl; + std::cout << "is a face of Sigma\n"; std::cout << " | isnan(filtration(Tau)=" << isnan(filtration(f_boundary)) << std::endl; #endif // DEBUG_TRACES // ### If filt(Tau) is not NaN diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp index 5633d2c7..3aa835ec 100644 --- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp @@ -141,8 +141,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { // Init of an alpha complex from the list of points // ---------------------------------------------------------------------------- double max_alpha_square_value = 1e10; - Gudhi::alphacomplex::Alpha_complex<Kernel_s> alpha_complex_from_points(3, points.size(), points.begin(), points.end(), - max_alpha_square_value); + Gudhi::alphacomplex::Alpha_complex<Kernel_s> alpha_complex_from_points(3, points, max_alpha_square_value); std::cout << "========== Alpha_complex_from_points ==========" << std::endl; diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 590ae373..cd7f4991 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -77,7 +77,7 @@ else() # Install the GUDHIConfig.cmake and GUDHIConfigVersion.cmake install(FILES - "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/GUDHIConfig.cmake" + "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" DESTINATION share/gudhi) diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h index dfce8d1b..349bb7d8 100644 --- a/src/Contraction/include/gudhi/Edge_contraction.h +++ b/src/Contraction/include/gudhi/Edge_contraction.h @@ -37,7 +37,7 @@ namespace Gudhi { namespace contraction { -/** \defgroup contr Contraction +/** \defgroup contr Edge contraction \author David Salinas @@ -226,7 +226,7 @@ Time to simplify and enumerate simplices: \copyright GNU General Public License v3. -\verbatim Contact: David Salinas, david.salinas@inria.fr \endverbatim +\verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup } // namespace contraction diff --git a/src/Doxyfile b/src/Doxyfile index 90884779..81f55e29 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 = "1.1.0" +PROJECT_NUMBER = "1.2.0" # 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 @@ -672,7 +672,8 @@ LAYOUT_FILE = # search path. Do not use file names with spaces, bibtex cannot handle them. See # also \cite for info how to create references. -CITE_BIB_FILES = biblio/bibliography.bib +CITE_BIB_FILES = biblio/bibliography.bib \ + biblio/how_to_cite_gudhi.bib #--------------------------------------------------------------------------- # Configuration options related to warning and progress messages @@ -811,7 +812,8 @@ EXCLUDE_SYMBOLS = # that contain example code fragments that are included (see the \include # command). -EXAMPLE_PATH = example/common/ \ +EXAMPLE_PATH = biblio/ + example/common/ \ example/Alpha_complex/ # If the value of the EXAMPLE_PATH tag contains directories, you can use the @@ -832,16 +834,10 @@ EXAMPLE_RECURSIVE = NO # that contain images that are to be included in the documentation (see the # \image command). -<<<<<<< .working IMAGE_PATH = doc/Skeleton_blocker/ \ doc/Alpha_complex/ \ doc/common/ \ doc/Contraction/ -======= -IMAGE_PATH = doc/Skeleton_blocker/ \ - doc/common/ \ - doc/Contraction/ ->>>>>>> .merge-right.r851 # The INPUT_FILTER tag can be used to specify a program that doxygen should @@ -1346,7 +1342,7 @@ ECLIPSE_DOC_ID = org.doxygen.Project # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. -DISABLE_INDEX = NO +DISABLE_INDEX = YES # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index # structure should be generated to display hierarchical information. If the tag @@ -1363,7 +1359,7 @@ DISABLE_INDEX = NO # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. -GENERATE_TREEVIEW = NO +GENERATE_TREEVIEW = YES # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that # doxygen will group on one line in the generated HTML documentation. diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 74c2e778..8caf7d8b 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -5,6 +5,10 @@ project(GUDHIExPersCohom) add_definitions( -DBOOST_ALL_NO_LIB ) add_definitions( -DBOOST_ALL_DYN_LINK ) +add_executable(plain_homology plain_homology.cpp) +target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY}) +add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology) + add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY}) add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0) diff --git a/src/Persistent_cohomology/example/performance_rips_persistence.cpp b/src/Persistent_cohomology/example/performance_rips_persistence.cpp index 0e912d57..fc48d6b1 100644 --- a/src/Persistent_cohomology/example/performance_rips_persistence.cpp +++ b/src/Persistent_cohomology/example/performance_rips_persistence.cpp @@ -63,10 +63,11 @@ void timing_persistence(FilteredComplex & cpx */ int main(int argc, char * argv[]) { std::chrono::time_point<std::chrono::system_clock> start, end; - int enlapsed_sec; + int elapsed_sec; + { - std::string filepoints = "../examples/Kl.txt"; - Filtration_value threshold = 0.3; + std::string filepoints = "../../../data/points/Kl.txt"; + Filtration_value threshold = 0.27; int dim_max = 3; int p = 2; int q = 1223; @@ -81,8 +82,8 @@ int main(int argc, char * argv[]) { Graph_t prox_graph = compute_proximity_graph(points, threshold , euclidean_distance<Point_t>); end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); - std::cout << "Compute Rips graph in " << enlapsed_sec << " sec.\n"; + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Compute Rips graph in " << elapsed_sec << " ms.\n"; // Construct the Rips complex in a Simplex Tree Simplex_tree<> st; @@ -94,8 +95,8 @@ int main(int argc, char * argv[]) { st.expansion(dim_max); end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); - std::cout << "Compute Rips complex in " << enlapsed_sec << " sec.\n"; + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Compute Rips complex in " << elapsed_sec << " ms.\n"; std::cout << " - dimension = " << st.dimension() << std::endl; std::cout << " - number of simplices = " << st.num_simplices() << std::endl; @@ -103,15 +104,26 @@ int main(int argc, char * argv[]) { start = std::chrono::system_clock::now(); st.initialize_filtration(); end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); - std::cout << "Order the simplices of the filtration in " << enlapsed_sec << " sec.\n"; + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Order the simplices of the filtration in " << elapsed_sec << " ms.\n"; + + // Copy the keys inside the simplices + start = std::chrono::system_clock::now(); + { + int count = 0; + for (auto sh : st.filtration_simplex_range()) + st.assign_key(sh, count++); + } + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Copied the keys inside the simplices in " << elapsed_sec << " ms.\n"; // Convert the simplex tree into a hasse diagram start = std::chrono::system_clock::now(); Hasse_complex<> hcpx(st); end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); - std::cout << "Convert the simplex tree into a Hasse diagram in " << enlapsed_sec << " sec.\n"; + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Convert the simplex tree into a Hasse diagram in " << elapsed_sec << " ms.\n"; std::cout << "Timings when using a simplex tree: \n"; @@ -124,6 +136,11 @@ int main(int argc, char * argv[]) { timing_persistence(hcpx, q); timing_persistence(hcpx, p, q); + start = std::chrono::system_clock::now(); + } + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << "Running the complex destructors in " << elapsed_sec << " ms.\n"; return 0; } @@ -132,19 +149,32 @@ void timing_persistence(FilteredComplex & cpx , int p) { std::chrono::time_point<std::chrono::system_clock> start, end; - int enlapsed_sec; - + int elapsed_sec; + { + start = std::chrono::system_clock::now(); Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx); + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Initialize pcoh in " << elapsed_sec << " ms.\n"; // initializes the coefficient field for homology + start = std::chrono::system_clock::now(); pcoh.init_coefficients(p); + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Initialize the coefficient field in " << elapsed_sec << " ms.\n"; start = std::chrono::system_clock::now(); pcoh.compute_persistent_cohomology(INFINITY); end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); - std::cout << " Compute persistent homology in Z/" << p << "Z in " << enlapsed_sec << " sec.\n"; + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Compute persistent homology in Z/" << p << "Z in " << elapsed_sec << " ms.\n"; + start = std::chrono::system_clock::now(); + } + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Run the persistence destructors in " << elapsed_sec << " ms.\n"; } template< typename FilteredComplex> @@ -153,11 +183,19 @@ timing_persistence(FilteredComplex & cpx , int p , int q) { std::chrono::time_point<std::chrono::system_clock> start, end; - int enlapsed_sec; - + int elapsed_sec; + { + start = std::chrono::system_clock::now(); Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx); + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Initialize pcoh in " << elapsed_sec << " ms.\n"; // initializes the coefficient field for homology + start = std::chrono::system_clock::now(); pcoh.init_coefficients(p, q); + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Initialize the coefficient field in " << elapsed_sec << " ms.\n"; // compute persistent homology, disgarding persistent features of life shorter than min_persistence start = std::chrono::system_clock::now(); @@ -165,7 +203,12 @@ timing_persistence(FilteredComplex & cpx pcoh.compute_persistent_cohomology(INFINITY); end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); std::cout << " Compute multi-field persistent homology in all coefficient fields Z/pZ " - << "with p in [" << p << ";" << q << "] in " << enlapsed_sec << " sec.\n"; + << "with p in [" << p << ";" << q << "] in " << elapsed_sec << " ms.\n"; + start = std::chrono::system_clock::now(); + } + end = std::chrono::system_clock::now(); + elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); + std::cout << " Run the persistence destructors in " << elapsed_sec << " ms.\n"; } diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp new file mode 100644 index 00000000..e293e013 --- /dev/null +++ b/src/Persistent_cohomology/example/plain_homology.cpp @@ -0,0 +1,80 @@ +/* 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): Marc Glisse + * + * Copyright (C) 2015 INRIA Saclay - Ile-de-France (France) + * + * 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/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> + +#include <iostream> + +using namespace Gudhi; + +struct MyOptions : Simplex_tree_options_full_featured { + // Implicitly use 0 as filtration value for all simplices + static const bool store_filtration = false; + // The persistence algorithm needs this + static const bool store_key = true; + // I have few vertices + typedef short Vertex_handle; +}; +typedef Simplex_tree<MyOptions> ST; + +int main() { + ST st; + + /* Complex to build. */ + /* 1 3 */ + /* o---o */ + /* /X\ / */ + /* o---o o */ + /* 2 0 4 */ + + const short triangle012[] = {0, 1, 2}; + const short edge03[] = {0, 3}; + const short edge13[] = {1, 3}; + const short vertex4[] = {4}; + st.insert_simplex_and_subfaces(triangle012); + st.insert_simplex_and_subfaces(edge03); + st.insert_simplex(edge13); + st.insert_simplex(vertex4); + // FIXME: Remove this line + st.set_dimension(2); + + // Sort the simplices in the order of the filtration + st.initialize_filtration(); + + // Class for homology computation + persistent_cohomology::Persistent_cohomology<ST, persistent_cohomology::Field_Zp> pcoh(st); + + // Initialize the coefficient field Z/2Z for homology + pcoh.init_coefficients(2); + + // Compute the persistence diagram of the complex + pcoh.compute_persistent_cohomology(); + + // Print the result. The format is, on each line: 2 dim 0 inf + // where 2 represents the field, dim the dimension of the feature. + // 2 0 0 inf + // 2 0 0 inf + // 2 1 0 inf + // means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=1. + pcoh.output_diagram(); +} diff --git a/src/Simplex_tree/concept/SimplexTreeOptions.h b/src/Simplex_tree/concept/SimplexTreeOptions.h index a50a2bf1..add3ebdd 100644 --- a/src/Simplex_tree/concept/SimplexTreeOptions.h +++ b/src/Simplex_tree/concept/SimplexTreeOptions.h @@ -34,8 +34,8 @@ struct SimplexTreeOptions { /// Must be a signed integer type. typedef SimplexKey Simplex_key; /// If true, each simplex has extra storage for one `Simplex_key`. Necessary for `Persistent_cohomology`. - static constexpr bool store_key; - /// If true, each simplex has extra storage for one `Filtration_value`, and this value is propagated by operations like `Gudhi::Simplex_tree<SimplexTreeOptions>::expansion`. Without it, `Persistent_cohomology` degenerates to computing usual (non-persistent) cohomology. - static constexpr bool store_filtration; + static const bool store_key; + /// If true, each simplex has extra storage for one `Filtration_value`, and this value is propagated by operations like `Gudhi::Simplex_tree::expansion`. Without it, `Persistent_cohomology` degenerates to computing usual (non-persistent) cohomology. + static const bool store_filtration; }; diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 1ca43ff9..35d839e2 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -778,12 +778,6 @@ class Simplex_tree { * assigned a Simplex_key corresponding to its order in the filtration (from 0 to m-1 for a * simplicial complex with m simplices). * - * The use of a depth-first traversal of the simplex tree, provided by - * complex_simplex_range(), combined with - * a stable sort is meant to optimize the order of simplices with same - * filtration value. The heuristic consists in inserting the cofaces of a - * simplex as soon as possible. - * * Will be automatically called when calling filtration_simplex_range() * if the filtration has never been initialized yet. */ void initialize_filtration() { @@ -792,7 +786,15 @@ class Simplex_tree { for (Simplex_handle sh : complex_simplex_range()) filtration_vect_.push_back(sh); - // the stable sort ensures the ordering heuristic + /* We use stable_sort here because with libstdc++ it is faster than sort. + * is_before_in_filtration is now a total order, but we used to call + * stable_sort for the following heuristic: + * The use of a depth-first traversal of the simplex tree, provided by + * complex_simplex_range(), combined with a stable sort is meant to + * optimize the order of simplices with same filtration value. The + * heuristic consists in inserting the cofaces of a simplex as soon as + * possible. + */ std::stable_sort(filtration_vect_.begin(), filtration_vect_.end(), is_before_in_filtration(this)); } diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h index 792a7994..3be480fd 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h @@ -241,7 +241,7 @@ their collaboration to write the two initial papers \copyright GNU General Public License v3. -\verbatim Contact: David Salinas, david.salinas@inria.fr \endverbatim +\verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h index 07f371a2..d26d12b0 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h @@ -1018,7 +1018,7 @@ class Skeleton_blocker_complex { } //@} - /** @Simplification operations + /** @name Simplification operations */ //@{ @@ -1131,7 +1131,7 @@ class Skeleton_blocker_complex { } //@} - /** @Edge contraction operations + /** @name Edge contraction operations */ //@{ diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 770d2216..0fd9a93e 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -1,74 +1,120 @@ -/** -\mainpage - -\image html "Gudhi_banner.jpg" "" width=20cm - -The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic C++ library for -topological analysis of high-dimensional data whose goal is to provide robust, efficient, flexible and easy to use -implementations of -state-of-the-art algorithms and data structures for computational topology. -This library is part of the <a href="https://project.inria.fr/gudhi/">Gudhi project</a>. - -The current release of the library allows to use several data-structures for simplicial complexes : -simplex tree, Hasse diagram or skeleton-blocker. Several operations can then be done on top of these -representations such as persistent homology computation or simplification. -All data-structures are generic and several of their aspects (such as stored elements, policies) -can be parameterized via template classes. -We refer to -\cite gudhilibrary_ICMS14 -for a detailed description of the design of the library. - -\section installation Gudhi installation - -As Gudhi is a header only library, there is no need to install the library. - -Examples of Gudhi headers inclusion can be found in \ref demos. - - -\section compiling Compiling - -The library uses c++11 and requires <a href="http://www.boost.org/">Boost</a> with version 1.48.0 or more recent. -It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013. - - -\subsection gmp GMP: -The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision -arithmetic, operating on signed integers, rational numbers, and floating point numbers. - -The following examples require the <a href="http://gmplib.org/">GNU Multiple Precision Arithmetic Library</a> (GMP) -and will not be built if GMP is not installed: - - Persistent_cohomology/rips_multifield_persistence - - Simplex_tree/simplex_tree_from_alpha_shapes_3 - -Having GMP version 4.2 or higher installed is recommended. - -\subsection cgal CGAL: -CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms. - -The following example requires the <a href="http://www.cgal.org/">Computational Geometry Algorithms Library</a> (CGAL) -and will not be built if CGAL is not installed: - - Simplex_tree/simplex_tree_from_alpha_shapes_3 - - Alpha_complex/Alpha_complex_from_off - - Alpha_complex/Alpha_complex_from_points - -Having CGAL version 4.7 or higher installed is recommended. The procedure to install this library according to -your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html - -\subsection demos Demos and examples - -To build the demos and libraries, run the following commands in a terminal: - -\verbatim -cd /path-to-gudhi/ -mkdir build -cd build/ -cmake .. -make -\endverbatim +/*! \mainpage + * \image html "Gudhi_banner.jpg" "" width=20cm + * + * \section Introduction Introduction + * The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic open source C++ library for + * Computational Topology and Topological Data Analysis + * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>). + * The GUDHI library is developed as part of the + * <a class="el" target="_blank" href="https://project.inria.fr/gudhi/">GUDHI project</a> supported by the European + * Research Council. The GUDHI library intends to help the development of new algorithmic solutions in TDA and their + * transfer to applications. It provides robust, efficient, flexible and easy to use implementations of + * state-of-the-art algorithms and data structures. + * + * The current release of the GUDHI library includes: + * + * \li Data structures to represent, construct and manipulate simplicial complexes. + * \li Algorithms to compute persistent homology and multi-field persistent homology. + * \li Simplication of simplicial complexes by edge contraction. + * + * All data-structures are generic and several of their aspects can be parameterized via template classes. + * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library. + * + * The library is available <a class="el" target="_blank" href="https://gforge.inria.fr/frs/?group_id=3865">here</a> + * and the documentation is available at this <a class="el" href="http://gudhi.gforge.inria.fr/doc/latest/"> + * webpage</a>. + * + * The library comes with data sets, \ref demos and \ref testsuites. + * + * Gudhi is also accessible though the + * <a class="el" target="_blank" href="https://cran.r-project.org/web/packages/TDA/index.html">R package TDA</a> + * (Statistical Tools for Topological Data Analysis). + * + * The development of the GUDHI library is steered by an Editorial Board composed of: + * + * \li <a class="el" target="_blank" href="http://www-sop.inria.fr/members/Jean-Daniel.Boissonnat/"> + * Jean-Daniel Boissonnat</a> | INRIA Sophia Antipolis - Méditerranée + * \li <a class="el" target="_blank" href="http://geometrica.saclay.inria.fr/team/Marc.Glisse/">Marc Glisse</a> | INRIA Saclay - Ile de France + * \li Clément Jamin | INRIA Sophia Antipolis - Méditerranée + * \li Vincent Rouvreau | INRIA Saclay - Ile de France + * +*/ -\details +/*! \page installation Gudhi installation + * As Gudhi is a header only library, there is no need to install the library. + * + * Examples of Gudhi headers inclusion can be found in \ref demos. + * + * \section compiling Compiling + * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or + * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013. + * + * \subsection gmp GMP: + * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision + * arithmetic, operating on signed integers, rational numbers, and floating point numbers. + * + * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic + * Library</a> (GMP) and will not be built if GMP is not installed: + * \li Persistent_cohomology/rips_multifield_persistence + * Having GMP version 4.2 or higher installed is recommended. + * + * \subsection cgal CGAL: + * CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms. + * + * The following examples require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms + * Library</a> (CGAL) and will not be built if CGAL is not installed: + * \li GudhUI + * \li Persistent_cohomology/alpha_shapes_persistence + * \li Simplex_tree/simplex_tree_from_alpha_shapes_3 + * \li Alpha_complex/Alpha_complex_from_off + * \li Alpha_complex/Alpha_complex_from_points + * + * Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to + * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html + * + * \subsection demos Demos and examples + * To build the demos and libraries, run the following commands in a terminal: + * \verbatim + * cd /path-to-gudhi/ + * mkdir build + * cd build/ + * cmake .. + * make + * \endverbatim + * + * \subsection testsuites Test suites + * To test your build, run the following command in a terminal: + * \verbatim + * make test + * \endverbatim + * + * \section Contributions Bug reports and contributions + * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: + * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim + * + * Gudhi is open to external contributions. If you want to join our development team, please contact us. + * +*/ -\copyright GNU General Public License v3. -\verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim +/*! \page Upcoming Upcoming + * + * The library is under active development. New packages to be released next include: + * \li Alpha complex. + * \li Bottleneck distance. + * \li Zig zag persistence. + * \li Witness complex. + * \li Tangential complex. + * \li Clustering. +*/ +/*! \page Citation Acknowledging the GUDHI library + * We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use + * of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages. + * Feel free to contact us in case you have any question or remark on this topic. + * + * We provide \ref GudhiBibtex entries for the modules of the User and Reference Manual, as well as for publications + * directly related to the GUDHI library. + * \section GudhiBibtex GUDHI bibtex + * \verbinclude biblio/how_to_cite_gudhi.bib */ + diff --git a/src/common/test/dtoffrw_unit_test.cpp b/src/common/test/dtoffrw_unit_test.cpp index cc6f283e..20094229 100644 --- a/src/common/test/dtoffrw_unit_test.cpp +++ b/src/common/test/dtoffrw_unit_test.cpp @@ -26,8 +26,9 @@ #include <CGAL/Delaunay_triangulation.h> #include <CGAL/Epick_d.h> -#include <stdio.h> #include <stdlib.h> + +#include <iostream> #include <string> #define BOOST_TEST_DYN_LINK |