diff options
34 files changed, 3138 insertions, 191 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt index 6bea06e2..bf01caeb 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -41,6 +41,11 @@ if (GPROF_PATH) message("gprof found in ${GPROF_PATH}") endif() +FIND_PROGRAM( DIFF_PATH diff ) +if (DIFF_PATH) + message("diff found in ${DIFF_PATH}") +endif() + if(NOT Boost_FOUND) message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.") @@ -57,6 +62,7 @@ else() message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS}) include_directories(src/common/include/) + include_directories(src/Alpha_complex/include/) include_directories(src/Bottleneck/include/) include_directories(src/Contraction/include/) include_directories(src/Hasse_complex/include/) @@ -64,6 +70,8 @@ else() include_directories(src/Simplex_tree/include/) include_directories(src/Skeleton_blocker/include/) + add_subdirectory(src/common/example) + add_subdirectory(src/common/test) add_subdirectory(src/Simplex_tree/test) add_subdirectory(src/Simplex_tree/example) add_subdirectory(src/Persistent_cohomology/test) @@ -72,6 +80,8 @@ else() add_subdirectory(src/Skeleton_blocker/example) add_subdirectory(src/Contraction/example) add_subdirectory(src/Hasse_complex/example) + add_subdirectory(src/Alpha_complex/example) + add_subdirectory(src/Alpha_complex/test) add_subdirectory(src/Bottleneck/example) add_subdirectory(src/Bottleneck/test) diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index 3fd1c10a..859696b4 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -897,6 +897,22 @@ language={English} bibsource = {DBLP, http://dblp.uni-trier.de} } +@ARTICLE{AlphaShapesDefinition, + author = {N. Akkiraju, H. Edelsbrunner, M. Facello, P. Fu, E. P. Mucke, and C. Varela}, + title = {\href{http://pub.ist.ac.at/~edels/Papers/1995-P-06-AlphaShapesSoftware.pdf}{Alpha shapes: definition and software}}, + journal = {Proc. Internat. Comput. Geom. Software Workshop 1995}, + year = {1995}, + bibsource = {http://pub.ist.ac.at} +} + +@ARTICLE{AlphaShapesIntroduction, + author = {Kaspar Fischer}, + title = {\href{http://www.cs.uu.nl/docs/vakken/ddm/texts/Delaunay/alphashapes.pdf}{Introduction to Alpha Shapes}}, + journal = {Unknown}, + year = {Unknown}, + bibsource = {http://www.cs.uu.nl} +} + misc{buddha_stanford_scan, author = "", title = "The Stanford 3D Scanning Repository", diff --git a/data/points/alphacomplexdoc.off b/data/points/alphacomplexdoc.off new file mode 100755 index 00000000..bb790193 --- /dev/null +++ b/data/points/alphacomplexdoc.off @@ -0,0 +1,10 @@ +nOFF +2 7 0 0 +1.0 1.0 +7.0 0.0 +4.0 6.0 +9.0 6.0 +0.0 14.0 +2.0 19.0 +9.0 17.0 + diff --git a/data/points/generator/hypergenerator.cpp b/data/points/generator/hypergenerator.cpp index f4ea6b07..32ef450d 100644 --- a/data/points/generator/hypergenerator.cpp +++ b/data/points/generator/hypergenerator.cpp @@ -86,8 +86,13 @@ int main(int argc, char **argv) { } std::ofstream diagram_out(argv[3]); - diagram_out << "OFF" << std::endl; - diagram_out << points_number << " 0 0" << std::endl; + if (dimension == 3) { + diagram_out << "OFF" << std::endl; + diagram_out << points_number << " 0 0" << std::endl; + } else { + diagram_out << "nOFF" << std::endl; + diagram_out << dimension << " " << points_number << " 0 0" << std::endl; + } if (diagram_out.is_open()) { // Instanciate a random point generator diff --git a/scripts/generate_version.sh b/scripts/generate_version.sh index 4d28cf53..e7575282 100755 --- a/scripts/generate_version.sh +++ b/scripts/generate_version.sh @@ -2,6 +2,8 @@ #usage bash generate_version.sh : dont generate if svn st non empty #usage bash generate_version.sh -f : generate even if svn is empty #usage bash generate_version.sh -f DIR : generate even if svn is empty and save library in dir +# +# 23/06/2015 - Remove source, add biblio, and doc # VERSION CHECK ROOT_DIR=.. VERSION_FILE="$ROOT_DIR/Version.txt" @@ -48,11 +50,13 @@ cp $ROOT_DIR/COPYING $VERSION_DIR cp -R $ROOT_DIR/data $VERSION_DIR cp $ROOT_DIR/src/CMakeLists.txt $VERSION_DIR cp $ROOT_DIR/src/Doxyfile $VERSION_DIR +cp -R $ROOT_DIR/biblio $VERSION_DIR # PACKAGE LEVEL COPY PACKAGE_INC_DIR="/include" -PACKAGE_SRC_DIR="/source" +#PACKAGE_SRC_DIR="/source" PACKAGE_EX_DIR="/example" +PACKAGE_DOC_DIR="/doc" for package in `ls $ROOT_DIR/src/` do echo $package @@ -77,20 +81,16 @@ do fi cp -R $ROOT_DIR/src/$package$PACKAGE_INC_DIR/* $VERSION_DIR$PACKAGE_INC_DIR/ fi - if [ -d "$ROOT_DIR/src/$package$PACKAGE_SRC_DIR" ] - then - if [ ! -d "$VERSION_DIR$PACKAGE_SRC_DIR" ] - then - # MUST CREATE DIRECTORY ON FIRST LOOP - mkdir $VERSION_DIR$PACKAGE_INC_DIR - fi - cp -R $ROOT_DIR/src/$package$PACKAGE_SRC_DIR/* $VERSION_DIR$PACKAGE_SRC_DIR/ - fi if [ -d "$ROOT_DIR/src/$package$PACKAGE_EX_DIR" ] then 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_DOC_DIR" ] + then + mkdir -p $VERSION_DIR$PACKAGE_DOC_DIR/$package + cp -R $ROOT_DIR/src/$package$PACKAGE_DOC_DIR/* $VERSION_DIR$PACKAGE_DOC_DIR/$package + fi fi fi done diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h new file mode 100644 index 00000000..34af2b98 --- /dev/null +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -0,0 +1,119 @@ +/* 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) 2015 INRIA Saclay (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/>. + */ + +// needs namespace for Doxygen to link on classes +namespace Gudhi { +// needs namespace for Doxygen to link on classes +namespace alphacomplex { + +/** \defgroup alpha_complex Alpha complex + * + * \author Vincent Rouvreau + * + * @{ + * + * \section definition Definition + * + * Alpha_complex is a Simplex_tree constructed from each finite cell of a Delaunay Triangulation. + * + * The filtration value of each simplex is computed from the alpha value of the simplex if it is Gabriel or + * from the alpha value of the simplex coface that makes the simplex not Gabriel. + * + * Please refer to \cite AlphaShapesDefinition for a more complete alpha complex definition. + * + * Alpha complex are interesting because it looks like an \ref alpha-shape "Alpha shape" as described in + * \cite AlphaShapesIntroduction (an alpha complex concept vulgarization). + * + * \section example Example + * + * This example loads points from an OFF file, builds the Delaunay triangulation from the points, and finally + * initialize the alpha complex with it. + * + * Then, it is asked to display information about the alpha complex. + * + * \include Alpha_complex_from_off.cpp + * + * When launching: + * + * \code $> ./alphaoffreader ../../data/points/alphacomplexdoc.off + * \endcode + * + * the program output is: + * + * \include alphaoffreader_for_doc.txt + * + * \section algorithm Algorithm + * + * <b>Data structure</b> + * + * In order to build the alpha complex, first, a Simplex tree is build from the cells of a Delaunay Triangulation. + * (The filtration value is set to NaN, which stands for unknown value): + * \image html "alpha_complex_doc.png" "Simplex tree structure construction example" + * + * <b>Filtration value computation algorithm</b> + * + * \f{algorithm}{ + * \caption{Filtration value computation algorithm}\label{alpha} + * \begin{algorithmic} + * \For{i : dimension $\rightarrow$ 1} + * \ForAll{$\sigma$ of dimension i} + * \If {filtration($\sigma$) is NaN} + * \State filtration($\sigma$) = $\alpha(\sigma)$ + * \EndIf + * \ForAll{$\tau$ face of $\sigma$} \Comment{propagate alpha filtration value} + * \If {filtration($\tau$) is not NaN} + * \State filtration($\tau$) = min (filtration($\tau$), filtration($\sigma$)) + * \Else + * \If {$\tau$ is not Gabriel for $\sigma$} + * \State filtration($\tau$) = filtration($\sigma$) + * \EndIf + * \EndIf + * \EndFor + * \EndFor + * \EndFor + * \end{algorithmic} + * \f} + * + * From the example above, it means the algorithm will look into each triangulation ([1,2,3], [2,3,4], [1,3,5], ...), + * will compute the filtration value of the triangulation, and then will propagate the filtration value as described + * here : + * \image html "alpha_complex_doc_135.png" "Filtration value propagation example" + * Then, the algorithm will look into each edge ([1,2], [2,3], [1,3], ...), + * will compute the filtration value of the edge (in this case, propagation will have no effect). + * + * Finally, the algorithm will look into each vertex ([1], [2], [3], [4], [5], [6] and [7]), + * will set the filtration value (0 in case of a vertex - propagation will have no effect). + * + * \section alpha-shape Alpha shape + * + * In the example above, the alpha shape of \f$\alpha_{74} < \alpha < \alpha_{73}\f$ is the alpha complex where the + * \f$\alpha_{74} <\f$ filtration value \f$< \alpha_{73}\f$ as described in \cite AlphaShapesIntroduction + * + * \image html "alpha_complex_doc_alpha_shape.png" "Alpha shape example" + * \copyright GNU General Public License v3. + * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim + */ +/** @} */ // end defgroup alpha_complex + +} // namespace alphacomplex + +} // namespace Gudhi diff --git a/src/Alpha_complex/doc/alpha_complex_doc.ipe b/src/Alpha_complex/doc/alpha_complex_doc.ipe new file mode 100644 index 00000000..6257b2f4 --- /dev/null +++ b/src/Alpha_complex/doc/alpha_complex_doc.ipe @@ -0,0 +1,438 @@ +<?xml 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height="6.42" depth="0" valign="baseline">5</text> +<path stroke="darkcyan" pen="heavier"> +406.093 497.775 m +446.094 418.092 l +</path> +<path stroke="darkcyan"> +44.5799 0 0 44.5799 425.934 457.774 e +</path> +<use name="mark/fdisk(sfx)" pos="425.934 457.774" size="normal" stroke="darkcyan" fill="white"/> +<path stroke="darkcyan"> +425.854 457.774 m +470.795 457.774 l +</path> +<text matrix="1 0 0 1 -48.9756 -209.799" transformations="translations" pos="380 530" stroke="darkcyan" type="label" width="231.798" height="8.965" depth="2.99" valign="baseline" size="large">[3,5] is Gabriel $\rightarrow$ $\alpha_{35}$ is not modified (NaN) +</text> +<path stroke="darkblue" arrow="normal/normal"> +205.028 596.091 m +110.946 544.02 l +</path> +<path stroke="darkblue" arrow="normal/normal"> +280.768 588.99 m +280.768 547.57 l +</path> +<path stroke="darkblue" arrow="normal/normal"> +341.123 594.316 m +413.904 554.079 l +</path> +<text matrix="1 0 0 1 39.645 -2.36686" 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m +300 680 l +</path> +<path stroke="black"> +280 660 m +300 640 l +</path> +<path stroke="black"> +370 660 m +350 680 l +</path> +<path stroke="black"> +370 660 m +350 640 l +</path> +<path stroke="black"> +290 670 m +360 670 l +</path> +<path stroke="black"> +290 650 m +360 650 l +</path> +<text matrix="1 0 0 1 2.36686 -1.77515" transformations="translations" pos="300 660" stroke="black" type="label" width="44.002" height="6.926" depth="1.93" valign="baseline">equivalent</text> +</page> +</ipe> diff --git a/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png b/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png Binary files differnew file mode 100644 index 00000000..516de126 --- /dev/null +++ b/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp new file mode 100644 index 00000000..b698d6d7 --- /dev/null +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -0,0 +1,50 @@ +#include <stdio.h> +#include <stdlib.h> + +#include <string> + +// to construct a Delaunay_triangulation from a OFF file +#include "gudhi/Delaunay_triangulation_off_io.h" +#include "gudhi/Alpha_complex.h" + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value" << std::endl; + std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0" << std::endl; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if (argc != 3) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; + usage(argv[0]); + } + + std::string off_file_name(argv[1]); + double alpha_square_max_value = atof(argv[2]); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from an OFF file + // ---------------------------------------------------------------------------- + typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; + Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name, alpha_square_max_value); + + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() << + " - " << alpha_complex_from_file.num_simplices() << " simplices - " << + alpha_complex_from_file.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) { + if (alpha_complex_from_file.filtration(f_simplex) <= alpha_complex_from_file.filtration()) { + std::cout << " ( "; + for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + } + return 0; +} diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp new file mode 100644 index 00000000..b160d702 --- /dev/null +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -0,0 +1,56 @@ +#include <stdio.h> +#include <stdlib.h> +#include <CGAL/Delaunay_triangulation.h> +#include <CGAL/Epick_d.h> + +#include <string> +#include <vector> + +// to construct a Delaunay_triangulation from a OFF file +#include "gudhi/Delaunay_triangulation_off_io.h" +#include "gudhi/Alpha_complex.h" + +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; +typedef Kernel::Point_d Point; +typedef std::vector<Point> Vector_of_points; + +int main(int argc, char **argv) { + // ---------------------------------------------------------------------------- + // Init of a list of points + // ---------------------------------------------------------------------------- + Vector_of_points 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 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); + + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Alpha complex is of dimension " << alpha_complex_from_points.dimension() << + " - " << alpha_complex_from_points.num_simplices() << " simplices - " << + alpha_complex_from_points.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + return 0; +} diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt new file mode 100644 index 00000000..04fc34af --- /dev/null +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -0,0 +1,32 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIAlphaShapesExample) + +# need CGAL 4.7 +# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../.. +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + include( ${CGAL_USE_FILE} ) + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + if (CMAKE_BUILD_TYPE MATCHES Debug) + # For programs to be more verbose + add_definitions(-DDEBUG_TRACES) + endif() + + add_executable ( alphaoffreader Alpha_complex_from_off.cpp ) + target_link_libraries(alphaoffreader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + + add_executable ( alphapoints Alpha_complex_from_points.cpp ) + target_link_libraries(alphapoints ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") + endif () +endif() diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc.txt b/src/Alpha_complex/example/alphaoffreader_for_doc.txt new file mode 100644 index 00000000..71f29a00 --- /dev/null +++ b/src/Alpha_complex/example/alphaoffreader_for_doc.txt @@ -0,0 +1,27 @@ +Alpha complex is of dimension 2 - 25 simplices - 7 vertices. +Iterator on alpha complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] + ( 6 2 ) -> [36.5] + ( 6 3 2 ) -> [36.5] + ( 6 4 2 ) -> [37.2449] + ( 4 0 ) -> [59.7107] + ( 4 2 0 ) -> [59.7107] diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h new file mode 100644 index 00000000..518d1792 --- /dev/null +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -0,0 +1,361 @@ +/* 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) 2015 INRIA Saclay (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/>. + */ + +#ifndef ALPHA_COMPLEX_H_ +#define ALPHA_COMPLEX_H_ + +// to construct a simplex_tree from Delaunay_triangulation +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Simplex_tree.h> + +#include <stdio.h> +#include <stdlib.h> +#include <math.h> // isnan, fmax + +#include <CGAL/Delaunay_triangulation.h> +#include <CGAL/Epick_d.h> +#include <CGAL/algorithm.h> +#include <CGAL/assertions.h> +#include <CGAL/enum.h> + +#include <iostream> +#include <vector> +#include <string> +#include <limits> // NaN +#include <map> +#include <utility> // std::pair + +namespace Gudhi { + +namespace alphacomplex { + +/** + * \brief Alpha complex data structure. + * + * \details + * The data structure can be constructed from a CGAL Delaunay triangulation (for more informations on CGAL Delaunay + * triangulation, please refer to the corresponding chapter in page http://doc.cgal.org/latest/Triangulation/) or from + * an OFF file (cf. Delaunay_triangulation_off_reader). + * + * Please refer to \ref alpha_complex for examples. + * + */ +template<class Kernel> +class Alpha_complex : public Simplex_tree<> { + private: + // From Simplex_tree + // Type required to insert into a simplex_tree (with or without subfaces). + typedef std::vector<Vertex_handle> Vector_vertex; + + // Simplex_result is the type returned from simplex_tree insert function. + typedef typename std::pair<Simplex_handle, bool> Simplex_result; + + // Delaunay_triangulation type required to create an alpha-complex. + typedef typename CGAL::Delaunay_triangulation<Kernel> Delaunay_triangulation; + + typedef typename Kernel::Compute_squared_radius_d Squared_Radius; + typedef typename Kernel::Side_of_bounded_sphere_d Is_Gabriel; + + typedef typename Kernel::Point_d Point_d; + + // Type required to compute squared radius, or side of bounded sphere on a vector of points. + typedef typename std::vector<Point_d> Vector_of_CGAL_points; + + // Vertex_iterator type from CGAL. + typedef typename Delaunay_triangulation::Vertex_iterator CGAL_vertex_iterator; + + // size_type type from CGAL. + typedef typename Delaunay_triangulation::size_type size_type; + + // Double map type to switch from CGAL vertex iterator to simplex tree vertex handle and vice versa. + typedef typename std::map< CGAL_vertex_iterator, Vertex_handle > Map_vertex_iterator_to_handle; + typedef typename std::map< Vertex_handle, CGAL_vertex_iterator > Map_vertex_handle_to_iterator; + + private: + /** \brief Map to switch from CGAL vertex iterator to simplex tree vertex handle.*/ + Map_vertex_iterator_to_handle vertex_iterator_to_handle_; + /** \brief Map to switch from simplex tree vertex handle to CGAL vertex iterator.*/ + Map_vertex_handle_to_iterator vertex_handle_to_iterator_; + /** \brief Pointer on the CGAL Delaunay triangulation.*/ + Delaunay_triangulation* triangulation_; + /** \brief Kernel for triangulation_ functions access.*/ + Kernel kernel_; + + public: + /** \brief Alpha_complex constructor from an OFF file name. + * Uses the Delaunay_triangulation_off_reader to construct the Delaunay triangulation required to initialize + * the Alpha_complex. + * + * @param[in] off_file_name OFF file [path and] name. + */ + Alpha_complex(const std::string& off_file_name, Filtration_value max_alpha_square) + : triangulation_(nullptr) { + Gudhi::Delaunay_triangulation_off_reader<Delaunay_triangulation> off_reader(off_file_name); + if (!off_reader.is_valid()) { + std::cerr << "Alpha_complex - Unable to read file " << off_file_name << std::endl; + exit(-1); // ----- >> + } + triangulation_ = off_reader.get_complex(); + set_filtration(max_alpha_square); + init(); + } + + /** \brief Alpha_complex constructor from a Delaunay triangulation. + * + * @param[in] triangulation_ptr Pointer on a Delaunay triangulation. + */ + Alpha_complex(Delaunay_triangulation* triangulation_ptr, Filtration_value max_alpha_square) + : triangulation_(triangulation_ptr) { + set_filtration(max_alpha_square); + init(); + } + + /** \brief Alpha_complex constructor from a list of points. + * Uses the Delaunay_triangulation_off_reader to construct the Delaunay triangulation required to initialize + * 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. + */ + template<typename ForwardIterator > + Alpha_complex(int dimension, size_type size, ForwardIterator firstPoint, ForwardIterator lastPoint, + Filtration_value max_alpha_square) + : 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; + exit(-1); // ----- >> + } + set_filtration(max_alpha_square); + init(); + } + + /** \brief Alpha_complex destructor from a Delaunay triangulation. + * + * @warning Deletes the Delaunay triangulation. + */ + ~Alpha_complex() { + delete triangulation_; + } + + /** \brief get_point returns the point corresponding to the vertex given as parameter. + * + * @param[in] vertex Vertex handle of the point to retrieve. + * @return The founded point. + * @warning Exception std::out_of_range is thrown in case vertex is not in the map vertex_handle_to_iterator_. + */ + Point_d get_point(Vertex_handle vertex) { + auto found_it = vertex_handle_to_iterator_.find(vertex); + if (found_it != vertex_handle_to_iterator_.end()) { + return found_it->second->point(); + } else { + throw std::out_of_range("Vertex out of vector range"); + } + } + + private: + /** \brief Initialize the Alpha_complex from the Delaunay triangulation. + * + * @warning Delaunay triangulation must be already constructed with at least one vertex and dimension must be more + * than 0. + * + * Initialization can be launched once. + */ + void init() { + if (triangulation_ == nullptr) { + std::cerr << "Alpha_complex init - Cannot init from a NULL triangulation" << std::endl; + return; // ----- >> + } + if (triangulation_->number_of_vertices() < 1) { + std::cerr << "Alpha_complex init - Cannot init from a triangulation without vertices" << std::endl; + return; // ----- >> + } + if (triangulation_->maximal_dimension() < 1) { + std::cerr << "Alpha_complex init - Cannot init from a zero-dimension triangulation" << std::endl; + return; // ----- >> + } + if (num_vertices() > 0) { + std::cerr << "Alpha_complex init - Cannot init twice" << std::endl; + return; // ----- >> + } + + set_dimension(triangulation_->maximal_dimension()); + + // -------------------------------------------------------------------------------------------- + // double map to retrieve simplex tree vertex handles from CGAL vertex iterator and vice versa + // Start to insert at handle = 0 - default integer value + Vertex_handle vertex_handle = Vertex_handle(); + // Loop on triangulation vertices list + for (CGAL_vertex_iterator vit = triangulation_->vertices_begin(); vit != triangulation_->vertices_end(); ++vit) { + if (!triangulation_->is_infinite(*vit)) { +#ifdef DEBUG_TRACES + std::cout << "Vertex insertion - " << vertex_handle << " -> " << vit->point() << std::endl; +#endif // DEBUG_TRACES + vertex_iterator_to_handle_.emplace(vit, vertex_handle); + vertex_handle_to_iterator_.emplace(vertex_handle, vit); + vertex_handle++; + } + } + // -------------------------------------------------------------------------------------------- + + // -------------------------------------------------------------------------------------------- + // Simplex_tree construction from loop on triangulation finite full cells list + for (auto cit = triangulation_->finite_full_cells_begin(); cit != triangulation_->finite_full_cells_end(); ++cit) { + Vector_vertex vertexVector; +#ifdef DEBUG_TRACES + std::cout << "Simplex_tree insertion "; +#endif // DEBUG_TRACES + for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) { + if (*vit != nullptr) { +#ifdef DEBUG_TRACES + std::cout << " " << vertex_iterator_to_handle_[*vit]; +#endif // DEBUG_TRACES + // Vector of vertex construction for simplex_tree structure + vertexVector.push_back(vertex_iterator_to_handle_[*vit]); + } + } +#ifdef DEBUG_TRACES + std::cout << std::endl; +#endif // DEBUG_TRACES + // Insert each simplex and its subfaces in the simplex tree - filtration is NaN + Simplex_result insert_result = insert_simplex_and_subfaces(vertexVector, + std::numeric_limits<double>::quiet_NaN()); + if (!insert_result.second) { + std::cerr << "Alpha_complex::init insert_simplex_and_subfaces failed" << std::endl; + exit(-1); // ----->> + } + } + // -------------------------------------------------------------------------------------------- + + // -------------------------------------------------------------------------------------------- + // ### For i : d -> 0 + for (int decr_dim = dimension(); decr_dim >= 0; decr_dim--) { + // ### Foreach Sigma of dim i + for (auto f_simplex : skeleton_simplex_range(decr_dim)) { + int f_simplex_dim = dimension(f_simplex); + if (decr_dim == f_simplex_dim) { + Vector_of_CGAL_points pointVector; +#ifdef DEBUG_TRACES + std::cout << "Sigma of dim " << decr_dim << " is"; +#endif // DEBUG_TRACES + for (auto vertex : simplex_vertex_range(f_simplex)) { + pointVector.push_back(get_point(vertex)); +#ifdef DEBUG_TRACES + std::cout << " " << vertex; +#endif // DEBUG_TRACES + } +#ifdef DEBUG_TRACES + std::cout << std::endl; +#endif // DEBUG_TRACES + // ### If filt(Sigma) is NaN : filt(Sigma) = alpha(Sigma) + if (isnan(filtration(f_simplex))) { + Filtration_value alpha_complex_filtration = 0.0; + // No need to compute squared_radius on a single point - alpha is 0.0 + if (f_simplex_dim > 0) { + // squared_radius function initialization + Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object(); + + alpha_complex_filtration = squared_radius(pointVector.begin(), pointVector.end()); + } + assign_filtration(f_simplex, alpha_complex_filtration); +#ifdef DEBUG_TRACES + std::cout << "filt(Sigma) is NaN : filt(Sigma) =" << filtration(f_simplex) << std::endl; +#endif // DEBUG_TRACES + } + propagate_alpha_filtration(f_simplex, decr_dim); + } + } + } + // -------------------------------------------------------------------------------------------- + } + + template<typename Simplex_handle> + void propagate_alpha_filtration(Simplex_handle f_simplex, int decr_dim) { + // ### Foreach Tau face of Sigma + for (auto f_boundary : boundary_simplex_range(f_simplex)) { +#ifdef DEBUG_TRACES + std::cout << " | --------------------------------------------------" << std::endl; + 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 << " | isnan(filtration(Tau)=" << isnan(filtration(f_boundary)) << std::endl; +#endif // DEBUG_TRACES + // ### If filt(Tau) is not NaN + if (!isnan(filtration(f_boundary))) { + // ### filt(Tau) = fmin(filt(Tau), filt(Sigma)) + Filtration_value alpha_complex_filtration = fmin(filtration(f_boundary), filtration(f_simplex)); + assign_filtration(f_boundary, alpha_complex_filtration); +#ifdef DEBUG_TRACES + std::cout << " | filt(Tau) = fmin(filt(Tau), filt(Sigma)) = " << filtration(f_boundary) << std::endl; +#endif // DEBUG_TRACES + // ### Else + } else { + // No need to compute is_gabriel for dimension <= 2 + // i.e. : Sigma = (3,1) => Tau = 1 + if (decr_dim > 1) { + // insert the Tau points in a vector for is_gabriel function + Vector_of_CGAL_points pointVector; + Vertex_handle vertexForGabriel = Vertex_handle(); + for (auto vertex : simplex_vertex_range(f_boundary)) { + pointVector.push_back(get_point(vertex)); + } + // Retrieve the Sigma point that is not part of Tau - parameter for is_gabriel function + for (auto vertex : simplex_vertex_range(f_simplex)) { + if (std::find(pointVector.begin(), pointVector.end(), get_point(vertex)) == pointVector.end()) { + // vertex is not found in Tau + vertexForGabriel = vertex; + // No need to continue loop + break; + } + } + // is_gabriel function initialization + Is_Gabriel is_gabriel = kernel_.side_of_bounded_sphere_d_object(); + bool is_gab = is_gabriel(pointVector.begin(), pointVector.end(), get_point(vertexForGabriel)) + != CGAL::ON_BOUNDED_SIDE; +#ifdef DEBUG_TRACES + std::cout << " | Tau is_gabriel(Sigma)=" << is_gab << " - vertexForGabriel=" << vertexForGabriel << std::endl; +#endif // DEBUG_TRACES + // ### If Tau is not Gabriel of Sigma + if (false == is_gab) { + // ### filt(Tau) = filt(Sigma) + Filtration_value alpha_complex_filtration = filtration(f_simplex); + assign_filtration(f_boundary, alpha_complex_filtration); +#ifdef DEBUG_TRACES + std::cout << " | filt(Tau) = filt(Sigma) = " << filtration(f_boundary) << std::endl; +#endif // DEBUG_TRACES + } + } + } + } + } +}; + +} // namespace alphacomplex + +} // namespace Gudhi + +#endif // ALPHA_COMPLEX_H_ diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp new file mode 100644 index 00000000..b2597eff --- /dev/null +++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp @@ -0,0 +1,214 @@ +/* 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) 2015 INRIA Saclay (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/>. + */ + +#define BOOST_TEST_MODULE alpha_complex +#include <boost/test/included/unit_test.hpp> +#include <boost/system/error_code.hpp> +#include <boost/chrono/thread_clock.hpp> +#include <CGAL/Delaunay_triangulation.h> +#include <CGAL/Epick_d.h> + +#include <cmath> // float comparison +#include <limits> +#include <string> +#include <vector> + +// to construct a Delaunay_triangulation from a OFF file +#include "gudhi/Delaunay_triangulation_off_io.h" +#include "gudhi/Alpha_complex.h" + +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel_d; +// The triangulation uses the default instantiation of the TriangulationDataStructure template parameter + +BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file) { + // ---------------------------------------------------------------------------- + // + // Init of an alpha-complex from a OFF file + // + // ---------------------------------------------------------------------------- + std::string off_file_name("../../../data/points/alphacomplexdoc.off"); + double max_alpha_square_value = 60.0; + std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" << + max_alpha_square_value << "==========" << std::endl; + + Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value); + + const int DIMENSION = 2; + std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl; + BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION); + + const int NUMBER_OF_VERTICES = 7; + std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl; + BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES); + + const int NUMBER_OF_SIMPLICES = 25; + std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl; + BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES); + +} + +BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file_filtered) { + // ---------------------------------------------------------------------------- + // + // Init of an alpha-complex from a OFF file + // + // ---------------------------------------------------------------------------- + std::string off_file_name("../../../data/points/alphacomplexdoc.off"); + double max_alpha_square_value = 59.0; + std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" << + max_alpha_square_value << "==========" << std::endl; + + Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value); + + const int DIMENSION = 2; + std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl; + BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION); + + const int NUMBER_OF_VERTICES = 7; + std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl; + BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES); + + const int NUMBER_OF_SIMPLICES = 25; + std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl; + BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES); + + int num_filtered_simplices = 0; + for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) { + if (alpha_complex_from_file.filtration(f_simplex) <= alpha_complex_from_file.filtration()) { + num_filtered_simplices++; + } + } + const int NUMBER_OF_FILTERED_SIMPLICES = 23; + std::cout << "num_filtered_simplices=" << num_filtered_simplices << std::endl; + BOOST_CHECK(num_filtered_simplices == NUMBER_OF_FILTERED_SIMPLICES); + +} + +bool are_almost_the_same(float a, float b) { + return std::fabs(a - b) < std::numeric_limits<float>::epsilon(); +} + +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Kernel_s; +typedef Kernel_s::Point_d Point; +typedef std::vector<Point> Vector_of_points; + + +bool is_point_in_list(Vector_of_points points_list, Point point) { + for (auto& point_in_list : points_list) { + if (point_in_list == point) { + return true; // point found + } + } + return false; // point not found +} + +BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { + // ---------------------------------------------------------------------------- + // Init of a list of points + // ---------------------------------------------------------------------------- + Vector_of_points 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 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); + + std::cout << "========== Alpha_complex_from_points ==========" << std::endl; + + // Another way to check num_simplices + std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + int num_simplices = 0; + for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) { + num_simplices++; + std::cout << " ( "; + for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + BOOST_CHECK(num_simplices == 15); + std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl; + BOOST_CHECK(alpha_complex_from_points.num_simplices() == 15); + + std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl; + BOOST_CHECK(alpha_complex_from_points.dimension() == 4); + std::cout << "alpha_complex_from_points.num_vertices()=" << alpha_complex_from_points.num_vertices() << std::endl; + BOOST_CHECK(alpha_complex_from_points.num_vertices() == 4); + + for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) { + switch (alpha_complex_from_points.dimension(f_simplex)) { + case 0: + BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 0.0)); + break; + case 1: + BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 1.0/2.0)); + break; + case 2: + BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 2.0/3.0)); + break; + case 3: + BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 3.0/4.0)); + break; + default: + BOOST_CHECK(false); // Shall not happen + break; + } + } + + Point p0 = alpha_complex_from_points.get_point(0); + std::cout << "alpha_complex_from_points.get_point(0)=" << p0 << std::endl; + BOOST_CHECK(4 == p0.dimension()); + BOOST_CHECK(is_point_in_list(points, p0)); + + Point p1 = alpha_complex_from_points.get_point(1); + std::cout << "alpha_complex_from_points.get_point(1)=" << p1 << std::endl; + BOOST_CHECK(4 == p1.dimension()); + BOOST_CHECK(is_point_in_list(points, p1)); + + Point p2 = alpha_complex_from_points.get_point(2); + std::cout << "alpha_complex_from_points.get_point(2)=" << p2 << std::endl; + BOOST_CHECK(4 == p2.dimension()); + BOOST_CHECK(is_point_in_list(points, p2)); + + Point p3 = alpha_complex_from_points.get_point(3); + std::cout << "alpha_complex_from_points.get_point(3)=" << p3 << std::endl; + BOOST_CHECK(4 == p3.dimension()); + BOOST_CHECK(is_point_in_list(points, p3)); + + // Test to the limit + BOOST_CHECK_THROW (alpha_complex_from_points.get_point(4), std::out_of_range); + BOOST_CHECK_THROW (alpha_complex_from_points.get_point(-1), std::out_of_range); + BOOST_CHECK_THROW (alpha_complex_from_points.get_point(1234), std::out_of_range); +} diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt new file mode 100644 index 00000000..87b05a3a --- /dev/null +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -0,0 +1,35 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIAlphaComplexTest) + +# need CGAL 4.7 +# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../.. +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + include( ${CGAL_USE_FILE} ) + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + include_directories (BEFORE "../../include") + if (CMAKE_BUILD_TYPE MATCHES Debug) + # For programs to be more verbose + add_definitions(-DDEBUG_TRACES) + endif() + + add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp ) + target_link_libraries(AlphaComplexUT ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no) + + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha complex feature.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha complex feature. Version 4.6.0 is required.") + endif () +endif() + diff --git a/src/Alpha_complex/test/README b/src/Alpha_complex/test/README new file mode 100644 index 00000000..45b87d91 --- /dev/null +++ b/src/Alpha_complex/test/README @@ -0,0 +1,12 @@ +To compile: +*********** + +cmake . +make + +To launch with details: +*********************** + +./AlphaComplexUnitTest --report_level=detailed --log_level=all + + ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 545b0b58..172f9128 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -38,11 +38,13 @@ else() LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) include_directories(include/) + add_subdirectory(example/common) add_subdirectory(example/Simplex_tree) add_subdirectory(example/Persistent_cohomology) add_subdirectory(example/Skeleton_blocker) add_subdirectory(example/Contraction) add_subdirectory(example/Hasse_complex) + add_subdirectory(example/Alpha_complex) add_subdirectory(example/Bottleneck) # GudhUI diff --git a/src/Doxyfile b/src/Doxyfile index 62412627..0724de1c 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -672,7 +672,7 @@ 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 #--------------------------------------------------------------------------- # Configuration options related to warning and progress messages @@ -811,7 +811,8 @@ EXCLUDE_SYMBOLS = # that contain example code fragments that are included (see the \include # command). -EXAMPLE_PATH = +EXAMPLE_PATH = example/common/ \ + example/Alpha_complex/ # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and @@ -831,9 +832,10 @@ EXAMPLE_RECURSIVE = NO # that contain images that are to be included in the documentation (see the # \image command). -IMAGE_PATH = Skeleton_blocker/doc/ \ - common/doc/ \ - Contraction/doc/ +IMAGE_PATH = doc/Skeleton_blocker/ \ + doc/Alpha_complex/ \ + doc/common/ \ + doc/Contraction/ # The INPUT_FILTER tag can be used to specify a program that doxygen should @@ -1595,7 +1597,7 @@ PAPER_TYPE = a4 # If left blank no extra packages will be included. # This tag requires that the tag GENERATE_LATEX is set to YES. -EXTRA_PACKAGES = amsfonts amsmath amssymb +EXTRA_PACKAGES = amsfonts amsmath amssymb algorithm algpseudocode # The LATEX_HEADER tag can be used to specify a personal LaTeX header for the # generated LaTeX document. The header should contain everything until the first diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 9487cce6..3276989d 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -28,8 +28,11 @@ if (NOT MSVC) target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if(CGAL_FOUND) - # uncomment to display debug traces - # add_definitions(-DDEBUG_TRACES) + if (CMAKE_BUILD_TYPE MATCHES Debug) + # For programs to be more verbose + add_definitions(-DDEBUG_TRACES) + endif() + add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp) target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index d4a52113..fe2faf90 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -38,7 +38,6 @@ #include <functional> // for greater<> namespace Gudhi { - /** \defgroup simplex_tree Filtered Complexes * * A simplicial complex \f$\mathbf{K}\f$ @@ -73,7 +72,6 @@ namespace Gudhi { * \copyright GNU General Public License v3. * @{ */ - /** * \brief Simplex Tree data structure for representing simplicial complexes. * @@ -282,7 +280,8 @@ class Simplex_tree { threshold_(0), root_(NULL, null_vertex_), filtration_vect_(), - dimension_(-1) { } + dimension_(-1) { + } /** \brief Destructor; deallocates the whole tree structure. */ ~Simplex_tree() { @@ -330,6 +329,15 @@ class Simplex_tree { } } + /** \brief Sets the filtration value of a simplex. + * + * No action if called on the null_simplex*/ + void assign_filtration(Simplex_handle sh, Filtration_value fv) { + if (sh != null_simplex()) { + sh->second.assign_filtration(fv); + } + } + /** \brief Returns an upper bound of the filtration values of the simplices. */ Filtration_value filtration() const { return threshold_; @@ -442,8 +450,7 @@ class Simplex_tree { Simplex_handle find_vertex(Vertex_handle v) { return root_.members_.begin() + v; } - //{ return root_.members_.find(v); } - + /** \brief Insert a simplex, represented by a range of Vertex_handles, in the simplicial complex. * * @param[in] simplex range of Vertex_handles, representing the vertices of the new simplex @@ -508,8 +515,9 @@ class Simplex_tree { * @param[in] filtration the filtration value assigned to the new N-simplex. */ template<class RandomAccessVertexRange> - void insert_simplex_and_subfaces(RandomAccessVertexRange& Nsimplex, - Filtration_value filtration = 0.0) { + std::pair<Simplex_handle, bool> insert_simplex_and_subfaces(RandomAccessVertexRange& Nsimplex, + Filtration_value filtration = 0.0) { + std::pair<Simplex_handle, bool> returned; if (Nsimplex.size() > 1) { for (unsigned int NIndex = 0; NIndex < Nsimplex.size(); NIndex++) { // insert N (N-1)-Simplex @@ -519,22 +527,21 @@ class Simplex_tree { NsimplexMinusOne.push_back(Nsimplex[(NIndex + NListIter) % Nsimplex.size()]); } // (N-1)-Simplex recursive call - insert_simplex_and_subfaces(NsimplexMinusOne, filtration); + returned = insert_simplex_and_subfaces(NsimplexMinusOne, filtration); } // N-Simplex insert - std::pair<Simplex_handle, bool> returned = insert_simplex(Nsimplex, filtration); + returned = insert_simplex(Nsimplex, filtration); + if (returned.second == true) { + } } else if (Nsimplex.size() == 1) { // 1-Simplex insert - End of recursivity - std::pair<Simplex_handle, bool> returned = insert_simplex(Nsimplex, filtration); + returned = insert_simplex(Nsimplex, filtration); + if (returned.second == true) { + } } else { // Nothing to insert - empty vector } - } - - /** \brief Assign a value 'key' to the key of the simplex - * represented by the Simplex_handle 'sh'. */ - void assign_key(Simplex_handle sh, Simplex_key key) { - sh->second.assign_key(key); + return returned; } public: @@ -921,7 +928,6 @@ class Simplex_tree { }; // Print a Simplex_tree in os. - template<typename...T> std::ostream& operator<<(std::ostream & os, Simplex_tree<T...> & st) { for (auto sh : st.filtration_simplex_range()) { diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 315aa0ac..770d2216 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -48,8 +48,10 @@ CGAL is a C++ library which provides easy access to efficient and reliable geome 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 4.4 or higher installed is recommended. The procedure to install this library according to +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 diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt new file mode 100644 index 00000000..4cb03dbe --- /dev/null +++ b/src/common/example/CMakeLists.txt @@ -0,0 +1,26 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIDelaunayTriangulationOffFileReadWrite) + +# need CGAL 4.6 +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.6.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + include( ${CGAL_USE_FILE} ) + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + + add_executable ( dtoffrw Delaunay_triangulation_off_rw.cpp ) + target_link_libraries(dtoffrw ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_test(dtoffrw ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off ${CMAKE_CURRENT_BINARY_DIR}/result.off) + + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") + endif () +endif() diff --git a/src/common/example/Delaunay_triangulation_off_rw.cpp b/src/common/example/Delaunay_triangulation_off_rw.cpp new file mode 100644 index 00000000..d1aa7988 --- /dev/null +++ b/src/common/example/Delaunay_triangulation_off_rw.cpp @@ -0,0 +1,55 @@ +// to construct a Delaunay_triangulation from a OFF file +#include "gudhi/Delaunay_triangulation_off_io.h" + +#include <CGAL/Delaunay_triangulation.h> +#include <CGAL/Epick_d.h> + +#include <stdio.h> +#include <stdlib.h> +#include <string> + +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K; +typedef CGAL::Delaunay_triangulation<K> T; +// The triangulation uses the default instantiation of the +// TriangulationDataStructure template parameter + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << " inputFile.off outputFile.off" << std::endl; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if (argc != 3) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; + usage(argv[0]); + } + + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulates points + Gudhi::Delaunay_triangulation_off_reader<T> off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + exit(-1); // ----- >> + } + + // Retrieve the triangulation + T* triangulation = off_reader.get_complex(); + // Operations on triangulation + std::cout << "Number of vertices= " << triangulation->number_of_vertices() << std::endl; + std::cout << "Number of finite full cells= " << triangulation->number_of_finite_full_cells() << std::endl; + + std::string outFileName(argv[2]); + std::string offOutputFile(outFileName); + // Write the OFF file (output file name given as parameter) with the points and triangulated cells as faces + Gudhi::Delaunay_triangulation_off_writer<T> off_writer(offOutputFile, triangulation); + + // Check the write operation was correct + if (!off_writer.is_valid()) { + std::cerr << "Unable to write file " << offOutputFile << std::endl; + exit(-1); // ----- >> + } + + return 0; +}
\ No newline at end of file diff --git a/src/common/example/dtoffrw_alphashapedoc_result.txt b/src/common/example/dtoffrw_alphashapedoc_result.txt new file mode 100644 index 00000000..57761d14 --- /dev/null +++ b/src/common/example/dtoffrw_alphashapedoc_result.txt @@ -0,0 +1,3 @@ +Number of vertices= 7 +Number of finite full cells= 6 + diff --git a/src/common/include/gudhi/Delaunay_triangulation_off_io.h b/src/common/include/gudhi/Delaunay_triangulation_off_io.h new file mode 100644 index 00000000..de5fa2af --- /dev/null +++ b/src/common/include/gudhi/Delaunay_triangulation_off_io.h @@ -0,0 +1,308 @@ +/* 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) 2015 INRIA Saclay (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/>. + */ +#ifndef SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_ +#define SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_ + +#include <string> +#include <vector> +#include <fstream> +#include <map> + +#include "gudhi/Off_reader.h" + +namespace Gudhi { + +/** \brief OFF file visitor implementation according to Off_reader in order to construct a CGAL Delaunay triangulation. + * + * For more informations on CGAL Delaunay triangulation, please refer to the corresponding chapter in page + * http://doc.cgal.org/latest/Triangulation/ + */ +template<typename Complex> +class Delaunay_triangulation_off_visitor_reader { + private: + Complex* _complex; + typedef typename Complex::Point Point; + + public: + + // TODO(VR) : Pass a Complex as a parameter is required, even if not used. Otherwise, compilation is KO. + + /** \brief Delaunay_triangulation_off_visitor_reader constructor + * + * @param[in] _complex_ptr pointer on a Delaunay triangulation. + */ + Delaunay_triangulation_off_visitor_reader(Complex* _complex_ptr) + : _complex(nullptr) { } + + /** \brief Off_reader visitor init implementation. + * + * The init parameters are set from OFF file header. + * Dimension value is required in order to construct Delaunay triangulation. + * + * @param[in] dim space dimension of vertices. + * @param[in] num_vertices number of vertices in the OFF file (not used). + * @param[in] num_faces number of faces in the OFF file (not used). + * @param[in] num_edges number of edges in the OFF file (not used). + */ + void init(int dim, int num_vertices, int num_faces, int num_edges) { +#ifdef DEBUG_TRACES + std::cout << "Delaunay_triangulation_off_visitor_reader::init - dim=" << dim << " - num_vertices=" << + num_vertices << " - num_faces=" << num_faces << " - num_edges=" << num_edges << std::endl; +#endif // DEBUG_TRACES + if (num_faces > 0) { + std::cerr << "Delaunay_triangulation_off_visitor_reader::init faces are not taken into account from OFF " << + "file for Delaunay triangulation - faces are computed." << std::endl; + } + if (num_edges > 0) { + std::cerr << "Delaunay_triangulation_off_visitor_reader::init edges are not taken into account from OFF " << + "file for Delaunay triangulation - edges are computed." << std::endl; + } + // Complex construction with dimension from file + _complex = new Complex(dim); + } + + /** \brief Off_reader visitor point implementation. + * + * The point function is called on each vertex line from OFF file. + * This function inserts the vertex in the Delaunay triangulation. + * + * @param[in] point vector of vertex coordinates. + */ + void point(const std::vector<double>& point) { +#ifdef DEBUG_TRACES + std::cout << "Delaunay_triangulation_off_visitor_reader::point "; + for (auto coordinate : point) { + std::cout << coordinate << " | "; + } + std::cout << std::endl; +#endif // DEBUG_TRACES + _complex->insert(Point(point.size(), point.begin(), point.end())); + } + + // Off_reader visitor maximal_face implementation - not used + void maximal_face(const std::vector<int>& face) { + // For Delaunay Triangulation, only points are read + } + + // Off_reader visitor done implementation - not used + void done() { + // Nothing to be done on end of OFF file read + } + + /** \brief Returns the constructed Delaunay triangulation. + * + * @return A pointer on the Delaunay triangulation. + * + * @warning The returned pointer can be nullptr. + */ + Complex* get_complex() const { + return _complex; + } +}; + +/** \brief OFF file reader implementation in order to construct a Delaunay triangulation. + * + * This class is using the Delaunay_triangulation_off_visitor_reader to visit the OFF file according to Off_reader. + * + * For more informations on CGAL Delaunay triangulation, please refer to the corresponding chapter in page + * http://doc.cgal.org/latest/Triangulation/ + * + * \section Example + * + * This example loads points from an OFF file and builds the Delaunay triangulation. + * Then, it is asked to display the number of vertices and finites full cells from the Delaunay triangulation. + * + * \include Delaunay_triangulation_off_rw.cpp + * + * When launching: + * + * \code $> ./dtoffrw ../../data/points/alphashapedoc.off triangulated.off + * \endcode + * + * the program output is: + * + * \include dtoffrw_alphashapedoc_result.txt + */ +template<typename Complex> +class Delaunay_triangulation_off_reader { + public: + + /** \brief Reads the OFF file and constructs the Delaunay triangulation from the points + * that are in the OFF file. + * + * @param[in] name_file OFF file to read. + * + * @warning Check with is_valid() function to see if read operation was successful. + */ + Delaunay_triangulation_off_reader(const std::string & name_file) + : valid_(false) { + std::ifstream stream(name_file); + if (stream.is_open()) { + Delaunay_triangulation_off_visitor_reader<Complex> off_visitor(_complex); + Off_reader off_reader(stream); + valid_ = off_reader.read(off_visitor); + if (valid_) { + _complex = off_visitor.get_complex(); + if (_complex == nullptr) { + std::cerr << "Delaunay_triangulation_off_reader::Delaunay_triangulation_off_reader off_visitor returns an empty pointer" << std::endl; + valid_ = false; + } + } + } else { + std::cerr << "Delaunay_triangulation_off_reader::Delaunay_triangulation_off_reader could not open file " << + name_file << std::endl; + } + + } + + /** \brief Returns if the OFF file read operation was successful or not. + * + * @return OFF file read status. + */ + bool is_valid() const { + return valid_; + } + + /** \brief Returns the constructed Delaunay triangulation. + * + * @return A pointer on the Delaunay triangulation. + * + * @warning The returned pointer can be nullptr. + */ + Complex* get_complex() const { + if (valid_) + return _complex; + return nullptr; + + } + + private: + /** \brief OFF file read status.*/ + bool valid_; + /** \brief A pointer on the Delaunay triangulation.*/ + Complex* _complex; +}; + +/** \brief OFF file writer from a Delaunay triangulation. + * + * This class constructs the OFF file header according to http://www.geomview.org/docs/html/OFF.html + * + * The header is followed by the list of points coordinates (Delaunay triangulation vertices) + * + * And finally is followed by the list of faces (Delaunay triangulation finite full cells) + * + * For more informations on CGAL Delaunay triangulation, please refer to the corresponding chapter in page + * http://doc.cgal.org/latest/Triangulation/ + * + * \section Example + * + * This example loads points from an OFF file and builds the Delaunay triangulation. + * Then, the Delaunay triangulation is saved in a new file including the triangulation as a list of faces. + * + * \include Delaunay_triangulation_off_rw.cpp + * + * When launching: + * + * \code $> ./dtoffrw ../../data/points/alphashapedoc.off triangulated.off + * \endcode + * + * The result will be an OFF file of dimension 2 with the 7 points from alphashapedoc.off followed by the 6 + * triangulations of dimension 3 (the first value on each faces): + * \include dtoffrw_alphashapedoc_result.off + */ +template<typename Complex> +class Delaunay_triangulation_off_writer { + public: + typedef typename Complex::Point Point; + + /** \brief Writes the OFF file from the Delaunay triangulation + * + * @param[in] name_file OFF file to write. + * @param[in] complex_ptr pointer on a Delaunay triangulation. + * + * @warning Check with is_valid() function to see if write operation was successful. + */ + Delaunay_triangulation_off_writer(const std::string & name_file, Complex* complex_ptr) + : valid_(false) { + std::ofstream stream(name_file); + if (stream.is_open()) { + if (complex_ptr->current_dimension() == 3) { + // OFF header + stream << "OFF" << std::endl; + // no endl on next line - don't know why... + stream << complex_ptr->number_of_vertices() << " " << complex_ptr->number_of_finite_full_cells() << " 0"; + } else { + // nOFF header + stream << "nOFF" << std::endl; + // no endl on next line - don't know why... + stream << complex_ptr->current_dimension() << " " << complex_ptr->number_of_vertices() << " " << + complex_ptr->number_of_finite_full_cells() << " 0"; + + } + + // bimap to retrieve vertex handles from points and vice versa + std::map< Point, int > points_to_vh; + // Start to insert at default handle value + int vertex_handle = int(); + + // Points list + for (auto vit = complex_ptr->vertices_begin(); vit != complex_ptr->vertices_end(); ++vit) { + for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) { + stream << *Coord << " "; + } + stream << std::endl; + points_to_vh[vit->point()] = vertex_handle; + vertex_handle++; + } + + for (auto cit = complex_ptr->finite_full_cells_begin(); cit != complex_ptr->finite_full_cells_end(); ++cit) { + std::vector<int> vertexVector; + stream << std::distance(cit->vertices_begin(), cit->vertices_end()) << " "; + for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) { + stream << points_to_vh[(*vit)->point()] << " "; + } + stream << std::endl; + } + stream.close(); + valid_ = true; + } else { + std::cerr << "Delaunay_triangulation_off_writer::Delaunay_triangulation_off_writer could not open file " << + name_file << std::endl; + } + } + + /** \brief Returns if the OFF write operation was successful or not. + * + * @return OFF file write status. + */ + bool is_valid() const { + return valid_; + } + + private: + /* \brief OFF file write status. */ + bool valid_; +}; + +} // namespace Gudhi + +#endif // SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_ diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h index e29218d8..a8abb507 100644 --- a/src/common/include/gudhi/Off_reader.h +++ b/src/common/include/gudhi/Off_reader.h @@ -7,7 +7,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (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 @@ -36,163 +36,150 @@ namespace Gudhi { -/** - * Read an off file and calls a visitor methods while reading it. - * An off file must have its first/snd line in this format : - * OFF - * num_vert num_faces num_edges - * - * A noff file must have its first/snd line in this format : - * nOFF - * dim num_vert num_faces num_edges - * - * The number of edges num_edges is optional and can be left to zero. +/** \brief OFF file reader top class visitor. + * + * OFF file must be conform to format described here : + * http://www.geomview.org/docs/html/OFF.html */ -class Off_reader{ -public: - Off_reader(std::ifstream& stream):stream_(stream){ - } -// Off_reader(const std::string& name):stream_(name){ -// if(!stream_.is_open()) -// std::cerr <<"could not open file \n"; -// } - - ~Off_reader(){ - stream_.close(); - } - - /** - * read an off file and calls the following methods : - * void init(int dim,int num_vertices,int num_faces,int num_edges); //num_edges may not be set - * void point(const std::vector<double>& point); - * void maximal_face(const std::list<int>& face); - * void done(); - * of the visitor when reading a point or a maximal face. - */ - template<typename OffVisitor> - bool read(OffVisitor& off_visitor){ - bool success_read_off_preambule = read_off_preambule(off_visitor); - if(!success_read_off_preambule) { - std::cerr <<"could not read off preambule\n"; - return false; - } - - bool success_read_off_points = read_off_points(off_visitor); - if(!success_read_off_points) { - std::cerr <<"could not read off points\n"; - return false; - } - - bool success_read_off_faces = read_off_faces(off_visitor); - if(!success_read_off_faces) { - std::cerr <<"could not read off faces\n"; - return false; - } - - off_visitor.done(); - return success_read_off_preambule && success_read_off_points && success_read_off_faces; - } - -private: - std::ifstream& stream_; - - struct Off_info{ - int dim; - int num_vertices; - int num_edges; - int num_faces; - }; - - Off_info off_info_; - - template<typename OffVisitor> - bool read_off_preambule(OffVisitor& off_visitor){ - std::string line; - if(!goto_next_uncomment_line(line)) return false; - - bool is_off_file = (line.find("OFF") != std::string::npos); - bool is_noff_file = (line.find("nOFF") != std::string::npos); - - if(!is_off_file && !is_noff_file) { - std::cerr << line<<std::endl; - std::cerr << "missing off header\n"; - return false; - } - - if(!goto_next_uncomment_line(line)) return false; - std::istringstream iss(line); - if(is_off_file){ - off_info_.dim = 3; - if(!(iss >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)){ - std::cerr << "incorrect number of vertices/faces/edges\n"; - return false; - } - } - else - if(!(iss >> off_info_.dim >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)){ - std::cerr << "incorrect number of vertices/faces/edges\n"; - return false; - } - off_visitor.init(off_info_.dim,off_info_.num_vertices,off_info_.num_faces,off_info_.num_edges); - - return true; - } - - bool goto_next_uncomment_line(std::string& uncomment_line){ - uncomment_line.clear(); - do - std::getline(stream_, uncomment_line); - while(uncomment_line[0] == '%');// || uncomment_line.empty()); - return (uncomment_line.size()>0 && uncomment_line[0] != '%'); - } - - - template<typename OffVisitor> - bool read_off_points(OffVisitor& visitor){ - int num_vertices_to_read = off_info_.num_vertices; - while(num_vertices_to_read--){ - std::string line; - if(!goto_next_uncomment_line(line)) return false; - std::vector<double> point; - std::istringstream iss(line); - point.assign(std::istream_iterator<double>(iss),std::istream_iterator<double>()); -// if(point.size() != off_info_.dim) return false; - visitor.point(point); - } - return true; - } - - template<typename OffVisitor> - bool read_off_faces(OffVisitor& visitor){ - std::string line; - while(goto_next_uncomment_line(line)){ - std::istringstream iss(line); - int num_face_vertices; - iss >> num_face_vertices; - std::vector<int> face; - face.assign(std::istream_iterator<int>(iss),std::istream_iterator<int>()); - if(!face.size() == off_info_.num_vertices) return false; - visitor.maximal_face(face); - } - return true; - } +class Off_reader { + public: + + Off_reader(std::ifstream& stream) : stream_(stream) { } + + ~Off_reader() { + stream_.close(); + } + + /** \brief + * Read an OFF file and calls the following methods : + * + * <CODE>void init(int dim,int num_vertices,int num_faces,int num_edges); // from file header - num_edges may not be set + * + * void point(const std::vector<double>& point); // for each point read + * + * void maximal_face(const std::list<int>& face); // for each face read + * + * void done(); // upon file read is finished</CODE> + * + * of the visitor when reading a point or a maximal face. Edges are not taken into account. + */ + template<typename OffVisitor> + bool read(OffVisitor& off_visitor) { + bool success_read_off_preambule = read_off_preambule(off_visitor); + if (!success_read_off_preambule) { + std::cerr << "could not read off preambule\n"; + return false; + } + + bool success_read_off_points = read_off_points(off_visitor); + if (!success_read_off_points) { + std::cerr << "could not read off points\n"; + return false; + } + + bool success_read_off_faces = read_off_faces(off_visitor); + if (!success_read_off_faces) { + std::cerr << "could not read off faces\n"; + return false; + } + + off_visitor.done(); + return success_read_off_preambule && success_read_off_points && success_read_off_faces; + } + + private: + std::ifstream& stream_; + + struct Off_info { + int dim; + int num_vertices; + int num_edges; + int num_faces; + }; + + Off_info off_info_; + + template<typename OffVisitor> + bool read_off_preambule(OffVisitor& off_visitor) { + std::string line; + if (!goto_next_uncomment_line(line)) return false; + + bool is_off_file = (line.find("OFF") != std::string::npos); + bool is_noff_file = (line.find("nOFF") != std::string::npos); + + if (!is_off_file && !is_noff_file) { + std::cerr << line << std::endl; + std::cerr << "missing off header\n"; + return false; + } + + if (!goto_next_uncomment_line(line)) return false; + std::istringstream iss(line); + if ((is_off_file) && (!is_noff_file)) { + off_info_.dim = 3; + if (!(iss >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) { + std::cerr << "incorrect number of vertices/faces/edges\n"; + return false; + } + } else + if (!(iss >> off_info_.dim >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) { + std::cerr << "incorrect number of vertices/faces/edges\n"; + return false; + } + off_visitor.init(off_info_.dim, off_info_.num_vertices, off_info_.num_faces, off_info_.num_edges); + + return true; + } + + bool goto_next_uncomment_line(std::string& uncomment_line) { + uncomment_line.clear(); + do + std::getline(stream_, uncomment_line); while (uncomment_line[0] == '%'); + return (uncomment_line.size() > 0 && uncomment_line[0] != '%'); + } + + template<typename OffVisitor> + bool read_off_points(OffVisitor& visitor) { + int num_vertices_to_read = off_info_.num_vertices; + while (num_vertices_to_read--) { + std::string line; + if (!goto_next_uncomment_line(line)) return false; + std::vector<double> point; + std::istringstream iss(line); + point.assign(std::istream_iterator<double>(iss), std::istream_iterator<double>()); + // if(point.size() != off_info_.dim) return false; + visitor.point(point); + } + return true; + } + + template<typename OffVisitor> + bool read_off_faces(OffVisitor& visitor) { + std::string line; + while (goto_next_uncomment_line(line)) { + std::istringstream iss(line); + int num_face_vertices; + iss >> num_face_vertices; + std::vector<int> face; + face.assign(std::istream_iterator<int>(iss), std::istream_iterator<int>()); + if (!face.size() == off_info_.num_vertices) return false; + visitor.maximal_face(face); + } + return true; + } }; - template<typename OFFVisitor> -void read_off(const std::string& name_file_off,OFFVisitor& vis){ - std::ifstream stream(name_file_off); - if(!stream.is_open()) - std::cerr <<"could not open file \n"; - else{ - Off_reader off_reader(stream); - off_reader.read(vis); - } +void read_off(const std::string& name_file_off, OFFVisitor& vis) { + std::ifstream stream(name_file_off); + if (!stream.is_open()) + std::cerr << "could not open file \n"; + else { + Off_reader off_reader(stream); + off_reader.read(vis); + } } - - } // namespace Gudhi - -#endif /* GUDHI_OFF_READER_H_ */ +#endif // GUDHI_OFF_READER_H_ diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt new file mode 100644 index 00000000..1b4dd6e0 --- /dev/null +++ b/src/common/test/CMakeLists.txt @@ -0,0 +1,41 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIDelaunayTriangulationOffFileReadWriteUT) + +if(NOT MSVC) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} --coverage") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage") +endif() + +# need CGAL 4.6 +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.6.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + include( ${CGAL_USE_FILE} ) + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + + add_executable ( dtoffrw_UT dtoffrw_unit_test.cpp ) + target_link_libraries(dtoffrw_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + + # Unitary tests + add_test(dtoffrw_UT ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw_UT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/dtoffrw_UT.xml --log_level=test_suite --report_level=no) + + if (DIFF_PATH) + add_test(dtoffrw_diff_files_UT ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/UT.off ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw_alphashapedoc_result.off) + endif() + + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") + endif () +endif() + diff --git a/src/common/test/README b/src/common/test/README new file mode 100644 index 00000000..f2a7eb5a --- /dev/null +++ b/src/common/test/README @@ -0,0 +1,14 @@ +To compile: +*********** + +cmake . +make + +To launch with details: +*********************** + +./dtoffrw_UT --report_level=detailed --log_level=all + + ==> echo $? returns 0 in case of success (non-zero otherwise) + + diff --git a/src/common/test/dtoffrw_alphashapedoc_result.off b/src/common/test/dtoffrw_alphashapedoc_result.off new file mode 100644 index 00000000..13c255c6 --- /dev/null +++ b/src/common/test/dtoffrw_alphashapedoc_result.off @@ -0,0 +1,15 @@ +nOFF +2 7 6 0 +1 1 +7 0 +4 6 +9 6 +0 14 +2 19 +9 17 +3 1 2 3 +3 4 3 2 +3 5 1 3 +3 5 3 7 +3 7 3 4 +3 6 5 7 diff --git a/src/common/test/dtoffrw_unit_test.cpp b/src/common/test/dtoffrw_unit_test.cpp new file mode 100644 index 00000000..d2705955 --- /dev/null +++ b/src/common/test/dtoffrw_unit_test.cpp @@ -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) 2015 INRIA Saclay (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/>. + */ + +#define BOOST_TEST_MODULE DelaunayTriangulationOffFileReadWrite test + +// to construct a Delaunay_triangulation from a OFF file +#include "gudhi/Delaunay_triangulation_off_io.h" + +#include <CGAL/Delaunay_triangulation.h> +#include <CGAL/Epick_d.h> + +#include <stdio.h> +#include <stdlib.h> +#include <string> + +#include <boost/test/included/unit_test.hpp> +#include <boost/system/error_code.hpp> +//#include <boost/chrono/thread_clock.hpp> + +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K; +typedef CGAL::Delaunay_triangulation<K> T; + +BOOST_AUTO_TEST_CASE( Delaunay_triangulation_doc_test ) +{ + // Read the OFF file (input file name given as parameter) and triangulates points + Gudhi::Delaunay_triangulation_off_reader<T> off_reader("../../../data/points/alphacomplexdoc.off"); + // Check the read operation was correct + BOOST_CHECK(off_reader.is_valid()); + + // Retrieve the triangulation + T* triangulation = off_reader.get_complex(); + BOOST_CHECK(triangulation != nullptr); + // Operations on triangulation + BOOST_CHECK(triangulation->number_of_vertices() == 7); + BOOST_CHECK(triangulation->number_of_finite_full_cells() == 6); + + // Write the OFF file (output file name given as parameter) with the points and triangulated cells as faces + Gudhi::Delaunay_triangulation_off_writer<T> off_writer("UT.off", triangulation); + + // Check the write operation was correct + BOOST_CHECK(off_writer.is_valid()); + + delete triangulation; +} + +BOOST_AUTO_TEST_CASE( Delaunay_triangulation_unexisting_file_read_test ) +{ + Gudhi::Delaunay_triangulation_off_reader<T> off_reader("pouetpouet_tralala.off"); + // Check the read operation was correct + BOOST_CHECK(!off_reader.is_valid()); + T* triangulation = off_reader.get_complex(); + BOOST_CHECK(triangulation == nullptr); +} + +BOOST_AUTO_TEST_CASE( Delaunay_triangulation_unexisting_file_write_test ) +{ + // Read the OFF file (input file name given as parameter) and triangulates points + Gudhi::Delaunay_triangulation_off_reader<T> off_reader("../../../data/points/alphacomplexdoc.off"); + + // Retrieve the triangulation + T* triangulation = off_reader.get_complex(); + + // Write the OFF file (output file name given as parameter) with the points and triangulated cells as faces + Gudhi::Delaunay_triangulation_off_writer<T> off_writer("/pouetpouet_tralala/pouetpouet_tralala/pouetpouet_tralala.off", triangulation); + + // Check the write operation was correct + BOOST_CHECK(!off_writer.is_valid()); + + delete triangulation; +} + |
