From 2f85df31681bb808a39fbeff9d0787ba7f632052 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 12 Jun 2019 11:44:01 +0200 Subject: Fix alpha complex 3d utilities and add links to utils pages --- .../doc/Intro_persistent_cohomology.h | 67 +++++++++++----------- 1 file changed, 35 insertions(+), 32 deletions(-) (limited to 'src') diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index 5fb9d4d2..3e0ad133 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -154,6 +154,8 @@ diagram. 3 1 0.104347 inf 3 2 0.138335 inf \endcode +More details on the Rips complex utilities dedicated page. + \li Persistent_cohomology/rips_multifield_persistence.cpp computes the Rips complex of a point cloud and outputs its persistence diagram with a family of field coefficients. @@ -166,6 +168,8 @@ The file should contain square or lower triangular distance matrix with semicolo The code do not check if it is dealing with a distance matrix. It is the user responsibility to provide a valid input. Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an example of a file. +More details on the Rips complex utilities dedicated page. + \li Rips_complex/rips_correlation_matrix_persistence.cpp computes the Rips complex of a correlation matrix and outputs its persistence diagram. @@ -175,6 +179,8 @@ It is the user responsibility to ensure that this is the case. The input is to b triangular matrix. Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv for an example of a file. +More details on the Rips complex utilities dedicated page. + \li Alpha_complex/alpha_complex_3d_persistence.cpp computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. @@ -185,48 +191,33 @@ Alpha_complex/alpha_complex_3d_persistence.cpp computes the persistent homol 2 1 0.0934117 1.00003 2 2 0.56444 1.03938 \endcode -\li -Alpha_complex/exact_alpha_complex_3d_persistence.cpp computes the persistent homology with -\f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. +More details on the Alpha complex utilities dedicated page. + Here, as CGAL computes the exact values, it is slower, but it is necessary when points are on a grid -for instance. -\code $> ./exact_alpha_complex_3d_persistence ../../data/points/sphere3D_pts_on_grid.off -p 2 -m 0.1 \endcode +for instance (the fast version `--fast` would give incorrect values). +\code $> ./alpha_complex_3d_persistence ../../data/points/sphere3D_pts_on_grid.off --exact -p 2 -m 0.1 \endcode \code Simplex_tree dim: 3 2 0 0 inf 2 2 0.0002 0.2028 \endcode -\li -Alpha_complex/weighted_alpha_complex_3d_persistence.cpp computes the persistent homology with +It can also compute the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the weighted alpha complex on points sampling from an OFF file and a weights file. -\code $> ./weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off -../../data/points/tore3D_300.weights -p 2 -m 0.45 \endcode +\code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off +--weight-file ../../data/points/tore3D_300.weights -p 2 -m 0.45 \endcode \code Simplex_tree dim: 3 2 0 -1 inf 2 1 -0.931784 0.000103311 2 1 -0.906588 2.60165e-05 2 2 -0.43556 0.0393798 \endcode -\li -Alpha_complex/alpha_complex_persistence.cpp computes the persistent homology with -\f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. -\code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode -\code Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. -Simplex_tree dim: 3 -2 0 0 inf -2 1 0.0682162 1.0001 -2 1 0.0934117 1.00003 -2 2 0.56444 1.03938 \endcode - -\li -Alpha_complex/periodic_alpha_complex_3d_persistence.cpp computes the persistent homology with +One can also compute the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file. The second parameter is a \ref FileFormatsIsoCuboid file with coordinates of the periodic cuboid. Note that the lengths of the sides of the periodic cuboid have to be the same. -\code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off -../../data/points/iso_cuboid_3_in_0_1.txt -p 3 -m 1.0 \endcode -\code Periodic Delaunay computed. -Simplex_tree dim: 3 +\code $> ./alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off +--cuboid-file ../../data/points/iso_cuboid_3_in_0_1.txt -p 3 -m 1.0 \endcode +\code Simplex_tree dim: 3 3 0 0 inf 3 1 0.0025 inf 3 1 0.0025 inf @@ -236,18 +227,17 @@ Simplex_tree dim: 3 3 2 0.005 inf 3 3 0.0075 inf \endcode -\li -Persistent_cohomology/weighted_periodic_alpha_complex_3d_persistence.cpp computes the persistent homology with +In order to compute the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on weighted points from an OFF file. The additional parameters of this program are:
(a) The file with the weights of points. The file consist of a sequence of numbers (as many as points). Note that the weight of each single point have to be bounded by 1/64 times the square of the cuboid edge length.
(b) A \ref FileFormatsIsoCuboid file with coordinates of the periodic cuboid. Note that the lengths of the sides of the periodic cuboid have to be the same.
-\code $> ./weighted_periodic_alpha_complex_3d_persistence ../../data/points/shifted_sphere.off -../../data/points/shifted_sphere.weights ../../data/points/iso_cuboid_3_in_0_10.txt 3 1.0 \endcode -\code Weighted Periodic Delaunay computed. -Simplex_tree dim: 3 +\code $> ./alpha_complex_3d_persistence ../../data/points/shifted_sphere.off +--weight-file ../../data/points/shifted_sphere.weights +--cuboid-file ../../data/points/iso_cuboid_3_in_0_10.txt -p 3 -m 1.0 \endcode +\code Simplex_tree dim: 3 3 0 -0.0001 inf 3 1 16.0264 inf 3 1 16.0273 inf @@ -257,6 +247,19 @@ Simplex_tree dim: 3 3 2 36.8838 inf 3 3 58.6783 inf \endcode +\li +Alpha_complex/alpha_complex_persistence.cpp computes the persistent homology with +\f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. +\code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode +\code Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. +Simplex_tree dim: 3 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 \endcode + +More details on the Alpha complex utilities dedicated page. + \li Persistent_cohomology/plain_homology.cpp computes the plain homology of a simple simplicial complex without filtration values. -- cgit v1.2.3