diff options
393 files changed, 2697 insertions, 1484 deletions
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt index cb07e55a..5e71f7eb 100644 --- a/CMakeGUDHIVersion.txt +++ b/CMakeGUDHIVersion.txt @@ -1,6 +1,6 @@ set (GUDHI_MAJOR_VERSION 2) set (GUDHI_MINOR_VERSION 1) -set (GUDHI_PATCH_VERSION 0.rc1) +set (GUDHI_PATCH_VERSION 0) set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION}) message(STATUS "GUDHI version : ${GUDHI_VERSION}") diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index b101cb76..16f43d6f 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -1,12 +1,12 @@ @inproceedings{gudhilibrary_ICMS14, - author = {Cl\'ement Maria and Jean-Daniel Boissonnat and + author = {Cl\'ement Maria and Jean-Daniel Boissonnat and Marc Glisse and Mariette Yvinec}, title = {The {G}udhi Library: Simplicial Complexes and Persistent Homology}, booktitle = {ICMS}, year = {2014}, } -@article{Carriere17c, +@article{Carriere17c, author = {Carri\`ere, Mathieu and Michel, Bertrand and Oudot, Steve}, title = {{Statistical Analysis and Parameter Selection for Mapper}}, journal = {CoRR}, @@ -20,7 +20,7 @@ booktitle = {Proceedings of the Twenty-ninth Annual Symposium on Computational Geometry}, year = {2013}, pages = {107--116}, -} +} @article{Carriere16, title={{Structure and Stability of the 1-Dimensional Mapper}}, @@ -70,7 +70,7 @@ language={English} publisher = {ACM Press/Addison-Wesley Publishing Co.}, address = {New York, NY, USA}, keywords = {level of detail, mutiresolution modeling, non-manifold, pair contraction, surface simplification}, -} +} @inproceedings{Lindstrom, @@ -85,7 +85,7 @@ language={English} numpages = {8}, publisher = {IEEE Computer Society Press}, address = {Los Alamitos, CA, USA}, -} +} @article{boissonnatmariacamalgorithmica, @@ -201,13 +201,13 @@ language={English}, bibsource = {DBLP, http://dblp.uni-trier.de} } @article{RS62, - author={J. B. Rosser and L. Schoenfeld}, - title={Approximate Formulas for some Functions of Prime Numbers}, - journal= {ijm}, - volume= 6, - year= 1962, - pages={64-94}, - mrnumber={25 \#1139} + author={J. B. Rosser and L. Schoenfeld}, + title={Approximate Formulas for some Functions of Prime Numbers}, + journal= {ijm}, + volume= 6, + year= 1962, + pages={64-94}, + mrnumber={25 \#1139} } @article{DBLP:journals/siamcomp/Furer09, author = {Martin F{\"u}rer}, @@ -410,7 +410,7 @@ url="http://dx.doi.org/10.1007/s00454-013-9557-2" edition = {2}, publisher = {Cambridge University Press}, address = {New York, NY, USA}, -} +} @book{DBLP:books/aw/AhoHU74, author = {Alfred V. Aho and John E. Hopcroft and @@ -508,7 +508,7 @@ proceedings{DBLP:conf/issac/1996, pages = {501--509}, numpages = {9}, keywords = {clique complexes, data structure, edge contraction, flag complexes, high dimensions, homotopy equivalence, shape reconstruction, shape simplification, simplicial complexes, vietoris-rips complexes}, -} +} @@ -571,7 +571,7 @@ note = "http://gmplib.org/", publisher = {ACM}, address = {New York, NY, USA}, keywords = {discrete and computational geometry, embedding theorem, persistent homology}, -} +} @article{Fredman:1984:SST:828.1884, author = {Fredman, Michael L. and Koml\'{o}s, J\'{a}nos and Szemer{\'e}di, Endre}, title = {Storing a Sparse Table with {O}(1) Worst Case Access Time}, @@ -589,7 +589,7 @@ note = "http://gmplib.org/", acmid = {1884}, publisher = {ACM}, address = {New York, NY, USA}, -} +} %------------------------------------------------------------------ @@ -739,7 +739,7 @@ inproceedings{DBLP:conf/soda/1997, publisher = {Kluwer Academic Publishers}, address = {Hingham, MA, USA}, keywords = {Filtration, Klein bottle, Manifold, Natural images, Persistent homology, Topology}, -} +} article{DBLP:journals/ijcv/LeePM03, author = {Ann B. Lee and @@ -767,7 +767,7 @@ pages={234115}, year={2010}, abstract={Understanding energy landscapes is a major challenge in chemistry and biology. Although a wide variety of methods have been invented and applied to this problem, very little is understood about the actual mathematical structures underlying such landscapes. Perhaps the most general assumption is the idea that energy landscapes are low-dimensional manifolds embedded in high-dimensional Euclidean space. While this is a very mild assumption, we have discovered an example of an energy landscape which is nonmanifold, demonstrating previously unknown mathematical complexity. The example occurs in the energy landscape of cyclo-octane, which was found to have the structure of a reducible algebraic variety, composed of the union of a sphere and a Klein bottle, intersecting in two rings.} } - + book{hatcher2002algebraic, title={Algebraic Topology}, @@ -803,7 +803,7 @@ book{hatcher2002algebraic, isbn = {0070131511}, edition = {2nd}, publisher = {McGraw-Hill Higher Education}, -} +} @article{DBLP:journals/focm/CarlssonS10, author = {Gunnar E. Carlsson and @@ -1017,7 +1017,7 @@ language={English} journal = {Journal of Symbolic Computation.}, year = {2016} } - + @ARTICLE{Fasy_Kim_Lecci_Maria_tda, author = {B. Fasy and J. Kim and F. Lecci and C. Maria}, title = {Introduction to the R package TDA.}, @@ -1064,11 +1064,42 @@ language={English} } @ARTICLE{Carriere_Oudot_Ovsjanikov_top_signatures_3d, - author = {M. Carrière and S. Oudot and M. Ovsjanikov}, + author = {M. Carri\`ere and S. Oudot and M. Ovsjanikov}, title = {Stable Topological Signatures for Points on 3D Shapes.}, journal = {Proc. Sympos. on Geometry Processing}, year = {2015} } - +@article{buchet16efficient, + title = {Efficient and Robust Persistent Homology for Measures}, + author = {Micka\"{e}l Buchet and Fr\'{e}d\'{e}ric Chazal and Steve Y. Oudot and Donald Sheehy}, + booktitle = {Computational Geometry: Theory and Applications}, + volume = {58}, + pages = {70--96}, + year = {2016} +} + +@inproceedings{cavanna15geometric, + author = {Nicholas J. Cavanna and Mahmoodreza Jahanseir and Donald R. Sheehy}, + booktitle = {Proceedings of the Canadian Conference on Computational Geometry}, + title = {A Geometric Perspective on Sparse Filtrations}, + year = {2015} +} + +@inproceedings{cavanna15visualizing, + author = {Nicholas J. Cavanna and Mahmoodreza Jahanseir and Donald R. Sheehy}, + booktitle = {Proceedings of the 31st International Symposium on Computational Geometry}, + title = {Visualizing Sparse Filtrations}, + year = {2015}, + doi = {10.4230/LIPIcs.SOCG.2015.23} +} +@article{sheehy13linear, + title = {Linear-Size Approximations to the {V}ietoris-{R}ips Filtration}, + author = {Donald R. Sheehy}, + journal = {Discrete \& Computational Geometry}, + volume = {49}, + number = {4}, + pages = {778--796}, + year = {2013} +} diff --git a/biblio/how_to_cite_gudhi.bib b/biblio/how_to_cite_gudhi.bib index 5994124a..942f8d7e 100644 --- a/biblio/how_to_cite_gudhi.bib +++ b/biblio/how_to_cite_gudhi.bib @@ -97,7 +97,7 @@ } @incollection{gudhi:RipsComplex -, author = "Cl\'ement Maria, Pawel Dlotko, Vincent Rouvreau" +, author = "Cl\'ement Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse" , title = "Rips complex" , publisher = "{GUDHI Editorial Board}" , booktitle = "{GUDHI} User and Reference Manual" diff --git a/data/correlation_matrix/lower_triangular_correlation_matrix.csv b/data/correlation_matrix/lower_triangular_correlation_matrix.csv new file mode 100644 index 00000000..99ad0b5d --- /dev/null +++ b/data/correlation_matrix/lower_triangular_correlation_matrix.csv @@ -0,0 +1,6 @@ + +0.4090538938 +0.2182708406;0.5664245836 +0.9109757412;0.5234453492;0.4239008464 +0.2426856242;0.7178816327;0.4748826202;0.8254894051 +0.0908790566;0.9369574252;0.9760741671;0.5256838992;0.0653515265 diff --git a/data/points/Kl.off b/data/points/Kl.off index 911bcd23..8930a321 100644 --- a/data/points/Kl.off +++ b/data/points/Kl.off @@ -1,5 +1,5 @@ -OFF -10000 0 0 +nOFF +5 10000 0 0 0.5 0 0 0 1 0.562791 0 0.125333 0 0.998027 0.625333 0 0.24869 0 0.992115 diff --git a/src/Alpha_complex/concept/SimplicialComplexForAlpha.h b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h index 2b8bff94..a51df127 100644 --- a/src/Alpha_complex/concept/SimplicialComplexForAlpha.h +++ b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Alpha_complex/doc/COPYRIGHT b/src/Alpha_complex/doc/COPYRIGHT index dbad2380..5f1d97cc 100644 --- a/src/Alpha_complex/doc/COPYRIGHT +++ b/src/Alpha_complex/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Vincent Rouvreau -Copyright (C) 2015 INRIA +Copyright (C) 2015 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index cf1a946a..db298ea6 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -31,7 +31,7 @@ namespace alpha_complex { /** \defgroup alpha_complex Alpha complex * * \author Vincent Rouvreau - * + * * @{ * * \section definition Definition @@ -195,8 +195,6 @@ namespace alpha_complex { * * \include Alpha_complex/alphaoffreader_for_doc_32.txt * - * \copyright GNU General Public License v3. - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup alpha_complex diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 63c6675c..4c07eddb 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -34,6 +34,7 @@ #include <CGAL/Epick_d.h> #include <CGAL/Spatial_sort_traits_adapter_d.h> #include <CGAL/property_map.h> // for CGAL::Identity_property_map +#include <CGAL/NT_converter.h> #include <iostream> #include <vector> @@ -323,8 +324,9 @@ class Alpha_complex { if (f_simplex_dim > 0) { // squared_radius function initialization Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object(); + CGAL::NT_converter<typename Geom_traits::FT, Filtration_value> cv; - alpha_complex_filtration = squared_radius(pointVector.begin(), pointVector.end()); + alpha_complex_filtration = cv(squared_radius(pointVector.begin(), pointVector.end())); } complex.assign_filtration(f_simplex, alpha_complex_filtration); #ifdef DEBUG_TRACES diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp index c3ad1a9c..622fcae8 100644 --- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h index a59f0654..a72fd96d 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h +++ b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index 8ef5ffb2..efa20db9 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp index 2105220a..42390b0e 100644 --- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp @@ -1,3 +1,25 @@ +/* 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) 2016 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + #include <boost/program_options.hpp> #include <CGAL/Epick_d.h> diff --git a/src/Alpha_complex/utilities/README b/src/Alpha_complex/utilities/alphacomplex.md index 1cd2ca95..0fe98837 100644 --- a/src/Alpha_complex/utilities/README +++ b/src/Alpha_complex/utilities/alphacomplex.md @@ -1,14 +1,33 @@ -# Alpha_complex #
+---
+layout: page
+title: "Alpha complex"
+meta_title: "Alpha complex"
+teaser: ""
+permalink: /alphacomplex/
+---
+{::comment}
+Leave the lines above as it is required by the web site generator 'Jekyll'
+{:/comment}
-## `alpha_complex_3d_persistence` ##
-This program computes the persistent homology with coefficient field Z/pZ of the 3D alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention:
-`p dim birth death`
+## alpha_complex_persistence ##
-where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number).
+This program computes the persistent homology with coefficient field Z/pZ of the dD alpha complex built from a dD point cloud.
+The output diagram contains one bar per line, written with the convention:
+
+```
+ p dim birth death
+```
+
+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature,
+and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number).
**Usage**
-`alpha_complex_3d_persistence [options] <input OFF file>`
+
+```
+ alpha_complex_persistence [options] <input OFF file>
+```
+
where
`<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).
@@ -16,47 +35,37 @@ where * `-h [ --help ]` Produce help message
* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.
-* `-p [ --field-charac ]` (default=11) Characteristic p of the coefficient field Z/pZ for computing homology.
+* `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value for the Alpha complex construction.
+* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.
* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
**Example**
-`alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45`
-outputs:
```
-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
+ alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off
```
-Here we retrieve expected Betti numbers on a tore 3D:
-```
-Betti numbers[0] = 1
-Betti numbers[1] = 2
-Betti numbers[2] = 1
-```
+N.B.:
-N.B.:
-* `alpha_complex_3d_persistence` only accepts OFF files in dimension 3.
* Filtration values are alpha square values.
+## alpha_complex_3d_persistence ##
+This program computes the persistent homology with coefficient field Z/pZ of the 3D alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention:
-## `exact_alpha_complex_3d_persistence` ##
-Same as `alpha_complex_3d_persistence`, but using exact computation. It is slower, but it is necessary when points are on a grid for instance.
+```
+p dim birth death
+```
+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number).
+**Usage**
-## `weighted_alpha_complex_3d_persistence` ##
-Same as `alpha_complex_3d_persistence`, but using weighted points.
+```
+ alpha_complex_3d_persistence [options] <input OFF file>
+```
-**Usage**
-`weighted_alpha_complex_3d_persistence [options] <input OFF file> <weights input file>`
-where
-`<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).
-`<input weights file>` is the path to the file containing the weights of the points (one value per line).
+where `<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).
**Allowed options**
@@ -66,112 +75,91 @@ where * `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
**Example**
-`weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off ../../data/points/tore3D_300.weights -p 2 -m 0.45`
-outputs:
```
-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
+alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45
```
N.B.:
-* Weights values are explained on CGAL [Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0)
-and [Regular triangulation](https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation) documentation.
+
+* `alpha_complex_3d_persistence` only accepts OFF files in dimension 3.
* Filtration values are alpha square values.
-## `periodic_alpha_complex_3d_persistence` ##
-Same as `alpha_complex_3d_persistence`, but using periodic alpha shape 3d.
-Refer to the [CGAL's 3D Periodic Triangulations User Manual](https://doc.cgal.org/latest/Periodic_3_triangulation_3/index.html) for more details.
+## exact_alpha_complex_3d_persistence ##
+
+Same as `alpha_complex_3d_persistence`, but using exact computation.
+It is slower, but it is necessary when points are on a grid for instance.
+
+
+
+## weighted_alpha_complex_3d_persistence ##
+
+Same as `alpha_complex_3d_persistence`, but using weighted points.
**Usage**
-`periodic_alpha_complex_3d_persistence [options] <input OFF file> <cuboid file>`
+
+```
+ weighted_alpha_complex_3d_persistence [options] <input OFF file> <weights input file>
+```
+
where
-`<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).
-`<cuboid file>` is the path to the file describing the periodic domain. It must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsIsoCuboid).
+
+* `<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).
+* `<input weights file>` is the path to the file containing the weights of the points (one value per line).
**Allowed options**
* `-h [ --help ]` Produce help message
* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.
* `-p [ --field-charac ]` (default=11) Characteristic p of the coefficient field Z/pZ for computing homology.
-* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals
-
+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
**Example**
-`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`
-outputs:
```
-Periodic Delaunay computed.
-Simplex_tree dim: 3
-3 0 0 inf
-3 1 0.0025 inf
-3 1 0.0025 inf
-3 1 0.0025 inf
-3 2 0.005 inf
-3 2 0.005 inf
-3 2 0.005 inf
-3 3 0.0075 inf
+ weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off ../../data/points/tore3D_300.weights -p 2 -m 0.45
```
-Here we retrieve expected Betti numbers on an 3D iso-oriented cuboids:
-```
-Betti numbers[0] = 1
-Betti numbers[1] = 3
-Betti numbers[2] = 3
-Betti numbers[3] = 1
-```
-
-N.B.:
-* Cuboid file must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsIsoCuboid).
-* Filtration values are alpha square values.
+N.B.:
+* Weights values are explained on CGAL [Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0)
+and [Regular triangulation](https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation) documentation.
+* Filtration values are alpha square values.
-## `alpha_complex_persistence` ##
-This program computes the persistent homology with coefficient field Z/pZ of the dD alpha complex built from a dD point cloud. The output diagram contains one bar per line, written with the convention:
+## periodic_alpha_complex_3d_persistence ##
+Same as `alpha_complex_3d_persistence`, but using periodic alpha shape 3d.
+Refer to the [CGAL's 3D Periodic Triangulations User Manual](https://doc.cgal.org/latest/Periodic_3_triangulation_3/index.html) for more details.
-`p dim birth death`
+**Usage**
-where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number).
+```
+ periodic_alpha_complex_3d_persistence [options] <input OFF file> <cuboid file>
+```
-**Usage**
-`alpha_complex_persistence [options] <input OFF file>`
where
-`<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).
+
+* `<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).
+* `<cuboid file>` is the path to the file describing the periodic domain. It must be in the format described
+[here](/doc/latest/fileformats.html#FileFormatsIsoCuboid).
**Allowed options**
* `-h [ --help ]` Produce help message
* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.
-* `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value for the Alpha complex construction.
-* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.
-* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
+* `-p [ --field-charac ]` (default=11) Characteristic p of the coefficient field Z/pZ for computing homology.
+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals
-**Example**
-`alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off`
-outputs:
-```
-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
-```
+**Example**
-Here we retrieve expected Betti numbers on a tore 3D:
```
-Betti numbers[0] = 1
-Betti numbers[1] = 2
-Betti numbers[2] = 1
+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
```
N.B.:
+
+* Cuboid file must be in the format described [here](/doc/latest/fileformats.html#FileFormatsIsoCuboid).
* Filtration values are alpha square values.
diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp index cceac46e..54c074c4 100644 --- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp index 188cf604..7c6e1583 100644 --- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -5,7 +5,7 @@ * Author(s): Vincent Rouvreau * Pawel Dlotko - 2017 - Swansea University, UK * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp index 93be8a05..54483819 100644 --- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp index 5321bb0a..f03f29a7 100644 --- a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp @@ -5,7 +5,7 @@ * Author(s): Vincent Rouvreau * Pawel Dlotko - 2017 - Swansea University, UK * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bitmap_cubical_complex/doc/COPYRIGHT b/src/Bitmap_cubical_complex/doc/COPYRIGHT index bcd46b23..2b14dcb9 100644 --- a/src/Bitmap_cubical_complex/doc/COPYRIGHT +++ b/src/Bitmap_cubical_complex/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Pawel Dlotko -Copyright (C) 2015 INRIA +Copyright (C) 2015 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h index ee84e201..d1836ef0 100644 --- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h +++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -105,7 +105,6 @@ namespace cubical_complex { * \section BitmapExamples Examples * End user programs are available in example/Bitmap_cubical_complex and utilities/Bitmap_cubical_complex folders. * - * \copyright GNU General Public License v3. */ /** @} */ // end defgroup cubical_complex diff --git a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp index f70558f2..6eb24040 100644 --- a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp +++ b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h index 969daba6..cc19b8b5 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -383,7 +383,7 @@ class Bitmap_cubical_complex : public T { std::vector<std::size_t> bdry = this->get_boundary_of_a_cell(sh); if (globalDbg) { std::cerr << "std::pair<Simplex_handle, Simplex_handle> endpoints( Simplex_handle sh )\n"; - std::cerr << "bdry.size() : " << bdry.size() << std::endl; + std::cerr << "bdry.size() : " << bdry.size() << "\n"; } // this method returns two first elements from the boundary of sh. if (bdry.size() < 2) diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h index 705b68a0..f82d4cc3 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h index bf257be1..47e71f8a 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h index 4a0d1c74..97070cda 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bitmap_cubical_complex/test/Bitmap_test.cpp b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp index 4af699e9..ca7bd986 100644 --- a/src/Bitmap_cubical_complex/test/Bitmap_test.cpp +++ b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bitmap_cubical_complex/utilities/README b/src/Bitmap_cubical_complex/utilities/README deleted file mode 100644 index ddff7034..00000000 --- a/src/Bitmap_cubical_complex/utilities/README +++ /dev/null @@ -1,18 +0,0 @@ -# Bitmap_cubical_complex #
-
-## `cubical_complex_persistence` ##
-This program computes persistent homology, by using the Bitmap_cubical_complex class, of cubical complexes provided in text files in Perseus style. See [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPerseus) for a description of the file format.
-
-Example:
-
-* Create a Cubical Complex from the Perseus style file `CubicalTwoSphere.txt`, computes Persistence cohomology from it and writes the results in a persistence file `CubicalTwoSphere.txt_persistence`:
-`cubical_complex_persistence data/bitmap/CubicalTwoSphere.txt`
-
-## `periodic_cubical_complex_persistence` ##
-
-Same as above, but with periodic boundary conditions.
-
-Example:
-
-* Create a Periodical Cubical Complex from the Perseus style file `3d_torus.txt`, computes Persistence cohomology from it and writes the results in a persistence file `3d_torus.txt_persistence`:
-`periodic_cubical_complex_persistence data/bitmap/3d_torus.txt`
diff --git a/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp b/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp index 9d1bc08c..170aa684 100644 --- a/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp +++ b/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md new file mode 100644 index 00000000..5b0404c3 --- /dev/null +++ b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md @@ -0,0 +1,37 @@ +---
+layout: page
+title: "Cubical complex"
+meta_title: "Cubical complex"
+teaser: ""
+permalink: /cubicalcomplex/
+---
+{::comment}
+Leave the lines above as it is required by the web site generator 'Jekyll'
+{:/comment}
+
+
+## cubical_complex_persistence ##
+This program computes persistent homology, by using the Bitmap_cubical_complex class, of cubical complexes provided in text files in Perseus style.
+See [here](/doc/latest/fileformats.html#FileFormatsPerseus) for a description of the file format.
+
+**Example**
+
+```
+ cubical_complex_persistence data/bitmap/CubicalTwoSphere.txt
+```
+
+* Creates a Cubical Complex from the Perseus style file `CubicalTwoSphere.txt`,
+computes Persistence cohomology from it and writes the results in a persistence file `CubicalTwoSphere.txt_persistence`.
+
+## periodic_cubical_complex_persistence ##
+
+Same as above, but with periodic boundary conditions.
+
+**Example**
+
+```
+ periodic_cubical_complex_persistence data/bitmap/3d_torus.txt
+```
+
+* Creates a Periodical Cubical Complex from the Perseus style file `3d_torus.txt`,
+computes Persistence cohomology from it and writes the results in a persistence file `3d_torus.txt_persistence`.
diff --git a/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp b/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp index c812cb3a..e9ba5495 100644 --- a/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp +++ b/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp b/src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp index 456c570b..acafb199 100644 --- a/src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index b157f22a..d016faf4 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -4,7 +4,7 @@ * * Author: François Godi * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/doc/COPYRIGHT b/src/Bottleneck_distance/doc/COPYRIGHT index 179740a6..1c2016b1 100644 --- a/src/Bottleneck_distance/doc/COPYRIGHT +++ b/src/Bottleneck_distance/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): François Godi -Copyright (C) 2015 INRIA +Copyright (C) 2015 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 3998fe8d..f8fce96c 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -4,7 +4,7 @@ * * Author: François Godi * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp index fd164b22..1e27887c 100644 --- a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp +++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/example/bottleneck_basic_example.cpp b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp index d0ca4e20..3df7d12d 100644 --- a/src/Bottleneck_distance/example/bottleneck_basic_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp @@ -4,7 +4,7 @@ * * Authors: Francois Godi, small modifications by Pawel Dlotko * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 7aee07bb..41f8b16a 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h index f51e22e9..313e7d9c 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h index 0b2d26fe..7f350f64 100644 --- a/src/Bottleneck_distance/include/gudhi/Internal_point.h +++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index 87c7cee5..36a63ea0 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index 622b0691..cb163623 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index e39613b3..bce88e13 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/utilities/README b/src/Bottleneck_distance/utilities/README deleted file mode 100644 index d9fdd252..00000000 --- a/src/Bottleneck_distance/utilities/README +++ /dev/null @@ -1,10 +0,0 @@ -# Bottleneck_distance #
-
-## `bottleneck_read_file_example` ##
-This program computes the Bottleneck distance between two persistence diagram files.
-
-Usage:
-`bottleneck_read_file_example <file_1.pers> <file_2.pers> [<tolerance>]`
-where
-`<file_1.pers>` and `<file_2.pers>` must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPers).
-`<tolerance>` is an error bound on the bottleneck distance (set by default to the smallest positive double value).
diff --git a/src/Bottleneck_distance/utilities/bottleneck_distance.cpp b/src/Bottleneck_distance/utilities/bottleneck_distance.cpp index 9dd52b31..8f724f95 100644 --- a/src/Bottleneck_distance/utilities/bottleneck_distance.cpp +++ b/src/Bottleneck_distance/utilities/bottleneck_distance.cpp @@ -4,7 +4,7 @@ * * Authors: Francois Godi, small modifications by Pawel Dlotko * - * Copyright (C) 2015 INRIA + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/utilities/bottleneckdistance.md b/src/Bottleneck_distance/utilities/bottleneckdistance.md new file mode 100644 index 00000000..939eb911 --- /dev/null +++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md @@ -0,0 +1,26 @@ +---
+layout: page
+title: "Bottleneck distance"
+meta_title: "Bottleneck distance"
+teaser: ""
+permalink: /bottleneckdistance/
+---
+{::comment}
+Leave the lines above as it is required by the web site generator 'Jekyll'
+{:/comment}
+
+
+## bottleneck_read_file_example ##
+
+This program computes the Bottleneck distance between two persistence diagram files.
+
+**Usage**
+
+```
+ bottleneck_read_file_example <file_1.pers> <file_2.pers> [<tolerance>]
+```
+
+where
+
+* `<file_1.pers>` and `<file_2.pers>` must be in the format described [here](/doc/latest/fileformats.html#FileFormatsPers).
+* `<tolerance>` is an error bound on the bottleneck distance (set by default to the smallest positive double value).
diff --git a/src/Contraction/doc/COPYRIGHT b/src/Contraction/doc/COPYRIGHT index 1de850d7..5b606ac2 100644 --- a/src/Contraction/doc/COPYRIGHT +++ b/src/Contraction/doc/COPYRIGHT @@ -3,7 +3,7 @@ The files of this directory are part of the Gudhi Library. The Gudhi library computational topology. Author(s): David Salinas -Copyright (C) 2015 INRIA +Copyright (C) 2015 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp index 2b0dc973..08dd932e 100644 --- a/src/Contraction/example/Garland_heckbert.cpp +++ b/src/Contraction/example/Garland_heckbert.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-M�diterran�e (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h index e7dafaa0..8bd9b545 100644 --- a/src/Contraction/example/Garland_heckbert/Error_quadric.h +++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-M�diterran�e (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp index 501b0e87..7f9b150a 100644 --- a/src/Contraction/example/Rips_contraction.cpp +++ b/src/Contraction/example/Rips_contraction.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/include/gudhi/Contraction/Edge_profile.h b/src/Contraction/include/gudhi/Contraction/Edge_profile.h index e4910b27..30b1b80a 100644 --- a/src/Contraction/include/gudhi/Contraction/Edge_profile.h +++ b/src/Contraction/include/gudhi/Contraction/Edge_profile.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h b/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h index 7ee05aad..fa02308b 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h b/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h index f4d343ec..04ce36b6 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h b/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h index 5d329496..a5567454 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h b/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h index dac2d448..1b7a825b 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h b/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h index 1f68db0d..0b9f8775 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h +++ b/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h b/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h index 250bba27..8c869830 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h b/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h index 4b59f1b5..0ba23a35 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h b/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h index 34ffa49f..19509fad 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h b/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h index 78d61173..8a91f0b5 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h index 61f2d945..fcd06996 100644 --- a/src/Contraction/include/gudhi/Edge_contraction.h +++ b/src/Contraction/include/gudhi/Edge_contraction.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -210,7 +210,6 @@ int main (int argc, char *argv[]) } \endcode - \verbatim ./example/Contraction/RipsContraction ../../data/SO3_10000.off 0.3 [ 50%] [100%] Built target SkeletonBlockerIteration @@ -223,9 +222,6 @@ Time to simplify and enumerate simplices: 3.166621s wall, 3.150000s user + 0.010000s system = 3.160000s CPU (99.8%) \endverbatim - - -\copyright GNU General Public License v3. */ /** @} */ // end defgroup } // namespace contraction diff --git a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h index df884c93..13086161 100644 --- a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h +++ b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Doxyfile b/src/Doxyfile index 2d5adea1..f1981e2e 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -38,7 +38,7 @@ PROJECT_NAME = "GUDHI" # could be handy for archiving the generated documentation or if some version # control system is used. -PROJECT_NUMBER = "2.1.0.rc1" +PROJECT_NUMBER = "2.1.0" # 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 @@ -801,7 +801,7 @@ EXCLUDE_SYMLINKS = NO # Note that the wildcards are matched against the file with absolute path, so to # exclude all test directories for example use the pattern */test/* -EXCLUDE_PATTERNS = +EXCLUDE_PATTERNS = */utilities/*/*.md # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names # (namespaces, classes, functions, etc.) that should be excluded from the diff --git a/src/GudhUI/gui/MainWindow.cpp b/src/GudhUI/gui/MainWindow.cpp index 779ccd33..b11b80e9 100644 --- a/src/GudhUI/gui/MainWindow.cpp +++ b/src/GudhUI/gui/MainWindow.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/gui/MainWindow.h b/src/GudhUI/gui/MainWindow.h index 15664dcb..6076c2ee 100644 --- a/src/GudhUI/gui/MainWindow.h +++ b/src/GudhUI/gui/MainWindow.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/gui/Menu_edge_contraction.cpp b/src/GudhUI/gui/Menu_edge_contraction.cpp index a679b0bf..041bdf9e 100644 --- a/src/GudhUI/gui/Menu_edge_contraction.cpp +++ b/src/GudhUI/gui/Menu_edge_contraction.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/gui/Menu_edge_contraction.h b/src/GudhUI/gui/Menu_edge_contraction.h index 2d5640e8..0ef7b267 100644 --- a/src/GudhUI/gui/Menu_edge_contraction.h +++ b/src/GudhUI/gui/Menu_edge_contraction.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp b/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp index e24865f2..b1ad15c8 100644 --- a/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp +++ b/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/gui/Menu_k_nearest_neighbors.h b/src/GudhUI/gui/Menu_k_nearest_neighbors.h index 77303b67..56b5b63d 100644 --- a/src/GudhUI/gui/Menu_k_nearest_neighbors.h +++ b/src/GudhUI/gui/Menu_k_nearest_neighbors.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/gui/Menu_persistence.cpp b/src/GudhUI/gui/Menu_persistence.cpp index 016c076b..ec990559 100644 --- a/src/GudhUI/gui/Menu_persistence.cpp +++ b/src/GudhUI/gui/Menu_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/gui/Menu_persistence.h b/src/GudhUI/gui/Menu_persistence.h index 1a2a2408..32f0c5ca 100644 --- a/src/GudhUI/gui/Menu_persistence.h +++ b/src/GudhUI/gui/Menu_persistence.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/gui/Menu_uniform_neighbors.cpp b/src/GudhUI/gui/Menu_uniform_neighbors.cpp index 20e4f98f..7f392b6c 100644 --- a/src/GudhUI/gui/Menu_uniform_neighbors.cpp +++ b/src/GudhUI/gui/Menu_uniform_neighbors.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/gui/Menu_uniform_neighbors.h b/src/GudhUI/gui/Menu_uniform_neighbors.h index 61316966..88a3823b 100644 --- a/src/GudhUI/gui/Menu_uniform_neighbors.h +++ b/src/GudhUI/gui/Menu_uniform_neighbors.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/gui/gudhui.cpp b/src/GudhUI/gui/gudhui.cpp index 276c4a5f..2a100fd5 100644 --- a/src/GudhUI/gui/gudhui.cpp +++ b/src/GudhUI/gui/gudhui.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -28,7 +28,7 @@ int main(int argc, char** argv) { QApplication application(argc, argv); application.setOrganizationDomain("inria.fr"); - application.setOrganizationName("INRIA"); + application.setOrganizationName("Inria"); application.setApplicationName("GudhUI"); MainWindow mw; diff --git a/src/GudhUI/model/Complex_typedefs.h b/src/GudhUI/model/Complex_typedefs.h index a4df2c94..347db1e3 100644 --- a/src/GudhUI/model/Complex_typedefs.h +++ b/src/GudhUI/model/Complex_typedefs.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h index fc284cc6..1d5cc087 100644 --- a/src/GudhUI/model/Model.h +++ b/src/GudhUI/model/Model.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -74,7 +74,7 @@ class CGAL_geometric_flag_complex_wrapper { // std::cout << "size:" << vertices.size() << std::endl; for (std::size_t i = 0; i < vertices.size(); ++i) for (std::size_t j = i + 1; j < vertices.size(); ++j) - complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j])); + complex_.add_edge_without_blockers(Vertex_handle(vertices[i]), Vertex_handle(vertices[j])); } } diff --git a/src/GudhUI/utils/Bar_code_persistence.h b/src/GudhUI/utils/Bar_code_persistence.h index b527d684..49c87b3c 100644 --- a/src/GudhUI/utils/Bar_code_persistence.h +++ b/src/GudhUI/utils/Bar_code_persistence.h @@ -1,3 +1,26 @@ +/* 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): David Salinas + * + * Copyright (C) 2014 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + * + */ + #include <math.h> // isfinite #include <QtGui/QApplication> diff --git a/src/GudhUI/utils/Critical_points.h b/src/GudhUI/utils/Critical_points.h index 2a18e079..fbd690f8 100644 --- a/src/GudhUI/utils/Critical_points.h +++ b/src/GudhUI/utils/Critical_points.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -79,7 +79,7 @@ template<typename SkBlComplex> class Critical_points { unsigned pos = 0; for (Edge e : edges) { std::cout << "edge " << pos++ << "/" << edges.size() << "\n"; - auto eh = filled_complex_.add_edge(e.first, e.second); + auto eh = filled_complex_.add_edge_without_blockers(e.first, e.second); int is_contractible(is_link_reducible(eh)); switch (is_contractible) { diff --git a/src/GudhUI/utils/Edge_collapsor.h b/src/GudhUI/utils/Edge_collapsor.h index 151e9b01..b3cc7df7 100644 --- a/src/GudhUI/utils/Edge_collapsor.h +++ b/src/GudhUI/utils/Edge_collapsor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/utils/Edge_contractor.h b/src/GudhUI/utils/Edge_contractor.h index 8a29ff4b..090baabe 100644 --- a/src/GudhUI/utils/Edge_contractor.h +++ b/src/GudhUI/utils/Edge_contractor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/utils/Furthest_point_epsilon_net.h b/src/GudhUI/utils/Furthest_point_epsilon_net.h index 98346daa..dbb6661c 100644 --- a/src/GudhUI/utils/Furthest_point_epsilon_net.h +++ b/src/GudhUI/utils/Furthest_point_epsilon_net.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/utils/Is_manifold.h b/src/GudhUI/utils/Is_manifold.h index d0974463..732df607 100644 --- a/src/GudhUI/utils/Is_manifold.h +++ b/src/GudhUI/utils/Is_manifold.h @@ -7,7 +7,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/utils/K_nearest_builder.h b/src/GudhUI/utils/K_nearest_builder.h index 7be0a4f4..14851d96 100644 --- a/src/GudhUI/utils/K_nearest_builder.h +++ b/src/GudhUI/utils/K_nearest_builder.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -81,7 +81,7 @@ template<typename SkBlComplex> class K_nearest_builder { for (auto it = ++search.begin(); it != search.end(); ++it) { Vertex_handle q(std::get<1>(it->first)); if (p != q && complex_.contains_vertex(p) && complex_.contains_vertex(q)) - complex_.add_edge(p, q); + complex_.add_edge_without_blockers(p, q); } } } diff --git a/src/GudhUI/utils/Lloyd_builder.h b/src/GudhUI/utils/Lloyd_builder.h index 18ec9fac..67595d33 100644 --- a/src/GudhUI/utils/Lloyd_builder.h +++ b/src/GudhUI/utils/Lloyd_builder.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/utils/MClock.h b/src/GudhUI/utils/MClock.h index e8d8918a..992f6fa5 100644 --- a/src/GudhUI/utils/MClock.h +++ b/src/GudhUI/utils/MClock.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h index 2dc03c8e..c8afded9 100644 --- a/src/GudhUI/utils/Persistence_compute.h +++ b/src/GudhUI/utils/Persistence_compute.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/utils/Rips_builder.h b/src/GudhUI/utils/Rips_builder.h index b22f4db6..ed62c1c0 100644 --- a/src/GudhUI/utils/Rips_builder.h +++ b/src/GudhUI/utils/Rips_builder.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -60,7 +60,7 @@ template<typename SkBlComplex> class Rips_builder { std::cout.flush(); for (auto q = p; ++q != vertices.end(); /**/) if (squared_eucl_distance(complex_.point(*p), complex_.point(*q)) < 4 * alpha * alpha) - complex_.add_edge(*p, *q); + complex_.add_edge_without_blockers(*p, *q); } std::cout << std::endl; } diff --git a/src/GudhUI/utils/UI_utils.h b/src/GudhUI/utils/UI_utils.h index 9cc209d3..67a02869 100644 --- a/src/GudhUI/utils/UI_utils.h +++ b/src/GudhUI/utils/UI_utils.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/utils/Vertex_collapsor.h b/src/GudhUI/utils/Vertex_collapsor.h index 568dab2f..fca57f7d 100644 --- a/src/GudhUI/utils/Vertex_collapsor.h +++ b/src/GudhUI/utils/Vertex_collapsor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/view/Color.h b/src/GudhUI/view/Color.h index ba0592e1..808dc2d8 100644 --- a/src/GudhUI/view/Color.h +++ b/src/GudhUI/view/Color.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/view/FirstCoordProjector.h b/src/GudhUI/view/FirstCoordProjector.h index 1333f5d3..3f8a6fd9 100644 --- a/src/GudhUI/view/FirstCoordProjector.h +++ b/src/GudhUI/view/FirstCoordProjector.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/view/Projector3D.h b/src/GudhUI/view/Projector3D.h index 2a756541..a1421f51 100644 --- a/src/GudhUI/view/Projector3D.h +++ b/src/GudhUI/view/Projector3D.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/view/View_parameter.h b/src/GudhUI/view/View_parameter.h index 9805abc2..578a0268 100644 --- a/src/GudhUI/view/View_parameter.h +++ b/src/GudhUI/view/View_parameter.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/view/Viewer.cpp b/src/GudhUI/view/Viewer.cpp index c6c2b345..42e35d6c 100644 --- a/src/GudhUI/view/Viewer.cpp +++ b/src/GudhUI/view/Viewer.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/view/Viewer.h b/src/GudhUI/view/Viewer.h index 797ddc53..414044ef 100644 --- a/src/GudhUI/view/Viewer.h +++ b/src/GudhUI/view/Viewer.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/view/Viewer_instructor.cpp b/src/GudhUI/view/Viewer_instructor.cpp index 1ddd4d8b..a9dc4525 100644 --- a/src/GudhUI/view/Viewer_instructor.cpp +++ b/src/GudhUI/view/Viewer_instructor.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/GudhUI/view/Viewer_instructor.h b/src/GudhUI/view/Viewer_instructor.h index 05c5c1fc..4b06acb8 100644 --- a/src/GudhUI/view/Viewer_instructor.h +++ b/src/GudhUI/view/Viewer_instructor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Hasse_complex/include/gudhi/Hasse_complex.h b/src/Hasse_complex/include/gudhi/Hasse_complex.h index e67f7609..efcaea55 100644 --- a/src/Hasse_complex/include/gudhi/Hasse_complex.h +++ b/src/Hasse_complex/include/gudhi/Hasse_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Nerve_GIC/doc/COPYRIGHT b/src/Nerve_GIC/doc/COPYRIGHT index 0c36a526..6b33053e 100644 --- a/src/Nerve_GIC/doc/COPYRIGHT +++ b/src/Nerve_GIC/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Mathieu Carrière -Copyright (C) 2017 INRIA +Copyright (C) 2017 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index 7578cc53..bc8aecc3 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carriere * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -70,15 +70,15 @@ namespace cover_complex { * * When launching: * - * \code $> ./Nerve ../../data/points/human.off 2 10 0.3 --v + * \code $> ./Nerve ../../data/points/human.off 2 10 0.3 -v * \endcode * * the program output is: * * \include Nerve_GIC/Nerve.txt * - * The program also writes a file SC.txt. The first three lines in this file are the location of the input point cloud - * and the function used to compute the cover. + * The program also writes a file ../../data/points/human_sc.txt. The first three lines in this file are the location + * of the input point cloud and the function used to compute the cover. * The fourth line contains the number of vertices nv and edges ne of the Nerve. * The next nv lines represent the vertices. Each line contains the vertex ID, * the number of data points it contains, and their average color function value. @@ -113,12 +113,12 @@ namespace cover_complex { * * When launching: * - * \code $> ./VoronoiGIC ../../data/points/human.off 700 --v + * \code $> ./VoronoiGIC ../../data/points/human.off 700 -v * \endcode * * the program outputs SC.off. Using e.g. * - * \code $> geomview SC.off + * \code $> geomview ../../data/points/human_sc.off * \endcode * * one can obtain the following visualization: @@ -146,7 +146,7 @@ namespace cover_complex { * * When launching: * - * \code $> ./CoordGIC ../../data/points/KleinBottle5D.off 0 --v + * \code $> ./CoordGIC ../../data/points/KleinBottle5D.off 0 -v * \endcode * * the program outputs SC.dot. Using e.g. @@ -169,15 +169,13 @@ namespace cover_complex { * * When launching: * - * \code $> ./FuncGIC ../../data/points/COIL_database/lucky_cat.off ../../data/points/COIL_database/lucky_cat_PCA1 --v + * \code $> ./FuncGIC ../../data/points/COIL_database/lucky_cat.off ../../data/points/COIL_database/lucky_cat_PCA1 -v * \endcode * * the program outputs again SC.dot which gives the following visualization after using neato: * * \image html "funcGICvisu.jpg" "Visualization with neato" * - * \copyright GNU General Public License v3. - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup cover_complex @@ -186,31 +184,3 @@ namespace cover_complex { } // namespace Gudhi #endif // DOC_COVER_COMPLEX_INTRO_COVER_COMPLEX_H_ - - -/* * \subsection gicexample Example with cover from function - * - * This example builds the GIC of a point cloud sampled on a 3D human shape (human.off). - * The cover C comes from the preimages of intervals (with length 0.075 and gain 0) - * covering the height function (coordinate 2), - * and the graph G comes from a Rips complex built with threshold 0.075. - * Note that if the gain is too big, the number of cliques increases a lot, - * which make the computation time much larger. - * - * \include Nerve_GIC/GIC.cpp - * - * When launching: - * - * \code $> ./GIC ../../data/points/human.off 0.075 2 0.075 0 --v - * \endcode - * - * the program outputs SC.txt, which can be visualized with python and firefox as before: - * - * \image html "gicvisu.jpg" "Visualization with KeplerMapper" - * */ - - -/* * Using e.g. - * - * \code $> python KeplerMapperVisuFromTxtFile.py && firefox SC.html - * \endcode */ diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt index 73728dc0..542c6af4 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -3,31 +3,27 @@ project(Nerve_GIC_examples) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - add_executable ( Nerve Nerve.cpp ) add_executable ( CoordGIC CoordGIC.cpp ) add_executable ( FuncGIC FuncGIC.cpp ) - add_executable ( VoronoiGIC VoronoiGIC.cpp ) if (TBB_FOUND) - target_link_libraries(Nerve ${TBB_LIBRARIES}) target_link_libraries(CoordGIC ${TBB_LIBRARIES}) target_link_libraries(FuncGIC ${TBB_LIBRARIES}) - target_link_libraries(VoronoiGIC ${TBB_LIBRARIES}) endif() - file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - - add_test(NAME Nerve_GIC_example_nerve COMMAND $<TARGET_FILE:Nerve> - "${CMAKE_SOURCE_DIR}/data/points/human.off" "2" "10" "0.3") - - add_test(NAME Nerve_GIC_example_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC> - "${CMAKE_SOURCE_DIR}/data/points/human.off" "100") + # Copy files for not to pollute sources when testing + file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0") + "tore3D_1307.off" "0") add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC> - "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" - "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1") + "lucky_cat.off" + "lucky_cat_PCA1") + + install(TARGETS CoordGIC DESTINATION bin) + install(TARGETS FuncGIC DESTINATION bin) endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Nerve_GIC/example/CoordGIC.cpp b/src/Nerve_GIC/example/CoordGIC.cpp index 7e595382..73edae18 100644 --- a/src/Nerve_GIC/example/CoordGIC.cpp +++ b/src/Nerve_GIC/example/CoordGIC.cpp @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carrière * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -27,8 +27,8 @@ void usage(int nbArgs, char *const progName) { std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " filename.off coordinate [--v] \n"; - std::cerr << " i.e.: " << progName << " ../../data/points/human.off 2 --v \n"; + std::cerr << "Usage: " << progName << " filename.off coordinate [-v] \n"; + std::cerr << " i.e.: " << progName << " ../../data/points/human.off 2 -v \n"; exit(-1); // ----- >> } diff --git a/src/Nerve_GIC/example/FuncGIC.cpp b/src/Nerve_GIC/example/FuncGIC.cpp index 3762db4e..1f5de999 100644 --- a/src/Nerve_GIC/example/FuncGIC.cpp +++ b/src/Nerve_GIC/example/FuncGIC.cpp @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carrière * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -27,9 +27,9 @@ void usage(int nbArgs, char *const progName) { std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " filename.off function [--v] \n"; + std::cerr << "Usage: " << progName << " filename.off function [-v] \n"; std::cerr << " i.e.: " << progName << " ../../data/points/COIL_database/lucky_cat.off " - "../../data/points/COIL_database/lucky_cat_PCA1 --v \n"; + "../../data/points/COIL_database/lucky_cat_PCA1 -v \n"; exit(-1); // ----- >> } diff --git a/src/Nerve_GIC/example/GIC.cpp b/src/Nerve_GIC/example/GIC.cpp deleted file mode 100644 index 2bc24a4d..00000000 --- a/src/Nerve_GIC/example/GIC.cpp +++ /dev/null @@ -1,95 +0,0 @@ -/* 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): Mathieu Carrière - * - * Copyright (C) 2017 INRIA - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/GIC.h> - -#include <string> -#include <vector> - -void usage(int nbArgs, char *const progName) { - std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " filename.off threshold coordinate resolution gain [--v] \n"; - std::cerr << " i.e.: " << progName << " ../../data/points/human.off 0.075 2 0.075 0 --v \n"; - exit(-1); // ----- >> -} - -int main(int argc, char **argv) { - if ((argc != 6) && (argc != 7)) usage(argc, argv[0]); - - using Point = std::vector<float>; - - std::string off_file_name(argv[1]); - double threshold = atof(argv[2]); - int coord = atoi(argv[3]); - double resolution = atof(argv[4]); - double gain = atof(argv[5]); - bool verb = 0; - if (argc == 7) verb = 1; - - // ---------------------------------------------------------------------------- - // Init of a graph induced complex from an OFF file - // ---------------------------------------------------------------------------- - - Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC; - GIC.set_verbose(verb); - - bool check = GIC.read_point_cloud(off_file_name); - - if (!check) { - std::cout << "Incorrect OFF file." << std::endl; - } else { - GIC.set_color_from_coordinate(coord); - GIC.set_function_from_coordinate(coord); - - GIC.set_graph_from_rips(threshold, Gudhi::Euclidean_distance()); - - GIC.set_resolution_with_interval_length(resolution); - GIC.set_gain(gain); - GIC.set_cover_from_function(); - - GIC.find_GIC_simplices(); - - GIC.plot_TXT_for_KeplerMapper(); - - Gudhi::Simplex_tree<> stree; - GIC.create_complex(stree); - - // ---------------------------------------------------------------------------- - // Display information about the graph induced complex - // ---------------------------------------------------------------------------- - - if (verb) { - std::cout << "Graph induced complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() - << " simplices - " << stree.num_vertices() << " vertices." << std::endl; - - std::cout << "Iterator on graph induced complex simplices" << std::endl; - for (auto f_simplex : stree.filtration_simplex_range()) { - for (auto vertex : stree.simplex_vertex_range(f_simplex)) { - std::cout << vertex << " "; - } - std::cout << std::endl; - } - } - } - - return 0; -} diff --git a/src/Nerve_GIC/example/KeplerMapperVisuFromTxtFile.py b/src/Nerve_GIC/example/KeplerMapperVisuFromTxtFile.py deleted file mode 100755 index d2897774..00000000 --- a/src/Nerve_GIC/example/KeplerMapperVisuFromTxtFile.py +++ /dev/null @@ -1,72 +0,0 @@ -#!/usr/bin/env python - -import km -import numpy as np -from collections import defaultdict - -"""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): Mathieu Carriere - - Copyright (C) 2017 INRIA - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -""" - -__author__ = "Mathieu Carriere" -__copyright__ = "Copyright (C) 2017 INRIA" -__license__ = "GPL v3" - -network = {} -mapper = km.KeplerMapper(verbose=0) -data = np.zeros((3,3)) -projected_data = mapper.fit_transform( data, projection="sum", scaler=None ) - -f = open('SC.txt','r') -nodes = defaultdict(list) -links = defaultdict(list) -custom = defaultdict(list) - -dat = f.readline() -lens = f.readline() -color = f.readline(); -param = [float(i) for i in f.readline().split(" ")] - -nums = [int(i) for i in f.readline().split(" ")] -num_nodes = nums[0] -num_edges = nums[1] - -for i in range(0,num_nodes): - point = [float(j) for j in f.readline().split(" ")] - nodes[ str(int(point[0])) ] = [ int(point[0]), point[1], int(point[2]) ] - links[ str(int(point[0])) ] = [] - custom[ int(point[0]) ] = point[1] - -m = min([custom[i] for i in range(0,num_nodes)]) -M = max([custom[i] for i in range(0,num_nodes)]) - -for i in range(0,num_edges): - edge = [int(j) for j in f.readline().split(" ")] - links[ str(edge[0]) ].append( str(edge[1]) ) - links[ str(edge[1]) ].append( str(edge[0]) ) - -network["nodes"] = nodes -network["links"] = links -network["meta"] = lens - -mapper.visualize(network, color_function = color, path_html="SC.html", title=dat, -graph_link_distance=30, graph_gravity=0.1, graph_charge=-120, custom_tooltips=custom, width_html=0, -height_html=0, show_tooltips=True, show_title=True, show_meta=True, res=param[0],gain=param[1], minimum=m,maximum=M) diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index e6c508fc..8834858c 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -4,7 +4,7 @@ * * Author: Mathieu Carriere * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -63,6 +63,7 @@ namespace Gudhi { namespace cover_complex { using Simplex_tree = Gudhi::Simplex_tree<>; +using Simplex_handle = Simplex_tree::Simplex_handle; using Filtration_value = Simplex_tree::Filtration_value; using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; using Persistence_diagram = std::vector<std::pair<double, double> >; @@ -269,6 +270,7 @@ class Cover_complex { point_cloud.emplace_back(point.begin(), point.begin() + data_dimension); boost::add_vertex(one_skeleton_OFF); vertices.push_back(boost::add_vertex(one_skeleton)); cover.emplace_back(); + cover.emplace_back(); i++; } } @@ -369,9 +371,8 @@ class Cover_complex { double d; std::vector<double> zeros(n); for (int i = 0; i < n; i++) distances.push_back(zeros); - std::string distance = point_cloud_name; - distance.append("_dist"); - std::ifstream input(distance.c_str(), std::ios::out | std::ios::binary); + std::string distance = point_cloud_name + "_dist"; + std::ifstream input(distance, std::ios::out | std::ios::binary); if (input.good()) { if (verbose) std::cout << "Reading distances..." << std::endl; @@ -487,7 +488,7 @@ class Cover_complex { char coordinate[100]; sprintf(coordinate, "coordinate %d", k); functional_cover = true; - cover_name = coordinate; + cover_name = "coordinate " + std::to_string(k); } public: // Set function from vector. @@ -955,8 +956,7 @@ class Cover_complex { * of its 1-skeleton in a .pdf file. */ void plot_DOT() { - char mapp[100]; - sprintf(mapp, "%s_sc.dot", point_cloud_name.c_str()); + std::string mapp = point_cloud_name + "_sc.dot"; std::ofstream graphic(mapp); double maxv = std::numeric_limits<double>::lowest(); @@ -996,7 +996,7 @@ class Cover_complex { } graphic << "}"; graphic.close(); - std::cout << ".dot file generated. It can be visualized with e.g. neato." << std::endl; + std::cout << mapp << " file generated. It can be visualized with e.g. neato." << std::endl; } public: // Create a .txt file that can be compiled with KeplerMapper. @@ -1006,8 +1006,7 @@ class Cover_complex { void write_info() { int num_simplices = simplices.size(); int num_edges = 0; - char mapp[100]; - sprintf(mapp, "%s_sc.txt", point_cloud_name.c_str()); + std::string mapp = point_cloud_name + "_sc.txt"; std::ofstream graphic(mapp); for (int i = 0; i < num_simplices; i++) @@ -1033,7 +1032,8 @@ class Cover_complex { if (cover_color[simplices[i][0]].first > mask && cover_color[simplices[i][1]].first > mask) graphic << name2id[simplices[i][0]] << " " << name2id[simplices[i][1]] << std::endl; graphic.close(); - std::cout << ".txt generated. It can be visualized with e.g. python KeplerMapperVisuFromTxtFile.py and firefox." + std::cout << mapp + << " generated. It can be visualized with e.g. python KeplerMapperVisuFromTxtFile.py and firefox." << std::endl; } @@ -1051,9 +1051,8 @@ class Cover_complex { std::vector<std::vector<int> > edges, faces; int numsimplices = simplices.size(); - char gic[100]; - sprintf(gic, "%s_sc.off", point_cloud_name.c_str()); - std::ofstream graphic(gic); + std::string mapp = point_cloud_name + "_sc.off"; + std::ofstream graphic(mapp); graphic << "OFF" << std::endl; for (int i = 0; i < numsimplices; i++) { @@ -1080,7 +1079,7 @@ class Cover_complex { for (int i = 0; i < numfaces; i++) graphic << 3 << " " << faces[i][0] << " " << faces[i][1] << " " << faces[i][2] << std::endl; graphic.close(); - std::cout << ".off generated. It can be visualized with e.g. geomview." << std::endl; + std::cout << mapp << " generated. It can be visualized with e.g. geomview." << std::endl; } // ******************************************************************************************************************* @@ -1111,8 +1110,9 @@ class Cover_complex { for (std::map<int, double>::iterator it = cover_std.begin(); it != cover_std.end(); it++) { int vertex = it->first; float val = it->second; int vert[] = {vertex}; int edge[] = {vertex, -2}; - st.assign_filtration(st.find(vert), -2 + (val - minf)/(maxf - minf)); - st.assign_filtration(st.find(edge), 2 - (val - minf)/(maxf - minf)); + Simplex_handle shv = st.find(vert); Simplex_handle she = st.find(edge); + if(shv != st.null_simplex()) st.assign_filtration(shv, -2 + (val - minf)/(maxf - minf)); + if(she != st.null_simplex()) st.assign_filtration(she, 2 - (val - minf)/(maxf - minf)); } st.make_filtration_non_decreasing(); @@ -1167,7 +1167,7 @@ class Cover_complex { Cboot.point_cloud.push_back(this->point_cloud[id]); Cboot.cover.emplace_back(); Cboot.func.push_back(this->func[id]); boost::add_vertex(Cboot.one_skeleton_OFF); Cboot.vertices.push_back(boost::add_vertex(Cboot.one_skeleton)); } - Cboot.set_color_from_vector(Cboot.func); + Cboot.set_color_from_vector(Cboot.func); for (int j = 0; j < n; j++) { std::vector<double> dist(n); diff --git a/src/Nerve_GIC/test/test_GIC.cpp b/src/Nerve_GIC/test/test_GIC.cpp index e3067d35..0db2cce2 100644 --- a/src/Nerve_GIC/test/test_GIC.cpp +++ b/src/Nerve_GIC/test/test_GIC.cpp @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carrière * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt new file mode 100644 index 00000000..7a838a8c --- /dev/null +++ b/src/Nerve_GIC/utilities/CMakeLists.txt @@ -0,0 +1,28 @@ +cmake_minimum_required(VERSION 2.6) +project(Nerve_GIC_examples) + +if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + + add_executable ( Nerve Nerve.cpp ) + add_executable ( VoronoiGIC VoronoiGIC.cpp ) + + if (TBB_FOUND) + target_link_libraries(Nerve ${TBB_LIBRARIES}) + target_link_libraries(VoronoiGIC ${TBB_LIBRARIES}) + endif() + + file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + # Copy files for not to pollute sources when testing + file(COPY "${CMAKE_SOURCE_DIR}/data/points/human.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + + add_test(NAME Nerve_GIC_utilities_nerve COMMAND $<TARGET_FILE:Nerve> + "human.off" "2" "10" "0.3") + + add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC> + "human.off" "100") + + install(TARGETS Nerve DESTINATION bin) + install(TARGETS VoronoiGIC DESTINATION bin) + install(FILES KeplerMapperVisuFromTxtFile.py km.py km.py.COPYRIGHT DESTINATION bin) + +endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py new file mode 100755 index 00000000..701e7a52 --- /dev/null +++ b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py @@ -0,0 +1,89 @@ +#!/usr/bin/env python + +import km +import numpy as np +from collections import defaultdict +import argparse + +"""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): Mathieu Carriere + + Copyright (C) 2017 Inria + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. +""" + +__author__ = "Mathieu Carriere" +__copyright__ = "Copyright (C) 2017 Inria" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='Creates an html Keppler Mapper ' + 'file to visualize a SC.txt file.', + epilog='Example: ' + './KeplerMapperVisuFromTxtFile.py ' + '-f ../../data/points/human.off_sc.txt' + '- Constructs an human.off_sc.html file.') +parser.add_argument("-f", "--file", type=str, required=True) + +args = parser.parse_args() + +with open(args.file, 'r') as f: + network = {} + mapper = km.KeplerMapper(verbose=0) + data = np.zeros((3,3)) + projected_data = mapper.fit_transform( data, projection="sum", scaler=None ) + + nodes = defaultdict(list) + links = defaultdict(list) + custom = defaultdict(list) + + dat = f.readline() + lens = f.readline() + color = f.readline(); + param = [float(i) for i in f.readline().split(" ")] + + nums = [int(i) for i in f.readline().split(" ")] + num_nodes = nums[0] + num_edges = nums[1] + + for i in range(0,num_nodes): + point = [float(j) for j in f.readline().split(" ")] + nodes[ str(int(point[0])) ] = [ int(point[0]), point[1], int(point[2]) ] + links[ str(int(point[0])) ] = [] + custom[ int(point[0]) ] = point[1] + + m = min([custom[i] for i in range(0,num_nodes)]) + M = max([custom[i] for i in range(0,num_nodes)]) + + for i in range(0,num_edges): + edge = [int(j) for j in f.readline().split(" ")] + links[ str(edge[0]) ].append( str(edge[1]) ) + links[ str(edge[1]) ].append( str(edge[0]) ) + + network["nodes"] = nodes + network["links"] = links + network["meta"] = lens + + html_output_filename = args.file.rsplit('.', 1)[0] + '.html' + mapper.visualize(network, color_function = color, path_html=html_output_filename, title=dat, + graph_link_distance=30, graph_gravity=0.1, graph_charge=-120, custom_tooltips=custom, width_html=0, + height_html=0, show_tooltips=True, show_title=True, show_meta=True, res=param[0],gain=param[1], minimum=m,maximum=M) + message = repr(html_output_filename) + " is generated. You can now use your favorite web browser to visualize it." + print(message) + + + f.close() diff --git a/src/Nerve_GIC/example/Nerve.cpp b/src/Nerve_GIC/utilities/Nerve.cpp index 6abdedc7..667129e0 100644 --- a/src/Nerve_GIC/example/Nerve.cpp +++ b/src/Nerve_GIC/utilities/Nerve.cpp @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carrière * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -27,8 +27,8 @@ void usage(int nbArgs, char *const progName) { std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " filename.off coordinate resolution gain [--v] \n"; - std::cerr << " i.e.: " << progName << " ../../data/points/human.off 2 10 0.3 --v \n"; + std::cerr << "Usage: " << progName << " filename.off coordinate resolution gain [-v] \n"; + std::cerr << " i.e.: " << progName << " ../../data/points/human.off 2 10 0.3 -v \n"; exit(-1); // ----- >> } diff --git a/src/Nerve_GIC/example/Nerve.txt b/src/Nerve_GIC/utilities/Nerve.txt index 839ff45e..839ff45e 100644 --- a/src/Nerve_GIC/example/Nerve.txt +++ b/src/Nerve_GIC/utilities/Nerve.txt diff --git a/src/Nerve_GIC/example/VoronoiGIC.cpp b/src/Nerve_GIC/utilities/VoronoiGIC.cpp index 32431cc2..33deca40 100644 --- a/src/Nerve_GIC/example/VoronoiGIC.cpp +++ b/src/Nerve_GIC/utilities/VoronoiGIC.cpp @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carrière * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -27,8 +27,8 @@ void usage(int nbArgs, char *const progName) { std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " filename.off N [--v] \n"; - std::cerr << " i.e.: " << progName << " ../../data/points/human.off 100 --v \n"; + std::cerr << "Usage: " << progName << " filename.off N [-v] \n"; + std::cerr << " i.e.: " << progName << " ../../data/points/human.off 100 -v \n"; exit(-1); // ----- >> } diff --git a/src/Nerve_GIC/utilities/covercomplex.md b/src/Nerve_GIC/utilities/covercomplex.md new file mode 100644 index 00000000..683c1b75 --- /dev/null +++ b/src/Nerve_GIC/utilities/covercomplex.md @@ -0,0 +1,69 @@ +--- +layout: page +title: "Cover complex" +meta_title: "Cover complex" +teaser: "" +permalink: /covercomplex/ +--- +{::comment} +Leave the lines above as it is required by the web site generator 'Jekyll' +{:/comment} + + +## Nerve ## +This program builds the Nerve of a point cloud sampled on an OFF file. +The cover C comes from the preimages of intervals covering a coordinate function, +which are then refined into their connected components using the triangulation of the .OFF file. + +The program also writes a file SC.txt. +The first three lines in this file are the location of the input point cloud and the function used to compute the cover. +The fourth line contains the number of vertices nv and edges ne of the Nerve. The next nv lines represent the vertices. +Each line contains the vertex ID, the number of data points it contains, and their average color function value. +Finally, the next ne lines represent the edges, characterized by the ID of their vertices. + +**Usage** + +`Nerve <OFF input file> coordinate resolution gain [-v]` + +where + +* `coordinate` is the coordinate function to cover +* `resolution` is the number of the intervals +* `gain` is the gain for each interval +* `-v` is optional, it activates verbose mode. + +**Example** + +`Nerve ../../data/points/human.off 2 10 0.3` + +* Builds the Nerve of a point cloud sampled on a 3D human shape (human.off). +The cover C comes from the preimages of intervals (10 intervals with gain 0.3) covering the height function (coordinate 2). + +`python KeplerMapperVisuFromTxtFile.py -f ../../data/points/human.off_sc.txt` + +* Constructs `human.off_sc.html` file. You can now use your favorite web browser to visualize it. + +## VoronoiGIC ## + +This util builds the Graph Induced Complex (GIC) of a point cloud. +It subsamples *N* points in the point cloud, which act as seeds of a geodesic Voronoï diagram. +Each cell of the diagram is then an element of C. + +The program also writes a file `*_sc.off`, that is an OFF file that can be visualized with GeomView. + +**Usage** + +`VoroniGIC <OFF input file> samples_number [-v]` + +where + +* `samples_number` is the number of samples to take from the point cloud +* `-v` is optional, it activates verbose mode. + +**Example** + +`VoroniGIC ../../data/points/human.off 700` + +* Builds the Voronoi Graph Induced Complex with 700 subsamples from `human.off` file. +`../../data/points/human_sc.off` can be visualized with GeomView. + diff --git a/src/Nerve_GIC/example/km.py b/src/Nerve_GIC/utilities/km.py index 53024aab..53024aab 100755 --- a/src/Nerve_GIC/example/km.py +++ b/src/Nerve_GIC/utilities/km.py diff --git a/src/Nerve_GIC/example/km.py.COPYRIGHT b/src/Nerve_GIC/utilities/km.py.COPYRIGHT index bef7b121..bef7b121 100644 --- a/src/Nerve_GIC/example/km.py.COPYRIGHT +++ b/src/Nerve_GIC/utilities/km.py.COPYRIGHT diff --git a/src/Persistence_representations/concept/Real_valued_topological_data.h b/src/Persistence_representations/concept/Real_valued_topological_data.h index 1d3595ad..22ef6d72 100644 --- a/src/Persistence_representations/concept/Real_valued_topological_data.h +++ b/src/Persistence_representations/concept/Real_valued_topological_data.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/concept/Topological_data_with_averages.h b/src/Persistence_representations/concept/Topological_data_with_averages.h index 9ebd105f..aa64467f 100644 --- a/src/Persistence_representations/concept/Topological_data_with_averages.h +++ b/src/Persistence_representations/concept/Topological_data_with_averages.h @@ -5,7 +5,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/concept/Topological_data_with_distances.h b/src/Persistence_representations/concept/Topological_data_with_distances.h index a6a62307..c8eb2b34 100644 --- a/src/Persistence_representations/concept/Topological_data_with_distances.h +++ b/src/Persistence_representations/concept/Topological_data_with_distances.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/concept/Topological_data_with_scalar_product.h b/src/Persistence_representations/concept/Topological_data_with_scalar_product.h index 2e506ca9..0f08b8c6 100644 --- a/src/Persistence_representations/concept/Topological_data_with_scalar_product.h +++ b/src/Persistence_representations/concept/Topological_data_with_scalar_product.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/concept/Vectorized_topological_data.h b/src/Persistence_representations/concept/Vectorized_topological_data.h index b6b5b109..365105d6 100644 --- a/src/Persistence_representations/concept/Vectorized_topological_data.h +++ b/src/Persistence_representations/concept/Vectorized_topological_data.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/doc/Persistence_representations_doc.h b/src/Persistence_representations/doc/Persistence_representations_doc.h index 978fb5bd..4d850a02 100644 --- a/src/Persistence_representations/doc/Persistence_representations_doc.h +++ b/src/Persistence_representations/doc/Persistence_representations_doc.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA Sophia-Saclay (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -67,7 +67,7 @@ namespace Persistence_representations { \li Concept of representation of persistence that allows computations of distances. \li Concept of representation of persistence that allows computations of scalar products. \li Concept of representation of persistence that allows vectorization. - \li Concept of representation of persistence that allows computations of real--valued characteristics of objects. + \li Concept of representation of persistence that allows computations of real-valued characteristics of objects. At the moment an implementation of the following representations of persistence are available (further details of @@ -250,7 +250,6 @@ namespace Persistence_representations { absolute value of differences between coordinates. A scalar product is a sum of products of values at the corresponding positions of two vectors. - \copyright GNU General Public License v3. */ /** @} */ // end defgroup Persistence_representations diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt index b8ce8ea6..54d719ac 100644 --- a/src/Persistence_representations/example/CMakeLists.txt +++ b/src/Persistence_representations/example/CMakeLists.txt @@ -2,31 +2,28 @@ cmake_minimum_required(VERSION 2.6) project(Persistence_representations_example) add_executable ( Persistence_representations_example_landscape_on_grid persistence_landscape_on_grid.cpp ) -target_link_libraries(Persistence_representations_example_landscape_on_grid ${Boost_SYSTEM_LIBRARY}) add_test(NAME Persistence_representations_example_landscape_on_grid COMMAND $<TARGET_FILE:Persistence_representations_example_landscape_on_grid>) +install(TARGETS Persistence_representations_example_landscape_on_grid DESTINATION bin) add_executable ( Persistence_representations_example_landscape persistence_landscape.cpp ) -target_link_libraries(Persistence_representations_example_landscape ${Boost_SYSTEM_LIBRARY}) add_test(NAME Persistence_representations_example_landscape COMMAND $<TARGET_FILE:Persistence_representations_example_landscape>) +install(TARGETS Persistence_representations_example_landscape DESTINATION bin) add_executable ( Persistence_representations_example_intervals persistence_intervals.cpp ) -target_link_libraries(Persistence_representations_example_intervals ${Boost_SYSTEM_LIBRARY}) add_test(NAME Persistence_representations_example_intervals COMMAND $<TARGET_FILE:Persistence_representations_example_intervals> "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers") +install(TARGETS Persistence_representations_example_intervals DESTINATION bin) add_executable ( Persistence_representations_example_vectors persistence_vectors.cpp ) -target_link_libraries(Persistence_representations_example_vectors ${Boost_SYSTEM_LIBRARY}) add_test(NAME Persistence_representations_example_vectors COMMAND $<TARGET_FILE:Persistence_representations_example_vectors>) +install(TARGETS Persistence_representations_example_vectors DESTINATION bin) add_executable ( Persistence_representations_example_heat_maps persistence_heat_maps.cpp ) -target_link_libraries(Persistence_representations_example_heat_maps ${Boost_SYSTEM_LIBRARY}) add_test(NAME Persistence_representations_example_heat_maps COMMAND $<TARGET_FILE:Persistence_representations_example_heat_maps>) - - - +install(TARGETS Persistence_representations_example_heat_maps DESTINATION bin) diff --git a/src/Persistence_representations/example/persistence_heat_maps.cpp b/src/Persistence_representations/example/persistence_heat_maps.cpp index 2a472ac6..323b57e9 100644 --- a/src/Persistence_representations/example/persistence_heat_maps.cpp +++ b/src/Persistence_representations/example/persistence_heat_maps.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/example/persistence_intervals.cpp b/src/Persistence_representations/example/persistence_intervals.cpp index c1ceb458..b5dcf25c 100644 --- a/src/Persistence_representations/example/persistence_intervals.cpp +++ b/src/Persistence_representations/example/persistence_intervals.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/example/persistence_landscape.cpp b/src/Persistence_representations/example/persistence_landscape.cpp index 400a9ae1..27542cf7 100644 --- a/src/Persistence_representations/example/persistence_landscape.cpp +++ b/src/Persistence_representations/example/persistence_landscape.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/example/persistence_landscape_on_grid.cpp b/src/Persistence_representations/example/persistence_landscape_on_grid.cpp index b201b397..0f471a67 100644 --- a/src/Persistence_representations/example/persistence_landscape_on_grid.cpp +++ b/src/Persistence_representations/example/persistence_landscape_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/example/persistence_vectors.cpp b/src/Persistence_representations/example/persistence_vectors.cpp index 834ae644..072e530d 100644 --- a/src/Persistence_representations/example/persistence_vectors.cpp +++ b/src/Persistence_representations/example/persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/include/gudhi/PSSK.h b/src/Persistence_representations/include/gudhi/PSSK.h index 630f5623..e1174455 100644 --- a/src/Persistence_representations/include/gudhi/PSSK.h +++ b/src/Persistence_representations/include/gudhi/PSSK.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h index a80c3c40..35e51e63 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h +++ b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals.h b/src/Persistence_representations/include/gudhi/Persistence_intervals.h index 3d04d8b7..76eac7d7 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_intervals.h +++ b/src/Persistence_representations/include/gudhi/Persistence_intervals.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h index 79908883..f48d1a3b 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h +++ b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape.h b/src/Persistence_representations/include/gudhi/Persistence_landscape.h index c5aa7867..4381a55b 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_landscape.h +++ b/src/Persistence_representations/include/gudhi/Persistence_landscape.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h b/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h index 84fd22ed..fd8a181c 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h +++ b/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/include/gudhi/Persistence_vectors.h b/src/Persistence_representations/include/gudhi/Persistence_vectors.h index 63577e46..9c04be1d 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_vectors.h +++ b/src/Persistence_representations/include/gudhi/Persistence_vectors.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/include/gudhi/common_persistence_representations.h b/src/Persistence_representations/include/gudhi/common_persistence_representations.h index 44e125a7..3d03f1f6 100644 --- a/src/Persistence_representations/include/gudhi/common_persistence_representations.h +++ b/src/Persistence_representations/include/gudhi/common_persistence_representations.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h index 83b89d0e..e0fc7107 100644 --- a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h +++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/test/CMakeLists.txt b/src/Persistence_representations/test/CMakeLists.txt index 4483de07..335a71ef 100644 --- a/src/Persistence_representations/test/CMakeLists.txt +++ b/src/Persistence_representations/test/CMakeLists.txt @@ -6,38 +6,38 @@ include(GUDHI_test_coverage) # copy data directory for tests purpose. file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_executable ( Persistence_intervals_test_unit persistence_intervals_test.cpp ) -target_link_libraries(Persistence_intervals_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Persistence_intervals_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) gudhi_add_coverage_test(Persistence_intervals_test_unit) add_executable (Vector_representation_test_unit vector_representation_test.cpp ) -target_link_libraries(Vector_representation_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Vector_representation_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) gudhi_add_coverage_test(Vector_representation_test_unit) add_executable (Persistence_lanscapes_test_unit persistence_lanscapes_test.cpp ) -target_link_libraries(Persistence_lanscapes_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Persistence_lanscapes_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) gudhi_add_coverage_test(Persistence_lanscapes_test_unit) add_executable ( Persistence_lanscapes_on_grid_test_unit persistence_lanscapes_on_grid_test.cpp ) -target_link_libraries(Persistence_lanscapes_on_grid_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Persistence_lanscapes_on_grid_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) gudhi_add_coverage_test(Persistence_lanscapes_on_grid_test_unit) add_executable (Persistence_heat_maps_test_unit persistence_heat_maps_test.cpp ) -target_link_libraries(Persistence_heat_maps_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Persistence_heat_maps_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) gudhi_add_coverage_test(Persistence_heat_maps_test_unit) add_executable ( Read_persistence_from_file_test_unit read_persistence_from_file_test.cpp ) -target_link_libraries(Read_persistence_from_file_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Read_persistence_from_file_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) gudhi_add_coverage_test(Read_persistence_from_file_test_unit) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) add_executable (Persistence_intervals_with_distances_test_unit persistence_intervals_with_distances_test.cpp ) - target_link_libraries(Persistence_intervals_with_distances_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + target_link_libraries(Persistence_intervals_with_distances_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Persistence_intervals_with_distances_test_unit ${TBB_LIBRARIES}) endif(TBB_FOUND) diff --git a/src/Persistence_representations/test/persistence_heat_maps_test.cpp b/src/Persistence_representations/test/persistence_heat_maps_test.cpp index e36108b7..5fad8051 100644 --- a/src/Persistence_representations/test/persistence_heat_maps_test.cpp +++ b/src/Persistence_representations/test/persistence_heat_maps_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/test/persistence_intervals_test.cpp b/src/Persistence_representations/test/persistence_intervals_test.cpp index f555e243..a89db9e3 100644 --- a/src/Persistence_representations/test/persistence_intervals_test.cpp +++ b/src/Persistence_representations/test/persistence_intervals_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp b/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp index 631e4d70..6ba9a470 100644 --- a/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp +++ b/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp b/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp index 130ac8cc..7eca413b 100644 --- a/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp +++ b/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/test/persistence_lanscapes_test.cpp b/src/Persistence_representations/test/persistence_lanscapes_test.cpp index e98ef894..27ad0987 100644 --- a/src/Persistence_representations/test/persistence_lanscapes_test.cpp +++ b/src/Persistence_representations/test/persistence_lanscapes_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/test/read_persistence_from_file_test.cpp b/src/Persistence_representations/test/read_persistence_from_file_test.cpp index 276b92ab..c3e8cb4e 100644 --- a/src/Persistence_representations/test/read_persistence_from_file_test.cpp +++ b/src/Persistence_representations/test/read_persistence_from_file_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/test/vector_representation_test.cpp b/src/Persistence_representations/test/vector_representation_test.cpp index c545dce7..a6b9314e 100644 --- a/src/Persistence_representations/test/vector_representation_test.cpp +++ b/src/Persistence_representations/test/vector_representation_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/CMakeLists.txt b/src/Persistence_representations/utilities/CMakeLists.txt index 137eb0c1..fc51b1d6 100644 --- a/src/Persistence_representations/utilities/CMakeLists.txt +++ b/src/Persistence_representations/utilities/CMakeLists.txt @@ -10,6 +10,8 @@ function(add_persistence_representation_creation_utility creation_utility) add_test(NAME Persistence_representation_utilities_${creation_utility} COMMAND $<TARGET_FILE:${creation_utility}> ${ARGN} "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "${CMAKE_CURRENT_BINARY_DIR}/../second.pers") + + install(TARGETS ${creation_utility} DESTINATION bin) endfunction(add_persistence_representation_creation_utility) function(add_persistence_representation_plot_utility plot_utility tool_extension) @@ -26,6 +28,8 @@ function(add_persistence_representation_plot_utility plot_utility tool_extension #add_test(NAME Persistence_representation_utilities_${plot_utility}_second_gnuplot COMMAND ${GNUPLOT_PATH} # "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}_GnuplotScript'") endif() + + install(TARGETS ${plot_utility} DESTINATION bin) endfunction(add_persistence_representation_plot_utility) function(add_persistence_representation_function_utility function_utility tool_extension) @@ -44,6 +48,8 @@ function(add_persistence_representation_function_utility function_utility tool_e "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}" "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") endif() + + install(TARGETS ${function_utility} DESTINATION bin) endfunction(add_persistence_representation_function_utility) add_subdirectory(persistence_heat_maps) diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp index 6739e0b6..2cbd812b 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp index ed8278a2..14d0db8f 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp index 63626853..12fceedc 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp index b4a1daa5..21c553b9 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * -* Copyright (C) 2016 INRIA (France) +* Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp index c50f9ddb..99b0bd17 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp index 59ff3c24..a4b6e458 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp index 25cd1067..5960a89f 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp index 97ddb8f0..04f33915 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp index 63711d83..e4402589 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt index 897e12a3..875ff45e 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt @@ -7,6 +7,8 @@ add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals add_test(NAME plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths> "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1") +install(TARGETS plot_histogram_of_intervals_lengths DESTINATION bin) + add_persistence_representation_plot_utility(plot_persistence_intervals "") add_persistence_representation_plot_utility(plot_persistence_Betti_numbers "") @@ -18,6 +20,8 @@ add_test(NAME Persistence_representation_utilities_compute_number_of_dominant_in COMMAND $<TARGET_FILE:compute_number_of_dominant_intervals> "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1" "2") +install(TARGETS compute_number_of_dominant_intervals DESTINATION bin) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) add_executable ( compute_bottleneck_distance compute_bottleneck_distance.cpp ) @@ -29,4 +33,6 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) "-1" "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "${CMAKE_CURRENT_BINARY_DIR}/../second.pers") + + install(TARGETS compute_bottleneck_distance DESTINATION bin) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp index 9102da79..3be3de8f 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp index c8290845..a6953b98 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp index b3d126f0..4f052f42 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp index ccb5b645..f283971b 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp index b433c2b3..1cacbcd0 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp index 33387802..f92d5782 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp index 1a59be8c..4048f508 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp index 5062f521..253fa273 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp index 5b5e9fa3..11fe2886 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp index 6030e994..59aad2f3 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp index c797a7a8..f32a92a1 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp index 0b098d1a..47102087 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp index fd0fcd15..6cf2739d 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp index 01de3dee..9417be6b 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp index 78e8ef57..46e229bc 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp index dddb3615..39e438d2 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp index 0144e76f..45199838 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp index 7e66d25e..0db7dbec 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp index 303c6e3e..8e99251b 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp index cc5e5393..364284e5 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp index aa33107d..550e47c5 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp index 252e8aef..3b00d7a9 100644 --- a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp +++ b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/concept/CoefficientField.h b/src/Persistent_cohomology/concept/CoefficientField.h index 953b06c2..9d066cca 100644 --- a/src/Persistent_cohomology/concept/CoefficientField.h +++ b/src/Persistent_cohomology/concept/CoefficientField.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/concept/FilteredComplex.h b/src/Persistent_cohomology/concept/FilteredComplex.h index c19698df..178503c9 100644 --- a/src/Persistent_cohomology/concept/FilteredComplex.h +++ b/src/Persistent_cohomology/concept/FilteredComplex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -31,7 +31,7 @@ struct FilteredComplex typedef unspecified Simplex_handle; /** \brief Key associated to each simplex. * - * Must be a signed integer type. */ + * Must be an integer type. */ typedef unspecified Simplex_key; /** \brief Type for the value of the filtration function. * @@ -67,8 +67,8 @@ struct FilteredComplex Simplex_key key ( Simplex_handle sh ); /** \brief Returns the simplex that has index idx in the filtration. * - * This is never called on null_key(). */ - Simplex_handle simplex ( Simplex_key idx ); + * This is only called on valid indices. */ + Simplex_handle simplex ( size_t idx ); /** \brief Assign a key to a simplex. */ void assign_key(Simplex_handle sh, Simplex_key key); diff --git a/src/Persistent_cohomology/concept/PersistentHomology.h b/src/Persistent_cohomology/concept/PersistentHomology.h index 111723a5..f9a78763 100644 --- a/src/Persistent_cohomology/concept/PersistentHomology.h +++ b/src/Persistent_cohomology/concept/PersistentHomology.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/doc/COPYRIGHT b/src/Persistent_cohomology/doc/COPYRIGHT index 34345bef..6cde9520 100644 --- a/src/Persistent_cohomology/doc/COPYRIGHT +++ b/src/Persistent_cohomology/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Clément Maria -Copyright (C) 2015 INRIA +Copyright (C) 2015 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index ceaea505..5fb9d4d2 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -162,6 +162,19 @@ persistence diagram with a family of field coefficients. Rips_complex/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and outputs its persistence diagram. +The file should contain square or lower triangular distance matrix with semicolons as separators. +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. + +\li <a href="_rips_complex_2rips_correlation_matrix_persistence_8cpp-example.html"> +Rips_complex/rips_correlation_matrix_persistence.cpp</a> +computes the Rips complex of a correlation matrix and outputs its persistence diagram. + +Note that no check is performed if the matrix given as the input is a correlation matrix. +It is the user responsibility to ensure that this is the case. The input is to be given either as a square or a lower +triangular matrix. +Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv for an example of a file. + \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. @@ -248,7 +261,6 @@ Simplex_tree dim: 3 Persistent_cohomology/plain_homology.cpp</a> computes the plain homology of a simple simplicial complex without filtration values. - \copyright GNU General Public License v3. */ } // namespace persistent_cohomology diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp index 64f2a4dc..35366144 100644 --- a/src/Persistent_cohomology/example/custom_persistence_sort.cpp +++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp index eafa3fd5..c40434a4 100644 --- a/src/Persistent_cohomology/example/persistence_from_file.cpp +++ b/src/Persistent_cohomology/example/persistence_from_file.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp index 8ef479d4..ffccfd86 100644 --- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp +++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp index a5ae09c8..a2256060 100644 --- a/src/Persistent_cohomology/example/plain_homology.cpp +++ b/src/Persistent_cohomology/example/plain_homology.cpp @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2015 INRIA Saclay - Ile-de-France (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp index dae36ed2..626ec2ef 100644 --- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp index c1de0ef8..7c81fcfb 100644 --- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp +++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp index 9618f278..c7607dce 100644 --- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp +++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria, Marc Glisse * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index e0a147b3..c68b5c0b 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -285,7 +285,7 @@ class Persistent_cohomology { } } cpx_->assign_key(sigma, cpx_->null_key()); - } else { // If ku == kv, same connected component: create a 1-cocycle class. + } else if (dim_max_ > 1) { // If ku == kv, same connected component: create a 1-cocycle class. create_cocycle(sigma, coeff_field_.multiplicative_identity(), coeff_field_.characteristic()); } } diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h index 6db16e69..e98b4bb4 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h index 38bc08d1..2bae8654 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h index 5deb2d88..de6c0750 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Rips_complex/concept/SimplicialComplexForRips.h b/src/Rips_complex/concept/SimplicialComplexForRips.h index 7dab0615..3c5acecf 100644 --- a/src/Rips_complex/concept/SimplicialComplexForRips.h +++ b/src/Rips_complex/concept/SimplicialComplexForRips.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Rips_complex/doc/COPYRIGHT b/src/Rips_complex/doc/COPYRIGHT index 594b7d03..2c31a0d6 100644 --- a/src/Rips_complex/doc/COPYRIGHT +++ b/src/Rips_complex/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau -Copyright (C) 2015 INRIA +Copyright (C) 2015 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index 124dfec9..712d3b6e 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -29,28 +29,41 @@ namespace rips_complex { /** \defgroup rips_complex Rips complex * - * \author Clément Maria, Pawel Dlotko, Vincent Rouvreau + * \author Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse * * @{ * * \section ripsdefinition Rips complex definition * - * Rips_complex - * <a target="_blank" href="https://en.wikipedia.org/wiki/Vietoris%E2%80%93Rips_complex">(Wikipedia)</a> is a - * one skeleton graph that allows to construct a - * <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a> - * from it. - * The input can be a point cloud with a given distance function, or a distance matrix. - * - * The filtration value of each edge is computed from a user-given distance function, or directly from the distance - * matrix. + * The Vietoris-Rips complex + * <a target="_blank" href="https://en.wikipedia.org/wiki/Vietoris%E2%80%93Rips_complex">(Wikipedia)</a> + * is an abstract simplicial complex + * defined on a finite metric space, where each simplex corresponds to a subset + * of point whose diameter is smaller that some given threshold. + * Varying the threshold, we can also see the Rips complex as a filtration of + * the \f$(n-1)-\f$dimensional simplex, where the filtration value of each + * simplex is the diameter of the corresponding subset of points. + * + * This filtered complex is most often used as an approximation of the + * ÄŒech complex. After rescaling (Rips using the length of the edges and ÄŒech + * the half-length), they share the same 1-skeleton and are multiplicatively + * 2-interleaved or better. While it is slightly bigger, it is also much + * easier to compute. + * + * The number of simplices in the full Rips complex is exponential in the + * number of vertices, it is thus usually restricted, by excluding all the + * simplices with filtration value larger than some threshold, and keeping only + * the dim_max-skeleton. + * + * In order to build this complex, the algorithm first builds the graph. + * The filtration value of each edge is computed from a user-given distance + * function, or directly read from the distance matrix. + * In a second step, this graph is inserted in a simplicial complex, which then + * gets expanded to a flag complex. * - * All edges that have a filtration value strictly greater than a given threshold value are not inserted into - * the complex. + * The input can be given as a range of points and a distance function, or as a + * distance matrix. * - * When creating a simplicial complex from this one skeleton graph, Rips inserts the one skeleton graph into the data - * structure, and then expands the simplicial complex when required. - * * Vertex name correspond to the index of the point in the given range (aka. the point cloud). * * \image html "rips_complex_representation.png" "Rips-complex one skeleton graph representation" @@ -61,7 +74,36 @@ namespace rips_complex { * * If the Rips_complex interfaces are not detailed enough for your need, please refer to * <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html"> - * rips_persistence_step_by_step.cpp</a> example, where the graph construction over the Simplex_tree is more detailed. + * rips_persistence_step_by_step.cpp</a> example, where the constructions of the graph and + * the Simplex_tree are more detailed. + * + * \section sparserips Sparse Rips complex + * + * Even truncated in filtration value and dimension, the Rips complex remains + * quite large. However, it is possible to approximate it by a much smaller + * filtered simplicial complex (linear size, with constants that depend on + * ε and the doubling dimension of the space) that is + * \f$(1+O(\epsilon))-\f$interleaved with it (in particular, their persistence + * diagrams are at log-bottleneck distance at most \f$O(\epsilon)\f$). + * + * The sparse Rips filtration was introduced by Don Sheehy + * \cite sheehy13linear. We are using the version described in + * \cite buchet16efficient (except that we multiply all filtration values + * by 2, to match the usual Rips complex), which proves a + * \f$\frac{1+\epsilon}{1-\epsilon}\f$-interleaving, although in practice the + * error is usually smaller. + * A more intuitive presentation of the idea is available in + * \cite cavanna15geometric, and in a video \cite cavanna15visualizing. + * + * The interface of `Sparse_rips_complex` is similar to the one for the usual + * `Rips_complex`, except that one has to specify the approximation factor, and + * there is no option to limit the maximum filtration value (the way the + * approximation is done means that larger filtration values are much cheaper + * to handle than low filtration values, so the gain would be too small). + * + * Theoretical guarantees are only available for \f$\epsilon<1\f$. The + * construction accepts larger values of ε, and the size of the complex + * keeps decreasing, but there is no guarantee on the quality of the result. * * \section ripspointsdistance Point cloud and distance function * @@ -104,6 +146,24 @@ namespace rips_complex { * * \include Rips_complex/full_skeleton_rips_for_doc.txt * + * + * \subsection sparseripspointscloudexample Example of a sparse Rips from a point cloud + * + * This example builds the full sparse Rips of a set of 2D Euclidean points, then prints some minimal + * information about the complex. + * + * \include Rips_complex/example_sparse_rips.cpp + * + * When launching: + * + * \code $> ./Rips_complex_example_sparse + * \endcode + * + * the program output may be (the exact output varies from one run to the next): + * + * \code Sparse Rips complex is of dimension 2 - 19 simplices - 7 vertices. + * \endcode + * * * * \section ripsdistancematrix Distance matrix @@ -146,8 +206,33 @@ namespace rips_complex { * * \include Rips_complex/full_skeleton_rips_for_doc.txt * - * \copyright GNU General Public License v3. - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim + * + * \section ripscorrelationematrix Correlation matrix + * + * Analogously to the case of distance matrix, Rips complexes can be also constructed based on correlation matrix. + * Given a correlation matrix M, comportment-wise 1-M is a distance matrix. + * This example builds the one skeleton graph from the given corelation matrix and threshold value. + * Then it creates a `Simplex_tree` with it. + * + * Then, it is asked to display information about the simplicial complex. + * + * \include Rips_complex/example_one_skeleton_rips_from_correlation_matrix.cpp + * + * When launching: + * + * \code $> ./example_one_skeleton_from_correlation_matrix + * \endcode + * + * the program output is: + * + * \include Rips_complex/one_skeleton_rips_from_correlation_matrix_for_doc.txt + * + * All the other constructions discussed for Rips complex for distance matrix can be also performed for Rips complexes + * construction from correlation matrices. + * + * @warning As persistence diagrams points will be under the diagonal, bottleneck distance and persistence graphical + * tool will not work properly, this is a known issue. + * */ /** @} */ // end defgroup rips_complex diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index 2940f164..af86636b 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -11,17 +11,29 @@ add_executable ( Rips_complex_example_one_skeleton_from_distance_matrix example_ add_executable ( Rips_complex_example_from_csv_distance_matrix example_rips_complex_from_csv_distance_matrix_file.cpp ) +# Sparse rips from points +add_executable ( Rips_complex_example_sparse example_sparse_rips.cpp ) + +# Correlation matrix +add_executable ( Rips_complex_example_one_skeleton_rips_from_correlation_matrix example_one_skeleton_rips_from_correlation_matrix.cpp ) + if (TBB_FOUND) target_link_libraries(Rips_complex_example_from_off ${TBB_LIBRARIES}) target_link_libraries(Rips_complex_example_one_skeleton_from_points ${TBB_LIBRARIES}) target_link_libraries(Rips_complex_example_one_skeleton_from_distance_matrix ${TBB_LIBRARIES}) target_link_libraries(Rips_complex_example_from_csv_distance_matrix ${TBB_LIBRARIES}) + target_link_libraries(Rips_complex_example_sparse ${TBB_LIBRARIES}) + target_link_libraries(Rips_complex_example_one_skeleton_rips_from_correlation_matrix ${TBB_LIBRARIES}) endif() add_test(NAME Rips_complex_example_one_skeleton_from_points COMMAND $<TARGET_FILE:Rips_complex_example_one_skeleton_from_points>) add_test(NAME Rips_complex_example_one_skeleton_from_distance_matrix COMMAND $<TARGET_FILE:Rips_complex_example_one_skeleton_from_distance_matrix>) +add_test(NAME Rips_complex_example_sparse + COMMAND $<TARGET_FILE:Rips_complex_example_sparse>) +add_test(NAME Rips_complex_example_one_skeleton_rips_from_correlation_matrix + COMMAND $<TARGET_FILE:Rips_complex_example_one_skeleton_rips_from_correlation_matrix>) add_test(NAME Rips_complex_example_from_off_doc_12_1 COMMAND $<TARGET_FILE:Rips_complex_example_from_off> "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "12.0" "1" "${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt") @@ -57,3 +69,4 @@ install(TARGETS Rips_complex_example_from_off DESTINATION bin) install(TARGETS Rips_complex_example_one_skeleton_from_points DESTINATION bin) install(TARGETS Rips_complex_example_one_skeleton_from_distance_matrix DESTINATION bin) install(TARGETS Rips_complex_example_from_csv_distance_matrix DESTINATION bin) +install(TARGETS Rips_complex_example_one_skeleton_rips_from_correlation_matrix DESTINATION bin) diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp new file mode 100644 index 00000000..1343f24d --- /dev/null +++ b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp @@ -0,0 +1,81 @@ +#include <gudhi/Rips_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/distance_functions.h> + +#include <iostream> +#include <string> +#include <vector> +#include <limits> // for std::numeric_limits + +int main() { + // Type definitions + using Simplex_tree = Gudhi::Simplex_tree<>; + using Filtration_value = Simplex_tree::Filtration_value; + using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; + using Distance_matrix = std::vector<std::vector<Filtration_value>>; + + // User defined correlation matrix is: + // |1 0.06 0.23 0.01 0.89| + // |0.06 1 0.74 0.01 0.61| + // |0.23 0.74 1 0.72 0.03| + // |0.01 0.01 0.72 1 0.7 | + // |0.89 0.61 0.03 0.7 1 | + + Distance_matrix correlations; + correlations.push_back({}); + correlations.push_back({0.06}); + correlations.push_back({0.23, 0.74}); + correlations.push_back({0.01, 0.01, 0.72}); + correlations.push_back({0.89, 0.61, 0.03, 0.7}); + + // ---------------------------------------------------------------------------- + // Convert correlation matrix to a distance matrix: + // ---------------------------------------------------------------------------- + double threshold = 0; + for (size_t i = 0; i != correlations.size(); ++i) { + for (size_t j = 0; j != correlations[i].size(); ++j) { + // Here we check if our data comes from corelation matrix. + if ((correlations[i][j] < -1) || (correlations[i][j] > 1)) { + std::cerr << "The input matrix is not a correlation matrix. The program will now terminate.\n"; + throw "The input matrix is not a correlation matrix. The program will now terminate.\n"; + } + correlations[i][j] = 1 - correlations[i][j]; + // Here we make sure that we will get the treshold value equal to maximal + // distance in the matrix. + if (correlations[i][j] > threshold) threshold = correlations[i][j]; + } + } + + //----------------------------------------------------------------------------- + // Now the correlation matrix is a distance matrix and can be processed further. + //----------------------------------------------------------------------------- + Distance_matrix distances = correlations; + + Rips_complex rips_complex_from_points(distances, threshold); + + Simplex_tree stree; + rips_complex_from_points.create_complex(stree, 1); + // ---------------------------------------------------------------------------- + // Display information about the one skeleton Rips complex. Note that + // the filtration displayed here comes from the distance matrix computed + // above, which is 1 - initial correlation matrix. Only this way, we obtain + // a complex with filtration. If a correlation matrix is used instead, we would + // have a reverse filtration (i.e. filtration of boundary of each simplex S + // is greater or equal to the filtration of S). + // ---------------------------------------------------------------------------- + std::cout << "Rips complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - " + << stree.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : stree.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " + << "[" << stree.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + + return 0; +} diff --git a/src/Rips_complex/example/example_sparse_rips.cpp b/src/Rips_complex/example/example_sparse_rips.cpp new file mode 100644 index 00000000..1c95b48c --- /dev/null +++ b/src/Rips_complex/example/example_sparse_rips.cpp @@ -0,0 +1,30 @@ +#include <gudhi/Sparse_rips_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/distance_functions.h> + +#include <iostream> +#include <vector> + +int main() { + using Point = std::vector<double>; + using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; + using Filtration_value = Simplex_tree::Filtration_value; + using Sparse_rips = Gudhi::rips_complex::Sparse_rips_complex<Filtration_value>; + + Point points[] = {{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}}; + + // ---------------------------------------------------------------------------- + // Init from Euclidean points + // ---------------------------------------------------------------------------- + double epsilon = 2; // very rough, no guarantees + Sparse_rips sparse_rips(points, Gudhi::Euclidean_distance(), epsilon); + + Simplex_tree stree; + sparse_rips.create_complex(stree, 10); + + // ---------------------------------------------------------------------------- + // Display information about the complex + // ---------------------------------------------------------------------------- + std::cout << "Sparse Rips complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() + << " simplices - " << stree.num_vertices() << " vertices." << std::endl; +} diff --git a/src/Rips_complex/example/one_skeleton_rips_from_correlation_matrix_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_from_correlation_matrix_for_doc.txt new file mode 100644 index 00000000..640d7083 --- /dev/null +++ b/src/Rips_complex/example/one_skeleton_rips_from_correlation_matrix_for_doc.txt @@ -0,0 +1,17 @@ +Rips complex is of dimension 1 - 15 simplices - 5 vertices. +Iterator on Rips complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 4 0 ) -> [0.11] + ( 2 1 ) -> [0.26] + ( 3 2 ) -> [0.28] + ( 4 3 ) -> [0.3] + ( 4 1 ) -> [0.39] + ( 2 0 ) -> [0.77] + ( 1 0 ) -> [0.94] + ( 4 2 ) -> [0.97] + ( 3 0 ) -> [0.99] + ( 3 1 ) -> [0.99] diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h index 1e4b76a7..f0fe57f4 100644 --- a/src/Rips_complex/include/gudhi/Rips_complex.h +++ b/src/Rips_complex/include/gudhi/Rips_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h new file mode 100644 index 00000000..19a44b28 --- /dev/null +++ b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h @@ -0,0 +1,175 @@ +/* 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) 2018 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef SPARSE_RIPS_COMPLEX_H_ +#define SPARSE_RIPS_COMPLEX_H_ + +#include <gudhi/Debug_utils.h> +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/choose_n_farthest_points.h> + +#include <boost/graph/adjacency_list.hpp> +#include <boost/range/metafunctions.hpp> + +#include <vector> + +namespace Gudhi { + +namespace rips_complex { + +// The whole interface is copied on Rips_complex. A redesign should be discussed with all complex creation classes in +// mind. + +/** + * \class Sparse_rips_complex + * \brief Sparse Rips complex data structure. + * + * \ingroup rips_complex + * + * \details + * This class is used to construct a sparse \f$(1+O(\epsilon))\f$-approximation of `Rips_complex`, i.e. a filtered + * simplicial complex that is multiplicatively \f$(1+O(\epsilon))\f$-interleaved with the Rips filtration. + * + * \tparam Filtration_value is the type used to store the filtration values of the simplicial complex. + */ +template <typename Filtration_value> +class Sparse_rips_complex { + private: + // TODO: use a different graph where we know we can safely insert in parallel. + typedef typename boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, + boost::property<vertex_filtration_t, Filtration_value>, + boost::property<edge_filtration_t, Filtration_value>> + Graph; + + typedef int Vertex_handle; + + public: + /** \brief Sparse_rips_complex constructor from a list of points. + * + * @param[in] points Range of points. + * @param[in] distance Distance function that returns a `Filtration_value` from 2 given points. + * @param[in] epsilon Approximation parameter. epsilon must be positive. + * + */ + template <typename RandomAccessPointRange, typename Distance> + Sparse_rips_complex(const RandomAccessPointRange& points, Distance distance, double epsilon) { + GUDHI_CHECK(epsilon > 0, "epsilon must be positive"); + std::vector<Vertex_handle> sorted_points; + std::vector<Filtration_value> params; + auto dist_fun = [&](Vertex_handle i, Vertex_handle j) { return distance(points[i], points[j]); }; + Ker<decltype(dist_fun)> kernel(dist_fun); + subsampling::choose_n_farthest_points(kernel, boost::irange<Vertex_handle>(0, boost::size(points)), -1, -1, + std::back_inserter(sorted_points), std::back_inserter(params)); + compute_sparse_graph(sorted_points, params, dist_fun, epsilon); + } + + /** \brief Sparse_rips_complex constructor from a distance matrix. + * + * @param[in] distance_matrix Range of range of distances. + * `distance_matrix[i][j]` returns the distance between points \f$i\f$ and + * \f$j\f$ as long as \f$ 0 \leqslant i < j \leqslant + * distance\_matrix.size().\f$ + * @param[in] epsilon Approximation parameter. epsilon must be positive. + */ + template <typename DistanceMatrix> + Sparse_rips_complex(const DistanceMatrix& distance_matrix, double epsilon) + : Sparse_rips_complex(boost::irange<Vertex_handle>(0, boost::size(distance_matrix)), + [&](Vertex_handle i, Vertex_handle j) { return distance_matrix[j][i]; }, epsilon) {} + + /** \brief Fills the simplicial complex with the sparse Rips graph and + * expands it with all the cliques, stopping at a given maximal dimension. + * + * \tparam SimplicialComplexForRips must meet `SimplicialComplexForRips` concept. + * + * @param[in] complex the complex to fill + * @param[in] dim_max maximal dimension of the simplicial complex. + * @exception std::invalid_argument In debug mode, if `complex.num_vertices()` does not return 0. + * + */ + template <typename SimplicialComplexForRips> + void create_complex(SimplicialComplexForRips& complex, int dim_max) { + GUDHI_CHECK(complex.num_vertices() == 0, + std::invalid_argument("Sparse_rips_complex::create_complex - simplicial complex is not empty")); + + complex.insert_graph(graph_); + complex.expansion(dim_max); + } + + private: + // choose_n_farthest_points wants the distance function in this form... + template <class Distance> + struct Ker { + typedef std::size_t Point_d; // index into point range + Ker(Distance& d) : dist(d) {} + // Despite the name, this is not squared... + typedef Distance Squared_distance_d; + Squared_distance_d& squared_distance_d_object() const { return dist; } + Distance& dist; + }; + + // PointRange must be random access. + template <typename PointRange, typename ParamRange, typename Distance> + void compute_sparse_graph(const PointRange& points, const ParamRange& params, Distance& dist, double epsilon) { + const int n = boost::size(points); + graph_.~Graph(); + new (&graph_) Graph(n); + // for(auto v : vertices(g)) // doesn't work :-( + typename boost::graph_traits<Graph>::vertex_iterator v_i, v_e; + for (std::tie(v_i, v_e) = vertices(graph_); v_i != v_e; ++v_i) { + auto v = *v_i; + // This whole loop might not be necessary, leave it until someone investigates if it is safe to remove. + put(vertex_filtration_t(), graph_, v, 0); + } + + // TODO: + // - make it parallel + // - only test near-enough neighbors + for (int i = 0; i < n; ++i) + for (int j = i + 1; j < n; ++j) { + auto&& pi = points[i]; + auto&& pj = points[j]; + auto d = dist(pi, pj); + auto li = params[i]; + auto lj = params[j]; + GUDHI_CHECK(lj <= li, "Bad furthest point sorting"); + Filtration_value alpha; + + // The paper has d/2 and d-lj/e to match the Cech, but we use doubles to match the Rips + if (d * epsilon <= 2 * lj) + alpha = d; + else if (d * epsilon <= li + lj && (epsilon >= 1 || d * epsilon <= lj * (1 + 1 / (1 - epsilon)))) + alpha = (d - lj / epsilon) * 2; + else + continue; + + add_edge(pi, pj, alpha, graph_); + } + } + + Graph graph_; +}; + +} // namespace rips_complex + +} // namespace Gudhi + +#endif // SPARSE_RIPS_COMPLEX_H_ diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp index 89afbc25..b8b444c9 100644 --- a/src/Rips_complex/test/test_rips_complex.cpp +++ b/src/Rips_complex/test/test_rips_complex.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA Saclay (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -31,6 +31,7 @@ #include <algorithm> // std::max #include <gudhi/Rips_complex.h> +#include <gudhi/Sparse_rips_complex.h> // to construct Rips_complex from a OFF file of points #include <gudhi/Points_off_io.h> #include <gudhi/Simplex_tree.h> @@ -43,6 +44,7 @@ using Point = std::vector<double>; using Simplex_tree = Gudhi::Simplex_tree<>; using Filtration_value = Simplex_tree::Filtration_value; using Rips_complex = Gudhi::rips_complex::Rips_complex<Simplex_tree::Filtration_value>; +using Sparse_rips_complex = Gudhi::rips_complex::Sparse_rips_complex<Simplex_tree::Filtration_value>; using Distance_matrix = std::vector<std::vector<Filtration_value>>; BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) { @@ -230,6 +232,71 @@ BOOST_AUTO_TEST_CASE(Rips_complex_from_points) { } } +BOOST_AUTO_TEST_CASE(Sparse_rips_complex_from_points) { + // This is a clone of the test above + // ---------------------------------------------------------------------------- + // 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 a Rips complex from the list of points + // ---------------------------------------------------------------------------- + // .001 is small enough that we get a deterministic result matching the exact Rips + Sparse_rips_complex sparse_rips(points, Custom_square_euclidean_distance(), .001); + + std::cout << "========== Sparse_rips_complex_from_points ==========" << std::endl; + Simplex_tree st; + const int DIMENSION = 3; + sparse_rips.create_complex(st, DIMENSION); + + // Another way to check num_simplices + std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" << std::endl; + int num_simplices = 0; + for (auto f_simplex : st.filtration_simplex_range()) { + num_simplices++; + std::cout << " ( "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << st.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + BOOST_CHECK(num_simplices == 15); + std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl; + BOOST_CHECK(st.num_simplices() == 15); + + std::cout << "st.dimension()=" << st.dimension() << std::endl; + BOOST_CHECK(st.dimension() == DIMENSION); + std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl; + BOOST_CHECK(st.num_vertices() == 4); + + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl; + switch (st.dimension(f_simplex)) { + case 0: + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.0); + break; + case 1: + case 2: + case 3: + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 2.0); + break; + default: + BOOST_CHECK(false); // Shall not happen + break; + } + } +} + BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) { // ---------------------------------------------------------------------------- // diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt index baa571fa..deb73ff0 100644 --- a/src/Rips_complex/utilities/CMakeLists.txt +++ b/src/Rips_complex/utilities/CMakeLists.txt @@ -7,15 +7,29 @@ target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_L add_executable(rips_persistence rips_persistence.cpp) target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) +add_executable(rips_correlation_matrix_persistence rips_correlation_matrix_persistence.cpp) +target_link_libraries(rips_correlation_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + +add_executable(sparse_rips_persistence sparse_rips_persistence.cpp) +target_link_libraries(sparse_rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + if (TBB_FOUND) target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) target_link_libraries(rips_persistence ${TBB_LIBRARIES}) + target_link_libraries(rips_correlation_matrix_persistence ${TBB_LIBRARIES}) + target_link_libraries(sparse_rips_persistence ${TBB_LIBRARIES}) endif() add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence> "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") add_test(NAME Rips_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") +add_test(NAME Rips_complex_utility_from_rips_correlation_matrix COMMAND $<TARGET_FILE:rips_correlation_matrix_persistence> + "${CMAKE_SOURCE_DIR}/data/correlation_matrix/lower_triangular_correlation_matrix.csv" "-c" "0.3" "-d" "3" "-p" "3" "-m" "0") +add_test(NAME Sparse_rips_complex_utility_on_tore_3D COMMAND $<TARGET_FILE:sparse_rips_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-e" "0.5" "-m" "0.2" "-d" "3" "-p" "2") install(TARGETS rips_distance_matrix_persistence DESTINATION bin) install(TARGETS rips_persistence DESTINATION bin) +install(TARGETS rips_correlation_matrix_persistence DESTINATION bin) +install(TARGETS sparse_rips_persistence DESTINATION bin) diff --git a/src/Rips_complex/utilities/README b/src/Rips_complex/utilities/README deleted file mode 100644 index 4d20c806..00000000 --- a/src/Rips_complex/utilities/README +++ /dev/null @@ -1,74 +0,0 @@ -# Rips_complex # - -## `rips_persistence` ## -This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention: - -`p dim birth death` - -where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number). - -**Usage** -`rips_persistence [options] <OFF input file>` - -**Allowed options** - -* `-h [ --help ]` Produce help message -* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. -* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction. -* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute. -* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. -* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. - -Beware: this program may use a lot of RAM and take a lot of time if `max-edge-length` is set to a large value. - -**Example 1 with Z/2Z coefficients** -`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2` - -outputs: -``` -2 0 0 inf -2 1 0.0983494 inf -2 1 0.104347 inf -2 2 0.138335 inf -``` - -**Example 2 with Z/3Z coefficients** - -rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 - -outputs: -``` -3 0 0 inf -3 1 0.0983494 inf -3 1 0.104347 inf -3 2 0.138335 inf -``` - - - - -## `rips_distance_matrix_persistence` ## -Same as `rips_persistence` but taking a distance matrix as input.
-
-**Usage** -`rips_persistence [options] <CSV input file>`
-where
-`<CSV input file>` is the path to the file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'. - -**Example** -`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` - -outputs: -``` -The complex contains 46 simplices - and has dimension 3 -3 0 0 inf -3 0 0 8.94427 -3 0 0 7.28011 -3 0 0 6.08276 -3 0 0 5.83095 -3 0 0 5.38516 -3 0 0 5 -3 1 11 12.0416 -3 1 6.32456 6.7082 -``` diff --git a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp new file mode 100644 index 00000000..d4671b45 --- /dev/null +++ b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp @@ -0,0 +1,170 @@ +/* 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): Pawel Dlotko, Vincent Rouvreau + * + * Copyright (C) 2016 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Rips_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/reader_utils.h> +#include <gudhi/writing_persistence_to_file.h> + +#include <boost/program_options.hpp> + +#include <string> +#include <vector> +#include <limits> // infinity + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = Simplex_tree::Filtration_value; +using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; +using Correlation_matrix = std::vector<std::vector<Filtration_value>>; +using intervals_common = Gudhi::Persistence_interval_common<double, int>; + +void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag, + Filtration_value& correlation_min, int& dim_max, int& p, Filtration_value& min_persistence); + +int main(int argc, char* argv[]) { + std::string csv_matrix_file; + std::string filediag; + Filtration_value correlation_min; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, csv_matrix_file, filediag, correlation_min, dim_max, p, min_persistence); + + Correlation_matrix correlations = + Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file); + + Filtration_value threshold = 0; + + // Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix: + for (size_t i = 0; i != correlations.size(); ++i) { + for (size_t j = 0; j != correlations[i].size(); ++j) { + correlations[i][j] = 1 - correlations[i][j]; + // Here we make sure that the values of corelations lie between -1 and 1. + // If not, we throw an exception. + if ((correlations[i][j] < -1) || (correlations[i][j] > 1)) { + std::cerr << "The input matrix is not a correlation matrix. The program will now terminate. \n"; + throw "The input matrix is not a correlation matrix. The program will now terminate. \n"; + } + if (correlations[i][j] > threshold) threshold = correlations[i][j]; + } + } + + Rips_complex rips_complex_from_file(correlations, threshold); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree simplex_tree; + + rips_complex_from_file.create_complex(simplex_tree, dim_max); + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + // compute persistence + pcoh.compute_persistent_cohomology(min_persistence); + + // invert the persistence diagram. The reason for this procedure is the following: + // The input to the program is a corelation matrix M. When processing it, it is + // turned into 1-M and the obtained persistence intervals are in '1-M' units. + // Below we reverse every (birth,death) pair into (1-birth, 1-death) pair + // so that the input and the output to the program is expressed in the same + // units. + auto pairs = pcoh.get_persistent_pairs(); + std::vector<intervals_common> processed_persistence_intervals; + processed_persistence_intervals.reserve(pairs.size()); + for (auto pair : pairs) { + double birth = 1 - simplex_tree.filtration(get<0>(pair)); + double death = 1 - simplex_tree.filtration(get<1>(pair)); + unsigned dimension = (unsigned)simplex_tree.dimension(get<0>(pair)); + int field = get<2>(pair); + processed_persistence_intervals.push_back(intervals_common(birth, death, dimension, field)); + } + + // sort the processed intervals: + std::sort(processed_persistence_intervals.begin(), processed_persistence_intervals.end()); + + // and write them to a file + if (filediag.empty()) { + write_persistence_intervals_to_stream(processed_persistence_intervals); + } else { + std::ofstream out(filediag); + write_persistence_intervals_to_stream(processed_persistence_intervals, out); + } + return 0; +} + +void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag, + Filtration_value& correlation_min, int& dim_max, int& p, Filtration_value& min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()( + "input-file", po::value<std::string>(&csv_matrix_file), + "Name of file containing a corelation matrix. Can be square or lower triangular matrix. Separator is ';'."); + po::options_description visible("Allowed options", 100); + visible.add_options()("help,h", "produce help message")( + "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout")( + "min-edge-corelation,c", po::value<Filtration_value>(&correlation_min)->default_value(0), + "Minimal corelation of an edge for the Rips complex construction.")( + "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.")( + "field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "min-persistence,m", po::value<Filtration_value>(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " + "intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a corelation matrix.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp index ca3c0327..53191ca7 100644 --- a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp +++ b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko, Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Rips_complex/utilities/rips_persistence.cpp b/src/Rips_complex/utilities/rips_persistence.cpp index 8405c014..7cee927e 100644 --- a/src/Rips_complex/utilities/rips_persistence.cpp +++ b/src/Rips_complex/utilities/rips_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md new file mode 100644 index 00000000..6df49310 --- /dev/null +++ b/src/Rips_complex/utilities/ripscomplex.md @@ -0,0 +1,109 @@ +--- +layout: page +title: "Rips complex" +meta_title: "Rips complex" +teaser: "" +permalink: /ripscomplex/ +--- +{::comment} +Leave the lines above as it is required by the web site generator 'Jekyll' +{:/comment} + + +## rips_persistence ## +This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points, using Euclidean distance. The output diagram contains one bar per line, written with the convention: + +`p dim birth death` + +where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number). + +**Usage** + +`rips_persistence [options] <OFF input file>` + +**Allowed options** + +* `-h [ --help ]` Produce help message +* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. +* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction. +* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. + +Beware: this program may use a lot of RAM and take a lot of time if `max-edge-length` is set to a large value. + +**Example 1 with Z/2Z coefficients** + +`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2` + +**Example 2 with Z/3Z coefficients** + +`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3` + + +## rips_distance_matrix_persistence ## + +Same as `rips_persistence` but taking a distance matrix as input. + +**Usage** + +`rips_distance_matrix_persistence [options] <CSV input file>` + +where +`<CSV input file>` is the path to the file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'. +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. + +**Example** + +`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` + + +## rips_correlation_matrix_persistence ## + +Same as `rips_distance_matrix_persistence` but taking a correlation matrix as input. + +**Usage** + +`rips_correlation_matrix_persistence [options] <CSV input file>` + +where +`<CSV input file>` is the path to the file containing a correlation matrix. Can be square or lower triangular matrix. Separator is ';'. +Note that no check is performed if the matrix given as the input is a correlation matrix. +It is the user responsibility to ensure that this is the case. +Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv for an example of a file. + +**Example** + +`rips_correlation_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` + +**Warning** + +As persistence diagrams points will be under the diagonal, bottleneck distance and persistence graphical tool will not work +properly, this is a known issue. + + +## sparse_rips_persistence ## +This program computes the persistent homology with coefficient field *Z/pZ* +of a sparse (1+epsilon)-approximation of the Rips complex defined on a set of input Euclidean points. The output diagram contains one bar per line, written with the convention: + +`p dim birth death` + +where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number). + +**Usage** + +`sparse_rips_persistence [options] <OFF input file>` + +**Allowed options** + +* `-h [ --help ]` Produce help message +* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. +* `-e [ --approximation ]` (default = .5) Epsilon, where the sparse Rips complex is a (1+epsilon)-approximation of the Rips complex. +* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. + +**Example with Z/2Z coefficients** + +`sparse_rips_persistence ../../data/points/tore3D_1307.off -e .5 -m .2 -d 3 -p 2` diff --git a/src/Rips_complex/utilities/sparse_rips_persistence.cpp b/src/Rips_complex/utilities/sparse_rips_persistence.cpp new file mode 100644 index 00000000..bcd5c2c5 --- /dev/null +++ b/src/Rips_complex/utilities/sparse_rips_persistence.cpp @@ -0,0 +1,133 @@ +/* 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, Clément Maria + * + * Copyright (C) 2018 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Sparse_rips_complex.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Points_off_io.h> + +#include <boost/program_options.hpp> + +#include <string> +#include <vector> + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = Simplex_tree::Filtration_value; +using Sparse_rips = Gudhi::rips_complex::Sparse_rips_complex<Filtration_value>; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; +using Point = std::vector<double>; +using Points_off_reader = Gudhi::Points_off_reader<Point>; + +void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, double& epsilon, + int& dim_max, int& p, Filtration_value& min_persistence); + +int main(int argc, char* argv[]) { + std::string off_file_points; + std::string filediag; + double epsilon; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, filediag, epsilon, dim_max, p, min_persistence); + + Points_off_reader off_reader(off_file_points); + Sparse_rips sparse_rips(off_reader.get_point_cloud(), Gudhi::Euclidean_distance(), epsilon); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree simplex_tree; + + sparse_rips.create_complex(simplex_tree, dim_max); + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + +void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, double& epsilon, + int& dim_max, int& p, Filtration_value& min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()("input-file", po::value<std::string>(&off_file_points), + "Name of an OFF file containing a point set.\n"); + + po::options_description visible("Allowed options", 100); + visible.add_options()("help,h", "produce help message")( + "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout")( + "approximation,e", po::value<double>(&epsilon)->default_value(.5), + "Epsilon, where the sparse Rips complex is a (1+epsilon)-approximation of the Rips complex.")( + "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.")( + "field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "min-persistence,m", po::value<Filtration_value>(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " + "intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a sparse (1+epsilon)-approximation of the Rips complex \ndefined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Simplex_tree/concept/FiltrationValue.h b/src/Simplex_tree/concept/FiltrationValue.h index 79ca06cc..f4dcf985 100644 --- a/src/Simplex_tree/concept/FiltrationValue.h +++ b/src/Simplex_tree/concept/FiltrationValue.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/concept/IndexingTag.h b/src/Simplex_tree/concept/IndexingTag.h index 1dcdd756..37e7e294 100644 --- a/src/Simplex_tree/concept/IndexingTag.h +++ b/src/Simplex_tree/concept/IndexingTag.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/concept/SimplexKey.h b/src/Simplex_tree/concept/SimplexKey.h index 9fbed401..c03f7da1 100644 --- a/src/Simplex_tree/concept/SimplexKey.h +++ b/src/Simplex_tree/concept/SimplexKey.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/concept/SimplexTreeOptions.h b/src/Simplex_tree/concept/SimplexTreeOptions.h index 89acdc18..6638da26 100644 --- a/src/Simplex_tree/concept/SimplexTreeOptions.h +++ b/src/Simplex_tree/concept/SimplexTreeOptions.h @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2015 INRIA Saclay - Ile-de-France (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/concept/VertexHandle.h b/src/Simplex_tree/concept/VertexHandle.h index 3efbba61..9d0642c3 100644 --- a/src/Simplex_tree/concept/VertexHandle.h +++ b/src/Simplex_tree/concept/VertexHandle.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/doc/COPYRIGHT b/src/Simplex_tree/doc/COPYRIGHT index 34345bef..6cde9520 100644 --- a/src/Simplex_tree/doc/COPYRIGHT +++ b/src/Simplex_tree/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Clément Maria -Copyright (C) 2015 INRIA +Copyright (C) 2015 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h index 769491d9..db399489 100644 --- a/src/Simplex_tree/doc/Intro_simplex_tree.h +++ b/src/Simplex_tree/doc/Intro_simplex_tree.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -79,7 +79,6 @@ Number of vertices = 10 Number of simplices = 98 \endcode * 1 incidence relations in a complex. It is consequently faster when accessing the boundary of a simplex, but is less * compact and harder to construct from scratch. * - * \copyright GNU General Public License v3. * @} */ diff --git a/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp b/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp index 9bd51106..08ed74bb 100644 --- a/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp +++ b/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Clément Maria + * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp index d8289ba9..290a9d9b 100644 --- a/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp +++ b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/example/graph_expansion_with_blocker.cpp b/src/Simplex_tree/example/graph_expansion_with_blocker.cpp index 0d458cbd..f675e353 100644 --- a/src/Simplex_tree/example/graph_expansion_with_blocker.cpp +++ b/src/Simplex_tree/example/graph_expansion_with_blocker.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/example/mini_simplex_tree.cpp b/src/Simplex_tree/example/mini_simplex_tree.cpp index 19e45361..e7c7177f 100644 --- a/src/Simplex_tree/example/mini_simplex_tree.cpp +++ b/src/Simplex_tree/example/mini_simplex_tree.cpp @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2015 INRIA Saclay - Ile-de-France (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp index 828977c2..d71b5608 100644 --- a/src/Simplex_tree/example/simple_simplex_tree.cpp +++ b/src/Simplex_tree/example/simple_simplex_tree.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp index d1b8b2de..6d70f3d1 100644 --- a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp +++ b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 7456cb1f..5d4ea30c 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h index ab7346d4..335bac1e 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h index 25d4888a..3a75ec72 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h index 1eca7f6f..ab2ca707 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h index 0adeb46d..ec4461f3 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h index d82425a0..fd806ff1 100644 --- a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h +++ b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h b/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h index 477464c4..d8521343 100644 --- a/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h +++ b/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/doc/COPYRIGHT b/src/Skeleton_blocker/doc/COPYRIGHT index 1de850d7..5b606ac2 100644 --- a/src/Skeleton_blocker/doc/COPYRIGHT +++ b/src/Skeleton_blocker/doc/COPYRIGHT @@ -3,7 +3,7 @@ The files of this directory are part of the Gudhi Library. The Gudhi library computational topology. Author(s): David Salinas -Copyright (C) 2015 INRIA +Copyright (C) 2015 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp index 076c6a53..f288e39c 100644 --- a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp +++ b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp index 08ff0264..4d008450 100644 --- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp +++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp index 58322038..2ec72128 100644 --- a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp +++ b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h index 32fe411c..e8b6fde8 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -239,9 +239,6 @@ their collaboration to write the two initial papers about this data-structure and also Dominique for leaving him use a prototype. - -\copyright GNU General Public License v3. - @} */ } // namespace skeleton_blocker diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h index ba3636bc..6c6a8638 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h index d4b60613..feab7b3f 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h index 747e60f1..56009daf 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h index 275376e6..22c1668e 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h index 3835cf77..144f1fd0 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h index aa6f2215..d7193157 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h index fadf6619..dbfb4042 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h index 2b681752..f80ca4fe 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h index 2c9602fa..7a5d38eb 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h index d2fff960..95c5f7ef 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h index b90dcf34..5c725aae 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h index 1351614f..8054e64f 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h index 2acdb555..e2024652 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h index 736941dd..a834fe1d 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h index 9e9ae961..3a638ae6 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h index 4f052ba5..addd8104 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h index 95331b7a..39b88ceb 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h index 4db075b0..428d4e9b 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h index 544e02e8..d5adb39d 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/test/test_skeleton_blocker_complex.cpp b/src/Skeleton_blocker/test/test_skeleton_blocker_complex.cpp index 4f9888ba..9760c74d 100644 --- a/src/Skeleton_blocker/test/test_skeleton_blocker_complex.cpp +++ b/src/Skeleton_blocker/test/test_skeleton_blocker_complex.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/test/test_skeleton_blocker_geometric_complex.cpp b/src/Skeleton_blocker/test/test_skeleton_blocker_geometric_complex.cpp index d035b2c3..f2d3bb27 100644 --- a/src/Skeleton_blocker/test/test_skeleton_blocker_geometric_complex.cpp +++ b/src/Skeleton_blocker/test/test_skeleton_blocker_geometric_complex.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Skeleton_blocker/test/test_skeleton_blocker_simplifiable.cpp b/src/Skeleton_blocker/test/test_skeleton_blocker_simplifiable.cpp index 360b91db..1f263c98 100644 --- a/src/Skeleton_blocker/test/test_skeleton_blocker_simplifiable.cpp +++ b/src/Skeleton_blocker/test/test_skeleton_blocker_simplifiable.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Spatial_searching/doc/Intro_spatial_searching.h b/src/Spatial_searching/doc/Intro_spatial_searching.h index 1ee5e92e..f387ab2f 100644 --- a/src/Spatial_searching/doc/Intro_spatial_searching.h +++ b/src/Spatial_searching/doc/Intro_spatial_searching.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -50,8 +50,6 @@ namespace spatial_searching { * * \include Spatial_searching/example_spatial_searching.cpp * - * \copyright GNU General Public License v3. - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup spatial_searching diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h index 96bbeb36..ad1054e5 100644 --- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h +++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Spatial_searching/test/test_Kd_tree_search.cpp b/src/Spatial_searching/test/test_Kd_tree_search.cpp index 8a8334c3..981a5850 100644 --- a/src/Spatial_searching/test/test_Kd_tree_search.cpp +++ b/src/Spatial_searching/test/test_Kd_tree_search.cpp @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Subsampling/doc/Intro_subsampling.h b/src/Subsampling/doc/Intro_subsampling.h index c84616dd..d88f6bf6 100644 --- a/src/Subsampling/doc/Intro_subsampling.h +++ b/src/Subsampling/doc/Intro_subsampling.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -58,8 +58,6 @@ namespace subsampling { * This example outputs a subset of 100 points picked randomly. * * \include Subsampling/example_pick_n_random_points.cpp - * \copyright GNU General Public License v3. - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup subsampling diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h index 8390b4c9..ab1c4c73 100644 --- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h +++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Subsampling/include/gudhi/pick_n_random_points.h b/src/Subsampling/include/gudhi/pick_n_random_points.h index 8c90b6bf..64821e5d 100644 --- a/src/Subsampling/include/gudhi/pick_n_random_points.h +++ b/src/Subsampling/include/gudhi/pick_n_random_points.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Subsampling/include/gudhi/sparsify_point_set.h b/src/Subsampling/include/gudhi/sparsify_point_set.h index 7d3b97fb..db10e0b1 100644 --- a/src/Subsampling/include/gudhi/sparsify_point_set.h +++ b/src/Subsampling/include/gudhi/sparsify_point_set.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Subsampling/test/test_choose_n_farthest_points.cpp b/src/Subsampling/test/test_choose_n_farthest_points.cpp index ee9d4c77..0e0eb29c 100644 --- a/src/Subsampling/test/test_choose_n_farthest_points.cpp +++ b/src/Subsampling/test/test_choose_n_farthest_points.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Subsampling/test/test_pick_n_random_points.cpp b/src/Subsampling/test/test_pick_n_random_points.cpp index 6c8dbea2..4baf4a5d 100644 --- a/src/Subsampling/test/test_pick_n_random_points.cpp +++ b/src/Subsampling/test/test_pick_n_random_points.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Subsampling/test/test_sparsify_point_set.cpp b/src/Subsampling/test/test_sparsify_point_set.cpp index f993d6d6..f414dda3 100644 --- a/src/Subsampling/test/test_sparsify_point_set.cpp +++ b/src/Subsampling/test/test_sparsify_point_set.cpp @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Tangential_complex/benchmark/RIB_exporter.h b/src/Tangential_complex/benchmark/RIB_exporter.h index 73c14041..59ca138a 100644 --- a/src/Tangential_complex/benchmark/RIB_exporter.h +++ b/src/Tangential_complex/benchmark/RIB_exporter.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Tangential_complex/benchmark/XML_exporter.h b/src/Tangential_complex/benchmark/XML_exporter.h index ed44f90a..4db5687f 100644 --- a/src/Tangential_complex/benchmark/XML_exporter.h +++ b/src/Tangential_complex/benchmark/XML_exporter.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Tangential_complex/benchmark/benchmark_tc.cpp b/src/Tangential_complex/benchmark/benchmark_tc.cpp index 6d6dd548..e3b2a04f 100644 --- a/src/Tangential_complex/benchmark/benchmark_tc.cpp +++ b/src/Tangential_complex/benchmark/benchmark_tc.cpp @@ -564,10 +564,6 @@ int main() { #endif #endif - unsigned int seed = static_cast<unsigned int> (time(NULL)); - CGAL::default_random = CGAL::Random(seed); // TODO(CJ): use set_default_random - std::cerr << "Random seed = " << seed << "\n"; - std::ifstream script_file; script_file.open(BENCHMARK_SCRIPT_FILENAME); // Script? diff --git a/src/Tangential_complex/doc/COPYRIGHT b/src/Tangential_complex/doc/COPYRIGHT index c4df0f64..f9f92471 100644 --- a/src/Tangential_complex/doc/COPYRIGHT +++ b/src/Tangential_complex/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Clement Jamin -Copyright (C) 2015 INRIA +Copyright (C) 2015 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software diff --git a/src/Tangential_complex/doc/Intro_tangential_complex.h b/src/Tangential_complex/doc/Intro_tangential_complex.h index 3d687c1d..f4fc8ac7 100644 --- a/src/Tangential_complex/doc/Intro_tangential_complex.h +++ b/src/Tangential_complex/doc/Intro_tangential_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -107,8 +107,6 @@ dimensions are known at compile-time. \include Tangential_complex/example_with_perturb.cpp -\copyright GNU General Public License v3. -\verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup tangential_complex diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index 6f061922..d8356520 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h index 65c74ca5..f79186b0 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex/config.h b/src/Tangential_complex/include/gudhi/Tangential_complex/config.h index ffefcd6b..e1af1ea6 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex/config.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex/config.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h b/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h index b2d6d674..2dd46118 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Tangential_complex/test/test_tangential_complex.cpp b/src/Tangential_complex/test/test_tangential_complex.cpp index 48156440..4e2d4f65 100644 --- a/src/Tangential_complex/test/test_tangential_complex.cpp +++ b/src/Tangential_complex/test/test_tangential_complex.cpp @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/concept/SimplicialComplexForWitness.h b/src/Witness_complex/concept/SimplicialComplexForWitness.h index d78cc83f..8b85f4e4 100644 --- a/src/Witness_complex/concept/SimplicialComplexForWitness.h +++ b/src/Witness_complex/concept/SimplicialComplexForWitness.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/doc/COPYRIGHT b/src/Witness_complex/doc/COPYRIGHT index 7d032c87..25a700cf 100644 --- a/src/Witness_complex/doc/COPYRIGHT +++ b/src/Witness_complex/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Siargey Kachanovich -Copyright (C) 2015 INRIA +Copyright (C) 2015 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h index 5d5c0735..62203054 100644 --- a/src/Witness_complex/doc/Witness_complex_doc.h +++ b/src/Witness_complex/doc/Witness_complex_doc.h @@ -117,9 +117,6 @@ int main(int argc, char * const argv[]) { \include Witness_complex/example_nearest_landmark_table.cpp - \copyright GNU General Public License v3. - - */ #endif // WITNESS_COMPLEX_DOC_H_ diff --git a/src/Witness_complex/example/example_nearest_landmark_table.cpp b/src/Witness_complex/example/example_nearest_landmark_table.cpp index b8594212..acaf7c54 100644 --- a/src/Witness_complex/example/example_nearest_landmark_table.cpp +++ b/src/Witness_complex/example/example_nearest_landmark_table.cpp @@ -1,25 +1,3 @@ -/* 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): Siargey Kachanovich - * - * Copyright (C) 2016 INRIA (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_PARAMETER_MAX_ARITY 12 #include <gudhi/Simplex_tree.h> diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp index 346bef6d..19f73836 100644 --- a/src/Witness_complex/example/example_strong_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp @@ -1,25 +1,3 @@ -/* 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): Siargey Kachanovich - * - * Copyright (C) 2016 INRIA (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/Euclidean_strong_witness_complex.h> #include <gudhi/pick_n_random_points.h> diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp index a6e9b11a..9e3c972d 100644 --- a/src/Witness_complex/example/example_witness_complex_sphere.cpp +++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp @@ -1,25 +1,3 @@ -/* 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): Siargey Kachanovich - * - * Copyright (C) 2016 INRIA (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_PARAMETER_MAX_ARITY 12 #include <gudhi/Simplex_tree.h> diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h index 7df43db5..81566824 100644 --- a/src/Witness_complex/example/generators.h +++ b/src/Witness_complex/example/generators.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h index d41a6811..8cb8662b 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h index 0a05173a..10d2ec52 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h index 4f3cef4f..ea97cd3f 100644 --- a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h index ff8bb139..1dacefa5 100644 --- a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index b3d00b11..fd6b3f38 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index 53c38520..67885258 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h index b68d75a1..c7b732b9 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h +++ b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/utilities/strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp index 2fba631b..9d23df74 100644 --- a/src/Witness_complex/utilities/strong_witness_persistence.cpp +++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/utilities/weak_witness_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp index 23fa93aa..1315d2ba 100644 --- a/src/Witness_complex/utilities/weak_witness_persistence.cpp +++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/utilities/README b/src/Witness_complex/utilities/witnesscomplex.md index 1141033e..da453cce 100644 --- a/src/Witness_complex/utilities/README +++ b/src/Witness_complex/utilities/witnesscomplex.md @@ -1,18 +1,31 @@ -# Witness_complex #
+---
+layout: page
+title: "Witness complex"
+meta_title: "Witness complex"
+teaser: ""
+permalink: /witnesscomplex/
+---
+{::comment}
+Leave the lines above as it is required by the web site generator 'Jekyll'
+{:/comment}
-For more details about the witness complex, please read the [user manual of the package](http://gudhi.gforge.inria.fr/doc/latest/group__witness__complex.html).
-## `weak_witness_persistence` ##
-This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:
+For more details about the witness complex, please read the [user manual of the package](/doc/latest/group__witness__complex.html).
+
+## weak_witness_persistence ##
+This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness complex defined on a set of input points.
+The output diagram contains one bar per line, written with the convention:
`p dim birth death`
-where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature,
+and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+
+**Usage**
-*Usage*
`weak_witness_persistence [options] <OFF input file>`
-*Allowed options*
+**Allowed options**
* `-h [ --help ]` Produce help message
* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.
@@ -22,33 +35,28 @@ where `dim` is the dimension of the homological feature, `birth` and `death` are * `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.
-*Example*
-`weak_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.006`
+**Example**
-outputs:
-```
-Successfully read 1307 points.
-Ambient dimension is 3.
-The complex contains 732 simplices and has dimension 8
-11 0 0 inf
-11 1 0 inf
-11 2 0.0275251 0.0534586
-11 1 0 0.0239952
-```
+`weak_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.006`
N.B.: output is random as the 20 landmarks are chosen randomly.
-## `strong_witness_persistence` ##
-This program computes the persistent homology with coefficient field *Z/pZ* of a Strong witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:
+
+## strong_witness_persistence ##
+
+This program computes the persistent homology with coefficient field *Z/pZ* of a Strong witness complex defined on a set of input points.
+The output diagram contains one bar per line, written with the convention:
`p dim birth death`
-where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature,
+and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+
+**Usage**
-*Usage*
`strong_witness_persistence [options] <OFF input file>`
-*Allowed options*
+**Allowed options**
* `-h [ --help ]` Produce help message
* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.
@@ -58,17 +66,8 @@ where `dim` is the dimension of the homological feature, `birth` and `death` are * `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.
-*Example*
-`strong_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.06`
+**Example**
-outputs:
-```
-Successfully read 1307 points.
-Ambient dimension is 3.
-The complex contains 1836 simplices and has dimension 8
-11 0 0 inf
-11 1 0.00674748 inf
-11 2 0.0937751 0.235354
-```
+`strong_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.06`
N.B.: output is random as the 20 landmarks are chosen randomly.
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 419c2581..a008dd0a 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -63,14 +63,18 @@ if(CGAL_FOUND) endif() endif() +option(WITH_GUDHI_USE_TBB "Build with Intel TBB parallelization" ON) + # Find TBB package for parallel sort - not mandatory, just optional. -set(TBB_FIND_QUIETLY ON) -find_package(TBB) -if (TBB_FOUND) - include(${TBB_USE_FILE}) - message("TBB found in ${TBB_LIBRARY_DIRS}") - add_definitions(-DGUDHI_USE_TBB) -endif() +if(WITH_GUDHI_USE_TBB) + set(TBB_FIND_QUIETLY ON) + find_package(TBB) + if (TBB_FOUND) + include(${TBB_USE_FILE}) + message("TBB found in ${TBB_LIBRARY_DIRS}") + add_definitions(-DGUDHI_USE_TBB) + endif() +endif(WITH_GUDHI_USE_TBB) set(CGAL_WITH_EIGEN3_VERSION 0.0.0) find_package(Eigen3 3.1.0) diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h new file mode 100644 index 00000000..40f202c7 --- /dev/null +++ b/src/common/doc/examples.h @@ -0,0 +1,99 @@ +// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments +// In user_version, `find . -name "*.cpp"` in example and utilities folders +/*! @file Examples + * @example Alpha_complex/Alpha_complex_from_off.cpp + * @example Alpha_complex/Alpha_complex_from_points.cpp + * @example Bottleneck_distance/bottleneck_basic_example.cpp + * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp + * @example Witness_complex/example_nearest_landmark_table.cpp + * @example Witness_complex/example_witness_complex_off.cpp + * @example Witness_complex/example_witness_complex_sphere.cpp + * @example Witness_complex/example_strong_witness_complex_off.cpp + * @example Simplex_tree/mini_simplex_tree.cpp + * @example Simplex_tree/graph_expansion_with_blocker.cpp + * @example Simplex_tree/simple_simplex_tree.cpp + * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp + * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp + * @example Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp + * @example Persistent_cohomology/plain_homology.cpp + * @example Persistent_cohomology/persistence_from_file.cpp + * @example Persistent_cohomology/rips_persistence_step_by_step.cpp + * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp + * @example Persistent_cohomology/custom_persistence_sort.cpp + * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp + * @example Persistent_cohomology/rips_multifield_persistence.cpp + * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp + * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp + * @example Skeleton_blocker/Skeleton_blocker_link.cpp + * @example Contraction/Garland_heckbert.cpp + * @example Contraction/Rips_contraction.cpp + * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp + * @example common/example_CGAL_3D_points_off_reader.cpp + * @example common/example_vector_double_points_off_reader.cpp + * @example common/example_CGAL_points_off_reader.cpp + * @example Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp + * @example Rips_complex/example_one_skeleton_rips_from_points.cpp + * @example Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp + * @example Rips_complex/example_rips_complex_from_off_file.cpp + * @example Persistence_representations/persistence_intervals.cpp + * @example Persistence_representations/persistence_vectors.cpp + * @example Persistence_representations/persistence_heat_maps.cpp + * @example Persistence_representations/persistence_landscape_on_grid.cpp + * @example Persistence_representations/persistence_landscape.cpp + * @example Tangential_complex/example_basic.cpp + * @example Tangential_complex/example_with_perturb.cpp + * @example Subsampling/example_custom_kernel.cpp + * @example Subsampling/example_choose_n_farthest_points.cpp + * @example Subsampling/example_sparsify_point_set.cpp + * @example Subsampling/example_pick_n_random_points.cpp + * @example Nerve_GIC/CoordGIC.cpp + * @example Nerve_GIC/Nerve.cpp + * @example Nerve_GIC/FuncGIC.cpp + * @example Nerve_GIC/VoronoiGIC.cpp + * @example Spatial_searching/example_spatial_searching.cpp + * @example Alpha_complex/alpha_complex_3d_persistence.cpp + * @example Alpha_complex/alpha_complex_persistence.cpp + * @example Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp + * @example Alpha_complex/weighted_alpha_complex_3d_persistence.cpp + * @example Alpha_complex/periodic_alpha_complex_3d_persistence.cpp + * @example Alpha_complex/exact_alpha_complex_3d_persistence.cpp + * @example Bottleneck_distance/bottleneck_distance.cpp + * @example Witness_complex/weak_witness_persistence.cpp + * @example Witness_complex/strong_witness_persistence.cpp + * @example Bitmap_cubical_complex/cubical_complex_persistence.cpp + * @example Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp + * @example common/off_file_from_shape_generator.cpp + * @example Rips_complex/rips_distance_matrix_persistence.cpp + * @example Rips_complex/rips_persistence.cpp + * @example Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp + * @example Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp + * @example Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp + * @example Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp + * @example Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp + * @example Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp + * @example Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp + * @example Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp + * @example Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp + * @example Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp + * @example Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp + * @example Persistence_representations/persistence_heat_maps/create_pssk.cpp + * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp + * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp + * @example Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp + * @example Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp + * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp + * @example Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp + * @example Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp + * @example Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp + * @example Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp + * @example Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp + * @example Persistence_representations/persistence_vectors/average_persistence_vectors.cpp + * @example Persistence_representations/persistence_vectors/create_persistence_vectors.cpp + * @example Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp + * @example Persistence_representations/persistence_landscapes/average_landscapes.cpp + * @example Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp + * @example Persistence_representations/persistence_landscapes/create_landscapes.cpp + * @example Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp + * @example Persistence_representations/persistence_landscapes/plot_landscapes.cpp + */ + diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h index c60ed15a..523153b8 100644 --- a/src/common/doc/file_formats.h +++ b/src/common/doc/file_formats.h @@ -4,7 +4,7 @@ * * Author(s): Clément Jamin * -* Copyright (C) 2017 INRIA +* Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/doc/footer.html b/src/common/doc/footer.html index 7b4cdc5c..a557922b 100644 --- a/src/common/doc/footer.html +++ b/src/common/doc/footer.html @@ -6,24 +6,18 @@ <!--BEGIN PROJECT_NAME--> $projectname <!--BEGIN PROJECT_NUMBER--> Version $projectnumber<!--END PROJECT_NUMBER--> <!--BEGIN PROJECT_BRIEF--> - $projectbrief<!--END PROJECT_BRIEF--> +<!--BEGIN PROJECT_BRIEF--> - Copyright : GPL v3<!--END PROJECT_BRIEF--> <!--END PROJECT_NAME--> </td> <td class="network-entypo"> <!--BEGIN GENERATE_TREEVIEW--> $generatedby <a href="http://www.doxygen.org/index.html"> - <img class="footer" src="$relpath^doxygen.png" alt="doxygen"/></a> $doxygenversion + Doxygen</a> $doxygenversion <!--END GENERATE_TREEVIEW--> </td> </tr> </table> -<!--BEGIN !GENERATE_TREEVIEW--> -<hr class="footer"/><address class="footer"><small> tralala -$generatedby  <a href="http://www.doxygen.org/index.html"> -<img class="footer" src="$relpath^doxygen.png" alt="doxygen"/> -</a> $doxygenversion -</small></address> -<!--END !GENERATE_TREEVIEW--> </body> </html> diff --git a/src/common/doc/header.html b/src/common/doc/header.html index 53b5c0a2..2f54e68d 100644 --- a/src/common/doc/header.html +++ b/src/common/doc/header.html @@ -9,7 +9,7 @@ <!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME--> <!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME--> <!-- GUDHI website css for header BEGIN --> -<link rel="stylesheet" type="text/css" href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/gudhi-doc-2.0.0/assets/css/styles_feeling_responsive.css" /> +<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" /> <!-- GUDHI website css for header END --> <link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/> <script type="text/javascript" src="$relpath^jquery.js"></script> @@ -56,6 +56,8 @@ $extrastylesheet <ul class="dropdown"> <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li> <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li> + <li><a href="https://gforge.inria.fr/frs/download.php/file/37365/2018-02-01-16-59-31_GUDHI_2.1.0_OSX_UTILS.tar.gz" target="_blank">Utils for Mac OSx</a></li> + <li><a href="https://gforge.inria.fr/frs/download.php/file/37366/2018-01-31-09-25-53_GUDHI_2.1.0_WIN64_UTILS.zip" target="_blank">Utils for Win x64</a></li> </ul> </li> <li class="divider"></li> @@ -66,6 +68,8 @@ $extrastylesheet <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li> <li><a href="http://gudhi.gforge.inria.fr/python/latest/">Python documentation</a></li> <li><a href="http://gudhi.gforge.inria.fr/python/latest/installation.html">Python installation manual</a></li> + <li><a href="http://gudhi.gforge.inria.fr/utils/">Utilities</a></li> + <li><a href="http://bertrand.michel.perso.math.cnrs.fr/Enseignements/TDA-Gudhi-Python.html" target="_blank">Tutorial</a></li> </ul> </li> <li class="divider"></li> diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h new file mode 100644 index 00000000..25675cc5 --- /dev/null +++ b/src/common/doc/installation.h @@ -0,0 +1,263 @@ +/*! \page installation GUDHI installation + * \tableofcontents + * 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 2015. + * + * \subsection demos Demos and examples + * To build the demos and examples, run the following commands in a terminal: +\verbatim cd /path-to-gudhi/ +mkdir build +cd build/ +cmake .. +make \endverbatim + * A list of examples is available <a href="examples.html">here</a>. + * + * \subsection testsuites Test suites + * To test your build, run the following command in a terminal: + * \verbatim make test \endverbatim + * + * \subsection documentationgeneration Documentation + * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> is required. + * Run the following command in a terminal: +\verbatim +make doxygen +# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/ +# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder` +\endverbatim + * + * \section optionallibrary Optional third-party library + * \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 <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> + * Persistent_cohomology/rips_multifield_persistence.cpp</a> + * + * Having GMP version 4.2 or higher installed is recommended. + * + * \subsection cgal CGAL + * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++ + * library which provides easy access to efficient and reliable geometric algorithms. + * + * \note There is no need to install CGAL, you can just <CODE>cmake . && make</CODE> CGAL (or even + * <CODE>cmake -DCGAL_HEADER_ONLY=ON .</CODE> for CGAL version ≥ 4.8.0), thereafter you will be able to compile + * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE> + * + * Having CGAL version 4.4.0 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 + * + * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms + * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: + * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> + * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> + * + * The following examples/utilities require CGAL version ≥ 4.6.0: + * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> + * Witness_complex/strong_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> + * Witness_complex/weak_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_strong_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html"> + * Witness_complex/example_witness_complex_sphere.cpp</a> + * + * The following example requires CGAL version ≥ 4.7.0: + * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_off.cpp</a> + * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> + * Persistent_cohomology/custom_persistence_sort.cpp</a> + * + * The following example requires CGAL version ≥ 4.8.1: + * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> + * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> + * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html"> + * Bottleneck_distance/bottleneck_basic_example.cpp</a> + * \li <a href="_bottleneck_distance_2bottleneck_read_file_8cpp-example.html"> + * Bottleneck_distance/bottleneck_distance.cpp</a> + * \li <a href="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html"> + * Nerve_GIC/CoordGIC.cpp</a> + * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html"> + * Nerve_GIC/FuncGIC.cpp</a> + * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html"> + * Nerve_GIC/Nerve.cpp</a> + * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html"> + * Nerve_GIC/VoronoiGIC.cpp</a> + * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> + * Spatial_searching/example_spatial_searching.cpp</a> + * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html"> + * Subsampling/example_choose_n_farthest_points.cpp</a> + * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> + * Subsampling/example_custom_kernel.cpp</a> + * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> + * Subsampling/example_pick_n_random_points.cpp</a> + * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> + * Subsampling/example_sparsify_point_set.cpp</a> + * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> + * Tangential_complex/example_basic.cpp</a> + * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> + * Tangential_complex/example_with_perturb.cpp</a> + * + * \subsection eigen3 Eigen3 + * The \ref alpha_complex data structure and few examples requires + * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra: + * matrices, vectors, numerical solvers, and related algorithms. + * + * The following examples/utilities require the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be + * built if Eigen3 is not installed: + * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_off.cpp</a> + * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> + * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> + * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> + * Persistent_cohomology/custom_persistence_sort.cpp</a> + * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> + * Spatial_searching/example_spatial_searching.cpp</a> + * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html"> + * Subsampling/example_choose_n_farthest_points.cpp</a> + * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> + * Subsampling/example_custom_kernel.cpp</a> + * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> + * Subsampling/example_pick_n_random_points.cpp</a> + * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> + * Subsampling/example_sparsify_point_set.cpp</a> + * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> + * Tangential_complex/example_basic.cpp</a> + * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> + * Tangential_complex/example_with_perturb.cpp</a> + * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> + * Witness_complex/strong_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> + * Witness_complex/weak_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_strong_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html"> + * Witness_complex/example_witness_complex_sphere.cpp</a> + * + * \subsection tbb Threading Building Blocks + * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel® TBB</a> lets you easily write parallel + * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have + * future-proof scalability. + * + * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. + * + * The following examples/utilities are using Intel® TBB if installed: + * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_off.cpp</a> + * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html"> + * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a> + * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html"> + * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp</a> + * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html"> + * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a> + * \li <a href="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html"> + * Nerve_GIC/CoordGIC.cpp</a> + * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html"> + * Nerve_GIC/FuncGIC.cpp</a> + * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html"> + * Nerve_GIC/Nerve.cpp</a> + * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html"> + * Nerve_GIC/VoronoiGIC.cpp</a> + * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html"> + * Simplex_tree/simple_simplex_tree.cpp</a> + * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> + * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> + * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html"> + * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> + * \li <a href="_simplex_tree_2graph_expansion_with_blocker_8cpp-example.html"> + * Simplex_tree/graph_expansion_with_blocker.cpp</a> + * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> + * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> + * Persistent_cohomology/alpha_complex_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html"> + * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a> + * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html"> + * Persistent_cohomology/persistence_from_file.cpp</a> + * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html"> + * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a> + * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html"> + * Persistent_cohomology/plain_homology.cpp</a> + * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> + * Persistent_cohomology/rips_multifield_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html"> + * Persistent_cohomology/rips_persistence_step_by_step.cpp</a> + * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html"> + * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> + * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> + * Persistent_cohomology/custom_persistence_sort.cpp</a> + * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html"> + * Rips_complex/example_one_skeleton_rips_from_points.cpp</a> + * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html"> + * Rips_complex/example_rips_complex_from_off_file.cpp</a> + * \li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html"> + * Rips_complex/rips_distance_matrix_persistence.cpp</a> + * \li <a href="_rips_complex_2rips_persistence_8cpp-example.html"> + * Rips_complex/rips_persistence.cpp</a> + * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> + * Witness_complex/strong_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> + * Witness_complex/weak_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2example_nearest_landmark_table_8cpp-example.html"> + * Witness_complex/example_nearest_landmark_table.cpp</a> + * + * \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. + * +*/ + +/*! \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/doc/main_page.h b/src/common/doc/main_page.h index 148ee670..b3e9ea03 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -93,7 +93,7 @@ </td> </tr> </table> - \subsection CoverComplexDataStructure Cover Complexes: Nerves and Graph Induced Complexes + \subsection CoverComplexDataStructure Cover Complexes \image html "gicvisu.jpg" "Graph Induced Complex of a point cloud." <table border="0"> <tr> @@ -101,6 +101,7 @@ <b>Author:</b> Mathieu Carrière<br> <b>Introduced in:</b> GUDHI 2.1.0<br> <b>Copyright:</b> GPL v3<br> + <b>Requires:</b> \ref cgal ≥ 4.8.1 </td> <td width="75%"> Nerves and Graph Induced Complexes are cover complexes, i.e. simplicial complexes that provably contain @@ -250,305 +251,3 @@ </table> */ - -/*! \page installation GUDHI installation - * \tableofcontents - * 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 2015. - * - * \subsection demos Demos and examples - * To build the demos and examples, run the following commands in a terminal: -\verbatim cd /path-to-gudhi/ -mkdir build -cd build/ -cmake .. -make \endverbatim - * A list of examples is available <a href="examples.html">here</a>. - * - * \subsection testsuites Test suites - * To test your build, run the following command in a terminal: - * \verbatim make test \endverbatim - * - * \subsection documentationgeneration Documentation - * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> is required. - * Run the following command in a terminal: -\verbatim -make doxygen -# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/ -# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder` -\endverbatim - * - * \section optionallibrary Optional third-party library - * \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 <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_multifield_persistence.cpp</a> - * - * Having GMP version 4.2 or higher installed is recommended. - * - * \subsection cgal CGAL - * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++ - * library which provides easy access to efficient and reliable geometric algorithms. - * - * \note There is no need to install CGAL, you can just <CODE>cmake . && make</CODE> CGAL (or even - * <CODE>cmake -DCGAL_HEADER_ONLY=ON .</CODE> for CGAL version ≥ 4.8.0), thereafter you will be able to compile - * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE> - * - * Having CGAL version 4.4.0 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 - * - * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms - * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: - * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> - * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> - * - * The following examples/utilities require CGAL version ≥ 4.6.0: - * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> - * Witness_complex/strong_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> - * Witness_complex/weak_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_strong_witness_complex_off.cpp</a> - * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_witness_complex_off.cpp</a> - * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html"> - * Witness_complex/example_witness_complex_sphere.cpp</a> - * - * The following example requires CGAL version ≥ 4.7.0: - * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_off.cpp</a> - * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> - * Persistent_cohomology/custom_persistence_sort.cpp</a> - * - * The following example requires CGAL version ≥ 4.8.1: - * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> - * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> - * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html"> - * Bottleneck_distance/bottleneck_basic_example.cpp</a> - * \li <a href="_bottleneck_distance_2bottleneck_read_file_8cpp-example.html"> - * Bottleneck_distance/bottleneck_distance.cpp</a> - * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> - * Spatial_searching/example_spatial_searching.cpp</a> - * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html"> - * Subsampling/example_choose_n_farthest_points.cpp</a> - * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> - * Subsampling/example_custom_kernel.cpp</a> - * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> - * Subsampling/example_pick_n_random_points.cpp</a> - * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> - * Subsampling/example_sparsify_point_set.cpp</a> - * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> - * Tangential_complex/example_basic.cpp</a> - * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> - * Tangential_complex/example_with_perturb.cpp</a> - * - * \subsection eigen3 Eigen3 - * The \ref alpha_complex data structure and few examples requires - * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra: - * matrices, vectors, numerical solvers, and related algorithms. - * - * The following examples/utilities require the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be - * built if Eigen3 is not installed: - * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_off.cpp</a> - * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> - * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> - * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> - * Persistent_cohomology/custom_persistence_sort.cpp</a> - * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> - * Spatial_searching/example_spatial_searching.cpp</a> - * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html"> - * Subsampling/example_choose_n_farthest_points.cpp</a> - * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> - * Subsampling/example_custom_kernel.cpp</a> - * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> - * Subsampling/example_pick_n_random_points.cpp</a> - * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> - * Subsampling/example_sparsify_point_set.cpp</a> - * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> - * Tangential_complex/example_basic.cpp</a> - * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> - * Tangential_complex/example_with_perturb.cpp</a> - * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> - * Witness_complex/strong_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> - * Witness_complex/weak_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_strong_witness_complex_off.cpp</a> - * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_witness_complex_off.cpp</a> - * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html"> - * Witness_complex/example_witness_complex_sphere.cpp</a> - * - * \subsection tbb Threading Building Blocks - * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel® TBB</a> lets you easily write parallel - * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have - * future-proof scalability. - * - * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. - * - * The following examples/utilities are using Intel® TBB if installed: - * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_off.cpp</a> - * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html"> - * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a> - * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html"> - * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp</a> - * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html"> - * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a> - * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html"> - * Simplex_tree/simple_simplex_tree.cpp</a> - * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> - * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> - * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html"> - * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> - * \li <a href="_simplex_tree_2graph_expansion_with_blocker_8cpp-example.html"> - * Simplex_tree/graph_expansion_with_blocker.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html"> - * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a> - * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html"> - * Persistent_cohomology/persistence_from_file.cpp</a> - * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html"> - * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a> - * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html"> - * Persistent_cohomology/plain_homology.cpp</a> - * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_multifield_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html"> - * Persistent_cohomology/rips_persistence_step_by_step.cpp</a> - * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> - * Persistent_cohomology/custom_persistence_sort.cpp</a> - * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html"> - * Rips_complex/example_one_skeleton_rips_from_points.cpp</a> - * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html"> - * Rips_complex/example_rips_complex_from_off_file.cpp</a> - * \li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html"> - * Rips_complex/rips_distance_matrix_persistence.cpp</a> - * \li <a href="_rips_complex_2rips_persistence_8cpp-example.html"> - * Rips_complex/rips_persistence.cpp</a> - * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> - * Witness_complex/strong_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> - * Witness_complex/weak_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2example_nearest_landmark_table_8cpp-example.html"> - * Witness_complex/example_nearest_landmark_table.cpp</a> - * - * \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. - * -*/ - -/*! \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 -*/ - -// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments -/*! @file Examples - * @example Alpha_complex/Alpha_complex_from_off.cpp - * @example Alpha_complex/Alpha_complex_from_points.cpp - * @example Alpha_complex/alpha_complex_3d_persistence.cpp - * @example Alpha_complex/alpha_complex_persistence.cpp - * @example Alpha_complex/exact_alpha_complex_3d_persistence.cpp - * @example Alpha_complex/periodic_alpha_complex_3d_persistence.cpp - * @example Alpha_complex/weighted_alpha_complex_3d_persistence.cpp - * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp - * @example Bottleneck_distance/bottleneck_basic_example.cpp - * @example Bottleneck_distance/bottleneck_distance.cpp - * @example Bitmap_cubical_complex/cubical_complex_persistence.cpp - * @example Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp - * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp - * @example common/example_CGAL_3D_points_off_reader.cpp - * @example common/example_CGAL_points_off_reader.cpp - * @example Contraction/Garland_heckbert.cpp - * @example Contraction/Rips_contraction.cpp - * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp - * @example Persistent_cohomology/persistence_from_file.cpp - * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp - * @example Persistent_cohomology/plain_homology.cpp - * @example Persistent_cohomology/rips_multifield_persistence.cpp - * @example Persistent_cohomology/custom_persistence_sort.cpp - * @example Persistent_cohomology/rips_persistence_step_by_step.cpp - * @example Rips_complex/example_one_skeleton_rips_from_points.cpp - * @example Rips_complex/example_rips_complex_from_off_file.cpp - * @example Rips_complex/rips_persistence.cpp - * @example Rips_complex/rips_distance_matrix_persistence.cpp - * @example Simplex_tree/mini_simplex_tree.cpp - * @example Simplex_tree/simple_simplex_tree.cpp - * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp - * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp - * @example Simplex_tree/graph_expansion_with_blocker.cpp - * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp - * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp - * @example Skeleton_blocker/Skeleton_blocker_link.cpp - * @example Spatial_searching/example_spatial_searching.cpp - * @example Subsampling/example_choose_n_farthest_points.cpp - * @example Subsampling/example_custom_kernel.cpp - * @example Subsampling/example_pick_n_random_points.cpp - * @example Subsampling/example_sparsify_point_set.cpp - * @example Tangential_complex/example_basic.cpp - * @example Tangential_complex/example_with_perturb.cpp - * @example Witness_complex/example_nearest_landmark_table.cpp - * @example Witness_complex/example_strong_witness_complex_off.cpp - * @example Witness_complex/example_witness_complex_off.cpp - * @example Witness_complex/example_witness_complex_sphere.cpp - * @example Witness_complex/weak_witness_persistence.cpp - * @example Witness_complex/strong_witness_persistence.cpp - */ - diff --git a/src/common/doc/offline_header.html b/src/common/doc/offline_header.html new file mode 100644 index 00000000..6a02a895 --- /dev/null +++ b/src/common/doc/offline_header.html @@ -0,0 +1,41 @@ +<!-- HTML header for doxygen 1.8.6--> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<!-- GUDHI website : class="no-js" lang="en" is necessary --> +<html xmlns="http://www.w3.org/1999/xhtml" class="no-js" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> +<meta http-equiv="X-UA-Compatible" content="IE=9"/> +<meta name="generator" content="Doxygen $doxygenversion"/> +<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME--> +<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME--> +<!-- GUDHI website css for header END --> +<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/> +<script type="text/javascript" src="$relpath^jquery.js"></script> +<script type="text/javascript" src="$relpath^dynsections.js"></script> +$treeview +$search +$mathjax +<link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" /> +$extrastylesheet +</head> +<body> + + +<div id="top"><!-- do not remove this div, it is closed by doxygen! --> + +<!--BEGIN TITLEAREA--> +<div id="titlearea"> +<table cellspacing="0" cellpadding="0"> + <tbody> + <tr style="height: 30px;"> + <!--BEGIN DISABLE_INDEX--> + <!--BEGIN SEARCHENGINE--> + <td>$searchbox</td> + <!--END SEARCHENGINE--> + <!--END DISABLE_INDEX--> + </tr> + </tbody> +</table> +</div> +<!--END TITLEAREA--> +<!-- end header part --> diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt index afe865d4..1273c699 100644 --- a/src/common/example/CMakeLists.txt +++ b/src/common/example/CMakeLists.txt @@ -3,11 +3,20 @@ project(Common_examples) add_executable ( vector_double_off_reader example_vector_double_points_off_reader.cpp ) target_link_libraries(vector_double_off_reader ${CGAL_LIBRARY}) +file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_test(NAME Common_example_vector_double_off_reader COMMAND $<TARGET_FILE:vector_double_off_reader> - "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off") + "alphacomplexdoc.off") install(TARGETS vector_double_off_reader DESTINATION bin) +if (DIFF_PATH) + # Do not forget to copy test results files in current binary dir + file(COPY "vectordoubleoffreader_result.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + + add_test(Common_example_vector_double_off_reader_diff_files ${DIFF_PATH} + ${CMAKE_CURRENT_BINARY_DIR}/vectordoubleoffreader_result.txt ${CMAKE_CURRENT_BINARY_DIR}/alphacomplexdoc.off.txt) +endif() + if(CGAL_FOUND) add_executable ( cgal_3D_off_reader example_CGAL_3D_points_off_reader.cpp ) target_link_libraries(cgal_3D_off_reader ${CGAL_LIBRARY}) diff --git a/src/common/example/example_CGAL_3D_points_off_reader.cpp b/src/common/example/example_CGAL_3D_points_off_reader.cpp index 665b7a29..4658d8d5 100644 --- a/src/common/example/example_CGAL_3D_points_off_reader.cpp +++ b/src/common/example/example_CGAL_3D_points_off_reader.cpp @@ -20,12 +20,12 @@ int main(int argc, char **argv) { usage(argv[0]); } - std::string offInputFile(argv[1]); + std::string off_input_file(argv[1]); // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile); + Gudhi::Points_3D_off_reader<Point_3> off_reader(off_input_file); // Check the read operation was correct if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << offInputFile << std::endl; + std::cerr << "Unable to read file " << off_input_file << std::endl; usage(argv[0]); } diff --git a/src/common/example/example_CGAL_points_off_reader.cpp b/src/common/example/example_CGAL_points_off_reader.cpp index 8c6a6b54..f45683a5 100644 --- a/src/common/example/example_CGAL_points_off_reader.cpp +++ b/src/common/example/example_CGAL_points_off_reader.cpp @@ -22,12 +22,12 @@ int main(int argc, char **argv) { usage(argv[0]); } - std::string offInputFile(argv[1]); + std::string off_input_file(argv[1]); // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_off_reader<Point_d> off_reader(offInputFile); + Gudhi::Points_off_reader<Point_d> off_reader(off_input_file); // Check the read operation was correct if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << offInputFile << std::endl; + std::cerr << "Unable to read file " << off_input_file << std::endl; usage(argv[0]); } diff --git a/src/common/example/example_vector_double_points_off_reader.cpp b/src/common/example/example_vector_double_points_off_reader.cpp index 8aecb26e..5093da85 100644 --- a/src/common/example/example_vector_double_points_off_reader.cpp +++ b/src/common/example/example_vector_double_points_off_reader.cpp @@ -17,25 +17,27 @@ int main(int argc, char **argv) { usage(argv[0]); } - std::string offInputFile(argv[1]); + std::string off_input_file(argv[1]); // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_off_reader<Point_d> off_reader(offInputFile); + Gudhi::Points_off_reader<Point_d> off_reader(off_input_file); // Check the read operation was correct if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << offInputFile << std::endl; + std::cerr << "Unable to read file " << off_input_file << std::endl; usage(argv[0]); } // Retrieve the triangulation std::vector<Point_d> point_cloud = off_reader.get_point_cloud(); + std::ofstream output_file(off_input_file + ".txt"); int n {0}; for (auto point : point_cloud) { - std::cout << "Point[" << n << "] = "; + output_file << "Point[" << n << "] = "; for (std::size_t i {0}; i < point.size(); i++) - std::cout << point[i] << " "; - std::cout << "\n"; + output_file << point[i] << " "; + output_file << "\n"; ++n; } + output_file.close(); return 0; } diff --git a/src/common/example/cgaloffreader_result.txt b/src/common/example/vectordoubleoffreader_result.txt index 1deb8dbd..1deb8dbd 100644 --- a/src/common/example/cgaloffreader_result.txt +++ b/src/common/example/vectordoubleoffreader_result.txt diff --git a/src/common/include/gudhi/Clock.h b/src/common/include/gudhi/Clock.h index b83de2f5..cdf18cb2 100644 --- a/src/common/include/gudhi/Clock.h +++ b/src/common/include/gudhi/Clock.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/Debug_utils.h b/src/common/include/gudhi/Debug_utils.h index 90d3cf47..3f5cb04f 100644 --- a/src/common/include/gudhi/Debug_utils.h +++ b/src/common/include/gudhi/Debug_utils.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/Null_output_iterator.h b/src/common/include/gudhi/Null_output_iterator.h index 42e6e449..c700af5f 100644 --- a/src/common/include/gudhi/Null_output_iterator.h +++ b/src/common/include/gudhi/Null_output_iterator.h @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h index 4fcd2af2..024f0568 100644 --- a/src/common/include/gudhi/Off_reader.h +++ b/src/common/include/gudhi/Off_reader.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -105,25 +105,26 @@ class Off_reader { 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 (is_noff_file) { + // Should be on a separate line, but we accept it on the same line as the number of vertices + stream_ >> off_info_.dim; + } else { + off_info_.dim = 3; + } + 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)) { + 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; - } } off_visitor.init(off_info_.dim, off_info_.num_vertices, off_info_.num_faces, off_info_.num_edges); @@ -131,10 +132,12 @@ class Off_reader { } 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] != '%'); + do { + // skip whitespace, including empty lines + if (!std::ifstream::sentry(stream_)) return false; + std::getline(stream_, uncomment_line); + } while (uncomment_line[0] == '#'); + return (bool)stream_; } template<typename OffVisitor> diff --git a/src/common/include/gudhi/Point.h b/src/common/include/gudhi/Point.h index 0479e71e..345a8465 100644 --- a/src/common/include/gudhi/Point.h +++ b/src/common/include/gudhi/Point.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/Points_3D_off_io.h b/src/common/include/gudhi/Points_3D_off_io.h index b0d24998..704f73a7 100644 --- a/src/common/include/gudhi/Points_3D_off_io.h +++ b/src/common/include/gudhi/Points_3D_off_io.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h index 29af8a8a..38029658 100644 --- a/src/common/include/gudhi/Points_off_io.h +++ b/src/common/include/gudhi/Points_off_io.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -126,9 +126,9 @@ class Points_off_visitor_reader { * \code $> ./vector_double_off_reader ../../data/points/alphacomplexdoc.off * \endcode * - * the program output is: + * the program outputs a file ../../data/points/alphacomplexdoc.off.txt: * - * \include common/cgaloffreader_result.txt + * \include common/vectordoubleoffreader_result.txt */ template<typename Point_d> class Points_off_reader { diff --git a/src/common/include/gudhi/Simple_object_pool.h b/src/common/include/gudhi/Simple_object_pool.h index fb9c8e23..47283521 100644 --- a/src/common/include/gudhi/Simple_object_pool.h +++ b/src/common/include/gudhi/Simple_object_pool.h @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2015 INRIA Saclay - Ile de France + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/Unitary_tests_utils.h b/src/common/include/gudhi/Unitary_tests_utils.h index 8394a062..e07c8d42 100644 --- a/src/common/include/gudhi/Unitary_tests_utils.h +++ b/src/common/include/gudhi/Unitary_tests_utils.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/allocator.h b/src/common/include/gudhi/allocator.h index 4ede14e4..3de16a49 100644 --- a/src/common/include/gudhi/allocator.h +++ b/src/common/include/gudhi/allocator.h @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2015 INRIA Saclay - Ile de France + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/console_color.h b/src/common/include/gudhi/console_color.h index c4671da3..a493e0d0 100644 --- a/src/common/include/gudhi/console_color.h +++ b/src/common/include/gudhi/console_color.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA Sophia-Antipolis (France) + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index 3a5d1fd5..f7baed6f 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index d84421b2..6ab7b0b4 100644 --- a/src/common/include/gudhi/graph_simplicial_complex.h +++ b/src/common/include/gudhi/graph_simplicial_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h index 9df77760..1f8f2cd8 100644 --- a/src/common/include/gudhi/random_point_generators.h +++ b/src/common/include/gudhi/random_point_generators.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 90be4fc7..26eeb76d 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -4,7 +4,7 @@ * * Author(s): Clement Maria, Pawel Dlotko, Clement Jamin * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/writing_persistence_to_file.h b/src/common/include/gudhi/writing_persistence_to_file.h new file mode 100644 index 00000000..4c5ce918 --- /dev/null +++ b/src/common/include/gudhi/writing_persistence_to_file.h @@ -0,0 +1,117 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2017 Swansea University, UK + * + * 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 WRITING_PERSISTENCE_TO_FILE_H +#define WRITING_PERSISTENCE_TO_FILE_H + +#include <iostream> +#include <string> +#include <limits> + +namespace Gudhi { + +/** +* This is a class to store persistence intervals. Its main purpose is to +* exchange data in between different packages and provide unified way +* of writing a collection of persistence intervals to file. +**/ +template <typename Filtration_type, typename Coefficient_field> +class Persistence_interval_common { + public: + /** + * Constructor taking as an input birth and death of the pair. + **/ + Persistence_interval_common(Filtration_type birth, Filtration_type death) + : birth_(birth), + death_(death), + dimension_(std::numeric_limits<unsigned>::max()), + arith_element_(std::numeric_limits<Coefficient_field>::max()) {} + + /** + * Constructor taking as an input birth, death and dimension of the pair. + **/ + Persistence_interval_common(Filtration_type birth, Filtration_type death, unsigned dim) + : birth_(birth), death_(death), dimension_(dim), arith_element_(std::numeric_limits<Coefficient_field>::max()) {} + + /** +* Constructor taking as an input birth, death, dimension of the pair as well +* as the number p such that this interval is present over Z_p field. +**/ + Persistence_interval_common(Filtration_type birth, Filtration_type death, unsigned dim, Coefficient_field field) + : birth_(birth), death_(death), dimension_(dim), arith_element_(field) {} + + /** + * Operator to compare two persistence pairs. During the comparision all the + * fields: birth, death, dimensiona and arith_element_ are taken into account + * and they all have to be equal for two pairs to be equal. + **/ + bool operator==(const Persistence_interval_common& i2) const { + return ((this->birth_ == i2.birth_) && (this->death_ == i2.death_) && (this->dimension_ == i2.dimension_) && + (this->arith_element_ == i2.arith_element_)); + } + + /** + * Check if two persistence paris are not equal. + **/ + bool operator!=(const Persistence_interval_common& i2) const { return (!((*this) == i2)); } + + /** + * Operator to compare objects of a type Persistence_interval_common. + * One intervals is smaller than the other if it has lower persistence. + * Note that this operator do not take Arith_element into account when doing comparisions. + **/ + bool operator<(const Persistence_interval_common& i2) const { + return fabs(this->death_ - this->birth_) < fabs(i2.death_ - i2.birth_); + } + + friend std::ostream& operator<<(std::ostream& out, const Persistence_interval_common& it) { + if (it.arith_element_ != std::numeric_limits<Coefficient_field>::max()) { + out << it.arith_element_ << " "; + } + if (it.dimension_ != std::numeric_limits<unsigned>::max()) { + out << it.dimension_ << " "; + } + out << it.birth_ << " " << it.death_ << " "; + return out; + } + + private: + Filtration_type birth_; + Filtration_type death_; + unsigned dimension_; + Coefficient_field arith_element_; +}; + +/** + * This function write a vector<Persistence_interval_common> to a stream +**/ +template <typename Persistence_interval_range> +void write_persistence_intervals_to_stream(const Persistence_interval_range& intervals, + std::ostream& out = std::cout) { + for (auto interval : intervals) { + out << interval << "\n"; + } +} + +} + +#endif // WRITING_PERSISTENCE_TO_FILE_H diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp index 656e6f2e..6fee86e2 100644 --- a/src/common/test/test_distance_matrix_reader.cpp +++ b/src/common/test/test_distance_matrix_reader.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/test/test_persistence_intervals_reader.cpp b/src/common/test/test_persistence_intervals_reader.cpp index be299376..b7ece9bd 100644 --- a/src/common/test/test_persistence_intervals_reader.cpp +++ b/src/common/test/test_persistence_intervals_reader.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/test/test_points_off_reader.cpp b/src/common/test/test_points_off_reader.cpp index 0a78d190..ba3bab71 100644 --- a/src/common/test/test_points_off_reader.cpp +++ b/src/common/test/test_points_off_reader.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 + * Copyright (C) 2015 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/utilities/README b/src/common/utilities/README deleted file mode 100644 index 18fa8cc4..00000000 --- a/src/common/utilities/README +++ /dev/null @@ -1,19 +0,0 @@ -# Pointset generator # - -## `off_file_from_shape_generator` ## - -Generates a pointset and save it in an OFF file. Command-line is: -`off_file_from_shape_generator on|in sphere|cube|curve|torus|klein <filename> <num_points> <dimension> <parameter1> <parameter2>...` - -Warning: "on cube" generator is not available! - -Examples: - -* Generate an onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2: -`off_file_from_shape_generator on sphere onSphere.off 1000 3 15.2` - -* Generate an inSphere.off file with 100 points randomized in a sphere of dimension 2 (circle) and radius 1.0 (default): -`off_file_from_shape_generator in sphere inSphere.off 100 2` - -* Generates a inCube.off file with 10000 points randomized in a cube of dimension 3 and side 5.8: -`off_file_from_shape_generator in cube inCube.off 10000 3 5.8` diff --git a/src/common/utilities/off_file_from_shape_generator.cpp b/src/common/utilities/off_file_from_shape_generator.cpp index afcd558c..5e3da7f7 100644 --- a/src/common/utilities/off_file_from_shape_generator.cpp +++ b/src/common/utilities/off_file_from_shape_generator.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/utilities/pointsetgenerator.md b/src/common/utilities/pointsetgenerator.md new file mode 100644 index 00000000..c8c819b7 --- /dev/null +++ b/src/common/utilities/pointsetgenerator.md @@ -0,0 +1,39 @@ +--- +layout: page +title: "OFF point set generator" +meta_title: "OFF point set generator" +teaser: "" +permalink: /pointsetgenerator/ +--- +{::comment} +Leave the lines above as it is required by the web site generator 'Jekyll' +{:/comment} + + +Generates a pointset and save it in an OFF file. Command-line is: + +``` +off_file_from_shape_generator on|in sphere|cube|curve|torus|klein <filename> <num_points> <dimension> <parameter1> <parameter2>... +``` + +Warning: "on cube" generator is not available! + +**Examples** + +``` +off_file_from_shape_generator on sphere onSphere.off 1000 3 15.2 +``` + +* Generates an onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2. + +``` +off_file_from_shape_generator in sphere inSphere.off 100 2 +``` + +* Generates an inSphere.off file with 100 points randomized in a sphere of dimension 2 (circle) and radius 1.0 (default). + +``` +off_file_from_shape_generator in cube inCube.off 10000 3 5.8 +``` + +* Generates a inCube.off file with 10000 points randomized in a cube of dimension 3 and side 5.8. diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index afca9d60..b19cc550 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -1,6 +1,8 @@ cmake_minimum_required(VERSION 2.8) project(Cython) +include(CheckCXXSourceCompiles) + function( add_gudhi_cython_lib THE_LIB ) if(EXISTS ${THE_LIB}) get_filename_component(THE_LIB_FILE_NAME ${THE_LIB} NAME_WE) @@ -32,35 +34,6 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") - # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h - # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac). - # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h - # #if __has_feature(cxx_thread_local) || \ - # ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ - # ( _MSC_VER >= 1900 ) - # #define CGAL_CAN_USE_CXX11_THREAD_LOCAL - # #endif - set(CGAL_CAN_USE_CXX11_THREAD_LOCAL " - int main() { - #ifndef __has_feature - #define __has_feature(x) 0 // Compatibility with non-clang compilers. - #endif - #if __has_feature(cxx_thread_local) || \ - ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ - ( _MSC_VER >= 1900 ) - bool has_feature_thread_local = true; - #else - // Explicit error of compilation for CMake test purpose - has_feature_thread_local is not defined - #endif - bool result = has_feature_thread_local; - } ") - check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) - - if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) - add_gudhi_cython_lib(${Boost_THREAD_LIBRARY}) - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") - endif() - # Gudhi and CGAL compilation option if(MSVC) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ") @@ -99,6 +72,35 @@ if(CYTHON_FOUND) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) if(CGAL_FOUND) + # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h + # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac). + # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h + # #if __has_feature(cxx_thread_local) || \ + # ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ + # ( _MSC_VER >= 1900 ) + # #define CGAL_CAN_USE_CXX11_THREAD_LOCAL + # #endif + set(CGAL_CAN_USE_CXX11_THREAD_LOCAL " + int main() { + #ifndef __has_feature + #define __has_feature(x) 0 // Compatibility with non-clang compilers. + #endif + #if __has_feature(cxx_thread_local) || \ + ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ + ( _MSC_VER >= 1900 ) + bool has_feature_thread_local = true; + #else + // Explicit error of compilation for CMake test purpose - has_feature_thread_local is not defined + #endif + bool result = has_feature_thread_local; + } ") + check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) + + if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) + add_gudhi_cython_lib(${Boost_THREAD_LIBRARY}) + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") + endif() + # Add CGAL compilation args if(CGAL_HEADER_ONLY) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") @@ -135,7 +137,7 @@ if(CYTHON_FOUND) endforeach() set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ") - if (TBB_FOUND) + if (TBB_FOUND AND WITH_GUDHI_USE_TBB) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY}) add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY}) diff --git a/src/cython/cython/alpha_complex.pyx b/src/cython/cython/alpha_complex.pyx index a0e8f9b7..4f772e31 100644 --- a/src/cython/cython/alpha_complex.pyx +++ b/src/cython/cython/alpha_complex.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -28,7 +28,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Alpha_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/bottleneck_distance.pyx b/src/cython/cython/bottleneck_distance.pyx index 9fb377ff..76ef81f4 100644 --- a/src/cython/cython/bottleneck_distance.pyx +++ b/src/cython/cython/bottleneck_distance.pyx @@ -9,7 +9,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -26,7 +26,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Bottleneck_distance_interface.h" namespace "Gudhi::persistence_diagram": diff --git a/src/cython/cython/cubical_complex.pyx b/src/cython/cython/cubical_complex.pyx index ffc85130..a98a3ec3 100644 --- a/src/cython/cython/cubical_complex.pyx +++ b/src/cython/cython/cubical_complex.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -28,7 +28,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Cubical_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/euclidean_strong_witness_complex.pyx b/src/cython/cython/euclidean_strong_witness_complex.pyx index c1523892..62b7cf71 100644 --- a/src/cython/cython/euclidean_strong_witness_complex.pyx +++ b/src/cython/cython/euclidean_strong_witness_complex.pyx @@ -8,7 +8,7 @@ from libcpp.utility cimport pair Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ from libcpp.utility cimport pair """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Euclidean_strong_witness_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/euclidean_witness_complex.pyx b/src/cython/cython/euclidean_witness_complex.pyx index 7c443b6b..c10ca73d 100644 --- a/src/cython/cython/euclidean_witness_complex.pyx +++ b/src/cython/cython/euclidean_witness_complex.pyx @@ -8,7 +8,7 @@ from libcpp.utility cimport pair Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ from libcpp.utility cimport pair """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Euclidean_witness_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/off_reader.pyx b/src/cython/cython/off_reader.pyx index b6e107ef..b939013f 100644 --- a/src/cython/cython/off_reader.pyx +++ b/src/cython/cython/off_reader.pyx @@ -9,7 +9,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -26,7 +26,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Off_reader_interface.h" namespace "Gudhi": @@ -46,4 +46,5 @@ def read_off(off_file=''): return read_points_from_OFF_file(str.encode(off_file)) else: print("file " + off_file + " not found.") + return [] diff --git a/src/cython/cython/periodic_cubical_complex.pyx b/src/cython/cython/periodic_cubical_complex.pyx index 3025f125..c25b83e9 100644 --- a/src/cython/cython/periodic_cubical_complex.pyx +++ b/src/cython/cython/periodic_cubical_complex.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -28,7 +28,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Cubical_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index fb837e29..e2405e96 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -8,7 +8,7 @@ import os Author(s): Vincent Rouvreau, Bertrand Michel - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ import os """ __author__ = "Vincent Rouvreau, Bertrand Michel" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" def __min_birth_max_death(persistence, band_boot=0.): diff --git a/src/cython/cython/reader_utils.pyx b/src/cython/cython/reader_utils.pyx index 3a17c5a0..e4572db0 100644 --- a/src/cython/cython/reader_utils.pyx +++ b/src/cython/cython/reader_utils.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2017 INRIA + Copyright (C) 2017 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -28,7 +28,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2017 INRIA" +__copyright__ = "Copyright (C) 2017 Inria" __license__ = "GPL v3" cdef extern from "Reader_utils_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx index ad9b0a4d..59c16bff 100644 --- a/src/cython/cython/rips_complex.pyx +++ b/src/cython/cython/rips_complex.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -28,14 +28,12 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Rips_complex_interface.h" namespace "Gudhi": cdef cppclass Rips_complex_interface "Gudhi::rips_complex::Rips_complex_interface": Rips_complex_interface(vector[vector[double]] values, double threshold, bool euclidean) - # bool from_file is a workaround for cython to find the correct signature - Rips_complex_interface(string file_name, double threshold, bool euclidean, bool from_file) void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) # RipsComplex python interface @@ -49,7 +47,7 @@ cdef class RipsComplex: cdef Rips_complex_interface * thisptr # Fake constructor that does nothing but documenting the constructor - def __init__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')): + def __init__(self, points=None, distance_matrix=None, max_edge_length=float('inf')): """RipsComplex constructor. :param max_edge_length: Rips value. @@ -60,41 +58,14 @@ cdef class RipsComplex: Or - :param off_file: An OFF file style name. - :type off_file: string - - Or - :param distance_matrix: A distance matrix (full square or lower triangular). :type points: list of list of double - - Or - - :param csv_file: A csv file style name containing a full square or a - lower triangular distance matrix. - :type csv_file: string """ # The real cython constructor - def __cinit__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')): - if off_file is not '': - if os.path.isfile(off_file): - self.thisptr = new Rips_complex_interface(str.encode(off_file), - max_edge_length, - True, - True) - else: - print("file " + off_file + " not found.") - elif csv_file is not '': - if os.path.isfile(csv_file): - self.thisptr = new Rips_complex_interface(str.encode(csv_file), - max_edge_length, - False, - True) - else: - print("file " + csv_file + " not found.") - elif distance_matrix is not None: + def __cinit__(self, points=None, distance_matrix=None, max_edge_length=float('inf')): + if distance_matrix is not None: self.thisptr = new Rips_complex_interface(distance_matrix, max_edge_length, False) else: if points is None: diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx index 0cb575d2..8abeb5f8 100644 --- a/src/cython/cython/simplex_tree.pyx +++ b/src/cython/cython/simplex_tree.pyx @@ -10,7 +10,7 @@ from libcpp.string cimport string Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -27,7 +27,7 @@ from libcpp.string cimport string """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/strong_witness_complex.pyx b/src/cython/cython/strong_witness_complex.pyx index 770b46f5..74c5cb05 100644 --- a/src/cython/cython/strong_witness_complex.pyx +++ b/src/cython/cython/strong_witness_complex.pyx @@ -8,7 +8,7 @@ from libcpp.utility cimport pair Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ from libcpp.utility cimport pair """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Strong_witness_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/subsampling.pyx b/src/cython/cython/subsampling.pyx index 894a4fbe..ac09b7a3 100644 --- a/src/cython/cython/subsampling.pyx +++ b/src/cython/cython/subsampling.pyx @@ -10,7 +10,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -27,7 +27,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Subsampling_interface.h" namespace "Gudhi::subsampling": diff --git a/src/cython/cython/tangential_complex.pyx b/src/cython/cython/tangential_complex.pyx index d55bb050..10fa1468 100644 --- a/src/cython/cython/tangential_complex.pyx +++ b/src/cython/cython/tangential_complex.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -28,7 +28,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Tangential_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/witness_complex.pyx b/src/cython/cython/witness_complex.pyx index 96d122bb..8591465a 100644 --- a/src/cython/cython/witness_complex.pyx +++ b/src/cython/cython/witness_complex.pyx @@ -8,7 +8,7 @@ from libcpp.utility cimport pair Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ from libcpp.utility cimport pair """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Witness_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html index 243f33c6..c9356116 100644 --- a/src/cython/doc/_templates/layout.html +++ b/src/cython/doc/_templates/layout.html @@ -198,6 +198,8 @@ <ul class="dropdown"> <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li> <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li> + <li><a href="https://gforge.inria.fr/frs/download.php/file/37365/2018-02-01-16-59-31_GUDHI_2.1.0_OSX_UTILS.tar.gz" target="_blank">Utils for Mac OSx</a></li> + <li><a href="https://gforge.inria.fr/frs/download.php/file/37366/2018-01-31-09-25-53_GUDHI_2.1.0_WIN64_UTILS.zip" target="_blank">Utils for Win x64</a></li> </ul> </li> <li class="divider"></li> @@ -208,6 +210,8 @@ <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li> <li><a href="http://gudhi.gforge.inria.fr/python/latest/">Python documentation</a></li> <li><a href="http://gudhi.gforge.inria.fr/python/latest/installation.html">Python installation manual</a></li> + <li><a href="http://gudhi.gforge.inria.fr/utils/">Utilities</a></li> + <li><a href="http://bertrand.michel.perso.math.cnrs.fr/Enseignements/TDA-Gudhi-Python.html" target="_blank">Tutorial</a></li> </ul> </li> <li class="divider"></li> @@ -255,7 +259,7 @@ {%- if hasdoc('copyright') %} {% trans path=pathto('copyright'), copyright=copyright|e %}© <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %} {%- else %} - {% trans copyright=copyright|e %}© Copyright {{ copyright }}.{% endtrans %} + {% trans copyright=copyright|e %} {{ copyright }}.{% endtrans %} {%- endif %} {%- endif %} {%- if last_updated %} diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py index 19a880d4..a13c9751 100755 --- a/src/cython/doc/conf.py +++ b/src/cython/doc/conf.py @@ -62,7 +62,7 @@ import gudhi # General information about the project. project = gudhi.__name__ -copyright = gudhi.__copyright__ +copyright = gudhi.__copyright__ + ' - ' + gudhi.__license__ # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -158,7 +158,7 @@ html_static_path = ['_static'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' +html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index 34598f02..dd82ad93 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst @@ -152,6 +152,6 @@ End user programs are available in cython/example/ folder. Bibliography ============ -.. bibliography:: ../../bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 9033331f..a5523d23 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -58,8 +58,8 @@ This function can display the persistence result as a diagram: import gudhi - rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ - '/data/points/tore3D_1307.off', max_edge_length=0.2) + point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off') + rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) @@ -69,8 +69,8 @@ This function can display the persistence result as a diagram: import gudhi - rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ - '/data/points/tore3D_1307.off', max_edge_length=0.2) + point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off') + rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py index c2fbf801..ac20bf47 100755 --- a/src/cython/doc/pyplots/diagram_persistence.py +++ b/src/cython/doc/pyplots/diagram_persistence.py @@ -1,7 +1,8 @@ import gudhi -rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ - '/data/points/tore3D_1307.off', max_edge_length=0.2) +point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + \ + '/data/points/tore3D_1307.off') +rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index 96ba9944..7738aef0 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -101,8 +101,8 @@ Finally, it is asked to display information about the Rips complex. .. testcode:: import gudhi - rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ - '/data/points/alphacomplexdoc.off', max_edge_length=12.0) + point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off') + rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=12.0) simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ @@ -197,7 +197,7 @@ Example from csv file ^^^^^^^^^^^^^^^^^^^^^ This example builds the :doc:`Rips_complex <rips_complex_ref>` from the given -points in an OFF file, and max_edge_length value. +distance matrix in a csv file, and max_edge_length value. Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it. Finally, it is asked to display information about the Rips complex. @@ -206,8 +206,9 @@ Finally, it is asked to display information about the Rips complex. .. testcode:: import gudhi - rips_complex = gudhi.RipsComplex(csv_file=gudhi.__root_source_dir__ + \ - '/data/distance_matrix/full_square_distance_matrix.csv', max_edge_length=12.0) + distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=gudhi.__root_source_dir__ + \ + '/data/distance_matrix/full_square_distance_matrix.csv') + rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, max_edge_length=12.0) simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ @@ -240,3 +241,72 @@ the program output is: [0, 3] -> 9.43 [4, 6] -> 9.49 [3, 6] -> 11.00 + +Correlation matrix +--------------- + +Example from a correlation matrix +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Analogously to the case of distance matrix, Rips complexes can be also constructed based on correlation matrix. +Given a correlation matrix M, comportment-wise 1-M is a distance matrix. +This example builds the one skeleton graph from the given corelation matrix and threshold value. +Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it. + +Finally, it is asked to display information about the simplicial complex. + +.. testcode:: + + import gudhi + import numpy as np + + # User defined correlation matrix is: + # |1 0.06 0.23 0.01 0.89| + # |0.06 1 0.74 0.01 0.61| + # |0.23 0.74 1 0.72 0.03| + # |0.01 0.01 0.72 1 0.7 | + # |0.89 0.61 0.03 0.7 1 | + correlation_matrix=np.array([[1., 0.06, 0.23, 0.01, 0.89], + [0.06, 1., 0.74, 0.01, 0.61], + [0.23, 0.74, 1., 0.72, 0.03], + [0.01, 0.01, 0.72, 1., 0.7], + [0.89, 0.61, 0.03, 0.7, 1.]], float) + + distance_matrix = np.ones((correlation_matrix.shape),float) - correlation_matrix + rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, max_edge_length=1.0) + + simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) + result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ + repr(simplex_tree.num_simplices()) + ' simplices - ' + \ + repr(simplex_tree.num_vertices()) + ' vertices.' + print(result_str) + fmt = '%s -> %.2f' + for filtered_value in simplex_tree.get_filtration(): + print(fmt % tuple(filtered_value)) + +When launching (Rips maximal distance between 2 points is 12.0, is expanded +until dimension 1 - one skeleton graph in other words), the output is: + +.. testoutput:: + + Rips complex is of dimension 1 - 15 simplices - 5 vertices. + [0] -> 0.00 + [1] -> 0.00 + [2] -> 0.00 + [3] -> 0.00 + [4] -> 0.00 + [0, 4] -> 0.11 + [1, 2] -> 0.26 + [2, 3] -> 0.28 + [3, 4] -> 0.30 + [1, 4] -> 0.39 + [0, 2] -> 0.77 + [0, 1] -> 0.94 + [2, 4] -> 0.97 + [0, 3] -> 0.99 + [1, 3] -> 0.99 + +.. note:: + As persistence diagrams points will be under the diagonal, + bottleneck distance and persistence graphical tool will not work properly, + this is a known issue. diff --git a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py index b4487be4..27550025 100755 --- a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='AlphaComplex creation from ' diff --git a/src/cython/example/alpha_complex_from_points_example.py b/src/cython/example/alpha_complex_from_points_example.py index 7d6278ce..ad73c744 100755 --- a/src/cython/example/alpha_complex_from_points_example.py +++ b/src/cython/example/alpha_complex_from_points_example.py @@ -8,7 +8,7 @@ from gudhi import AlphaComplex, SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ from gudhi import AlphaComplex, SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py index ab5fc1e9..b51fa7a8 100755 --- a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py +++ b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py @@ -10,7 +10,7 @@ import math Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -27,7 +27,7 @@ import math """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='AlphaComplex and RipsComplex ' @@ -45,13 +45,14 @@ args = parser.parse_args() with open(args.file, 'r') as f: first_line = f.readline() if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): + point_cloud = gudhi.read_off(off_file=args.file) print("#####################################################################") print("RipsComplex creation from points read in a OFF file") message = "RipsComplex with max_edge_length=" + repr(args.threshold) print(message) - rips_complex = gudhi.RipsComplex(off_file=args.file, + rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=args.threshold) rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) @@ -67,7 +68,7 @@ with open(args.file, 'r') as f: message = "AlphaComplex with max_edge_length=" + repr(args.threshold) print(message) - alpha_complex = gudhi.AlphaComplex(off_file=args.file) + alpha_complex = gudhi.AlphaComplex(points=point_cloud) alpha_stree = alpha_complex.create_simplex_tree(max_alpha_square=(args.threshold * args.threshold)) message = "Number of simplices=" + repr(alpha_stree.num_simplices()) diff --git a/src/cython/example/bottleneck_basic_example.py b/src/cython/example/bottleneck_basic_example.py index 31cecb29..287956e7 100755 --- a/src/cython/example/bottleneck_basic_example.py +++ b/src/cython/example/bottleneck_basic_example.py @@ -8,7 +8,7 @@ import gudhi Author(s): Francois Godi, Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,11 +25,9 @@ import gudhi """ __author__ = "Francois Godi, Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" -import gudhi - diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]] diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]] diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index e3f362dc..1c142d9a 100755 --- a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='EuclideanStrongWitnessComplex creation from ' diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index c236d992..216fcff2 100755 --- a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from ' diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py index ed87806b..9f37efc0 100755 --- a/src/cython/example/gudhi_graphical_tools_example.py +++ b/src/cython/example/gudhi_graphical_tools_example.py @@ -8,7 +8,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index 00334121..5f968bf1 100755 --- a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" def is_file_perseus(file): diff --git a/src/cython/example/random_cubical_complex_persistence_example.py b/src/cython/example/random_cubical_complex_persistence_example.py index c832d6bf..80ff2452 100755 --- a/src/cython/example/random_cubical_complex_persistence_example.py +++ b/src/cython/example/random_cubical_complex_persistence_example.py @@ -13,7 +13,7 @@ import operator Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -30,7 +30,7 @@ import operator """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='Random cubical complex.', diff --git a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py new file mode 100755 index 00000000..4142fa99 --- /dev/null +++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -0,0 +1,84 @@ +#!/usr/bin/env python + +import gudhi +import sys +import argparse + +"""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) 2017 Inria + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2017 Inria" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='RipsComplex creation from ' + 'a correlation matrix read in a csv file.', + epilog='Example: ' + 'example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py ' + '-f ../data/correlation_matrix/lower_triangular_correlation_matrix.csv -e 12.0 -d 3' + '- Constructs a Rips complex with the ' + 'correlation matrix from the given csv file.') +parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument("-c", "--min_edge_correlation", type=float, default=0.5) +parser.add_argument("-d", "--max_dimension", type=int, default=1) +parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') + +args = parser.parse_args() + +if not (-1. < args.min_edge_correlation < 1.): + print("Wrong value of the treshold corelation (should be between -1 and 1).") + sys.exit(1) + +print("#####################################################################") +print("Caution: as persistence diagrams points will be under the diagonal,") +print("bottleneck distance and persistence graphical tool will not work") +print("properly, this is a known issue.") + +print("#####################################################################") +print("RipsComplex creation from correlation matrix read in a csv file") + +message = "RipsComplex with min_edge_correlation=" + repr(args.min_edge_correlation) +print(message) + +correlation_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file) +# Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix: +distance_matrix = [[1.-correlation_matrix[i][j] for j in range(len(correlation_matrix[i]))] for i in range(len(correlation_matrix))] + +rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, + max_edge_length=1.-args.min_edge_correlation) +simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) + +message = "Number of simplices=" + repr(simplex_tree.num_simplices()) +print(message) + +diag = simplex_tree.persistence() + +print("betti_numbers()=") +print(simplex_tree.betti_numbers()) + +# invert the persistence diagram +invert_diag = [(diag[pers][0],(1.-diag[pers][1][0], 1.-diag[pers][1][1])) for pers in range(len(diag))] + +if args.no_diagram == False: + pplot = gudhi.plot_persistence_diagram(invert_diag, band_boot=args.band_boot) + pplot.show() diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 3baebd17..01d1f38a 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -26,16 +26,16 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='RipsComplex creation from ' - 'a distance matrix read in a OFF file.', + 'a distance matrix read in a csv file.', epilog='Example: ' 'example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py ' '-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3' '- Constructs a Rips complex with the ' - 'points from the given OFF file.') + 'distance matrix from the given csv file.') parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-e", "--max_edge_length", type=float, default=0.5) parser.add_argument("-d", "--max_dimension", type=int, default=1) @@ -50,7 +50,8 @@ print("RipsComplex creation from distance matrix read in a csv file") message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) print(message) -rips_complex = gudhi.RipsComplex(csv_file=args.file, max_edge_length=args.max_edge_length) +distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file) +rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, max_edge_length=args.max_edge_length) simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) message = "Number of simplices=" + repr(simplex_tree.num_simplices()) diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py index 5951eedf..865c66b6 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='RipsComplex creation from ' @@ -53,7 +53,8 @@ with open(args.file, 'r') as f: message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) print(message) - rips_complex = gudhi.RipsComplex(off_file=args.file, max_edge_length=args.max_edge_length) + point_cloud = gudhi.read_off(off_file=args.file) + rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=args.max_edge_length) simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) message = "Number of simplices=" + repr(simplex_tree.num_simplices()) diff --git a/src/cython/example/rips_complex_from_points_example.py b/src/cython/example/rips_complex_from_points_example.py index 5d411b1a..ffa9d91f 100755 --- a/src/cython/example/rips_complex_from_points_example.py +++ b/src/cython/example/rips_complex_from_points_example.py @@ -8,7 +8,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py index 9bfea41c..7a6a9f46 100755 --- a/src/cython/example/rips_persistence_diagram.py +++ b/src/cython/example/rips_persistence_diagram.py @@ -8,7 +8,7 @@ import gudhi Author(s): Marc Glisse - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ import gudhi """ __author__ = "Marc Glisse" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py index 51a60e73..28679015 100755 --- a/src/cython/example/simplex_tree_example.py +++ b/src/cython/example/simplex_tree_example.py @@ -8,7 +8,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py index 6145e7f2..680a8bf8 100755 --- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='TangentialComplex creation from ' diff --git a/src/cython/example/witness_complex_from_nearest_landmark_table.py b/src/cython/example/witness_complex_from_nearest_landmark_table.py index 92ed970b..e6b295ee 100755 --- a/src/cython/example/witness_complex_from_nearest_landmark_table.py +++ b/src/cython/example/witness_complex_from_nearest_landmark_table.py @@ -8,7 +8,7 @@ from gudhi import StrongWitnessComplex, SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ from gudhi import StrongWitnessComplex, SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in index a8dd9f80..b94f2251 100644 --- a/src/cython/gudhi.pyx.in +++ b/src/cython/gudhi.pyx.in @@ -4,7 +4,7 @@ Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -21,7 +21,7 @@ """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" __version__ = "@GUDHI_VERSION@" # This variable is used by doctest to find files diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h index d47db71f..8cf527fc 100644 --- a/src/cython/include/Alpha_complex_interface.h +++ b/src/cython/include/Alpha_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Bottleneck_distance_interface.h b/src/cython/include/Bottleneck_distance_interface.h index d5fbf6ea..5ad9d77d 100644 --- a/src/cython/include/Bottleneck_distance_interface.h +++ b/src/cython/include/Bottleneck_distance_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Cubical_complex_interface.h b/src/cython/include/Cubical_complex_interface.h index fad92c2c..85b717b3 100644 --- a/src/cython/include/Cubical_complex_interface.h +++ b/src/cython/include/Cubical_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Euclidean_strong_witness_complex_interface.h b/src/cython/include/Euclidean_strong_witness_complex_interface.h index b9dd8177..d86355d6 100644 --- a/src/cython/include/Euclidean_strong_witness_complex_interface.h +++ b/src/cython/include/Euclidean_strong_witness_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Euclidean_witness_complex_interface.h b/src/cython/include/Euclidean_witness_complex_interface.h index 2a09b3b5..dc303533 100644 --- a/src/cython/include/Euclidean_witness_complex_interface.h +++ b/src/cython/include/Euclidean_witness_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Off_reader_interface.h b/src/cython/include/Off_reader_interface.h index 0ca55500..f6b14f38 100644 --- a/src/cython/include/Off_reader_interface.h +++ b/src/cython/include/Off_reader_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h index 55028fd0..a86b1187 100644 --- a/src/cython/include/Persistent_cohomology_interface.h +++ b/src/cython/include/Persistent_cohomology_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Reader_utils_interface.h b/src/cython/include/Reader_utils_interface.h index 8ec34f61..5f7527d9 100644 --- a/src/cython/include/Reader_utils_interface.h +++ b/src/cython/include/Reader_utils_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h index 02985727..8b6c9c35 100644 --- a/src/cython/include/Rips_complex_interface.h +++ b/src/cython/include/Rips_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -25,9 +25,7 @@ #include <gudhi/Simplex_tree.h> #include <gudhi/Rips_complex.h> -#include <gudhi/Points_off_io.h> #include <gudhi/distance_functions.h> -#include <gudhi/reader_utils.h> #include "Simplex_tree_interface.h" @@ -56,21 +54,6 @@ class Rips_complex_interface { } } - Rips_complex_interface(const std::string& file_name, double threshold, bool euclidean, bool from_file = true) { - if (euclidean) { - // Rips construction where file_name is an OFF file - Gudhi::Points_off_reader<Point_d> off_reader(file_name); - rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(off_reader.get_point_cloud(), - threshold, - Gudhi::Euclidean_distance()); - } else { - // Rips construction where values is a distance matrix - Distance_matrix distances = - Gudhi::read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name); - rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(distances, threshold); - } - } - ~Rips_complex_interface() { delete rips_complex_; } diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h index 54a4f824..3481eeff 100644 --- a/src/cython/include/Simplex_tree_interface.h +++ b/src/cython/include/Simplex_tree_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Strong_witness_complex_interface.h b/src/cython/include/Strong_witness_complex_interface.h index d05eaac5..3c72c916 100644 --- a/src/cython/include/Strong_witness_complex_interface.h +++ b/src/cython/include/Strong_witness_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Subsampling_interface.h b/src/cython/include/Subsampling_interface.h index b0f4a50a..f990da0c 100644 --- a/src/cython/include/Subsampling_interface.h +++ b/src/cython/include/Subsampling_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h index 0c3a510e..2772460a 100644 --- a/src/cython/include/Tangential_complex_interface.h +++ b/src/cython/include/Tangential_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h index 6501cc35..01b372e7 100644 --- a/src/cython/include/Witness_complex_interface.h +++ b/src/cython/include/Witness_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * Copyright (C) 2016 Inria * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in index fefa36bb..b6ca4bcb 100644 --- a/src/cython/setup.py.in +++ b/src/cython/setup.py.in @@ -7,7 +7,7 @@ from Cython.Build import cythonize Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -23,8 +23,8 @@ from Cython.Build import cythonize along with this program. If not, see <http://www.gnu.org/licenses/>. """ -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__author__ = "GUDHI Editorial Board" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" gudhi = Extension( @@ -41,7 +41,7 @@ gudhi = Extension( setup( name = 'gudhi', - author='Vincent Rouvreau', + author='GUDHI Editorial Board', author_email='gudhi-contact@lists.gforge.inria.fr', version='@GUDHI_VERSION@', url='http://gudhi.gforge.inria.fr/', diff --git a/src/cython/test/test_alpha_complex.py b/src/cython/test/test_alpha_complex.py index 2c76d9d7..e97f2530 100755 --- a/src/cython/test/test_alpha_complex.py +++ b/src/cython/test/test_alpha_complex.py @@ -6,7 +6,7 @@ from gudhi import AlphaComplex, SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -23,7 +23,7 @@ from gudhi import AlphaComplex, SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_bottleneck_distance.py b/src/cython/test/test_bottleneck_distance.py index 3d982d34..4eb5848f 100755 --- a/src/cython/test/test_bottleneck_distance.py +++ b/src/cython/test/test_bottleneck_distance.py @@ -6,7 +6,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -23,7 +23,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py index 0e81554d..79d39aa8 100755 --- a/src/cython/test/test_cubical_complex.py +++ b/src/cython/test/test_cubical_complex.py @@ -6,7 +6,7 @@ from gudhi import CubicalComplex Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -23,7 +23,7 @@ from gudhi import CubicalComplex """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_euclidean_witness_complex.py b/src/cython/test/test_euclidean_witness_complex.py index 737f1ef4..2f77210a 100755 --- a/src/cython/test/test_euclidean_witness_complex.py +++ b/src/cython/test/test_euclidean_witness_complex.py @@ -6,7 +6,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -23,7 +23,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_reader_utils.py b/src/cython/test/test_reader_utils.py index 25591fb3..b240c84f 100755 --- a/src/cython/test/test_reader_utils.py +++ b/src/cython/test/test_reader_utils.py @@ -6,7 +6,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2017 INRIA + Copyright (C) 2017 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -23,7 +23,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2017 INRIA" +__copyright__ = "Copyright (C) 2017 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py index c7d2ead4..c37b5400 100755 --- a/src/cython/test/test_rips_complex.py +++ b/src/cython/test/test_rips_complex.py @@ -7,7 +7,7 @@ from math import sqrt Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -24,7 +24,7 @@ from math import sqrt """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py index 6dec5d94..029e7729 100755 --- a/src/cython/test/test_simplex_tree.py +++ b/src/cython/test/test_simplex_tree.py @@ -6,7 +6,7 @@ from gudhi import SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -23,7 +23,7 @@ from gudhi import SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_subsampling.py b/src/cython/test/test_subsampling.py index 2caf4ddb..96906a6f 100755 --- a/src/cython/test/test_subsampling.py +++ b/src/cython/test/test_subsampling.py @@ -6,7 +6,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -23,7 +23,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_tangential_complex.py b/src/cython/test/test_tangential_complex.py index 8aa4023c..fe623c7b 100755 --- a/src/cython/test/test_tangential_complex.py +++ b/src/cython/test/test_tangential_complex.py @@ -6,7 +6,7 @@ from gudhi import TangentialComplex, SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -23,7 +23,7 @@ from gudhi import TangentialComplex, SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_witness_complex.py b/src/cython/test/test_witness_complex.py index 7d1fb6be..bcbc521b 100755 --- a/src/cython/test/test_witness_complex.py +++ b/src/cython/test/test_witness_complex.py @@ -6,7 +6,7 @@ from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + Copyright (C) 2016 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -23,7 +23,7 @@ from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" |