From 06ff6fac211d2823c7d14a6d2f4a4db03f48d2e3 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 26 Jan 2018 14:01:39 +0000 Subject: Seperate installation and examples from main page Move cover complex utilities from examples GIC.cpp example was not compiled, nor tested. It is removed. Persistence representation : no need to link with Boost_SYSTEM git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3164 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: cf2bfa6c6de2ed359aaa165b9f80bca7e06defb1 --- src/Nerve_GIC/doc/Intro_graph_induced_complex.h | 29 -- src/Nerve_GIC/example/CMakeLists.txt | 12 - src/Nerve_GIC/example/GIC.cpp | 95 ----- .../example/KeplerMapperVisuFromTxtFile.py | 72 ---- src/Nerve_GIC/example/Nerve.cpp | 96 ----- src/Nerve_GIC/example/Nerve.txt | 63 ---- src/Nerve_GIC/example/VoronoiGIC.cpp | 90 ----- src/Nerve_GIC/example/km.py | 390 --------------------- src/Nerve_GIC/example/km.py.COPYRIGHT | 26 -- src/Nerve_GIC/utilities/CMakeLists.txt | 22 ++ .../utilities/KeplerMapperVisuFromTxtFile.py | 72 ++++ src/Nerve_GIC/utilities/Nerve.cpp | 96 +++++ src/Nerve_GIC/utilities/Nerve.txt | 63 ++++ src/Nerve_GIC/utilities/VoronoiGIC.cpp | 90 +++++ src/Nerve_GIC/utilities/km.py | 390 +++++++++++++++++++++ src/Nerve_GIC/utilities/km.py.COPYRIGHT | 26 ++ 16 files changed, 759 insertions(+), 873 deletions(-) delete mode 100644 src/Nerve_GIC/example/GIC.cpp delete mode 100755 src/Nerve_GIC/example/KeplerMapperVisuFromTxtFile.py delete mode 100644 src/Nerve_GIC/example/Nerve.cpp delete mode 100644 src/Nerve_GIC/example/Nerve.txt delete mode 100644 src/Nerve_GIC/example/VoronoiGIC.cpp delete mode 100755 src/Nerve_GIC/example/km.py delete mode 100644 src/Nerve_GIC/example/km.py.COPYRIGHT create mode 100644 src/Nerve_GIC/utilities/CMakeLists.txt create mode 100755 src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py create mode 100644 src/Nerve_GIC/utilities/Nerve.cpp create mode 100644 src/Nerve_GIC/utilities/Nerve.txt create mode 100644 src/Nerve_GIC/utilities/VoronoiGIC.cpp create mode 100755 src/Nerve_GIC/utilities/km.py create mode 100644 src/Nerve_GIC/utilities/km.py.COPYRIGHT (limited to 'src/Nerve_GIC') diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index 7578cc53..344cb031 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -177,7 +177,6 @@ namespace cover_complex { * \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 +185,3 @@ 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..434637fa 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -3,26 +3,14 @@ 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 $ - "${CMAKE_SOURCE_DIR}/data/points/human.off" "2" "10" "0.3") - - add_test(NAME Nerve_GIC_example_VoronoiGIC COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/human.off" "100") - add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0") 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 . - */ - -#include - -#include -#include - -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; - - 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 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 . -""" - -__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/example/Nerve.cpp b/src/Nerve_GIC/example/Nerve.cpp deleted file mode 100644 index 6abdedc7..00000000 --- a/src/Nerve_GIC/example/Nerve.cpp +++ /dev/null @@ -1,96 +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 . - */ - -#include - -#include -#include - -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"; - exit(-1); // ----- >> -} - -int main(int argc, char **argv) { - if ((argc != 5) && (argc != 6)) usage(argc, argv[0]); - - using Point = std::vector; - - std::string off_file_name(argv[1]); - int coord = atoi(argv[2]); - int resolution = atoi(argv[3]); - double gain = atof(argv[4]); - bool verb = 0; - if (argc == 6) verb = 1; - - // -------------------------------- - // Init of a Nerve from an OFF file - // -------------------------------- - - Gudhi::cover_complex::Cover_complex SC; - SC.set_verbose(verb); - - bool check = SC.read_point_cloud(off_file_name); - - if (!check) { - std::cout << "Incorrect OFF file." << std::endl; - } else { - SC.set_type("Nerve"); - - SC.set_color_from_coordinate(coord); - SC.set_function_from_coordinate(coord); - - SC.set_graph_from_OFF(); - SC.set_resolution_with_interval_number(resolution); - SC.set_gain(gain); - SC.set_cover_from_function(); - - SC.find_simplices(); - - SC.write_info(); - - Gudhi::Simplex_tree<> stree; - SC.create_complex(stree); - SC.compute_PD(); - - // ---------------------------------------------------------------------------- - // Display information about the graph induced complex - // ---------------------------------------------------------------------------- - - if (verb) { - std::cout << "Nerve is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - " - << stree.num_vertices() << " vertices." << std::endl; - - std::cout << "Iterator on Nerve 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/Nerve.txt b/src/Nerve_GIC/example/Nerve.txt deleted file mode 100644 index 839ff45e..00000000 --- a/src/Nerve_GIC/example/Nerve.txt +++ /dev/null @@ -1,63 +0,0 @@ -Min function value = -0.979672 and Max function value = 0.816414 -Interval 0 = [-0.979672, -0.761576] -Interval 1 = [-0.838551, -0.581967] -Interval 2 = [-0.658942, -0.402359] -Interval 3 = [-0.479334, -0.22275] -Interval 4 = [-0.299725, -0.0431415] -Interval 5 = [-0.120117, 0.136467] -Interval 6 = [0.059492, 0.316076] -Interval 7 = [0.239101, 0.495684] -Interval 8 = [0.418709, 0.675293] -Interval 9 = [0.598318, 0.816414] -Computing preimages... -Computing connected components... -.txt generated. It can be visualized with e.g. python KeplerMapperVisuFromTxtFile.py and firefox. -5 interval(s) in dimension 0: - [-0.909111, 0.00817529] - [-0.171433, 0.367392] - [-0.171433, 0.367392] - [-0.909111, 0.745853] -0 interval(s) in dimension 1: -Nerve is of dimension 1 - 41 simplices - 21 vertices. -Iterator on Nerve simplices -1 -0 -4 -4 0 -2 -2 1 -8 -8 2 -5 -5 4 -9 -9 8 -13 -13 5 -14 -14 9 -19 -19 13 -25 -32 -20 -32 20 -33 -33 25 -26 -26 14 -26 19 -42 -42 26 -34 -34 33 -27 -27 20 -35 -35 27 -35 34 -42 35 -44 -44 35 -54 -54 44 \ No newline at end of file diff --git a/src/Nerve_GIC/example/VoronoiGIC.cpp b/src/Nerve_GIC/example/VoronoiGIC.cpp deleted file mode 100644 index 32431cc2..00000000 --- a/src/Nerve_GIC/example/VoronoiGIC.cpp +++ /dev/null @@ -1,90 +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 . - */ - -#include - -#include -#include - -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"; - exit(-1); // ----- >> -} - -int main(int argc, char **argv) { - if ((argc != 3) && (argc != 4)) usage(argc, argv[0]); - - using Point = std::vector; - - std::string off_file_name(argv[1]); - int m = atoi(argv[2]); - bool verb = 0; - if (argc == 4) verb = 1; - - // ---------------------------------------------------------------------------- - // Init of a graph induced complex from an OFF file - // ---------------------------------------------------------------------------- - - Gudhi::cover_complex::Cover_complex 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_type("GIC"); - - GIC.set_color_from_coordinate(); - - GIC.set_graph_from_OFF(); - GIC.set_cover_from_Voronoi(Gudhi::Euclidean_distance(), m); - - GIC.find_simplices(); - - GIC.plot_OFF(); - - 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/km.py b/src/Nerve_GIC/example/km.py deleted file mode 100755 index 53024aab..00000000 --- a/src/Nerve_GIC/example/km.py +++ /dev/null @@ -1,390 +0,0 @@ -from __future__ import division -import numpy as np -from collections import defaultdict -import json -import itertools -from sklearn import cluster, preprocessing, manifold -from datetime import datetime -import sys - -class KeplerMapper(object): - # With this class you can build topological networks from (high-dimensional) data. - # - # 1) Fit a projection/lens/function to a dataset and transform it. - # For instance "mean_of_row(x) for x in X" - # 2) Map this projection with overlapping intervals/hypercubes. - # Cluster the points inside the interval - # (Note: we cluster on the inverse image/original data to lessen projection loss). - # If two clusters/nodes have the same members (due to the overlap), then: - # connect these with an edge. - # 3) Visualize the network using HTML and D3.js. - # - # functions - # --------- - # fit_transform: Create a projection (lens) from a dataset - # map: Apply Mapper algorithm on this projection and build a simplicial complex - # visualize: Turns the complex dictionary into a HTML/D3.js visualization - - def __init__(self, verbose=2): - self.verbose = verbose - - self.chunk_dist = [] - self.overlap_dist = [] - self.d = [] - self.nr_cubes = 0 - self.overlap_perc = 0 - self.clusterer = False - - def fit_transform(self, X, projection="sum", scaler=preprocessing.MinMaxScaler()): - # Creates the projection/lens from X. - # - # Input: X. Input features as a numpy array. - # Output: projected_X. original data transformed to a projection (lens). - # - # parameters - # ---------- - # projection: Projection parameter is either a string, - # a scikit class with fit_transform, like manifold.TSNE(), - # or a list of dimension indices. - # scaler: if None, do no scaling, else apply scaling to the projection - # Default: Min-Max scaling - - self.scaler = scaler - self.projection = str(projection) - - # Detect if projection is a class (for scikit-learn) - #if str(type(projection))[1:6] == "class": #TODO: de-ugly-fy - # reducer = projection - # if self.verbose > 0: - # try: - # projection.set_params(**{"verbose":self.verbose}) - # except: - # pass - # print("\n..Projecting data using: \n\t%s\n"%str(projection)) - # X = reducer.fit_transform(X) - - # Detect if projection is a string (for standard functions) - if isinstance(projection, str): - if self.verbose > 0: - print("\n..Projecting data using: %s"%(projection)) - # Stats lenses - if projection == "sum": # sum of row - X = np.sum(X, axis=1).reshape((X.shape[0],1)) - if projection == "mean": # mean of row - X = np.mean(X, axis=1).reshape((X.shape[0],1)) - if projection == "median": # mean of row - X = np.median(X, axis=1).reshape((X.shape[0],1)) - if projection == "max": # max of row - X = np.max(X, axis=1).reshape((X.shape[0],1)) - if projection == "min": # min of row - X = np.min(X, axis=1).reshape((X.shape[0],1)) - if projection == "std": # std of row - X = np.std(X, axis=1).reshape((X.shape[0],1)) - - if projection == "dist_mean": # Distance of x to mean of X - X_mean = np.mean(X, axis=0) - X = np.sum(np.sqrt((X - X_mean)**2), axis=1).reshape((X.shape[0],1)) - - # Detect if projection is a list (with dimension indices) - if isinstance(projection, list): - if self.verbose > 0: - print("\n..Projecting data using: %s"%(str(projection))) - X = X[:,np.array(projection)] - - # Scaling - if scaler is not None: - if self.verbose > 0: - print("\n..Scaling with: %s\n"%str(scaler)) - X = scaler.fit_transform(X) - - return X - - def map(self, projected_X, inverse_X=None, clusterer=cluster.DBSCAN(eps=0.5,min_samples=3), nr_cubes=10, overlap_perc=0.1): - # This maps the data to a simplicial complex. Returns a dictionary with nodes and links. - # - # Input: projected_X. A Numpy array with the projection/lens. - # Output: complex. A dictionary with "nodes", "links" and "meta information" - # - # parameters - # ---------- - # projected_X projected_X. A Numpy array with the projection/lens. Required. - # inverse_X Numpy array or None. If None then the projection itself is used for clustering. - # clusterer Scikit-learn API compatible clustering algorithm. Default: DBSCAN - # nr_cubes Int. The number of intervals/hypercubes to create. - # overlap_perc Float. The percentage of overlap "between" the intervals/hypercubes. - - start = datetime.now() - - # Helper function - def cube_coordinates_all(nr_cubes, nr_dimensions): - # Helper function to get origin coordinates for our intervals/hypercubes - # Useful for looping no matter the number of cubes or dimensions - # Example: if there are 4 cubes per dimension and 3 dimensions - # return the bottom left (origin) coordinates of 64 hypercubes, - # as a sorted list of Numpy arrays - # TODO: elegance-ify... - l = [] - for x in range(nr_cubes): - l += [x] * nr_dimensions - return [np.array(list(f)) for f in sorted(set(itertools.permutations(l,nr_dimensions)))] - - nodes = defaultdict(list) - links = defaultdict(list) - complex = {} - self.nr_cubes = nr_cubes - self.clusterer = clusterer - self.overlap_perc = overlap_perc - - if self.verbose > 0: - print("Mapping on data shaped %s using dimensions\n"%(str(projected_X.shape))) - - # If inverse image is not provided, we use the projection as the inverse image (suffer projection loss) - if inverse_X is None: - inverse_X = projected_X - - # We chop up the min-max column ranges into 'nr_cubes' parts - self.chunk_dist = (np.max(projected_X, axis=0) - np.min(projected_X, axis=0))/nr_cubes - - # We calculate the overlapping windows distance - self.overlap_dist = self.overlap_perc * self.chunk_dist - - # We find our starting point - self.d = np.min(projected_X, axis=0) - - # Use a dimension index array on the projected X - # (For now this uses the entire dimensionality, but we keep for experimentation) - di = np.array([x for x in range(projected_X.shape[1])]) - - # Prefix'ing the data with ID's - ids = np.array([x for x in range(projected_X.shape[0])]) - projected_X = np.c_[ids,projected_X] - inverse_X = np.c_[ids,inverse_X] - - # Subdivide the projected data X in intervals/hypercubes with overlap - if self.verbose > 0: - total_cubes = len(cube_coordinates_all(nr_cubes,projected_X.shape[1])) - print("Creating %s hypercubes."%total_cubes) - - for i, coor in enumerate(cube_coordinates_all(nr_cubes,di.shape[0])): - # Slice the hypercube - hypercube = projected_X[ np.invert(np.any((projected_X[:,di+1] >= self.d[di] + (coor * self.chunk_dist[di])) & - (projected_X[:,di+1] < self.d[di] + (coor * self.chunk_dist[di]) + self.chunk_dist[di] + self.overlap_dist[di]) == False, axis=1 )) ] - - if self.verbose > 1: - print("There are %s points in cube_%s / %s with starting range %s"% - (hypercube.shape[0],i,total_cubes,self.d[di] + (coor * self.chunk_dist[di]))) - - # If at least one sample inside the hypercube - if hypercube.shape[0] > 0: - # Cluster the data point(s) in the cube, skipping the id-column - # Note that we apply clustering on the inverse image (original data samples) that fall inside the cube. - inverse_x = inverse_X[[int(nn) for nn in hypercube[:,0]]] - - clusterer.fit(inverse_x[:,1:]) - - if self.verbose > 1: - print("Found %s clusters in cube_%s\n"%(np.unique(clusterer.labels_[clusterer.labels_ > -1]).shape[0],i)) - - #Now for every (sample id in cube, predicted cluster label) - for a in np.c_[hypercube[:,0],clusterer.labels_]: - if a[1] != -1: #if not predicted as noise - cluster_id = str(coor[0])+"_"+str(i)+"_"+str(a[1])+"_"+str(coor)+"_"+str(self.d[di] + (coor * self.chunk_dist[di])) # TODO: de-rudimentary-ify - nodes[cluster_id].append( int(a[0]) ) # Append the member id's as integers - else: - if self.verbose > 1: - print("Cube_%s is empty.\n"%(i)) - - # Create links when clusters from different hypercubes have members with the same sample id. - candidates = itertools.combinations(nodes.keys(),2) - for candidate in candidates: - # if there are non-unique members in the union - if len(nodes[candidate[0]]+nodes[candidate[1]]) != len(set(nodes[candidate[0]]+nodes[candidate[1]])): - links[candidate[0]].append( candidate[1] ) - - # Reporting - if self.verbose > 0: - nr_links = 0 - for k in links: - nr_links += len(links[k]) - print("\ncreated %s edges and %s nodes in %s."%(nr_links,len(nodes),str(datetime.now()-start))) - - complex["nodes"] = nodes - complex["links"] = links - complex["meta"] = self.projection - - return complex - - def visualize(self, complex, color_function="", path_html="mapper_visualization_output.html", title="My Data", - graph_link_distance=30, graph_gravity=0.1, graph_charge=-120, custom_tooltips=None, width_html=0, - height_html=0, show_tooltips=True, show_title=True, show_meta=True, res=0,gain=0,minimum=0,maximum=0): - # Turns the dictionary 'complex' in a html file with d3.js - # - # Input: complex. Dictionary (output from calling .map()) - # Output: a HTML page saved as a file in 'path_html'. - # - # parameters - # ---------- - # color_function string. Not fully implemented. Default: "" (distance to origin) - # path_html file path as string. Where to save the HTML page. - # title string. HTML page document title and first heading. - # graph_link_distance int. Edge length. - # graph_gravity float. "Gravity" to center of layout. - # graph_charge int. charge between nodes. - # custom_tooltips None or Numpy Array. You could use "y"-label array for this. - # width_html int. Width of canvas. Default: 0 (full width) - # height_html int. Height of canvas. Default: 0 (full height) - # show_tooltips bool. default:True - # show_title bool. default:True - # show_meta bool. default:True - - # Format JSON for D3 graph - json_s = {} - json_s["nodes"] = [] - json_s["links"] = [] - k2e = {} # a key to incremental int dict, used for id's when linking - - for e, k in enumerate(complex["nodes"]): - # Tooltip and node color formatting, TODO: de-mess-ify - if custom_tooltips is not None: - tooltip_s = "

Cluster %s

"%k + " ".join(str(custom_tooltips[complex["nodes"][k][0]]).split(" ")) - if maximum == minimum: - tooltip_i = 0 - else: - tooltip_i = int(30*(custom_tooltips[complex["nodes"][k][0]]-minimum)/(maximum-minimum)) - json_s["nodes"].append({"name": str(k), "tooltip": tooltip_s, "group": 2 * int(np.log(complex["nodes"][k][2])), "color": tooltip_i}) - else: - tooltip_s = "

Cluster %s

Contains %s members."%(k,len(complex["nodes"][k])) - json_s["nodes"].append({"name": str(k), "tooltip": tooltip_s, "group": 2 * int(np.log(len(complex["nodes"][k]))), "color": str(k.split("_")[0])}) - k2e[k] = e - for k in complex["links"]: - for link in complex["links"][k]: - json_s["links"].append({"source": k2e[k], "target":k2e[link],"value":1}) - - # Width and height of graph in HTML output - if width_html == 0: - width_css = "100%" - width_js = 'document.getElementById("holder").offsetWidth-20' - else: - width_css = "%spx" % width_html - width_js = "%s" % width_html - if height_html == 0: - height_css = "100%" - height_js = 'document.getElementById("holder").offsetHeight-20' - else: - height_css = "%spx" % height_html - height_js = "%s" % height_html - - # Whether to show certain UI elements or not - if show_tooltips == False: - tooltips_display = "display: none;" - else: - tooltips_display = "" - - if show_meta == False: - meta_display = "display: none;" - else: - meta_display = "" - - if show_title == False: - title_display = "display: none;" - else: - title_display = "" - - with open(path_html,"wb") as outfile: - html = """ - - - %s | KeplerMapper - - - -
-

%s

-

- Lens
%s

- Length of intervals
%s

- Overlap percentage
%s%%

- Color Function
%s -

-
- - """%(title,width_css, height_css, title_display, meta_display, tooltips_display, title,complex["meta"],res,gain*100,color_function,width_js,height_js,graph_charge,graph_link_distance,graph_gravity,json.dumps(json_s)) - outfile.write(html.encode("utf-8")) - if self.verbose > 0: - print("\nWrote d3.js graph to '%s'"%path_html) diff --git a/src/Nerve_GIC/example/km.py.COPYRIGHT b/src/Nerve_GIC/example/km.py.COPYRIGHT deleted file mode 100644 index bef7b121..00000000 --- a/src/Nerve_GIC/example/km.py.COPYRIGHT +++ /dev/null @@ -1,26 +0,0 @@ -km.py is a fork of https://github.com/MLWave/kepler-mapper. -Only the visualization part has been kept (Mapper part has been removed). - -This file has te following Copyright : - -The MIT License (MIT) - -Copyright (c) 2015 Triskelion - HJ van Veen - info@mlwave.com - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE. diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt new file mode 100644 index 00000000..a0508dc2 --- /dev/null +++ b/src/Nerve_GIC/utilities/CMakeLists.txt @@ -0,0 +1,22 @@ +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}/) + + add_test(NAME Nerve_GIC_utilities_nerve COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/human.off" "2" "10" "0.3") + + add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/human.off" "100") + +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..d2897774 --- /dev/null +++ b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py @@ -0,0 +1,72 @@ +#!/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 . +""" + +__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/utilities/Nerve.cpp b/src/Nerve_GIC/utilities/Nerve.cpp new file mode 100644 index 00000000..6abdedc7 --- /dev/null +++ b/src/Nerve_GIC/utilities/Nerve.cpp @@ -0,0 +1,96 @@ +/* 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 . + */ + +#include + +#include +#include + +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"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if ((argc != 5) && (argc != 6)) usage(argc, argv[0]); + + using Point = std::vector; + + std::string off_file_name(argv[1]); + int coord = atoi(argv[2]); + int resolution = atoi(argv[3]); + double gain = atof(argv[4]); + bool verb = 0; + if (argc == 6) verb = 1; + + // -------------------------------- + // Init of a Nerve from an OFF file + // -------------------------------- + + Gudhi::cover_complex::Cover_complex SC; + SC.set_verbose(verb); + + bool check = SC.read_point_cloud(off_file_name); + + if (!check) { + std::cout << "Incorrect OFF file." << std::endl; + } else { + SC.set_type("Nerve"); + + SC.set_color_from_coordinate(coord); + SC.set_function_from_coordinate(coord); + + SC.set_graph_from_OFF(); + SC.set_resolution_with_interval_number(resolution); + SC.set_gain(gain); + SC.set_cover_from_function(); + + SC.find_simplices(); + + SC.write_info(); + + Gudhi::Simplex_tree<> stree; + SC.create_complex(stree); + SC.compute_PD(); + + // ---------------------------------------------------------------------------- + // Display information about the graph induced complex + // ---------------------------------------------------------------------------- + + if (verb) { + std::cout << "Nerve is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - " + << stree.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on Nerve 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/utilities/Nerve.txt b/src/Nerve_GIC/utilities/Nerve.txt new file mode 100644 index 00000000..839ff45e --- /dev/null +++ b/src/Nerve_GIC/utilities/Nerve.txt @@ -0,0 +1,63 @@ +Min function value = -0.979672 and Max function value = 0.816414 +Interval 0 = [-0.979672, -0.761576] +Interval 1 = [-0.838551, -0.581967] +Interval 2 = [-0.658942, -0.402359] +Interval 3 = [-0.479334, -0.22275] +Interval 4 = [-0.299725, -0.0431415] +Interval 5 = [-0.120117, 0.136467] +Interval 6 = [0.059492, 0.316076] +Interval 7 = [0.239101, 0.495684] +Interval 8 = [0.418709, 0.675293] +Interval 9 = [0.598318, 0.816414] +Computing preimages... +Computing connected components... +.txt generated. It can be visualized with e.g. python KeplerMapperVisuFromTxtFile.py and firefox. +5 interval(s) in dimension 0: + [-0.909111, 0.00817529] + [-0.171433, 0.367392] + [-0.171433, 0.367392] + [-0.909111, 0.745853] +0 interval(s) in dimension 1: +Nerve is of dimension 1 - 41 simplices - 21 vertices. +Iterator on Nerve simplices +1 +0 +4 +4 0 +2 +2 1 +8 +8 2 +5 +5 4 +9 +9 8 +13 +13 5 +14 +14 9 +19 +19 13 +25 +32 +20 +32 20 +33 +33 25 +26 +26 14 +26 19 +42 +42 26 +34 +34 33 +27 +27 20 +35 +35 27 +35 34 +42 35 +44 +44 35 +54 +54 44 \ No newline at end of file diff --git a/src/Nerve_GIC/utilities/VoronoiGIC.cpp b/src/Nerve_GIC/utilities/VoronoiGIC.cpp new file mode 100644 index 00000000..32431cc2 --- /dev/null +++ b/src/Nerve_GIC/utilities/VoronoiGIC.cpp @@ -0,0 +1,90 @@ +/* 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 . + */ + +#include + +#include +#include + +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"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if ((argc != 3) && (argc != 4)) usage(argc, argv[0]); + + using Point = std::vector; + + std::string off_file_name(argv[1]); + int m = atoi(argv[2]); + bool verb = 0; + if (argc == 4) verb = 1; + + // ---------------------------------------------------------------------------- + // Init of a graph induced complex from an OFF file + // ---------------------------------------------------------------------------- + + Gudhi::cover_complex::Cover_complex 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_type("GIC"); + + GIC.set_color_from_coordinate(); + + GIC.set_graph_from_OFF(); + GIC.set_cover_from_Voronoi(Gudhi::Euclidean_distance(), m); + + GIC.find_simplices(); + + GIC.plot_OFF(); + + 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/utilities/km.py b/src/Nerve_GIC/utilities/km.py new file mode 100755 index 00000000..53024aab --- /dev/null +++ b/src/Nerve_GIC/utilities/km.py @@ -0,0 +1,390 @@ +from __future__ import division +import numpy as np +from collections import defaultdict +import json +import itertools +from sklearn import cluster, preprocessing, manifold +from datetime import datetime +import sys + +class KeplerMapper(object): + # With this class you can build topological networks from (high-dimensional) data. + # + # 1) Fit a projection/lens/function to a dataset and transform it. + # For instance "mean_of_row(x) for x in X" + # 2) Map this projection with overlapping intervals/hypercubes. + # Cluster the points inside the interval + # (Note: we cluster on the inverse image/original data to lessen projection loss). + # If two clusters/nodes have the same members (due to the overlap), then: + # connect these with an edge. + # 3) Visualize the network using HTML and D3.js. + # + # functions + # --------- + # fit_transform: Create a projection (lens) from a dataset + # map: Apply Mapper algorithm on this projection and build a simplicial complex + # visualize: Turns the complex dictionary into a HTML/D3.js visualization + + def __init__(self, verbose=2): + self.verbose = verbose + + self.chunk_dist = [] + self.overlap_dist = [] + self.d = [] + self.nr_cubes = 0 + self.overlap_perc = 0 + self.clusterer = False + + def fit_transform(self, X, projection="sum", scaler=preprocessing.MinMaxScaler()): + # Creates the projection/lens from X. + # + # Input: X. Input features as a numpy array. + # Output: projected_X. original data transformed to a projection (lens). + # + # parameters + # ---------- + # projection: Projection parameter is either a string, + # a scikit class with fit_transform, like manifold.TSNE(), + # or a list of dimension indices. + # scaler: if None, do no scaling, else apply scaling to the projection + # Default: Min-Max scaling + + self.scaler = scaler + self.projection = str(projection) + + # Detect if projection is a class (for scikit-learn) + #if str(type(projection))[1:6] == "class": #TODO: de-ugly-fy + # reducer = projection + # if self.verbose > 0: + # try: + # projection.set_params(**{"verbose":self.verbose}) + # except: + # pass + # print("\n..Projecting data using: \n\t%s\n"%str(projection)) + # X = reducer.fit_transform(X) + + # Detect if projection is a string (for standard functions) + if isinstance(projection, str): + if self.verbose > 0: + print("\n..Projecting data using: %s"%(projection)) + # Stats lenses + if projection == "sum": # sum of row + X = np.sum(X, axis=1).reshape((X.shape[0],1)) + if projection == "mean": # mean of row + X = np.mean(X, axis=1).reshape((X.shape[0],1)) + if projection == "median": # mean of row + X = np.median(X, axis=1).reshape((X.shape[0],1)) + if projection == "max": # max of row + X = np.max(X, axis=1).reshape((X.shape[0],1)) + if projection == "min": # min of row + X = np.min(X, axis=1).reshape((X.shape[0],1)) + if projection == "std": # std of row + X = np.std(X, axis=1).reshape((X.shape[0],1)) + + if projection == "dist_mean": # Distance of x to mean of X + X_mean = np.mean(X, axis=0) + X = np.sum(np.sqrt((X - X_mean)**2), axis=1).reshape((X.shape[0],1)) + + # Detect if projection is a list (with dimension indices) + if isinstance(projection, list): + if self.verbose > 0: + print("\n..Projecting data using: %s"%(str(projection))) + X = X[:,np.array(projection)] + + # Scaling + if scaler is not None: + if self.verbose > 0: + print("\n..Scaling with: %s\n"%str(scaler)) + X = scaler.fit_transform(X) + + return X + + def map(self, projected_X, inverse_X=None, clusterer=cluster.DBSCAN(eps=0.5,min_samples=3), nr_cubes=10, overlap_perc=0.1): + # This maps the data to a simplicial complex. Returns a dictionary with nodes and links. + # + # Input: projected_X. A Numpy array with the projection/lens. + # Output: complex. A dictionary with "nodes", "links" and "meta information" + # + # parameters + # ---------- + # projected_X projected_X. A Numpy array with the projection/lens. Required. + # inverse_X Numpy array or None. If None then the projection itself is used for clustering. + # clusterer Scikit-learn API compatible clustering algorithm. Default: DBSCAN + # nr_cubes Int. The number of intervals/hypercubes to create. + # overlap_perc Float. The percentage of overlap "between" the intervals/hypercubes. + + start = datetime.now() + + # Helper function + def cube_coordinates_all(nr_cubes, nr_dimensions): + # Helper function to get origin coordinates for our intervals/hypercubes + # Useful for looping no matter the number of cubes or dimensions + # Example: if there are 4 cubes per dimension and 3 dimensions + # return the bottom left (origin) coordinates of 64 hypercubes, + # as a sorted list of Numpy arrays + # TODO: elegance-ify... + l = [] + for x in range(nr_cubes): + l += [x] * nr_dimensions + return [np.array(list(f)) for f in sorted(set(itertools.permutations(l,nr_dimensions)))] + + nodes = defaultdict(list) + links = defaultdict(list) + complex = {} + self.nr_cubes = nr_cubes + self.clusterer = clusterer + self.overlap_perc = overlap_perc + + if self.verbose > 0: + print("Mapping on data shaped %s using dimensions\n"%(str(projected_X.shape))) + + # If inverse image is not provided, we use the projection as the inverse image (suffer projection loss) + if inverse_X is None: + inverse_X = projected_X + + # We chop up the min-max column ranges into 'nr_cubes' parts + self.chunk_dist = (np.max(projected_X, axis=0) - np.min(projected_X, axis=0))/nr_cubes + + # We calculate the overlapping windows distance + self.overlap_dist = self.overlap_perc * self.chunk_dist + + # We find our starting point + self.d = np.min(projected_X, axis=0) + + # Use a dimension index array on the projected X + # (For now this uses the entire dimensionality, but we keep for experimentation) + di = np.array([x for x in range(projected_X.shape[1])]) + + # Prefix'ing the data with ID's + ids = np.array([x for x in range(projected_X.shape[0])]) + projected_X = np.c_[ids,projected_X] + inverse_X = np.c_[ids,inverse_X] + + # Subdivide the projected data X in intervals/hypercubes with overlap + if self.verbose > 0: + total_cubes = len(cube_coordinates_all(nr_cubes,projected_X.shape[1])) + print("Creating %s hypercubes."%total_cubes) + + for i, coor in enumerate(cube_coordinates_all(nr_cubes,di.shape[0])): + # Slice the hypercube + hypercube = projected_X[ np.invert(np.any((projected_X[:,di+1] >= self.d[di] + (coor * self.chunk_dist[di])) & + (projected_X[:,di+1] < self.d[di] + (coor * self.chunk_dist[di]) + self.chunk_dist[di] + self.overlap_dist[di]) == False, axis=1 )) ] + + if self.verbose > 1: + print("There are %s points in cube_%s / %s with starting range %s"% + (hypercube.shape[0],i,total_cubes,self.d[di] + (coor * self.chunk_dist[di]))) + + # If at least one sample inside the hypercube + if hypercube.shape[0] > 0: + # Cluster the data point(s) in the cube, skipping the id-column + # Note that we apply clustering on the inverse image (original data samples) that fall inside the cube. + inverse_x = inverse_X[[int(nn) for nn in hypercube[:,0]]] + + clusterer.fit(inverse_x[:,1:]) + + if self.verbose > 1: + print("Found %s clusters in cube_%s\n"%(np.unique(clusterer.labels_[clusterer.labels_ > -1]).shape[0],i)) + + #Now for every (sample id in cube, predicted cluster label) + for a in np.c_[hypercube[:,0],clusterer.labels_]: + if a[1] != -1: #if not predicted as noise + cluster_id = str(coor[0])+"_"+str(i)+"_"+str(a[1])+"_"+str(coor)+"_"+str(self.d[di] + (coor * self.chunk_dist[di])) # TODO: de-rudimentary-ify + nodes[cluster_id].append( int(a[0]) ) # Append the member id's as integers + else: + if self.verbose > 1: + print("Cube_%s is empty.\n"%(i)) + + # Create links when clusters from different hypercubes have members with the same sample id. + candidates = itertools.combinations(nodes.keys(),2) + for candidate in candidates: + # if there are non-unique members in the union + if len(nodes[candidate[0]]+nodes[candidate[1]]) != len(set(nodes[candidate[0]]+nodes[candidate[1]])): + links[candidate[0]].append( candidate[1] ) + + # Reporting + if self.verbose > 0: + nr_links = 0 + for k in links: + nr_links += len(links[k]) + print("\ncreated %s edges and %s nodes in %s."%(nr_links,len(nodes),str(datetime.now()-start))) + + complex["nodes"] = nodes + complex["links"] = links + complex["meta"] = self.projection + + return complex + + def visualize(self, complex, color_function="", path_html="mapper_visualization_output.html", title="My Data", + graph_link_distance=30, graph_gravity=0.1, graph_charge=-120, custom_tooltips=None, width_html=0, + height_html=0, show_tooltips=True, show_title=True, show_meta=True, res=0,gain=0,minimum=0,maximum=0): + # Turns the dictionary 'complex' in a html file with d3.js + # + # Input: complex. Dictionary (output from calling .map()) + # Output: a HTML page saved as a file in 'path_html'. + # + # parameters + # ---------- + # color_function string. Not fully implemented. Default: "" (distance to origin) + # path_html file path as string. Where to save the HTML page. + # title string. HTML page document title and first heading. + # graph_link_distance int. Edge length. + # graph_gravity float. "Gravity" to center of layout. + # graph_charge int. charge between nodes. + # custom_tooltips None or Numpy Array. You could use "y"-label array for this. + # width_html int. Width of canvas. Default: 0 (full width) + # height_html int. Height of canvas. Default: 0 (full height) + # show_tooltips bool. default:True + # show_title bool. default:True + # show_meta bool. default:True + + # Format JSON for D3 graph + json_s = {} + json_s["nodes"] = [] + json_s["links"] = [] + k2e = {} # a key to incremental int dict, used for id's when linking + + for e, k in enumerate(complex["nodes"]): + # Tooltip and node color formatting, TODO: de-mess-ify + if custom_tooltips is not None: + tooltip_s = "

Cluster %s

"%k + " ".join(str(custom_tooltips[complex["nodes"][k][0]]).split(" ")) + if maximum == minimum: + tooltip_i = 0 + else: + tooltip_i = int(30*(custom_tooltips[complex["nodes"][k][0]]-minimum)/(maximum-minimum)) + json_s["nodes"].append({"name": str(k), "tooltip": tooltip_s, "group": 2 * int(np.log(complex["nodes"][k][2])), "color": tooltip_i}) + else: + tooltip_s = "

Cluster %s

Contains %s members."%(k,len(complex["nodes"][k])) + json_s["nodes"].append({"name": str(k), "tooltip": tooltip_s, "group": 2 * int(np.log(len(complex["nodes"][k]))), "color": str(k.split("_")[0])}) + k2e[k] = e + for k in complex["links"]: + for link in complex["links"][k]: + json_s["links"].append({"source": k2e[k], "target":k2e[link],"value":1}) + + # Width and height of graph in HTML output + if width_html == 0: + width_css = "100%" + width_js = 'document.getElementById("holder").offsetWidth-20' + else: + width_css = "%spx" % width_html + width_js = "%s" % width_html + if height_html == 0: + height_css = "100%" + height_js = 'document.getElementById("holder").offsetHeight-20' + else: + height_css = "%spx" % height_html + height_js = "%s" % height_html + + # Whether to show certain UI elements or not + if show_tooltips == False: + tooltips_display = "display: none;" + else: + tooltips_display = "" + + if show_meta == False: + meta_display = "display: none;" + else: + meta_display = "" + + if show_title == False: + title_display = "display: none;" + else: + title_display = "" + + with open(path_html,"wb") as outfile: + html = """ + + + %s | KeplerMapper + + + +
+

%s

+

+ Lens
%s

+ Length of intervals
%s

+ Overlap percentage
%s%%

+ Color Function
%s +

+
+ + """%(title,width_css, height_css, title_display, meta_display, tooltips_display, title,complex["meta"],res,gain*100,color_function,width_js,height_js,graph_charge,graph_link_distance,graph_gravity,json.dumps(json_s)) + outfile.write(html.encode("utf-8")) + if self.verbose > 0: + print("\nWrote d3.js graph to '%s'"%path_html) diff --git a/src/Nerve_GIC/utilities/km.py.COPYRIGHT b/src/Nerve_GIC/utilities/km.py.COPYRIGHT new file mode 100644 index 00000000..bef7b121 --- /dev/null +++ b/src/Nerve_GIC/utilities/km.py.COPYRIGHT @@ -0,0 +1,26 @@ +km.py is a fork of https://github.com/MLWave/kepler-mapper. +Only the visualization part has been kept (Mapper part has been removed). + +This file has te following Copyright : + +The MIT License (MIT) + +Copyright (c) 2015 Triskelion - HJ van Veen - info@mlwave.com + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. -- cgit v1.2.3 From b674e9a5fae8bdbb22eadb9a7c0013ce84451743 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 26 Jan 2018 14:55:28 +0000 Subject: Move documentation Copyright in footer Removed from each module git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3167 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7595f2d18cdc3773bbd96fa9fed414876ff9fdc7 --- src/Alpha_complex/doc/Intro_alpha_complex.h | 4 +--- src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h | 1 - src/Contraction/include/gudhi/Edge_contraction.h | 4 ---- src/Nerve_GIC/doc/Intro_graph_induced_complex.h | 1 - .../doc/Persistence_representations_doc.h | 1 - src/Persistent_cohomology/doc/Intro_persistent_cohomology.h | 1 - src/Rips_complex/doc/Intro_rips_complex.h | 2 -- src/Simplex_tree/doc/Intro_simplex_tree.h | 1 - src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h | 3 --- src/Spatial_searching/doc/Intro_spatial_searching.h | 2 -- src/Subsampling/doc/Intro_subsampling.h | 2 -- src/Tangential_complex/doc/Intro_tangential_complex.h | 2 -- src/Witness_complex/doc/Witness_complex_doc.h | 3 --- src/common/doc/footer.html | 10 ++-------- 14 files changed, 3 insertions(+), 34 deletions(-) (limited to 'src/Nerve_GIC') diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index cf1a946a..a08663ca 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -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/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h index ee84e201..a5d7b60f 100644 --- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h +++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h @@ -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/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h index 61f2d945..cf9a2c27 100644 --- a/src/Contraction/include/gudhi/Edge_contraction.h +++ b/src/Contraction/include/gudhi/Edge_contraction.h @@ -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/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index 344cb031..f2409087 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -176,7 +176,6 @@ namespace cover_complex { * * \image html "funcGICvisu.jpg" "Visualization with neato" * - * \copyright GNU General Public License v3. */ /** @} */ // end defgroup cover_complex diff --git a/src/Persistence_representations/doc/Persistence_representations_doc.h b/src/Persistence_representations/doc/Persistence_representations_doc.h index 978fb5bd..d781211a 100644 --- a/src/Persistence_representations/doc/Persistence_representations_doc.h +++ b/src/Persistence_representations/doc/Persistence_representations_doc.h @@ -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/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index ceaea505..4dbe82c7 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -248,7 +248,6 @@ Simplex_tree dim: 3 Persistent_cohomology/plain_homology.cpp 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/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index 124dfec9..8c517516 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -146,8 +146,6 @@ 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 */ /** @} */ // end defgroup rips_complex diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h index 769491d9..6b80d1c9 100644 --- a/src/Simplex_tree/doc/Intro_simplex_tree.h +++ b/src/Simplex_tree/doc/Intro_simplex_tree.h @@ -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/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h index 32fe411c..aca2aa57 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h @@ -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/Spatial_searching/doc/Intro_spatial_searching.h b/src/Spatial_searching/doc/Intro_spatial_searching.h index 1ee5e92e..52ed65e4 100644 --- a/src/Spatial_searching/doc/Intro_spatial_searching.h +++ b/src/Spatial_searching/doc/Intro_spatial_searching.h @@ -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/Subsampling/doc/Intro_subsampling.h b/src/Subsampling/doc/Intro_subsampling.h index c84616dd..ab9cdc37 100644 --- a/src/Subsampling/doc/Intro_subsampling.h +++ b/src/Subsampling/doc/Intro_subsampling.h @@ -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/Tangential_complex/doc/Intro_tangential_complex.h b/src/Tangential_complex/doc/Intro_tangential_complex.h index 3d687c1d..00e00c52 100644 --- a/src/Tangential_complex/doc/Intro_tangential_complex.h +++ b/src/Tangential_complex/doc/Intro_tangential_complex.h @@ -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/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/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 @@ $projectname  Version $projectnumber  - $projectbrief + - Copyright : GPL v3 $generatedby - doxygen $doxygenversion + Doxygen $doxygenversion - -
tralala -$generatedby   -doxygen - $doxygenversion -
- -- cgit v1.2.3 From 81b06fad98ac4210c5b1d04dddeed628a8e0accb Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 29 Jan 2018 08:24:41 +0000 Subject: Using std::string instead of char array for file names (overflow detected by fortify) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3171 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b590989d278e00aec79d6a7bc2b72088b5cb0e57 --- src/Nerve_GIC/include/gudhi/GIC.h | 22 ++++++++-------------- 1 file changed, 8 insertions(+), 14 deletions(-) (limited to 'src/Nerve_GIC') diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index 642b88b0..58831bbf 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -376,8 +376,7 @@ class Cover_complex { double d; std::vector zeros(n); for (int i = 0; i < n; i++) distances.push_back(zeros); - std::string distance = point_cloud_name; - distance.append("_dist"); + std::string distance = point_cloud_name + "_dist"; std::ifstream input(distance.c_str(), std::ios::out | std::ios::binary); if (input.good()) { @@ -481,10 +480,8 @@ class Cover_complex { */ void set_function_from_coordinate(int k) { for (int i = 0; i < n; i++) func.emplace(i, point_cloud[i][k]); - 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. @@ -897,9 +894,8 @@ 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::ofstream graphic(mapp); + std::string mapp = point_cloud_name + "_sc.dot"; + std::ofstream graphic(mapp.c_str()); double maxv = std::numeric_limits::lowest(); double minv = std::numeric_limits::max(); @@ -948,9 +944,8 @@ 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::ofstream graphic(mapp); + std::string mapp = point_cloud_name + "_sc.dot"; + std::ofstream graphic(mapp.c_str()); for (int i = 0; i < num_simplices; i++) if (simplices[i].size() == 2) @@ -993,9 +988,8 @@ class Cover_complex { std::vector > 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.dot"; + std::ofstream graphic(mapp.c_str()); graphic << "OFF" << std::endl; for (int i = 0; i < numsimplices; i++) { -- cgit v1.2.3 From c2d46e0e6cfea1927875219bd5e03962cef7b010 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 29 Jan 2018 16:31:18 +0000 Subject: Fix doc issue for utilities part on the web site git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3176 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3bafd9e13a5646ca93023144705d3ac7ed7c9b3a --- src/Alpha_complex/utilities/README | 148 ++++++++++----------- src/Bitmap_cubical_complex/utilities/README | 42 ++++-- src/Bottleneck_distance/utilities/README | 32 ++++- src/Nerve_GIC/doc/Intro_graph_induced_complex.h | 6 +- src/Nerve_GIC/include/gudhi/GIC.h | 11 +- .../utilities/KeplerMapperVisuFromTxtFile.py | 97 ++++++++------ src/Nerve_GIC/utilities/covercomplex.md | 73 ++++++++++ src/Rips_complex/utilities/README | 67 ++++------ src/Witness_complex/utilities/README | 70 +++++----- src/common/utilities/README | 46 +++++-- 10 files changed, 365 insertions(+), 227 deletions(-) create mode 100644 src/Nerve_GIC/utilities/covercomplex.md (limited to 'src/Nerve_GIC') diff --git a/src/Alpha_complex/utilities/README b/src/Alpha_complex/utilities/README index 1cd2ca95..56bce602 100644 --- a/src/Alpha_complex/utilities/README +++ b/src/Alpha_complex/utilities/README @@ -1,16 +1,35 @@ -# Alpha_complex # - -## `alpha_complex_3d_persistence` ## +--- +layout: page +title: "Alpha complex" +meta_title: "alphacomplex" +subheadline: "" +teaser: "" +permalink: "/alphacomplex/" +--- +{::comment} +These flags above are here for web site generation, please let them. +cf. https://gitlab.inria.fr/GUDHI/website +Must be in conformity with _data/navigation.yml +{:/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` +``` +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] ` -where -`` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). + +``` + alpha_complex_3d_persistence [options] +``` + +where `` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). **Allowed options** @@ -20,43 +39,38 @@ where * `-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_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45 ``` -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. +## 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. -## `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 ## -## `weighted_alpha_complex_3d_persistence` ## Same as `alpha_complex_3d_persistence`, but using weighted points. **Usage** -`weighted_alpha_complex_3d_persistence [options] ` + +``` + weighted_alpha_complex_3d_persistence [options] +``` + where -`` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). -`` is the path to the file containing the weights of the points (one value per line). + +* `` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). +* `` is the path to the file containing the weights of the points (one value per line). **Allowed options** @@ -66,32 +80,33 @@ 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 + weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off ../../data/points/tore3D_300.weights -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. * Filtration values are alpha square values. -## `periodic_alpha_complex_3d_persistence` ## +## 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. **Usage** -`periodic_alpha_complex_3d_persistence [options] ` + +``` + periodic_alpha_complex_3d_persistence [options] +``` + where -`` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). -`` 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). + +* `` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). +* `` 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). **Allowed options** @@ -102,46 +117,36 @@ where **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 +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 ``` -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.: -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. +## alpha_complex_persistence ## -## `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: +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` +``` + 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). +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_persistence [options] ` + +``` + alpha_complex_persistence [options] +``` + where `` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). @@ -154,24 +159,11 @@ where * `-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 -``` - -Here we retrieve expected Betti numbers on a tore 3D: -``` -Betti numbers[0] = 1 -Betti numbers[1] = 2 -Betti numbers[2] = 1 + alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off ``` N.B.: + * Filtration values are alpha square values. diff --git a/src/Bitmap_cubical_complex/utilities/README b/src/Bitmap_cubical_complex/utilities/README index ddff7034..393b2654 100644 --- a/src/Bitmap_cubical_complex/utilities/README +++ b/src/Bitmap_cubical_complex/utilities/README @@ -1,18 +1,40 @@ -# Bitmap_cubical_complex # +--- +layout: page +title: "Bitmap cubical complex" +meta_title: "cubicalcomplex" +subheadline: "" +teaser: "" +permalink: "/cubicalcomplex/" +--- +{::comment} +These flags above are here for web site generation, please let them. +cf. https://gitlab.inria.fr/GUDHI/website +Must be in conformity with _data/navigation.yml +{:/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](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPerseus) for a description of the file format. -Example: +## 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. -* 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` +**Example** -## `periodic_cubical_complex_persistence` ## +``` + 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: +**Example** + +``` + periodic_cubical_complex_persistence data/bitmap/3d_torus.txt +``` -* 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` +* 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/Bottleneck_distance/utilities/README b/src/Bottleneck_distance/utilities/README index d9fdd252..04e1c4bd 100644 --- a/src/Bottleneck_distance/utilities/README +++ b/src/Bottleneck_distance/utilities/README @@ -1,10 +1,30 @@ -# Bottleneck_distance # +--- +layout: page +title: "Bottleneck distance" +meta_title: "bottleneckdistance" +subheadline: "" +teaser: "" +permalink: "/bottleneckdistance/" +--- +{::comment} +These flags above are here for web site generation, please let them. +cf. https://gitlab.inria.fr/GUDHI/website +Must be in conformity with _data/navigation.yml +{:/comment} + + + +## bottleneck_read_file_example ## -## `bottleneck_read_file_example` ## This program computes the Bottleneck distance between two persistence diagram files. -Usage: -`bottleneck_read_file_example []` +**Usage** + +``` + bottleneck_read_file_example [] +``` + where -`` and `` must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPers). -`` is an error bound on the bottleneck distance (set by default to the smallest positive double value). + +* `` and `` must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPers). +* `` is an error bound on the bottleneck distance (set by default to the smallest positive double value). diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index f2409087..474f0f0e 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -77,8 +77,8 @@ namespace cover_complex { * * \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. @@ -118,7 +118,7 @@ namespace cover_complex { * * 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: diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index 58831bbf..ff95b913 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -934,7 +934,7 @@ 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. @@ -944,7 +944,7 @@ class Cover_complex { void write_info() { int num_simplices = simplices.size(); int num_edges = 0; - std::string mapp = point_cloud_name + "_sc.dot"; + std::string mapp = point_cloud_name + "_sc.txt"; std::ofstream graphic(mapp.c_str()); for (int i = 0; i < num_simplices; i++) @@ -970,7 +970,8 @@ 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; } @@ -988,7 +989,7 @@ class Cover_complex { std::vector > edges, faces; int numsimplices = simplices.size(); - std::string mapp = point_cloud_name + "_sc.dot"; + std::string mapp = point_cloud_name + "_sc.off"; std::ofstream graphic(mapp.c_str()); graphic << "OFF" << std::endl; @@ -1016,7 +1017,7 @@ 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; } // ******************************************************************************************************************* diff --git a/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py index d2897774..c811f610 100755 --- a/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py +++ b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py @@ -3,6 +3,7 @@ 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++ @@ -30,43 +31,59 @@ __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) +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/utilities/covercomplex.md b/src/Nerve_GIC/utilities/covercomplex.md new file mode 100644 index 00000000..692e44e7 --- /dev/null +++ b/src/Nerve_GIC/utilities/covercomplex.md @@ -0,0 +1,73 @@ +--- +layout: page +title: "Cover complex" +meta_title: "covercomplex" +subheadline: "" +teaser: "" +permalink: "/covercomplex/" +--- +{::comment} +These flags above are here for web site generation, please let them. +cf. https://gitlab.inria.fr/GUDHI/website +Must be in conformity with _data/navigation.yml +{:/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 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 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/Rips_complex/utilities/README b/src/Rips_complex/utilities/README index 4d20c806..44a37543 100644 --- a/src/Rips_complex/utilities/README +++ b/src/Rips_complex/utilities/README @@ -1,6 +1,20 @@ -# Rips_complex # - -## `rips_persistence` ## +--- +layout: page +title: "Rips complex" +meta_title: "ripscomplex" +subheadline: "" +teaser: "" +permalink: "/ripscomplex/" +--- +{::comment} +These flags above are here for web site generation, please let them. +cf. https://gitlab.inria.fr/GUDHI/website +Must be in conformity with _data/navigation.yml +{:/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. The output diagram contains one bar per line, written with the convention: `p dim birth death` @@ -8,6 +22,7 @@ This program computes the persistent homology with coefficient field *Z/pZ* of a 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] ` **Allowed options** @@ -22,53 +37,25 @@ where `dim` is the dimension of the homological feature, `birth` and `death` are 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 -``` +`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 - -outputs: -``` -3 0 0 inf -3 1 0.0983494 inf -3 1 0.104347 inf -3 2 0.138335 inf -``` +`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. -## `rips_distance_matrix_persistence` ## -Same as `rips_persistence` but taking a distance matrix as input. - **Usage** -`rips_persistence [options] ` -where + +`rips_persistence [options] ` + +where `` 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 -``` +`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` diff --git a/src/Witness_complex/utilities/README b/src/Witness_complex/utilities/README index 1141033e..5cdb1f88 100644 --- a/src/Witness_complex/utilities/README +++ b/src/Witness_complex/utilities/README @@ -1,18 +1,34 @@ -# Witness_complex # +--- +layout: page +title: "Witness complex" +meta_title: "witnesscomplex" +subheadline: "" +teaser: "" +permalink: "/witnesscomplex/" +--- +{::comment} +These flags above are here for web site generation, please let them. +cf. https://gitlab.inria.fr/GUDHI/website +Must be in conformity with _data/navigation.yml +{:/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: +## 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] ` -*Allowed options* +**Allowed options** * `-h [ --help ]` Produce help message * `-l [ --landmarks ]` Number of landmarks to choose from the point cloud. @@ -22,33 +38,28 @@ 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] ` -*Allowed options* +**Allowed options** * `-h [ --help ]` Produce help message * `-l [ --landmarks ]` Number of landmarks to choose from the point cloud. @@ -58,17 +69,8 @@ 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/common/utilities/README b/src/common/utilities/README index 18fa8cc4..f39c63b8 100644 --- a/src/common/utilities/README +++ b/src/common/utilities/README @@ -1,19 +1,43 @@ -# Pointset generator # +--- +layout: page +title: "Pointset generator" +meta_title: "pointsetgenerator" +subheadline: "" +teaser: "" +permalink: "/pointsetgenerator/" +--- +{::comment} +These flags above are here for web site generation, please let them. +cf. https://gitlab.inria.fr/GUDHI/website +Must be in conformity with _data/navigation.yml +{:/comment} -## `off_file_from_shape_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 ...` + +``` +off_file_from_shape_generator on|in sphere|cube|curve|torus|klein ... +``` Warning: "on cube" generator is not available! -Examples: +**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). -* 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` +``` +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: -`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. -- cgit v1.2.3 From 7f9f246f5bc7b5ae6c5a2ea8891f8329cbf9a3e3 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 29 Jan 2018 16:36:03 +0000 Subject: Code review : with C++11 fstream constructor from std::string is available git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3178 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 31485d70d2d4a475b70d0c07859084b36139b56f --- src/Nerve_GIC/include/gudhi/GIC.h | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'src/Nerve_GIC') diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index ff95b913..40ff7a4a 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -377,7 +377,7 @@ class Cover_complex { std::vector zeros(n); for (int i = 0; i < n; i++) distances.push_back(zeros); std::string distance = point_cloud_name + "_dist"; - std::ifstream input(distance.c_str(), std::ios::out | std::ios::binary); + std::ifstream input(distance, std::ios::out | std::ios::binary); if (input.good()) { if (verbose) std::cout << "Reading distances..." << std::endl; @@ -895,7 +895,7 @@ class Cover_complex { */ void plot_DOT() { std::string mapp = point_cloud_name + "_sc.dot"; - std::ofstream graphic(mapp.c_str()); + std::ofstream graphic(mapp); double maxv = std::numeric_limits::lowest(); double minv = std::numeric_limits::max(); @@ -945,7 +945,7 @@ class Cover_complex { int num_simplices = simplices.size(); int num_edges = 0; std::string mapp = point_cloud_name + "_sc.txt"; - std::ofstream graphic(mapp.c_str()); + std::ofstream graphic(mapp); for (int i = 0; i < num_simplices; i++) if (simplices[i].size() == 2) @@ -990,7 +990,7 @@ class Cover_complex { int numsimplices = simplices.size(); std::string mapp = point_cloud_name + "_sc.off"; - std::ofstream graphic(mapp.c_str()); + std::ofstream graphic(mapp); graphic << "OFF" << std::endl; for (int i = 0; i < numsimplices; i++) { -- cgit v1.2.3 From b92ea601f15a239957ec6beba78ee2deee3d32d6 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 30 Jan 2018 08:54:00 +0000 Subject: Fix --v to -v for Cover complex git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3182 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 46e36af1a3e9aae8f1b12d2ee7fc749eb531f505 --- src/Nerve_GIC/doc/Intro_graph_induced_complex.h | 8 ++++---- src/Nerve_GIC/example/CoordGIC.cpp | 4 ++-- src/Nerve_GIC/example/FuncGIC.cpp | 4 ++-- src/Nerve_GIC/utilities/Nerve.cpp | 4 ++-- src/Nerve_GIC/utilities/VoronoiGIC.cpp | 4 ++-- src/Nerve_GIC/utilities/covercomplex.md | 8 ++++---- .../doc/Persistence_representations_doc.h | 2 +- 7 files changed, 17 insertions(+), 17 deletions(-) (limited to 'src/Nerve_GIC') diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index 474f0f0e..2b648425 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -70,7 +70,7 @@ 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: @@ -113,7 +113,7 @@ 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. @@ -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. @@ -169,7 +169,7 @@ 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: diff --git a/src/Nerve_GIC/example/CoordGIC.cpp b/src/Nerve_GIC/example/CoordGIC.cpp index c03fcbb3..c92cf235 100644 --- a/src/Nerve_GIC/example/CoordGIC.cpp +++ b/src/Nerve_GIC/example/CoordGIC.cpp @@ -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..cb0f0d63 100644 --- a/src/Nerve_GIC/example/FuncGIC.cpp +++ b/src/Nerve_GIC/example/FuncGIC.cpp @@ -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/utilities/Nerve.cpp b/src/Nerve_GIC/utilities/Nerve.cpp index 6abdedc7..aefc3874 100644 --- a/src/Nerve_GIC/utilities/Nerve.cpp +++ b/src/Nerve_GIC/utilities/Nerve.cpp @@ -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/utilities/VoronoiGIC.cpp b/src/Nerve_GIC/utilities/VoronoiGIC.cpp index 32431cc2..54bb871e 100644 --- a/src/Nerve_GIC/utilities/VoronoiGIC.cpp +++ b/src/Nerve_GIC/utilities/VoronoiGIC.cpp @@ -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 index 692e44e7..41489b66 100644 --- a/src/Nerve_GIC/utilities/covercomplex.md +++ b/src/Nerve_GIC/utilities/covercomplex.md @@ -27,14 +27,14 @@ Finally, the next ne lines represent the edges, characterized by the ID of their **Usage** -`Nerve coordinate resolution gain [--v]` +`Nerve 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. +* `-v` is optional, it activates verbose mode. **Example** @@ -57,12 +57,12 @@ The program also writes a file `*_sc.off`, that is an OFF file that can be visua **Usage** -`VoroniGIC samples_number [--v]` +`VoroniGIC samples_number [-v]` where * `samples_number` is the number of samples to take from the point cloud -* `--v` is optional, it activates verbose mode. +* `-v` is optional, it activates verbose mode. **Example** diff --git a/src/Persistence_representations/doc/Persistence_representations_doc.h b/src/Persistence_representations/doc/Persistence_representations_doc.h index d781211a..38bd3a21 100644 --- a/src/Persistence_representations/doc/Persistence_representations_doc.h +++ b/src/Persistence_representations/doc/Persistence_representations_doc.h @@ -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 -- cgit v1.2.3 From 0fe356ae3a1071950382ab308b03fd4a647ae796 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 30 Jan 2018 15:39:37 +0000 Subject: Copy test files in build directory for not to pollute sources git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3185 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4926f0a4e3c02ce77bdbf5847d421b6152a24a65 --- src/Nerve_GIC/example/CMakeLists.txt | 11 ++++++++--- src/Nerve_GIC/utilities/CMakeLists.txt | 6 ++++-- 2 files changed, 12 insertions(+), 5 deletions(-) (limited to 'src/Nerve_GIC') diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt index 434637fa..f2626927 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -11,11 +11,16 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) target_link_libraries(FuncGIC ${TBB_LIBRARIES}) endif() + # Copy files for not to pollute sources when testing + file(COPY "${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 $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0") + "tore3D_1307.off" "0") add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" - "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1") + "lucky_cat.off" + "lucky_cat_PCA1") endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt index a0508dc2..7762c8a0 100644 --- a/src/Nerve_GIC/utilities/CMakeLists.txt +++ b/src/Nerve_GIC/utilities/CMakeLists.txt @@ -12,11 +12,13 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) 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 $ - "${CMAKE_SOURCE_DIR}/data/points/human.off" "2" "10" "0.3") + "human.off" "2" "10" "0.3") add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/human.off" "100") + "human.off" "100") endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) -- cgit v1.2.3 From 37ded65d83935d417fc3bc484594a83b36f63514 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 30 Jan 2018 17:05:03 +0000 Subject: Fix after web review git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3189 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fd42bab9b27a3c086adeaf75068c83a911ede000 --- src/Alpha_complex/utilities/alphacomplex.md | 100 +++++++++------------ .../utilities/cubicalcomplex.md | 17 +--- .../utilities/bottleneckdistance.md | 16 +--- src/Nerve_GIC/utilities/covercomplex.md | 15 +--- src/Rips_complex/utilities/ripscomplex.md | 16 +--- src/Witness_complex/utilities/witnesscomplex.md | 22 ++--- src/common/utilities/pointsetgenerator.md | 16 +--- 7 files changed, 62 insertions(+), 140 deletions(-) (limited to 'src/Nerve_GIC') diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md index 0e500e53..aace85d3 100644 --- a/src/Alpha_complex/utilities/alphacomplex.md +++ b/src/Alpha_complex/utilities/alphacomplex.md @@ -1,18 +1,47 @@ ---- -layout: page -title: "Alpha complex" -meta_title: "alphacomplex" -subheadline: "" -teaser: "" -permalink: "/alphacomplex/" ---- -{::comment} -These flags above are here for web site generation, please let them. -cf. https://gitlab.inria.fr/GUDHI/website -Must be in conformity with _data/navigation.yml -{:/comment} +# Alpha complex # + + +## 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: + +``` + 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_persistence [options] +``` + +where +`` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). + +**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. + +**Example** + +``` + alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off +``` + +N.B.: + +* 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: @@ -107,7 +136,7 @@ where * `` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). * `` is the path to the file describing the periodic domain. It must be in the format described -[here](../doc/latest/fileformats.html#FileFormatsIsoCuboid). +[here](/doc/latest/fileformats.html#FileFormatsIsoCuboid). **Allowed options** @@ -125,46 +154,5 @@ periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off N.B.: -* Cuboid file must be in the format described [here](../doc/latest/fileformats.html#FileFormatsIsoCuboid). -* 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: - -``` - 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_persistence [options] -``` - -where -`` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). - -**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. - -**Example** - -``` - alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off -``` - -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/Bitmap_cubical_complex/utilities/cubicalcomplex.md b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md index 3a9e6aac..6e1b2578 100644 --- a/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md +++ b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md @@ -1,21 +1,10 @@ ---- -layout: page -title: "Bitmap cubical complex" -meta_title: "cubicalcomplex" -subheadline: "" -teaser: "" -permalink: "/cubicalcomplex/" ---- -{::comment} -These flags above are here for web site generation, please let them. -cf. https://gitlab.inria.fr/GUDHI/website -Must be in conformity with _data/navigation.yml -{:/comment} +# 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](../doc/latest/fileformats.html#FileFormatsPerseus) for a description of the file format. +See [here](/doc/latest/fileformats.html#FileFormatsPerseus) for a description of the file format. **Example** diff --git a/src/Bottleneck_distance/utilities/bottleneckdistance.md b/src/Bottleneck_distance/utilities/bottleneckdistance.md index e9079058..526f5822 100644 --- a/src/Bottleneck_distance/utilities/bottleneckdistance.md +++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md @@ -1,18 +1,6 @@ ---- -layout: page -title: "Bottleneck distance" -meta_title: "bottleneckdistance" -subheadline: "" -teaser: "" -permalink: "/bottleneckdistance/" ---- -{::comment} -These flags above are here for web site generation, please let them. -cf. https://gitlab.inria.fr/GUDHI/website -Must be in conformity with _data/navigation.yml -{:/comment} +# Bottleneck distance # ## bottleneck_read_file_example ## @@ -26,5 +14,5 @@ This program computes the Bottleneck distance between two persistence diagram fi where -* `` and `` must be in the format described [here](../doc/latest/fileformats.html#FileFormatsPers). +* `` and `` must be in the format described [here](/doc/latest/fileformats.html#FileFormatsPers). * `` is an error bound on the bottleneck distance (set by default to the smallest positive double value). diff --git a/src/Nerve_GIC/utilities/covercomplex.md b/src/Nerve_GIC/utilities/covercomplex.md index 41489b66..f33cb2e0 100644 --- a/src/Nerve_GIC/utilities/covercomplex.md +++ b/src/Nerve_GIC/utilities/covercomplex.md @@ -1,18 +1,7 @@ ---- -layout: page -title: "Cover complex" -meta_title: "covercomplex" -subheadline: "" -teaser: "" -permalink: "/covercomplex/" ---- -{::comment} -These flags above are here for web site generation, please let them. -cf. https://gitlab.inria.fr/GUDHI/website -Must be in conformity with _data/navigation.yml -{:/comment} +# Cover complex # + ## Nerve ## This program builds the Nerve of a point cloud sampled on an OFF file. diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md index 44a37543..4291fae7 100644 --- a/src/Rips_complex/utilities/ripscomplex.md +++ b/src/Rips_complex/utilities/ripscomplex.md @@ -1,21 +1,9 @@ ---- -layout: page -title: "Rips complex" -meta_title: "ripscomplex" -subheadline: "" -teaser: "" -permalink: "/ripscomplex/" ---- -{::comment} -These flags above are here for web site generation, please let them. -cf. https://gitlab.inria.fr/GUDHI/website -Must be in conformity with _data/navigation.yml -{:/comment} +# 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: +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` diff --git a/src/Witness_complex/utilities/witnesscomplex.md b/src/Witness_complex/utilities/witnesscomplex.md index 40864871..2341759b 100644 --- a/src/Witness_complex/utilities/witnesscomplex.md +++ b/src/Witness_complex/utilities/witnesscomplex.md @@ -1,19 +1,9 @@ ---- -layout: page -title: "Witness complex" -meta_title: "witnesscomplex" -subheadline: "" -teaser: "" -permalink: "/witnesscomplex/" ---- -{::comment} -These flags above are here for web site generation, please let them. -cf. https://gitlab.inria.fr/GUDHI/website -Must be in conformity with _data/navigation.yml -{:/comment} - - -For more details about the witness complex, please read the [user manual of the package](../doc/latest/group__witness__complex.html). + + +# Witness complex # + + +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. diff --git a/src/common/utilities/pointsetgenerator.md b/src/common/utilities/pointsetgenerator.md index f39c63b8..284715d4 100644 --- a/src/common/utilities/pointsetgenerator.md +++ b/src/common/utilities/pointsetgenerator.md @@ -1,16 +1,6 @@ ---- -layout: page -title: "Pointset generator" -meta_title: "pointsetgenerator" -subheadline: "" -teaser: "" -permalink: "/pointsetgenerator/" ---- -{::comment} -These flags above are here for web site generation, please let them. -cf. https://gitlab.inria.fr/GUDHI/website -Must be in conformity with _data/navigation.yml -{:/comment} + + +# common # ## off_file_from_shape_generator ## -- cgit v1.2.3 From 265484997185f3bf900744406206a2d64ca0a20d Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 2 Feb 2018 14:15:49 +0000 Subject: Fix after version release of Cover complex and Persistence representation installations Fix utils download link git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3211 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9596df8b0d0cdc3d8df79aa367a26b34a96d7f5e --- src/Nerve_GIC/example/CMakeLists.txt | 3 +++ src/Nerve_GIC/utilities/CMakeLists.txt | 4 ++++ src/Persistence_representations/example/CMakeLists.txt | 8 +++++--- src/Persistence_representations/utilities/CMakeLists.txt | 6 ++++++ .../utilities/persistence_intervals/CMakeLists.txt | 6 ++++++ src/common/doc/header.html | 4 ++-- src/cython/doc/_templates/layout.html | 4 ++-- 7 files changed, 28 insertions(+), 7 deletions(-) (limited to 'src/Nerve_GIC') diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt index f2626927..542c6af4 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -23,4 +23,7 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) "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/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt index 7762c8a0..7a838a8c 100644 --- a/src/Nerve_GIC/utilities/CMakeLists.txt +++ b/src/Nerve_GIC/utilities/CMakeLists.txt @@ -21,4 +21,8 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $ "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/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt index eb3258f8..54d719ac 100644 --- a/src/Persistence_representations/example/CMakeLists.txt +++ b/src/Persistence_representations/example/CMakeLists.txt @@ -4,24 +4,26 @@ project(Persistence_representations_example) add_executable ( Persistence_representations_example_landscape_on_grid persistence_landscape_on_grid.cpp ) add_test(NAME Persistence_representations_example_landscape_on_grid COMMAND $) +install(TARGETS Persistence_representations_example_landscape_on_grid DESTINATION bin) add_executable ( Persistence_representations_example_landscape persistence_landscape.cpp ) add_test(NAME Persistence_representations_example_landscape COMMAND $) +install(TARGETS Persistence_representations_example_landscape DESTINATION bin) add_executable ( Persistence_representations_example_intervals persistence_intervals.cpp ) add_test(NAME Persistence_representations_example_intervals COMMAND $ "${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 ) add_test(NAME Persistence_representations_example_vectors COMMAND $) +install(TARGETS Persistence_representations_example_vectors DESTINATION bin) add_executable ( Persistence_representations_example_heat_maps persistence_heat_maps.cpp ) add_test(NAME Persistence_representations_example_heat_maps COMMAND $) - - - +install(TARGETS Persistence_representations_example_heat_maps DESTINATION bin) diff --git a/src/Persistence_representations/utilities/CMakeLists.txt b/src/Persistence_representations/utilities/CMakeLists.txt index 137eb0c1..fc51b1d6 100644 --- a/src/Persistence_representations/utilities/CMakeLists.txt +++ b/src/Persistence_representations/utilities/CMakeLists.txt @@ -10,6 +10,8 @@ function(add_persistence_representation_creation_utility creation_utility) add_test(NAME Persistence_representation_utilities_${creation_utility} COMMAND $ ${ARGN} "${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_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 $ "${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 $ "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1" "2") +install(TARGETS compute_number_of_dominant_intervals DESTINATION bin) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) add_executable ( compute_bottleneck_distance compute_bottleneck_distance.cpp ) @@ -29,4 +33,6 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) "-1" "${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/common/doc/header.html b/src/common/doc/header.html index 9c514381..d69b28fa 100644 --- a/src/common/doc/header.html +++ b/src/common/doc/header.html @@ -56,8 +56,8 @@ $extrastylesheet
  • diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html index 8e4eba40..c9356116 100644 --- a/src/cython/doc/_templates/layout.html +++ b/src/cython/doc/_templates/layout.html @@ -198,8 +198,8 @@
  • -- cgit v1.2.3 From b77699a3188d6674427cffaa35f26ec57aadec8b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 8 Mar 2018 17:13:25 +0000 Subject: Web site review after Editorial Board Do not need to import gudhi twice in py git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3270 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7d7a4bba27f4cbcad5f8b18cb86587a15e6a8435 --- src/Alpha_complex/utilities/alphacomplex.md | 10 ++++++++++ src/Bitmap_cubical_complex/utilities/cubicalcomplex.md | 10 ++++++++++ src/Bottleneck_distance/utilities/bottleneckdistance.md | 10 ++++++++++ src/Nerve_GIC/utilities/covercomplex.md | 10 ++++++++++ src/Rips_complex/utilities/ripscomplex.md | 10 ++++++++++ src/Witness_complex/utilities/witnesscomplex.md | 10 ++++++++++ src/common/utilities/pointsetgenerator.md | 16 +++++++++++++--- src/cython/example/bottleneck_basic_example.py | 2 -- 8 files changed, 73 insertions(+), 5 deletions(-) (limited to 'src/Nerve_GIC') diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md index aace85d3..ede749a9 100644 --- a/src/Alpha_complex/utilities/alphacomplex.md +++ b/src/Alpha_complex/utilities/alphacomplex.md @@ -1,3 +1,13 @@ +--- +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 # diff --git a/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md index 6e1b2578..a1bb9007 100644 --- a/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md +++ b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md @@ -1,3 +1,13 @@ +--- +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# diff --git a/src/Bottleneck_distance/utilities/bottleneckdistance.md b/src/Bottleneck_distance/utilities/bottleneckdistance.md index 526f5822..f2749acc 100644 --- a/src/Bottleneck_distance/utilities/bottleneckdistance.md +++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md @@ -1,3 +1,13 @@ +--- +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 distance # diff --git a/src/Nerve_GIC/utilities/covercomplex.md b/src/Nerve_GIC/utilities/covercomplex.md index f33cb2e0..6d16d16f 100644 --- a/src/Nerve_GIC/utilities/covercomplex.md +++ b/src/Nerve_GIC/utilities/covercomplex.md @@ -1,3 +1,13 @@ +--- +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} # Cover complex # diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md index 4291fae7..c1f2210e 100644 --- a/src/Rips_complex/utilities/ripscomplex.md +++ b/src/Rips_complex/utilities/ripscomplex.md @@ -1,3 +1,13 @@ +--- +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 complex # diff --git a/src/Witness_complex/utilities/witnesscomplex.md b/src/Witness_complex/utilities/witnesscomplex.md index 2341759b..3be9bc55 100644 --- a/src/Witness_complex/utilities/witnesscomplex.md +++ b/src/Witness_complex/utilities/witnesscomplex.md @@ -1,3 +1,13 @@ +--- +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} # Witness complex # diff --git a/src/common/utilities/pointsetgenerator.md b/src/common/utilities/pointsetgenerator.md index 284715d4..3b23e668 100644 --- a/src/common/utilities/pointsetgenerator.md +++ b/src/common/utilities/pointsetgenerator.md @@ -1,6 +1,16 @@ - - -# common # +--- +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} + + +# Miscellaneous # ## off_file_from_shape_generator ## diff --git a/src/cython/example/bottleneck_basic_example.py b/src/cython/example/bottleneck_basic_example.py index 31cecb29..a7fa01c1 100755 --- a/src/cython/example/bottleneck_basic_example.py +++ b/src/cython/example/bottleneck_basic_example.py @@ -28,8 +28,6 @@ __author__ = "Francois Godi, Vincent Rouvreau" __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')]] -- cgit v1.2.3 From 9cceba4f1ed5cca6daa273166a2ec38fe0ab6c91 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 28 Mar 2018 10:09:36 +0000 Subject: Merge last Nerve_GIC development from eponym branch git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3311 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c57e5f6f364b6162f607edd07f3a31577e640fcb --- src/Nerve_GIC/include/gudhi/GIC.h | 254 +++++++++++++++++++++++--------------- src/Nerve_GIC/test/test_GIC.cpp | 3 + 2 files changed, 157 insertions(+), 100 deletions(-) (limited to 'src/Nerve_GIC') diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index 40ff7a4a..f5b67be6 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -23,6 +23,11 @@ #ifndef GIC_H_ #define GIC_H_ +#ifdef GUDHI_USE_TBB +#include +#include +#endif + #include #include #include @@ -99,9 +104,8 @@ class Cover_complex { int data_dimension; // dimension of input data. int n; // number of points. - std::map func; // function used to compute the output simplicial complex. - std::map - func_color; // function used to compute the colors of the nodes of the output simplicial complex. + std::vector func; // function used to compute the output simplicial complex. + std::vector func_color; // function used to compute the colors of the nodes of the output simplicial complex. bool functional_cover = false; // whether we use a cover with preimages of a function or not. Graph one_skeleton_OFF; // one-skeleton given by the input OFF file (if it exists). @@ -114,8 +118,8 @@ class Cover_complex { Persistence_diagram PD; std::vector distribution; - std::map > - cover; // function associating to each data point its vectors of cover elements to which it belongs. + std::vector > + cover; // function associating to each data point the vector of cover elements to which it belongs. std::map > cover_back; // inverse of cover, in order to get the data points associated to a specific cover element. std::map cover_std; // standard function (induced by func) used to compute the extended persistence @@ -140,8 +144,8 @@ class Cover_complex { // Point comparator struct Less { - Less(std::map func) { Fct = func; } - std::map Fct; + Less(std::vector func) { Fct = func; } + std::vector Fct; bool operator()(int a, int b) { if (Fct[a] == Fct[b]) return a < b; @@ -276,6 +280,7 @@ 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)); + std::vector dummy; dummy.clear(); cover.push_back(dummy); i++; } } @@ -430,17 +435,29 @@ class Cover_complex { if (distances.size() == 0) compute_pairwise_distances(distance); - // #pragma omp parallel for - for (int i = 0; i < N; i++) { - SampleWithoutReplacement(n, m, samples); - double hausdorff_dist = 0; - for (int j = 0; j < n; j++) { - double mj = distances[j][samples[0]]; - for (int k = 1; k < m; k++) mj = std::min(mj, distances[j][samples[k]]); - hausdorff_dist = std::max(hausdorff_dist, mj); + #ifdef GUDHI_USE_TBB + tbb::parallel_for(0, N, [&](int i){ + SampleWithoutReplacement(n, m, samples); + double hausdorff_dist = 0; + for (int j = 0; j < n; j++) { + double mj = distances[j][samples[0]]; + for (int k = 1; k < m; k++) mj = std::min(mj, distances[j][samples[k]]); + hausdorff_dist = std::max(hausdorff_dist, mj); + } + delta += hausdorff_dist / N; + }); + #else + for (int i = 0; i < N; i++) { + SampleWithoutReplacement(n, m, samples); + double hausdorff_dist = 0; + for (int j = 0; j < n; j++) { + double mj = distances[j][samples[0]]; + for (int k = 1; k < m; k++) mj = std::min(mj, distances[j][samples[k]]); + hausdorff_dist = std::max(hausdorff_dist, mj); + } + delta += hausdorff_dist / N; } - delta += hausdorff_dist / N; - } + #endif if (verbose) std::cout << "delta = " << delta << std::endl; set_graph_from_rips(delta, distance); @@ -465,7 +482,7 @@ class Cover_complex { while (std::getline(input, line)) { std::stringstream stream(line); stream >> f; - func.emplace(i, f); + func.push_back(f); i++; } functional_cover = true; @@ -479,7 +496,7 @@ class Cover_complex { * */ void set_function_from_coordinate(int k) { - for (int i = 0; i < n; i++) func.emplace(i, point_cloud[i][k]); + for (int i = 0; i < n; i++) func.push_back(point_cloud[i][k]); functional_cover = true; cover_name = "coordinate " + std::to_string(k); } @@ -492,7 +509,7 @@ class Cover_complex { */ template void set_function_from_range(InputRange const& function) { - for (int i = 0; i < n; i++) func.emplace(i, function[i]); + for (int i = 0; i < n; i++) func.push_back(function[i]); functional_cover = true; } @@ -710,37 +727,69 @@ class Cover_complex { funcstd[i] = 0.5 * (u + v); } - if (verbose) std::cout << "Computing connected components..." << std::endl; - // #pragma omp parallel for - for (int i = 0; i < res; i++) { - // Compute connected components - Graph G = one_skeleton.create_subgraph(); - int num = preimages[i].size(); - std::vector component(num); - for (int j = 0; j < num; j++) boost::add_vertex(index[vertices[preimages[i][j]]], G); - boost::connected_components(G, &component[0]); - int max = 0; - - // For each point in preimage - for (int j = 0; j < num; j++) { - // Update number of components in preimage - if (component[j] > max) max = component[j]; - - // Identify component with Cantor polynomial N^2 -> N - int identifier = (std::pow(i + component[j], 2) + 3 * i + component[j]) / 2; - - // Update covers - cover[preimages[i][j]].push_back(identifier); - cover_back[identifier].push_back(preimages[i][j]); - cover_fct[identifier] = i; - cover_std[identifier] = funcstd[i]; - cover_color[identifier].second += func_color[preimages[i][j]]; - cover_color[identifier].first += 1; - } + #ifdef GUDHI_USE_TBB + if (verbose) std::cout << "Computing connected components (parallelized)..." << std::endl; + tbb::parallel_for(0, res, [&](int i){ + // Compute connected components + Graph G = one_skeleton.create_subgraph(); + int num = preimages[i].size(); + std::vector component(num); + for (int j = 0; j < num; j++) boost::add_vertex(index[vertices[preimages[i][j]]], G); + boost::connected_components(G, &component[0]); + int max = 0; + + // For each point in preimage + for (int j = 0; j < num; j++) { + // Update number of components in preimage + if (component[j] > max) max = component[j]; + + // Identify component with Cantor polynomial N^2 -> N + int identifier = ((i + component[j])*(i + component[j]) + 3 * i + component[j]) / 2; + + // Update covers + cover[preimages[i][j]].push_back(identifier); + cover_back[identifier].push_back(preimages[i][j]); + cover_fct[identifier] = i; + cover_std[identifier] = funcstd[i]; + cover_color[identifier].second += func_color[preimages[i][j]]; + cover_color[identifier].first += 1; + } - // Maximal dimension is total number of connected components - id += max + 1; - } + // Maximal dimension is total number of connected components + id += max + 1; + }); + #else + if (verbose) std::cout << "Computing connected components..." << std::endl; + for (int i = 0; i < res; i++) { + // Compute connected components + Graph G = one_skeleton.create_subgraph(); + int num = preimages[i].size(); + std::vector component(num); + for (int j = 0; j < num; j++) boost::add_vertex(index[vertices[preimages[i][j]]], G); + boost::connected_components(G, &component[0]); + int max = 0; + + // For each point in preimage + for (int j = 0; j < num; j++) { + // Update number of components in preimage + if (component[j] > max) max = component[j]; + + // Identify component with Cantor polynomial N^2 -> N + int identifier = (std::pow(i + component[j], 2) + 3 * i + component[j]) / 2; + + // Update covers + cover[preimages[i][j]].push_back(identifier); + cover_back[identifier].push_back(preimages[i][j]); + cover_fct[identifier] = i; + cover_std[identifier] = funcstd[i]; + cover_color[identifier].second += func_color[preimages[i][j]]; + cover_color[identifier].first += 1; + } + + // Maximal dimension is total number of connected components + id += max + 1; + } + #endif maximal_dim = id - 1; for (std::map >::iterator iit = cover_color.begin(); iit != cover_color.end(); iit++) @@ -803,24 +852,46 @@ class Cover_complex { for (int j = 0; j < n; j++) mindist[j] = std::numeric_limits::max(); // Compute the geodesic distances to subsamples with Dijkstra - // #pragma omp parallel for - for (int i = 0; i < m; i++) { - if (verbose) std::cout << "Computing geodesic distances to seed " << i << "..." << std::endl; - int seed = voronoi_subsamples[i]; - std::vector dmap(n); - boost::dijkstra_shortest_paths( - one_skeleton, vertices[seed], - boost::weight_map(weight).distance_map(boost::make_iterator_property_map(dmap.begin(), index))); - - for (int j = 0; j < n; j++) - if (mindist[j] > dmap[j]) { - mindist[j] = dmap[j]; - if (cover[j].size() == 0) - cover[j].push_back(i); - else - cover[j][0] = i; - } - } + #ifdef GUDHI_USE_TBB + if (verbose) std::cout << "Computing geodesic distances (parallelized)..." << std::endl; + tbb::mutex coverMutex; tbb::mutex mindistMutex; + tbb::parallel_for(0, m, [&](int i){ + int seed = voronoi_subsamples[i]; + std::vector dmap(n); + boost::dijkstra_shortest_paths( + one_skeleton, vertices[seed], + boost::weight_map(weight).distance_map(boost::make_iterator_property_map(dmap.begin(), index))); + + coverMutex.lock(); mindistMutex.lock(); + for (int j = 0; j < n; j++) + if (mindist[j] > dmap[j]) { + mindist[j] = dmap[j]; + if (cover[j].size() == 0) + cover[j].push_back(i); + else + cover[j][0] = i; + } + coverMutex.unlock(); mindistMutex.unlock(); + }); + #else + for (int i = 0; i < m; i++) { + if (verbose) std::cout << "Computing geodesic distances to seed " << i << "..." << std::endl; + int seed = voronoi_subsamples[i]; + std::vector dmap(n); + boost::dijkstra_shortest_paths( + one_skeleton, vertices[seed], + boost::weight_map(weight).distance_map(boost::make_iterator_property_map(dmap.begin(), index))); + + for (int j = 0; j < n; j++) + if (mindist[j] > dmap[j]) { + mindist[j] = dmap[j]; + if (cover[j].size() == 0) + cover[j].push_back(i); + else + cover[j][0] = i; + } + } + #endif for (int i = 0; i < n; i++) { cover_back[cover[i][0]].push_back(i); @@ -860,7 +931,7 @@ class Cover_complex { while (std::getline(input, line)) { std::stringstream stream(line); stream >> f; - func_color.emplace(i, f); + func_color.push_back(f); i++; } color_name = color_file_name; @@ -873,7 +944,7 @@ class Cover_complex { * */ void set_color_from_coordinate(int k = 0) { - for (int i = 0; i < n; i++) func_color[i] = point_cloud[i][k]; + for (int i = 0; i < n; i++) func_color.push_back(point_cloud[i][k]); color_name = "coordinate "; color_name.append(std::to_string(k)); } @@ -885,7 +956,7 @@ class Cover_complex { * */ void set_color_from_vector(std::vector color) { - for (unsigned int i = 0; i < color.size(); i++) func_color[i] = color[i]; + for (unsigned int i = 0; i < color.size(); i++) func_color.push_back(color[i]); } public: // Create a .dot file that can be compiled with neato to produce a .pdf file. @@ -1039,45 +1110,29 @@ class Cover_complex { minf = std::min(minf, it->second); } + // Build filtration for (auto const& simplex : simplices) { - // Add a simplex and a cone on it - std::vector splx = simplex; - splx.push_back(-2); - st.insert_simplex_and_subfaces(splx); + std::vector splx = simplex; splx.push_back(-2); + st.insert_simplex_and_subfaces(splx, -3); } - // Build filtration - for (auto simplex : st.complex_simplex_range()) { - double filta = std::numeric_limits::lowest(); - double filts = filta; - bool ascending = true; - for (auto vertex : st.simplex_vertex_range(simplex)) { - if (vertex == -2) { - ascending = false; - continue; - } - filta = std::max(-2 + (cover_std[vertex] - minf) / (maxf - minf), filta); - filts = std::max(2 - (cover_std[vertex] - minf) / (maxf - minf), filts); - } - if (ascending) - st.assign_filtration(simplex, filta); - else - st.assign_filtration(simplex, filts); + for (std::map::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)); } - int magic[] = {-2}; - st.assign_filtration(st.find(magic), -3); + st.make_filtration_non_decreasing(); // Compute PD - st.initialize_filtration(); - Gudhi::persistent_cohomology::Persistent_cohomology pcoh(st); - pcoh.init_coefficients(2); + Gudhi::persistent_cohomology::Persistent_cohomology pcoh(st); pcoh.init_coefficients(2); pcoh.compute_persistent_cohomology(); // Output PD int max_dim = st.dimension(); for (int i = 0; i < max_dim; i++) { std::vector > bars = pcoh.intervals_in_dimension(i); - int num_bars = bars.size(); + int num_bars = bars.size(); if(i == 0) num_bars -= 1; if(verbose) std::cout << num_bars << " interval(s) in dimension " << i << ":" << std::endl; for (int j = 0; j < num_bars; j++) { double birth = bars[j].first; @@ -1206,8 +1261,7 @@ class Cover_complex { } if (type == "Nerve") { - for(auto& simplex : cover) - simplices.push_back(simplex.second); + for(int i = 0; i < n; i++) simplices.push_back(cover[i]); std::sort(simplices.begin(), simplices.end()); std::vector >::iterator it = std::unique(simplices.begin(), simplices.end()); simplices.resize(std::distance(simplices.begin(), it)); diff --git a/src/Nerve_GIC/test/test_GIC.cpp b/src/Nerve_GIC/test/test_GIC.cpp index d633753c..e3067d35 100644 --- a/src/Nerve_GIC/test/test_GIC.cpp +++ b/src/Nerve_GIC/test/test_GIC.cpp @@ -39,6 +39,7 @@ BOOST_AUTO_TEST_CASE(check_nerve) { N.set_type("Nerve"); std::string cloud_file_name("data/cloud"); N.read_point_cloud(cloud_file_name); + N.set_color_from_coordinate(); std::string graph_file_name("data/graph"); N.set_graph_from_file(graph_file_name); std::string cover_file_name("data/cover"); @@ -58,6 +59,7 @@ BOOST_AUTO_TEST_CASE(check_GIC) { GIC.set_type("GIC"); std::string cloud_file_name("data/cloud"); GIC.read_point_cloud(cloud_file_name); + GIC.set_color_from_coordinate(); std::string graph_file_name("data/graph"); GIC.set_graph_from_file(graph_file_name); std::string cover_file_name("data/cover"); @@ -77,6 +79,7 @@ BOOST_AUTO_TEST_CASE(check_voronoiGIC) { GIC.set_type("GIC"); std::string cloud_file_name("data/cloud"); GIC.read_point_cloud(cloud_file_name); + GIC.set_color_from_coordinate(); std::string graph_file_name("data/graph"); GIC.set_graph_from_file(graph_file_name); GIC.set_cover_from_Voronoi(Gudhi::Euclidean_distance(), 2); -- cgit v1.2.3 From d9b4497284de73f14387a170388bf8bcd4207436 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 4 Apr 2018 09:12:15 +0000 Subject: No need to repeat title, automatically done by the website git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3338 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 51d295377d2b3235e9316f199bf95d3c5aeaeab3 --- src/Alpha_complex/utilities/alphacomplex.md | 3 --- src/Bitmap_cubical_complex/utilities/cubicalcomplex.md | 2 -- src/Bottleneck_distance/utilities/bottleneckdistance.md | 2 -- src/Nerve_GIC/utilities/covercomplex.md | 3 --- src/Rips_complex/utilities/ripscomplex.md | 2 -- src/Witness_complex/utilities/witnesscomplex.md | 3 --- src/common/utilities/pointsetgenerator.md | 4 ---- 7 files changed, 19 deletions(-) (limited to 'src/Nerve_GIC') diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md index ede749a9..0fe98837 100644 --- a/src/Alpha_complex/utilities/alphacomplex.md +++ b/src/Alpha_complex/utilities/alphacomplex.md @@ -10,9 +10,6 @@ Leave the lines above as it is required by the web site generator 'Jekyll' {:/comment} -# Alpha complex # - - ## 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. diff --git a/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md index a1bb9007..5b0404c3 100644 --- a/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md +++ b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md @@ -10,8 +10,6 @@ Leave the lines above as it is required by the web site generator 'Jekyll' {:/comment} -# 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](/doc/latest/fileformats.html#FileFormatsPerseus) for a description of the file format. diff --git a/src/Bottleneck_distance/utilities/bottleneckdistance.md b/src/Bottleneck_distance/utilities/bottleneckdistance.md index f2749acc..939eb911 100644 --- a/src/Bottleneck_distance/utilities/bottleneckdistance.md +++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md @@ -10,8 +10,6 @@ Leave the lines above as it is required by the web site generator 'Jekyll' {:/comment} -# Bottleneck distance # - ## bottleneck_read_file_example ## This program computes the Bottleneck distance between two persistence diagram files. diff --git a/src/Nerve_GIC/utilities/covercomplex.md b/src/Nerve_GIC/utilities/covercomplex.md index 6d16d16f..683c1b75 100644 --- a/src/Nerve_GIC/utilities/covercomplex.md +++ b/src/Nerve_GIC/utilities/covercomplex.md @@ -10,9 +10,6 @@ Leave the lines above as it is required by the web site generator 'Jekyll' {:/comment} -# Cover complex # - - ## 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, diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md index 84f40cc1..6df49310 100644 --- a/src/Rips_complex/utilities/ripscomplex.md +++ b/src/Rips_complex/utilities/ripscomplex.md @@ -10,8 +10,6 @@ Leave the lines above as it is required by the web site generator 'Jekyll' {:/comment} -# 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, using Euclidean distance. The output diagram contains one bar per line, written with the convention: diff --git a/src/Witness_complex/utilities/witnesscomplex.md b/src/Witness_complex/utilities/witnesscomplex.md index 3be9bc55..da453cce 100644 --- a/src/Witness_complex/utilities/witnesscomplex.md +++ b/src/Witness_complex/utilities/witnesscomplex.md @@ -10,9 +10,6 @@ Leave the lines above as it is required by the web site generator 'Jekyll' {:/comment} -# Witness complex # - - For more details about the witness complex, please read the [user manual of the package](/doc/latest/group__witness__complex.html). ## weak_witness_persistence ## diff --git a/src/common/utilities/pointsetgenerator.md b/src/common/utilities/pointsetgenerator.md index 3b23e668..c8c819b7 100644 --- a/src/common/utilities/pointsetgenerator.md +++ b/src/common/utilities/pointsetgenerator.md @@ -10,10 +10,6 @@ Leave the lines above as it is required by the web site generator 'Jekyll' {:/comment} -# Miscellaneous # - -## off_file_from_shape_generator ## - Generates a pointset and save it in an OFF file. Command-line is: ``` -- cgit v1.2.3 From 3f770da9a2782f5a6c4811aa5bb079ee5bb27915 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 5 Apr 2018 08:25:34 +0000 Subject: Merge last modifications of Nerve_GIC branch git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3342 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 268968d6b446db88bdaab48bbdb5c91882d4a820 --- src/Nerve_GIC/example/CoordGIC.cpp | 3 ++ src/Nerve_GIC/include/gudhi/GIC.h | 58 ++++++++++++++++++-------------------- 2 files changed, 30 insertions(+), 31 deletions(-) (limited to 'src/Nerve_GIC') diff --git a/src/Nerve_GIC/example/CoordGIC.cpp b/src/Nerve_GIC/example/CoordGIC.cpp index c92cf235..d544db94 100644 --- a/src/Nerve_GIC/example/CoordGIC.cpp +++ b/src/Nerve_GIC/example/CoordGIC.cpp @@ -66,6 +66,9 @@ int main(int argc, char **argv) { GIC.find_simplices(); + GIC.compute_distribution(10); + GIC.compute_p_value(); + GIC.plot_DOT(); Gudhi::Simplex_tree<> stree; diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index f5b67be6..d6f3ded6 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -142,18 +142,6 @@ class Cover_complex { std::string point_cloud_name; std::string color_name; - // Point comparator - struct Less { - Less(std::vector func) { Fct = func; } - std::vector Fct; - bool operator()(int a, int b) { - if (Fct[a] == Fct[b]) - return a < b; - else - return Fct[a] < Fct[b]; - } - }; - // Remove all edges of a graph. void remove_edges(Graph& G) { boost::graph_traits::edge_iterator ei, ei_end; @@ -280,7 +268,7 @@ 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)); - std::vector dummy; dummy.clear(); cover.push_back(dummy); + cover.emplace_back(); i++; } } @@ -671,7 +659,7 @@ class Cover_complex { // Sort points according to function values std::vector points(n); for (int i = 0; i < n; i++) points[i] = i; - std::sort(points.begin(), points.end(), Less(this->func)); + std::sort(points.begin(), points.end(), [=](const int & p1, const int & p2){return (this->func[p1] < this->func[p2]);}); int id = 0; int pos = 0; @@ -1158,22 +1146,25 @@ class Cover_complex { * @param[in] N number of bootstrap iterations. * */ - template - void compute_distribution(int N = 100) { - if (distribution.size() >= N) { + void compute_distribution(unsigned int N = 100) { + unsigned int sz = distribution.size(); + if (sz >= N) { std::cout << "Already done!" << std::endl; } else { - for (int i = 0; i < N - distribution.size(); i++) { - Cover_complex Cboot; - Cboot.n = this->n; + for (unsigned int i = 0; i < N - sz; i++) { + if (verbose) std::cout << "Computing " << i << "th bootstrap, bottleneck distance = "; + + Cover_complex Cboot; Cboot.n = this->n; Cboot.data_dimension = this->data_dimension; Cboot.type = this->type; Cboot.functional_cover = true; + std::vector boot(this->n); for (int j = 0; j < this->n; j++) { double u = GetUniform(); - int id = std::floor(u * (this->n)); - boot[j] = id; - Cboot.point_cloud[j] = this->point_cloud[id]; - Cboot.func.emplace(j, this->func[id]); + int id = std::floor(u * (this->n)); boot[j] = id; + 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); + for (int j = 0; j < n; j++) { std::vector dist(n); for (int k = 0; k < n; k++) dist[k] = distances[boot[j]][boot[k]]; @@ -1186,8 +1177,9 @@ class Cover_complex { Cboot.set_cover_from_function(); Cboot.find_simplices(); Cboot.compute_PD(); - - distribution.push_back(Gudhi::persistence_diagram::bottleneck_distance(this->PD, Cboot.PD)); + double db = Gudhi::persistence_diagram::bottleneck_distance(this->PD, Cboot.PD); + if (verbose) std::cout << db << std::endl; + distribution.push_back(db); } std::sort(distribution.begin(), distribution.end()); @@ -1201,7 +1193,7 @@ class Cover_complex { * */ double compute_distance_from_confidence_level(double alpha) { - int N = distribution.size(); + unsigned int N = distribution.size(); return distribution[std::floor(alpha * N)]; } @@ -1212,9 +1204,11 @@ class Cover_complex { * */ double compute_confidence_level_from_distance(double d) { - int N = distribution.size(); - for (int i = 0; i < N; i++) - if (distribution[i] > d) return i * 1.0 / N; + unsigned int N = distribution.size(); + double level = 1; + for (unsigned int i = 0; i < N; i++) + if (distribution[i] > d){ level = i * 1.0 / N; break; } + return level; } public: @@ -1226,7 +1220,9 @@ class Cover_complex { double distancemin = -std::numeric_limits::lowest(); int N = PD.size(); for (int i = 0; i < N; i++) distancemin = std::min(distancemin, 0.5 * (PD[i].second - PD[i].first)); - return 1 - compute_confidence_level_from_distance(distancemin); + double p_value = 1 - compute_confidence_level_from_distance(distancemin); + if (verbose) std::cout << "p value = " << p_value << std::endl; + return p_value; } // ******************************************************************************************************************* -- cgit v1.2.3 From 4869d669f029886586d6211b40c8c549da85207b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 26 Apr 2018 15:54:12 +0000 Subject: Fix Copyrights git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/copyright_clarification_vincent@3400 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ff348beedf92656c6913c2a1df983b5804b33988 --- .../concept/SimplicialComplexForAlpha.h | 2 +- src/Alpha_complex/doc/COPYRIGHT | 2 +- src/Alpha_complex/doc/Intro_alpha_complex.h | 2 +- src/Alpha_complex/include/gudhi/Alpha_complex.h | 2 +- src/Alpha_complex/test/Alpha_complex_unit_test.cpp | 2 +- .../utilities/alpha_complex_3d_helper.h | 2 +- .../utilities/alpha_complex_3d_persistence.cpp | 2 +- .../utilities/alpha_complex_persistence.cpp | 22 +++++++++++++++++++++ .../exact_alpha_complex_3d_persistence.cpp | 2 +- .../periodic_alpha_complex_3d_persistence.cpp | 2 +- .../weighted_alpha_complex_3d_persistence.cpp | 2 +- ...ghted_periodic_alpha_complex_3d_persistence.cpp | 2 +- src/Bitmap_cubical_complex/doc/COPYRIGHT | 2 +- .../doc/Gudhi_Cubical_Complex_doc.h | 2 +- .../example/Random_bitmap_cubical_complex.cpp | 2 +- .../include/gudhi/Bitmap_cubical_complex.h | 2 +- .../include/gudhi/Bitmap_cubical_complex/counter.h | 2 +- .../include/gudhi/Bitmap_cubical_complex_base.h | 2 +- ...cal_complex_periodic_boundary_conditions_base.h | 2 +- src/Bitmap_cubical_complex/test/Bitmap_test.cpp | 2 +- .../utilities/cubical_complex_persistence.cpp | 2 +- .../periodic_cubical_complex_persistence.cpp | 2 +- .../benchmark/bottleneck_chrono.cpp | 2 +- .../concept/Persistence_diagram.h | 2 +- src/Bottleneck_distance/doc/COPYRIGHT | 2 +- .../doc/Intro_bottleneck_distance.h | 2 +- .../alpha_rips_persistence_bottleneck_distance.cpp | 2 +- .../example/bottleneck_basic_example.cpp | 2 +- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 2 +- .../include/gudhi/Graph_matching.h | 2 +- .../include/gudhi/Internal_point.h | 2 +- .../include/gudhi/Neighbors_finder.h | 2 +- .../include/gudhi/Persistence_graph.h | 2 +- .../test/bottleneck_unit_test.cpp | 2 +- .../utilities/bottleneck_distance.cpp | 2 +- src/Contraction/doc/COPYRIGHT | 2 +- src/Contraction/example/Garland_heckbert.cpp | 2 +- .../example/Garland_heckbert/Error_quadric.h | 2 +- src/Contraction/example/Rips_contraction.cpp | 2 +- .../include/gudhi/Contraction/Edge_profile.h | 2 +- .../Contraction/policies/Contraction_visitor.h | 2 +- .../gudhi/Contraction/policies/Cost_policy.h | 2 +- .../Contraction/policies/Dummy_valid_contraction.h | 2 +- .../gudhi/Contraction/policies/Edge_length_cost.h | 2 +- .../Contraction/policies/First_vertex_placement.h | 2 +- .../policies/Link_condition_valid_contraction.h | 2 +- .../gudhi/Contraction/policies/Middle_placement.h | 2 +- .../gudhi/Contraction/policies/Placement_policy.h | 2 +- .../policies/Valid_contraction_policy.h | 2 +- src/Contraction/include/gudhi/Edge_contraction.h | 2 +- .../include/gudhi/Skeleton_blocker_contractor.h | 2 +- src/GudhUI/gui/MainWindow.cpp | 2 +- src/GudhUI/gui/MainWindow.h | 2 +- src/GudhUI/gui/Menu_edge_contraction.cpp | 2 +- src/GudhUI/gui/Menu_edge_contraction.h | 2 +- src/GudhUI/gui/Menu_k_nearest_neighbors.cpp | 2 +- src/GudhUI/gui/Menu_k_nearest_neighbors.h | 2 +- src/GudhUI/gui/Menu_persistence.cpp | 2 +- src/GudhUI/gui/Menu_persistence.h | 2 +- src/GudhUI/gui/Menu_uniform_neighbors.cpp | 2 +- src/GudhUI/gui/Menu_uniform_neighbors.h | 2 +- src/GudhUI/gui/gudhui.cpp | 4 ++-- src/GudhUI/model/Complex_typedefs.h | 2 +- src/GudhUI/model/Model.h | 2 +- src/GudhUI/utils/Bar_code_persistence.h | 23 ++++++++++++++++++++++ src/GudhUI/utils/Critical_points.h | 2 +- src/GudhUI/utils/Edge_collapsor.h | 2 +- src/GudhUI/utils/Edge_contractor.h | 2 +- src/GudhUI/utils/Furthest_point_epsilon_net.h | 2 +- src/GudhUI/utils/Is_manifold.h | 2 +- src/GudhUI/utils/K_nearest_builder.h | 2 +- src/GudhUI/utils/Lloyd_builder.h | 2 +- src/GudhUI/utils/MClock.h | 2 +- src/GudhUI/utils/Persistence_compute.h | 2 +- src/GudhUI/utils/Rips_builder.h | 2 +- src/GudhUI/utils/UI_utils.h | 2 +- src/GudhUI/utils/Vertex_collapsor.h | 2 +- src/GudhUI/view/Color.h | 2 +- src/GudhUI/view/FirstCoordProjector.h | 2 +- src/GudhUI/view/Projector3D.h | 2 +- src/GudhUI/view/View_parameter.h | 2 +- src/GudhUI/view/Viewer.cpp | 2 +- src/GudhUI/view/Viewer.h | 2 +- src/GudhUI/view/Viewer_instructor.cpp | 2 +- src/GudhUI/view/Viewer_instructor.h | 2 +- src/Hasse_complex/include/gudhi/Hasse_complex.h | 2 +- src/Nerve_GIC/doc/COPYRIGHT | 2 +- src/Nerve_GIC/doc/Intro_graph_induced_complex.h | 2 +- src/Nerve_GIC/example/CoordGIC.cpp | 2 +- src/Nerve_GIC/example/FuncGIC.cpp | 2 +- src/Nerve_GIC/include/gudhi/GIC.h | 2 +- src/Nerve_GIC/test/test_GIC.cpp | 2 +- .../utilities/KeplerMapperVisuFromTxtFile.py | 4 ++-- src/Nerve_GIC/utilities/Nerve.cpp | 2 +- src/Nerve_GIC/utilities/VoronoiGIC.cpp | 2 +- .../concept/Real_valued_topological_data.h | 2 +- .../concept/Topological_data_with_averages.h | 2 +- .../concept/Topological_data_with_distances.h | 2 +- .../concept/Topological_data_with_scalar_product.h | 2 +- .../concept/Vectorized_topological_data.h | 2 +- .../doc/Persistence_representations_doc.h | 2 +- .../example/persistence_heat_maps.cpp | 2 +- .../example/persistence_intervals.cpp | 2 +- .../example/persistence_landscape.cpp | 2 +- .../example/persistence_landscape_on_grid.cpp | 2 +- .../example/persistence_vectors.cpp | 2 +- .../include/gudhi/PSSK.h | 2 +- .../include/gudhi/Persistence_heat_maps.h | 2 +- .../include/gudhi/Persistence_intervals.h | 2 +- .../gudhi/Persistence_intervals_with_distances.h | 2 +- .../include/gudhi/Persistence_landscape.h | 2 +- .../include/gudhi/Persistence_landscape_on_grid.h | 2 +- .../include/gudhi/Persistence_vectors.h | 2 +- .../gudhi/common_persistence_representations.h | 2 +- .../include/gudhi/read_persistence_from_file.h | 2 +- .../test/persistence_heat_maps_test.cpp | 2 +- .../test/persistence_intervals_test.cpp | 2 +- .../persistence_intervals_with_distances_test.cpp | 2 +- .../test/persistence_lanscapes_on_grid_test.cpp | 2 +- .../test/persistence_lanscapes_test.cpp | 2 +- .../test/read_persistence_from_file_test.cpp | 2 +- .../test/vector_representation_test.cpp | 2 +- .../average_persistence_heat_maps.cpp | 2 +- .../compute_distance_of_persistence_heat_maps.cpp | 2 +- ...ute_scalar_product_of_persistence_heat_maps.cpp | 2 +- ...h_m_weighted_by_arctan_of_their_persistence.cpp | 2 +- ...te_p_h_m_weighted_by_distance_from_diagonal.cpp | 2 +- ...ate_p_h_m_weighted_by_squared_diag_distance.cpp | 2 +- .../create_persistence_heat_maps.cpp | 2 +- .../persistence_heat_maps/create_pssk.cpp | 2 +- .../plot_persistence_heat_map.cpp | 2 +- ...te_birth_death_range_in_persistence_diagram.cpp | 2 +- .../compute_bottleneck_distance.cpp | 2 +- .../compute_number_of_dominant_intervals.cpp | 2 +- .../plot_histogram_of_intervals_lengths.cpp | 2 +- .../plot_persistence_Betti_numbers.cpp | 2 +- .../plot_persistence_intervals.cpp | 2 +- .../persistence_landscapes/average_landscapes.cpp | 2 +- .../compute_distance_of_landscapes.cpp | 2 +- .../compute_scalar_product_of_landscapes.cpp | 2 +- .../persistence_landscapes/create_landscapes.cpp | 2 +- .../persistence_landscapes/plot_landscapes.cpp | 2 +- .../average_landscapes_on_grid.cpp | 2 +- .../compute_distance_of_landscapes_on_grid.cpp | 2 +- ...ompute_scalar_product_of_landscapes_on_grid.cpp | 2 +- .../create_landscapes_on_grid.cpp | 2 +- .../plot_landscapes_on_grid.cpp | 2 +- .../average_persistence_vectors.cpp | 2 +- .../compute_distance_of_persistence_vectors.cpp | 2 +- ...mpute_scalar_product_of_persistence_vectors.cpp | 2 +- .../create_persistence_vectors.cpp | 2 +- .../plot_persistence_vectors.cpp | 2 +- .../benchmark/performance_rips_persistence.cpp | 2 +- .../concept/CoefficientField.h | 2 +- .../concept/FilteredComplex.h | 2 +- .../concept/PersistentHomology.h | 2 +- src/Persistent_cohomology/doc/COPYRIGHT | 2 +- .../doc/Intro_persistent_cohomology.h | 2 +- .../example/custom_persistence_sort.cpp | 2 +- .../example/persistence_from_file.cpp | 2 +- .../persistence_from_simple_simplex_tree.cpp | 2 +- .../example/plain_homology.cpp | 2 +- .../example/rips_multifield_persistence.cpp | 2 +- .../example/rips_persistence_step_by_step.cpp | 2 +- .../rips_persistence_via_boundary_matrix.cpp | 2 +- .../include/gudhi/Persistent_cohomology.h | 2 +- .../include/gudhi/Persistent_cohomology/Field_Zp.h | 2 +- .../gudhi/Persistent_cohomology/Multi_field.h | 2 +- .../Persistent_cohomology_column.h | 2 +- .../concept/SimplicialComplexForRips.h | 2 +- src/Rips_complex/doc/COPYRIGHT | 2 +- src/Rips_complex/doc/Intro_rips_complex.h | 2 +- src/Rips_complex/include/gudhi/Rips_complex.h | 2 +- .../include/gudhi/Sparse_rips_complex.h | 2 +- src/Rips_complex/test/test_rips_complex.cpp | 2 +- .../rips_correlation_matrix_persistence.cpp | 2 +- .../utilities/rips_distance_matrix_persistence.cpp | 2 +- src/Rips_complex/utilities/rips_persistence.cpp | 2 +- .../utilities/sparse_rips_persistence.cpp | 2 +- src/Simplex_tree/concept/FiltrationValue.h | 2 +- src/Simplex_tree/concept/IndexingTag.h | 2 +- src/Simplex_tree/concept/SimplexKey.h | 2 +- src/Simplex_tree/concept/SimplexTreeOptions.h | 2 +- src/Simplex_tree/concept/VertexHandle.h | 2 +- src/Simplex_tree/doc/COPYRIGHT | 2 +- src/Simplex_tree/doc/Intro_simplex_tree.h | 2 +- .../example/cech_complex_cgal_mini_sphere_3d.cpp | 4 ++-- ...e_alpha_shapes_3_simplex_tree_from_off_file.cpp | 2 +- .../example/graph_expansion_with_blocker.cpp | 2 +- src/Simplex_tree/example/mini_simplex_tree.cpp | 2 +- src/Simplex_tree/example/simple_simplex_tree.cpp | 2 +- .../example/simplex_tree_from_cliques_of_graph.cpp | 2 +- src/Simplex_tree/include/gudhi/Simplex_tree.h | 2 +- .../gudhi/Simplex_tree/Simplex_tree_iterators.h | 2 +- .../Simplex_tree_node_explicit_storage.h | 2 +- .../gudhi/Simplex_tree/Simplex_tree_siblings.h | 2 +- .../include/gudhi/Simplex_tree/indexing_tag.h | 2 +- src/Skeleton_blocker/concept/SkeletonBlockerDS.h | 2 +- .../concept/SkeletonBlockerGeometricDS.h | 2 +- src/Skeleton_blocker/doc/COPYRIGHT | 2 +- .../example/Skeleton_blocker_from_simplices.cpp | 2 +- .../example/Skeleton_blocker_iteration.cpp | 2 +- .../example/Skeleton_blocker_link.cpp | 2 +- .../include/gudhi/Skeleton_blocker.h | 2 +- .../Skeleton_blocker_complex_visitor.h | 2 +- .../Skeleton_blocker_link_superior.h | 2 +- .../Skeleton_blocker/Skeleton_blocker_off_io.h | 2 +- .../Skeleton_blocker_simple_geometric_traits.h | 2 +- .../Skeleton_blocker_simple_traits.h | 2 +- .../Skeleton_blocker/Skeleton_blocker_simplex.h | 2 +- .../Skeleton_blocker_sub_complex.h | 2 +- .../gudhi/Skeleton_blocker/internal/Top_faces.h | 2 +- .../include/gudhi/Skeleton_blocker/internal/Trie.h | 2 +- .../Skeleton_blockers_blockers_iterators.h | 2 +- .../iterators/Skeleton_blockers_edges_iterators.h | 2 +- .../iterators/Skeleton_blockers_iterators.h | 2 +- .../Skeleton_blockers_simplices_iterators.h | 2 +- .../Skeleton_blockers_triangles_iterators.h | 2 +- .../Skeleton_blockers_vertices_iterators.h | 2 +- .../include/gudhi/Skeleton_blocker_complex.h | 2 +- .../gudhi/Skeleton_blocker_geometric_complex.h | 2 +- .../include/gudhi/Skeleton_blocker_link_complex.h | 2 +- .../gudhi/Skeleton_blocker_simplifiable_complex.h | 2 +- .../test/test_skeleton_blocker_complex.cpp | 2 +- .../test_skeleton_blocker_geometric_complex.cpp | 2 +- .../test/test_skeleton_blocker_simplifiable.cpp | 2 +- .../doc/Intro_spatial_searching.h | 2 +- .../include/gudhi/Kd_tree_search.h | 2 +- src/Spatial_searching/test/test_Kd_tree_search.cpp | 2 +- src/Subsampling/doc/Intro_subsampling.h | 2 +- .../include/gudhi/choose_n_farthest_points.h | 2 +- .../include/gudhi/pick_n_random_points.h | 2 +- src/Subsampling/include/gudhi/sparsify_point_set.h | 2 +- .../test/test_choose_n_farthest_points.cpp | 2 +- src/Subsampling/test/test_pick_n_random_points.cpp | 2 +- src/Subsampling/test/test_sparsify_point_set.cpp | 2 +- src/Tangential_complex/benchmark/RIB_exporter.h | 2 +- src/Tangential_complex/benchmark/XML_exporter.h | 2 +- src/Tangential_complex/doc/COPYRIGHT | 2 +- .../doc/Intro_tangential_complex.h | 2 +- .../include/gudhi/Tangential_complex.h | 2 +- .../gudhi/Tangential_complex/Simplicial_complex.h | 2 +- .../include/gudhi/Tangential_complex/config.h | 2 +- .../include/gudhi/Tangential_complex/utilities.h | 2 +- .../test/test_tangential_complex.cpp | 2 +- .../concept/SimplicialComplexForWitness.h | 2 +- src/Witness_complex/doc/COPYRIGHT | 2 +- .../example/example_nearest_landmark_table.cpp | 22 --------------------- .../example/example_strong_witness_complex_off.cpp | 22 --------------------- .../example/example_witness_complex_sphere.cpp | 22 --------------------- src/Witness_complex/example/generators.h | 2 +- .../include/gudhi/Active_witness/Active_witness.h | 2 +- .../gudhi/Active_witness/Active_witness_iterator.h | 2 +- .../gudhi/Euclidean_strong_witness_complex.h | 2 +- .../include/gudhi/Euclidean_witness_complex.h | 2 +- .../include/gudhi/Strong_witness_complex.h | 2 +- .../include/gudhi/Witness_complex.h | 2 +- .../include/gudhi/Witness_complex/all_faces_in.h | 2 +- .../utilities/strong_witness_persistence.cpp | 2 +- .../utilities/weak_witness_persistence.cpp | 2 +- src/common/doc/file_formats.h | 2 +- src/common/include/gudhi/Clock.h | 2 +- src/common/include/gudhi/Debug_utils.h | 2 +- src/common/include/gudhi/Null_output_iterator.h | 2 +- src/common/include/gudhi/Off_reader.h | 2 +- src/common/include/gudhi/Point.h | 2 +- src/common/include/gudhi/Points_3D_off_io.h | 2 +- src/common/include/gudhi/Points_off_io.h | 2 +- src/common/include/gudhi/Simple_object_pool.h | 2 +- src/common/include/gudhi/Unitary_tests_utils.h | 2 +- src/common/include/gudhi/allocator.h | 2 +- src/common/include/gudhi/console_color.h | 2 +- src/common/include/gudhi/distance_functions.h | 2 +- .../include/gudhi/graph_simplicial_complex.h | 2 +- src/common/include/gudhi/random_point_generators.h | 2 +- src/common/include/gudhi/reader_utils.h | 2 +- src/common/test/test_distance_matrix_reader.cpp | 2 +- .../test/test_persistence_intervals_reader.cpp | 2 +- src/common/test/test_points_off_reader.cpp | 2 +- .../utilities/off_file_from_shape_generator.cpp | 2 +- src/cython/cython/alpha_complex.pyx | 4 ++-- src/cython/cython/bottleneck_distance.pyx | 4 ++-- src/cython/cython/cubical_complex.pyx | 4 ++-- .../cython/euclidean_strong_witness_complex.pyx | 4 ++-- src/cython/cython/euclidean_witness_complex.pyx | 4 ++-- src/cython/cython/off_reader.pyx | 4 ++-- src/cython/cython/periodic_cubical_complex.pyx | 4 ++-- src/cython/cython/persistence_graphical_tools.py | 4 ++-- src/cython/cython/reader_utils.pyx | 4 ++-- src/cython/cython/rips_complex.pyx | 4 ++-- src/cython/cython/simplex_tree.pyx | 4 ++-- src/cython/cython/strong_witness_complex.pyx | 4 ++-- src/cython/cython/subsampling.pyx | 4 ++-- src/cython/cython/tangential_complex.pyx | 4 ++-- src/cython/cython/witness_complex.pyx | 4 ++-- ...ex_diagram_persistence_from_off_file_example.py | 4 ++-- .../example/alpha_complex_from_points_example.py | 4 ++-- .../alpha_rips_persistence_bottleneck_distance.py | 4 ++-- src/cython/example/bottleneck_basic_example.py | 4 ++-- ...ex_diagram_persistence_from_off_file_example.py | 4 ++-- ...ex_diagram_persistence_from_off_file_example.py | 4 ++-- .../example/gudhi_graphical_tools_example.py | 4 ++-- ...arcode_persistence_from_perseus_file_example.py | 4 ++-- .../random_cubical_complex_persistence_example.py | 4 ++-- ...istence_from_correlation_matrix_file_example.py | 4 ++-- ...ersistence_from_distance_matrix_file_example.py | 4 ++-- ...ex_diagram_persistence_from_off_file_example.py | 4 ++-- .../example/rips_complex_from_points_example.py | 4 ++-- src/cython/example/rips_persistence_diagram.py | 4 ++-- src/cython/example/simplex_tree_example.py | 4 ++-- ...complex_plain_homology_from_off_file_example.py | 4 ++-- .../witness_complex_from_nearest_landmark_table.py | 4 ++-- src/cython/gudhi.pyx.in | 4 ++-- src/cython/include/Alpha_complex_interface.h | 2 +- src/cython/include/Bottleneck_distance_interface.h | 2 +- src/cython/include/Cubical_complex_interface.h | 2 +- .../Euclidean_strong_witness_complex_interface.h | 2 +- .../include/Euclidean_witness_complex_interface.h | 2 +- src/cython/include/Off_reader_interface.h | 2 +- .../include/Persistent_cohomology_interface.h | 2 +- src/cython/include/Reader_utils_interface.h | 2 +- src/cython/include/Rips_complex_interface.h | 2 +- src/cython/include/Simplex_tree_interface.h | 2 +- .../include/Strong_witness_complex_interface.h | 2 +- src/cython/include/Subsampling_interface.h | 2 +- src/cython/include/Tangential_complex_interface.h | 2 +- src/cython/include/Witness_complex_interface.h | 2 +- src/cython/setup.py.in | 4 ++-- src/cython/test/test_alpha_complex.py | 4 ++-- src/cython/test/test_bottleneck_distance.py | 4 ++-- src/cython/test/test_cubical_complex.py | 4 ++-- src/cython/test/test_euclidean_witness_complex.py | 4 ++-- src/cython/test/test_reader_utils.py | 4 ++-- src/cython/test/test_rips_complex.py | 4 ++-- src/cython/test/test_simplex_tree.py | 4 ++-- src/cython/test/test_subsampling.py | 4 ++-- src/cython/test/test_tangential_complex.py | 4 ++-- src/cython/test/test_witness_complex.py | 4 ++-- 338 files changed, 425 insertions(+), 446 deletions(-) (limited to 'src/Nerve_GIC') 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 a08663ca..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 diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 91305032..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 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 . + */ + #include #include 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 a5d7b60f..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 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 770eb55f..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 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/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/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/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/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 cf9a2c27..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 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/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 072d1185..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 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 . + * + */ + #include // isfinite #include diff --git a/src/GudhUI/utils/Critical_points.h b/src/GudhUI/utils/Critical_points.h index e7b9ef31..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 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 4000a331..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 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 59b4bee2..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 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 2b648425..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 diff --git a/src/Nerve_GIC/example/CoordGIC.cpp b/src/Nerve_GIC/example/CoordGIC.cpp index d544db94..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 diff --git a/src/Nerve_GIC/example/FuncGIC.cpp b/src/Nerve_GIC/example/FuncGIC.cpp index cb0f0d63..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 diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index d6f3ded6..aa6478e5 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 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/KeplerMapperVisuFromTxtFile.py b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py index c811f610..701e7a52 100755 --- a/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py +++ b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py @@ -11,7 +11,7 @@ import argparse 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 @@ -28,7 +28,7 @@ import argparse """ __author__ = "Mathieu Carriere" -__copyright__ = "Copyright (C) 2017 INRIA" +__copyright__ = "Copyright (C) 2017 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='Creates an html Keppler Mapper ' diff --git a/src/Nerve_GIC/utilities/Nerve.cpp b/src/Nerve_GIC/utilities/Nerve.cpp index aefc3874..667129e0 100644 --- a/src/Nerve_GIC/utilities/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 diff --git a/src/Nerve_GIC/utilities/VoronoiGIC.cpp b/src/Nerve_GIC/utilities/VoronoiGIC.cpp index 54bb871e..33deca40 100644 --- a/src/Nerve_GIC/utilities/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 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 38bd3a21..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 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/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/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/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 d6b662e9..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 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 3113a22c..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 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 a8c9afa3..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 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 5a551e60..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 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 index 1a9d6ebb..19a44b28 100644 --- a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h +++ b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2018 INRIA + * 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 diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp index 4e7b79d2..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 diff --git a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp index c2082fae..d4671b45 100644 --- a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp +++ b/src/Rips_complex/utilities/rips_correlation_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_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/sparse_rips_persistence.cpp b/src/Rips_complex/utilities/sparse_rips_persistence.cpp index d4bae3ba..bcd5c2c5 100644 --- a/src/Rips_complex/utilities/sparse_rips_persistence.cpp +++ b/src/Rips_complex/utilities/sparse_rips_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse, Clément Maria * - * Copyright (C) 2018 INRIA + * 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 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 6b80d1c9..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 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 aca2aa57..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 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 52ed65e4..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 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 ab9cdc37..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 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/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 00e00c52..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 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/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 . - */ - #define BOOST_PARAMETER_MAX_ARITY 12 #include 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 . - */ - #include #include #include 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 . - */ - #define BOOST_PARAMETER_MAX_ARITY 12 #include 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/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/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 32320e4d..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 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 08f324c6..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 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/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/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/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 266dae2c..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": 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 73b154b8..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 @@ -28,7 +28,7 @@ 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": 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/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 386f8457..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 ' diff --git a/src/cython/example/bottleneck_basic_example.py b/src/cython/example/bottleneck_basic_example.py index a7fa01c1..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 @@ -25,7 +25,7 @@ import gudhi """ __author__ = "Francois Godi, Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,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 index aa82ef71..4142fa99 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -10,7 +10,7 @@ import argparse 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 @@ -27,7 +27,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2017 INRIA" +__copyright__ = "Copyright (C) 2017 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='RipsComplex creation from ' 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 c8aac240..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 @@ -26,7 +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 ' 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 544b68c9..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 ' 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 f26befbc..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 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 c767e93d..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 @@ -24,7 +24,7 @@ from Cython.Build import cythonize """ __author__ = "GUDHI Editorial Board" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" gudhi = Extension( 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" -- cgit v1.2.3