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iCAPs/packages/gspbox/embedding/gsp_compute_coordinates.m
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gsp_compute_coordinates.m
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function coords = gsp_compute_coordinates(G, dim, method, param)
%GSP_COMPUTE_COORDINATES calculate coordinates
% Usage: coords = gsp_compute_coordinates( G , dim );
% coords = gsp_compute_coordinates( G , dim, method );
% coords = gsp_compute_coordinates( G , dim, method, param );
%
% Input parameters
% G : Graph
% dim : Number of lower dimentions
% method : Method to be used
% param : Structure of optional paramter
%
% Output parameters
% coords : New coordinates of graph that lives in a lower dimention
%
% This function computes coordinates from the weighted adjacency matrix.
% The available methods are:
%
% 'laplacian_eigenmaps' : Laplacian Eigenmaps. For further information,
% see the help of GSP_LAPLACIAN_EIGENMAPS (default)
% 'lle' : LLE (Loccaly Linear Embedding). For further
% information, see the help of GSP_LLE
% 'isomap' : Isomap. For further information, see the
% help of GSP_ISOMAP
%
% The coordinates can be insterted inside the graph structure with the
% function GSP_UPDATE_COORDINATES.
%
% param is a structure forwarding optiona paramter to the different
% functions.
%
% param.tol : Tolerance for the spectral gap (default 1e-6).
% For further parameters, check the selected method function's help.
%
% See also: gsp_update_coordinates gsp_isomap gsp_laplacian_eigenmaps gsp_lle
%
% Demo: gsp_demo_graph_embedding
%
%
% Url: http://lts2research.epfl.ch/gsp/doc/embedding/gsp_compute_coordinates.php
% Copyright (C) 2013-2016 Nathanael Perraudin, Johan Paratte, David I Shuman.
% This file is part of GSPbox version 0.7.0
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
% If you use this toolbox please kindly cite
% N. Perraudin, J. Paratte, D. Shuman, V. Kalofolias, P. Vandergheynst,
% and D. K. Hammond. GSPBOX: A toolbox for signal processing on graphs.
% ArXiv e-prints, Aug. 2014.
% http://arxiv.org/abs/1408.5781
% Authors : Dion O. E. Tzamarias
% Date : 20/11/2015
if nargin<4
param = struct;
end
if nargin<3
method = 'laplacian_eigenmaps';
end
if nargin<2
dim = 3;
end
if ~isfield(param,'tol'), param.tol = 1e-6; end
if iscell(G)
coords = cell(size(G));
for ii = 1: numel(G)
coords = gsp_compute_coordinates(G{ii}, dim, method, param);
end
end
if gsp_check_connectivity(G)==0
error('Graph is not connected')
warning('Use gsp_components to extract individual graph components')
[~, Gz, ~] = gsp_components(G);
% coords = cell(size(Gz));
% for ii=1:length(Gz)
% switch lower(method)
% case 'laplacian_eigenmaps'
% coords{ii} = gsp_laplacian_eigenmaps(Gz{ii}, dim, param);
% case 'lle'
% coords{ii} = gsp_lle(Gz{ii}, dim, param);
% case 'isomap'
% coords{ii} = gsp_isomap(Gz{ii}, dim);
% otherwise
% warning('Please specify param.method')
% end
% end
coords = gsp_compute_coordinates(G, dim, method, param);
else
switch lower(method)
case 'laplacian_eigenmaps'
coords = gsp_laplacian_eigenmaps(G, dim, param);
case 'lle'
coords = gsp_lle(G, dim, param);
case 'isomap'
coords = gsp_isomap(G, dim);
otherwise
warning('Please specify param.method')
end
end
end
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