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function P = sammon(D, P, varargin)
%SAMMON Computes Sammon's mapping of a data set.
%
% P = sammon(D, P, [value], [mode], [alpha], [Mdist])
%
% P = sammon(D,2); % projection to 2-dim space
% P = sammon(sMap,3); % projects the codebook vectors
% P = sammon(sMap,3,[],[],[],Md) % uses distance matrix Md
% som_grid(sMap,'Coord',P) % visualization of map projection
%
% Input and output arguments ([]'s are optional):
% D (matrix) size dlen x dim, data to be projected
% (struct) data or map struct
% P (scalar) output dimension
% (matrix) size dlen x odim, initial projection matrix
% [value] (scalar) all different modes (the next argument) require
% a value, default = 100
% [mode] (string) 'steps' or 'errlimit' or 'errchange' or 'seconds',
% see below, default is 'steps'
% [alpha] (scalar) iteration step size, default = 0.2
% [Dist] (matrix) pairwise distance matrix, size dlen x dlen.
% If the distances in the input space should
% be calculated otherwise than as euclidian
% distances, the distance from each vector
% to each other vector can be given here,
% size dlen x dlen. For example PDIST
% function can be used to calculate the
% distances: Dist = squareform(pdist(D,'mahal'));
%
% P (matrix) size dlen x odim, the projections
%
% The output dimension must be 2 or higher but (naturally) lower
% than data set dimension.
%
% The mode argument determines the end condition for iteration. If
% the mode argument is used, also the value argument has to be
% specified. Different mode possibilities are:
% 'steps' the iteration is terminated when it is run <value>
% 'errlimit' steps, the iteration is terminated when projection error
% is lower than <value>,
% 'errchange' the iteration is terminated when change between
% projection error on two successive iteration rounds
% is less than <value> percent of total error, and
% 'seconds' the iteration is terminated after <value> seconds
% of iteration.
%
% See also CCA, PCAPROJ, SOM_GRID.
% Reference: Sammon, J.W. Jr., "A nonlinear mapping for data
% structure analysis", IEEE Transactions on Computers, vol. C-18,
% no. 5, 1969, pp. 401-409.
% Contributed to SOM Toolbox vs2, February 2nd, 2000 by Juha Vesanto
% Copyright (c) by Juha Vesanto
% http://www.cis.hut.fi/projects/somtoolbox/
% juuso 040100
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% check arguments
error(nargchk(2, 6, nargin)); % check no. of input arguments is correct
% input data
if isstruct(D),
if isfield(D, 'data'), D = D.data; % data struct
elseif isfield(D, 'codebook'), D = D.codebook; % map struct
else error('Invalid structure');
end
end
if any(isnan(D(:))),
error('Cannot make Sammon''s projection for data with unknown components')
end
% compute data dimensions
orig_si = size(D);
dim = orig_si(end);
noc = prod(orig_si)/dim;
if length(orig_si)>2, D = reshape(D,[noc dim]); end
% output dimension / initial projection matrix
if prod(size(P))==1,
odim = P;
P = rand(noc,odim)-0.5;
else
si = size(P);
odim = si(end);
if prod(si) ~= noc*odim,
error('Initial projection matrix size does not match data size');
end
if length(si)>2, P = reshape(P,[noc odim]); end
inds = find(isnan(P));
if length(inds), P(inds) = rand(size(inds)); end
end
if odim > dim | odim < 2,
error('Output dimension must be within [2, dimension of data]');
end
% determine operating mode
if nargin < 3 | isempty(varargin{1}) | isnan(varargin{1}), value=100;
else value = varargin{1};
end
if nargin < 4 | isempty(varargin{2}) | isnan(varargin{2}), mode='steps';
else mode = varargin{2};
end
switch mode,
case 'steps', runlen = value;
case 'errlimit', errlimit = value;
case 'errchange', errchange = value; e_prev = 0;
case 'seconds', endtime = value;
otherwise, error(['Illegal mode: ' mode]);
end
% iteration step size
if nargin > 4, alpha = varargin{3}; else alpha = NaN; end
if isempty(alpha) | isnan(alpha), alpha = 0.2; end
% mutual distances
if nargin > 5, Mdist = varargin{4}; else Mdist = []; end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% initialization
% these are used quite frequently
noc_x_1 = ones(noc, 1);
odim_x_1 = ones(odim,1);
% compute mutual distances between vectors
if isempty(Mdist) | all(isnan(Mdist(:))),
fprintf(2, 'computing mutual distances\r');
dim_x_1 = ones(dim,1);
for i = 1:noc,
x = D(i,:);
Diff = D - x(noc_x_1,:);
N = isnan(Diff);
Diff(find(N)) = 0;
Mdist(:,i) = sqrt((Diff.^2)*dim_x_1);
N = find(sum(N')==dim); %mutual distance unknown
if ~isempty(N), Mdist(N,i) = NaN; end
end
else
% if the distance matrix is output from PDIST function
if size(Mdist,1)==1, Mdist = squareform(Mdist); end
if size(Mdist,1)~=noc,
error('Mutual distance matrix size and data set size do not match');
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% action
if strcmp(mode, 'seconds'), tic; end;
fprintf(2, 'iterating \r');
% sammon iteration
x = P ;
xu = zeros(noc, odim);
xd = zeros(noc, odim);
dq = zeros(noc, 1);
dr = zeros(noc, 1);
i = 0;
ready = 0;
while ~ready
for j = 1:noc,
xd = -x + x(j*noc_x_1,:);
xd2 = xd.^2;
dpj = sqrt(sum(xd2'))';
dq = Mdist(:,j) - dpj;
dr = Mdist(:,j) .* dpj;
ind = find(dr ~= 0);
term = dq(ind) ./ dr(ind);
e1 = sum(xd(ind,:) .* term(:,odim_x_1));
term2 = ((1.0 + dq(ind) ./ dpj(ind)) ./ dpj(ind)) ./ dr(ind);
e2 = sum(term) - sum(xd2(ind,:) .* term2(:,odim_x_1));
xu(j,:) = x(j,:) + alpha * e1 ./ abs(e2);
end
% move the center of mass to the center
c = sum(xu) / noc;
x = xu - c(noc_x_1, :);
i = i + 1;
% compute mapping error
% doing this adds about 25% to computing time
if 0,
e = 0; tot = 0;
for j = 2:noc,
d = Mdist(1:(j - 1), j);
tot = tot + sum(d);
ind = find(d ~= 0);
xd = -x(1:(j - 1), :) + x(j * ones(j - 1, 1), :);
ee = d - sqrt(sum(xd'.^2))';
e = e + sum(ee(ind).^2 ./ d(ind));
end
e = e/tot;
fprintf(2, '\r%d iterations, error %f', i, e);
else
fprintf(2, '\r%d iterations', i);
end
% determine is the iteration ready
switch mode
case 'steps',
if i == runlen, ready = 1; end;
case 'errlimit',
if e < errlimit, ready = 1; end;
case 'errchange',
if i > 1
change = 100 * abs(e - e_prev) / e_prev;
if change < errchange, ready = 1; end;
fprintf(2, ', change of error %f %% ', change);
end
e_prev = e;
case 'seconds'
if toc > endtime, ready = 1; end;
fprintf(2, ', elapsed time %f seconds ', toc);
end
fprintf(2, ' ');
% If you want to see the Sammon's projection plotted (in 2-D and 3-D case),
% execute the code below; it is not in use by default to speed up
% computation.
if 0,
clf
if odim == 1, plot(x(:,1), noc_x_1, 'o');
elseif odim == 2, plot(x(:,1), x(:,2), 'o');
else plot3(x(:,1), x(:,2), x(:,3), 'o')
end
drawnow
end
end
fprintf(2, '\n');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% clean up
% reshape
orig_si(end) = odim;
P = reshape(x, orig_si);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%