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function P = som_order_cplanes(sM, varargin)
%SOM_ORDER_CPLANES Orders and shows the SOM component planes.
%
% P = som_order_cplanes(sM, [[argID,] value, ...])
%
% som_order_cplanes(sM);
% som_order_cplanes(sM,'comp',1:30,'simil',C,'pca');
% P = som_order_cplanes(sM);
%
% Input and output arguments ([]'s are optional):
% sM (struct) map or data struct
% (matrix) a data matrix, size * x dim
% [argID, (string) See below. The values which are unambiguous can
% value] (varies) be given without the preceeding argID.
%
% P (matrix) size n x * (typically n x 2), the projection coordinates
%
% Here are the valid argument IDs and corresponding values. The values
% which are unambiguous (marked with '*') can be given without the
% preceeding argID.
% 'comp' (vector) size 1 x n, which components to project, 1:dim by default
% 'simil' *(string) similarity measure to use
% 'corr' linear correlation between component planes
% 'abs(corr)' absolute value of correlation (default)
% 'umat' as 'abs(corr)' but calculated from U-matrices
% 'mutu' mutual information (not implemented yet)
% (matrix) size n x n, a similarity matrix to be used
% 'proj' *(string) projection method to use: 'SOM' (default),
% 'pca', 'sammon', 'cca', 'order', 'ring'
% 'msize' (vector) size of the SOM that is used for projection
% 'show' *(string) how visualization is done: 'planes' (default),
% 'names', or 'none'
% 'mask' (vector) dim x 1, the mask to use, ones(dim,1) by default
% 'comp_names' (cell array) of strings, size dim x 1, the component names
%
% The visualized objects have a callback associated with them: by
% clicking on the object, the index and name of the component are printed
% to the standard output.
%
% See also SOM_SHOW.
% Copyright (c) 2000 by the SOM toolbox programming team.
% Contributed to SOM Toolbox on June 16th, 2000 by Juha Vesanto
% http://www.cis.hut.fi/projects/somtoolbox/
% Version 2.0beta juuso 120600 070601
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% check arguments
% sM
if isstruct(sM),
switch sM.type
case 'som_map',
D = sM.codebook; dim = size(D,2); cnames = sM.comp_names; mask = sM.mask;
ismap = 1;
case 'som_data',
D = sM.data; dim = size(D,2); cnames = sM.comp_names; mask = ones(dim,1);
ismap = 0;
otherwise, error('Invalid first argument.');
end
else
D = sM;
dim = size(D,2); mask = ones(dim,1);
cnames = cell(dim,1);
for i = 1:dim, cnames{i} = sprintf('Variable%d',i); end
ismap = 0;
end
% defaults
comps = 1:dim;
simil = 'abs(corr)';
proj = 'SOM';
show = 'planes';
mapsize = NaN;
% varargin
i=1;
while i<=length(varargin),
argok = 1;
if ischar(varargin{i}),
switch varargin{i},
% argument IDs
case 'mask', i=i+1; mask = varargin{i};
case 'comp_names', i=i+1; cnames = varargin{i};
case 'comp', i=i+1; comps = varargin{i};
case 'proj', i=i+1; proj = varargin{i};
case 'show', i=i+1; show = varargin{i};
case 'simil', i=i+1; simil = varargin{i};
case 'msize', i=i+1; mapsize = varargin{i};
% unambiguous values
case {'corr','abs(corr)','umat','mutu'}, simil = varargin{i};
case {'SOM','pca','sammon','cca','order','ring'}, proj = varargin{i};
case {'planes','names','none'}, show = varargin{i};
otherwise argok=0;
end
else
argok = 0;
end
if ~argok,
disp(['(som_order_cplanes) Ignoring invalid argument #' num2str(i+1)]);
end
i = i+1;
end
if strcmp(show,'planes') & ~ismap,
warning('Given data is not a map: using ''names'' visualization.');
show = 'names';
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% similarity matrix
fprintf(1,'Calculating similarity matrix\n');
% use U-matrix
if strcmp(simil,'umat'),
if ~ismap, error('Given data is not a map: cannot use U-matrix similarity.'); end
U = som_umat(sM);
D = zeros(prod(size(U)),dim);
m = zeros(dim,1);
for i=1:dim, m=m*0; m(i)=1; U = som_umat(sM,'mask',m); D(:,i) = U(:); end
end
% components
D = D(:,comps);
cnames = cnames(comps);
mask = mask(comps);
dim = length(comps);
% similarity matrix
if ischar(simil),
switch simil,
case {'corr','abs(corr)','umat'},
A = zeros(dim);
me = zeros(1,dim);
for i=1:dim,
me(i) = mean(D(isfinite(D(:,i)),i)); D(:,i) = D(:,i) - me(i);
end
for i=1:dim,
for j=i:dim,
c = D(:,i).*D(:,j); c = c(isfinite(c));
A(i,j) = sum(c)/length(c); A(j,i) = A(i,j);
end
end
s = diag(A);
A = A./sqrt(s*s');
switch simil,
case {'abs(corr)','umat'}, A = abs(A);
case 'corr', A = A + 1;
end
case 'mutu',
error('Mutual information not implemented yet.');
end
else
A = simil;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% projection
fprintf(1,'Projection\n');
mu = 2*dim;
switch proj,
case 'SOM',
if isnan(mapsize),
sMtmp = som_randinit(A,'munits',mu);
msize = sMtmp.topol.msize;
else
msize = mapsize;
end
sM2 = som_make(A,'msize',msize,'rect','tracking',0);
bm = assign_unique_bm(sM2,A);
Co = som_unit_coords(sM2);
P = Co(bm,:);
case 'ring',
if isnan(mapsize), msize = [1 mu]; else msize = mapsize; end
sM2 = som_make(A,'msize',msize,'cyl','rect','tracking',0);
bm = assign_unique_bm(sM2,A);
Co = som_unit_coords(sM2);
P = Co(bm,[1 3]);
case 'order',
if isnan(mapsize), msize = [1 mu]; else msize = mapsize; end
sM2 = som_make(A,'msize',msize,'tracking',0);
bm = assign_unique_bm(sM2,A);
[dummy,i] = sort(bm);
[dummy,P] = sort(i);
if size(P,2)>1, P = P'; end
if size(P,2)==1, P(:,2) = zeros(length(P),1); end
case {'pca','sammon','cca'},
P = pcaproj(A,2);
if strcmp(proj,'sammon'), P = sammon(A,P,50,'steps');
elseif strcmp(proj,'cca'), P = cca(A,P,50);
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% visualization
if ~strcmp(show,'none'),
fprintf(1,'Visualization\n');
cla
hold on
if strcmp(show,'planes')
s = findscaling(sM.topol.msize,P);
for i=1:dim,
C = som_normcolor(D(:,i));
if strcmp(simil,'umat'),
h=som_cplane([sM.topol.lattice 'U'],sM.topol.msize,C,1,s*P(i,:));
else
h=som_cplane(sM,C,1,s*P(i,:));
end
set(h,'edgecolor','none','Userdata',sprintf('[%d] %s',i,cnames{i}));
set(h,'ButtonDownFcn','fprintf(1,''%s\n'',get(gco,''UserData''))');
end
else
s=1;
a=[min(P(:,1))-1 max(P(:,1))+1 min(P(:,2))-1-3 max(P(:,2))+1-3];
axis(s*a);
end
h=text(s*P(:,1),s*P(:,2)-3,cnames);
for i=1:length(h), set(h(i),'Userdata',sprintf('[%d] %s',i,cnames{i})); end
set(h,'ButtonDownFcn','fprintf(1,''%s\n'',get(gco,''UserData''))');
hold off
axis on; axis equal; axis tight; set(gca,'XTick',[],'YTick',[],'Box','on');
end
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
%% subfunctions
function bm = assign_unique_bm(sM,D)
munits = size(sM.codebook,1);
[dlen dim] = size(D);
margin = max(0,dlen-munits);
[bm,qers] = som_bmus(sM,D);
bmi=ones(dim,1);
hits = som_hits(sM,D);
mult = find(hits>1);
while any(mult) & sum(hits(mult))-length(mult)>margin,
choices = find(bm==mult(1));
while length(choices)>1,
[dummy,mv] = max(qers(choices)); mv = choices(mv);
[mv_to,q] = som_bmus(sM,D(mv,:),bmi(mv));
bmi(mv)=bmi(mv)+1; qers(mv) = q; bm(mv) = mv_to;
choices = find(bm==mv_to);
end
for i=1:length(hits), hits(i)=sum(bm==i); end
mult = find(hits>1);
end
return;
function s = findscaling(msize,P)
d1 = median(abs(diff(unique(sort(P(:,1))))));
d2 = median(abs(diff(unique(sort(P(:,2))))));
if d1>0, s1 = 1.5*msize(2)/d1; else s1 = 0; end
if d2>0, s2 = 1.5*msize(1)/d2; else s2 = 0; end
s = max(s1,s2);
if s==0, s=1; end
return;
function alternative_SOM_plane_vis(sT,bm,simil,D,cnames)
clf
for i=1:size(D,2),
subplot(sT.msize(2),sT.msize(1),bm(i));
if strcmp(simil,'umat'), h=som_cplane([sT.lattice 'U'],sT.msize,D(:,i));
else h=som_cplane(sT,D(:,i));
end
set(h,'edgecolor','none');
title(cnames{i});
axis off
end
return;