mfbox_pos_denoise_run.m

toolbox for spm 5 for data, model free analysis

function [A,W,S,params,reliability]=mfbox_pos_denoise_run(A,W,S,X,params,runflag)
% denoise result
%
% Usage:
%  [A,W,S,params,reliability]=mfbox_pos_denoise_run(A,W,S,X,params,runflag)
%
%  X           - cell with
%                (NxT) data
%                (Tx3) grid
%                timeline
%                mask
%                design
%                reference
%  A           - (TxD) mixing matrix
%  W           - (DxT) demixing matrix
%  S           - struct with
%                dat              - (MxD) components (M<=N unique datapoints)
%                mask             - mask selecting unique subset of grid
%                part             - cell array containing the different parts 
%                                   of the analysis
%                map              - (TxC) maps (timestep,component) to element in
%                                   1...D (D>=C)
%                spatialnoisevar  - (Mx1) spatial variance of the noise
%                temporalnoisevar - (Tx1) temporal variance of the noise
%                names            - (Cx1) cell with names
%  params      - struct with
%                tempdelaydim - temporal delay dimension
%                tempclusters - temporal number of clusters
%                tempstepsize - temporal step size
%                tempmethod   - ica
%                               pca
%                spatdelaydim - spatial elay dimension
%                spatclusters - spatial number of clusters
%                spatstepsize - spatial step size
%                spatmethod   - ica
%                               pca
%                method       - actions to perform (method(1): temporal,
%                               method(2): spatial)
%  reliability - struct
%  runflag     - -1 get default parameter
%                 0 interactive ask parameters
%                 1 interactive ask parameters and run
%                 2 run
%
% Copyright by Peter Gruber and Fabian J. Theis
% Signal Processing & Information Theory group
% Institute of Biophysics, University of Regensburg, Germany
% Homepage: http://research.fabian.theis.name
%           http://www-aglang.uni-regensburg.de
%
% This file is free software, subject to the 
% GNU GENERAL PUBLIC LICENSE, see gpl.txt

error(nargchk(3,6,nargin));
error(nargchk(1,5,nargout));

if (nargin<4), X = []; end
if (nargin<5), params = []; end
if (nargin<6), runflag = 1; end

s = size(S.dat);
dim = s(1:(end-1));
n = size(S.map,2);
timesteps = size(A,1);

params = mfbox_checkparam(params,'pos','denoise', ...
    struct('tempdelaydim',30,'tempclusters',1, ...
    'tempstepsize',1,'tempmethod','ica','spatdelaydim',10, ...
    'spatclusters',10,'spatstepsize',2,'spatmethod','pca','method',[1,1]));
reliability = struct();

if (abs(runflag-0.5)<1)
    if (exist('OCTAVE_HOME')~=5)% matlab
        params = mfbox_pos_denoiseg(A,W,S,X,params);
    end
end

if (runflag>0 && isstruct(params))
    switch params.tempmethod
        case 'ica'
            redm = 'pearsonica';
            sortm = 'comb';
            rep = 3.5;
        case 'pca'
            redm = 'pca';
            sortm = 'var';
            rep = 2.5;
    end

    if (params.method(1)==1)
        A = reshape(mfbox_denoise(reshape(A,1,[]), ...
            params.tempdelaydim,params.tempclusters,params.tempstepsize, ...
            'kmeans',redm,'avg',sortm,'mdl',32,rep),size(A));
    end

    switch params.spatmethod
        case 'ica'
            redm = 'pearsonica';
            sortm = 'comb';
            rep = 1;
        case 'pca'
            redm = 'pca';
            sortm = 'var';
            rep = 1;
    end

    if (params.method(2)==1)
        for j=1:size(S.dat,2)
            grid = X{2};
            grid = grid(:,S.mask);
            tS = reshape(mfbox_denoise({S.dat,grid},params.spatdelaydim, ...
                params.spatclusters,params.spatstepsize, ...
                'kmeans',redm,'avg',sortm,'mdl',32,rep),[],1);
            S.dat(:,j) = tS(S.mask);
        end
    end
end