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# catci

## (Toolbox/catci.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    [Cmap,map]=catci(acti,Cmap,M,cThres)

### Help Text

    CATCI - computing color coding for activation on the vertices
     function [Cmap,map]=catci(acti,Cmap,M,cThres)

    	computing color coding for activation on the vertices

      inputs : acti : vector containing activation, Cmap : colormap containing deepness coding on the vertices; M a value that indicates the maximum of activation for relative color mapping
      outputs : Cmap : colormap containing deepnes and activation coding on the vertices, map : colormap for the coding of activation

### Cross-Reference Information

This function is called by

    bst_imaging_display                C:\BrainStorm_2001\Toolbox\bst_imaging_display.m
    c_activ                            C:\BrainStorm_2001\Toolbox\c_activ.m

### Listing of function C:\BrainStorm_2001\Toolbox\catci.m

    function [Cmap,map]=catci(acti,Cmap,M,cThres)
    %CATCI - computing color coding for activation on the vertices
    % function [Cmap,map]=catci(acti,Cmap,M,cThres)
    %
    %    computing color coding for activation on the vertices
    %
    %  inputs : acti : vector containing activation, Cmap : colormap containing deepness coding on the vertices; M a value that indicates the maximum of activation for relative color mapping
    %  outputs : Cmap : colormap containing deepnes and activation coding on the vertices, map : colormap for the coding of activation
    %

    %<autobegin> ---------------------- 26-May-2004 11:29:53 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Visualization
    %
    % At Check-in: $Author: Mosher $  $Revision: 15 $  $Date: 5/26/04 9:59a $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 24-May-2004
    %
    % Principal Investigators and Developers:
    % ** Richard M. Leahy, PhD, Signal & Image Processing Institute,
    %    University of Southern California, Los Angeles, CA
    % ** John C. Mosher, PhD, Biophysics Group,
    %    Los Alamos National Laboratory, Los Alamos, NM
    % ** Sylvain Baillet, PhD, Cognitive Neuroscience & Brain Imaging Laboratory,
    %    CNRS, Hopital de la Salpetriere, Paris, France
    %
    % See BrainStorm website at http://neuroimage.usc.edu for further information.
    %
    % Copyright (c) 2004 BrainStorm by the University of Southern California
    % This software distributed  under the terms of the GNU General Public License
    % as published by the Free Software Foundation. Further details on the GPL
    % license can be found at http://www.gnu.org/copyleft/gpl.html .
    %
    % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
    % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
    % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
    % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
    % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
    %<autoend> ------------------------ 26-May-2004 11:29:53 -----------------------

    % threshold for activation
    MaxActi = max(abs(acti(:)));
    acti=abs(acti)/MaxActi;

    if nargin == 2
        M = MaxActi;
        cThres = 0;
    elseif nargin == 3
        cThres = 0;
    end

    MAX = MaxActi/M; % Colormapping relative to maximum M
    v_actthres=find(MAX*acti>=cThres/100);
    acti_thres=acti(v_actthres);

    % spreading of activationsize9)
    %acti_thres = (acti_thres-min(acti))/(max(acti_thres-min(acti)));
    %acti_thres = MAX*acti_thres/max(acti_thres);
    acti_thres = acti_thres/max(acti_thres);

    clear acti;

    %C_contrast=sum(Cmap,2)/3;
    %C_contrast=.35*ones(size(Cmap(:,1)));%Cmap(:,1); % Assume grey levels for depth coding
    C_contrast = Cmap(v_actthres,1); % Assume grey levels for depth coding / do .8*Cmap(v_actthres,1) for darker colors

    % coding of activation itself
    CR=ones(size(v_actthres,1),1);
    CG=CR;
    CB=CR;

    % % Processing of the RED colormap
    % maxx = MAX./C_contrast;
    % minn = ones(size(maxx));
    % x1 = 0; x2 = 48/128;
    % I1=find(acti_thres<=x2);
    % CR(I1)= ((acti_thres(I1)-x1)/(x2-x1)).*(maxx(I1)-minn(I1))+minn(I1);
    % I1=find(acti_thres>x2);
    % CR(I1) = maxx(I1);%*(ones(size(I1,1),1));
    %
    % %Processing of the GREEN & BLUE colormaps
    % x1 = 0; x2 = 64/128;
    % I1=find(acti_thres<=x2);
    % CG(I1) = minn(I1);%*(ones(size(I1,1),1));
    % CB(I1) = minn(I1);%*(ones(size(I1,1),1));
    %
    % x1 = 64/128; x2 = 128/128;
    % I1=find(acti_thres>x1 & acti_thres<=x2);
    % CG(I1)= ((acti_thres(I1)-x1)/(x2-x1)).*(maxx(I1)-minn(I1))+minn(I1);
    % CB(I1) = minn(I1);%*(ones(size(I1,1),1));
    %

    % Processing of the RED colormap
    maxx = 1./C_contrast;
    minn = ones(size(maxx));
    x1 = 0; x2 = 84/128/MAX;
    K = 1;

    I1=find(acti_thres<=x2);
    CR(I1)= ((acti_thres(I1)-x1)/(x2-x1)).*(maxx(I1)-K*minn(I1))+K*minn(I1);
    CG(I1)= K*minn(I1);
    CB(I1)= K*minn(I1);

    I1=find(acti_thres > x2);
    CR(I1) = maxx(I1);%*(ones(size(I1,1),1));

    %Processing of the GREEN & BLUE colormaps
    x1 = 84/MAX/128; x2 = 128/MAX/128;
    I1=find(acti_thres >x1 & acti_thres<=x2);
    CG(I1)= ((acti_thres(I1)-x1)/(x2-x1)).*(maxx(I1)-K*minn(I1))+K*minn(I1);
    CB(I1) = K*minn(I1);%*(ones(size(I1,1),1));

    %Processing of the GREEN & BLUE colormaps
    x1 = 190/MAX/128; x2 = 128/MAX/128;
    I1=find(acti_thres >x1 & acti_thres<=x2);
    CG(I1)= maxx(I1);
    CB(I1) = ((acti_thres(I1)-x1)/(x2-x1)).*(maxx(I1)-K*minn(I1))+K*minn(I1);

    if ~isempty(v_actthres) % No source above the threshold
        % coding of deepness and activation on the vertices
        Cmap(v_actthres,:) = [C_contrast.*CR C_contrast.*CG C_contrast.*CB];
    end

    % compute the colormap for activation coding
    load('bst_cactivcmap','map') % Load colormap map from file (modifies HOT(128) colormap)
    return

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