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# c_activ

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

### Function Synopsis

    [Cmap,map]=c_activ(FV,connectivity_cell,prop_thres,ref_map,acti,cmap);

### Help Text

    C_ACTIV - Finding a colormap to code deepness and activation
     function [Cmap,map]=c_activ(FV,connectivity_cell,prop_thres,ref_map,acti,cmap);

      Finding a colormap to code deepness and activation

      inputs : FV : Face Vertex Data, connectivity_cell : neighbors of the vertices (result of vertices_connectivity)
               prop_thres : percentage of gyri and sulci, ref_map : colors for gyri and sulci,
               acti : vector containing activation, cmap : colormap containing deepness coding on the vertices, if it has already been done.
      outputs : Cmap : colormap containing deepness coding [and activation coding] on the vertices, map : colormap for activation coding

### Cross-Reference Information

This function calls

    catci                              C:\BrainStorm_2001\Toolbox\catci.m
    contraste                          C:\BrainStorm_2001\Toolbox\contraste.m
    separation                         C:\BrainStorm_2001\Toolbox\separation.m

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

    function [Cmap,map]=c_activ(FV,connectivity_cell,prop_thres,ref_map,acti,cmap);
    %C_ACTIV - Finding a colormap to code deepness and activation
    % function [Cmap,map]=c_activ(FV,connectivity_cell,prop_thres,ref_map,acti,cmap);
    %
    %  Finding a colormap to code deepness and activation
    %
    %  inputs : FV : Face Vertex Data, connectivity_cell : neighbors of the vertices (result of vertices_connectivity)
    %           prop_thres : percentage of gyri and sulci, ref_map : colors for gyri and sulci,
    %           acti : vector containing activation, cmap : colormap containing deepness coding on the vertices, if it has already been done.
    %  outputs : Cmap : colormap containing deepness coding [and activation coding] on the vertices, map : colormap for activation coding
    %

    %<autobegin> ---------------------- 26-May-2004 11:29:56 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Visualization
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\catci.m
    %   toolbox\contraste.m
    %   toolbox\separation.m
    %
    % At Check-in: $Author: Mosher $  $Revision: 14 $  $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 11:29:56 -----------------------

    % tic
    if nargin<=3    % default parameters
         %BEST ref_map=[0.6 0.6 0.6;0.2 0.2 0.2];
       % ref_map=[0.8 0.8 0.8;0.4 0.4 0.4];
        ref_map = [0.35 0.35 0.35;0.2 0.2 0.2];

        if nargin==2
            prop_thres=0.6;
        end
    end
    maxicm=max(max(ref_map));

    vu=FV.vertices;
    fu=FV.faces;

    % centering of the brain
    v(:,1)=vu(:,1)-sum(sum(vu(:,1)))/size(vu,1).*ones(size(vu,1),1);
    v(:,2)=vu(:,2)-sum(sum(vu(:,2)))/size(vu,1).*ones(size(vu,1),1);
    v(:,3)=vu(:,3)-sum(sum(vu(:,3)))/size(vu,1).*ones(size(vu,1),1);
    clear vu;

    % find short and long axes
    larg1=max(max(v(:,1)))-min(min(v(:,1)));
    larg2=max(max(v(:,2)))-min(min(v(:,2)));
    if larg1<larg2
        short_axe=1;
    else
        short_axe=2;
    end

    [I_pos,I_neg]=separation(v,connectivity_cell);
    v_pos=zeros(size(v,1),3);
    v_neg=zeros(size(v,1),3);
    v_pos(I_pos,:)=v(I_pos,:);
    v_neg(I_neg,:)=v(I_neg,:);
    v_neg(I_neg,short_axe)=v_neg(I_neg,short_axe)-min(min(v(I_neg,short_axe)))/2;
    v_pos(I_pos,short_axe)=v_pos(I_pos,short_axe)-max(max(v(I_pos,short_axe)))/2;

    if nargin <= 4
        Cmap=contraste(v,v_pos,v_neg,connectivity_cell,I_pos,I_neg,prop_thres,ref_map);
        map = [];
    elseif nargin==5
        Cmap=contraste(v,v_pos,v_neg,connectivity_cell,I_pos,I_neg,prop_thres,ref_map);
        [Cmap,map]=catci(acti,Cmap);
    elseif nargin==6
        Cmap=cmap;
        [Cmap,map]=catci(acti,Cmap);
    end
    % toc

    % Cmap_pos=Cmap;
    % Cmap_neg=Cmap;
    % Cmap_pos(I_neg,:)=ones(size(I_neg,1),1)*[0 0 0];
    % Cmap_neg(I_pos,:)=ones(size(I_pos,1),1)*[0 0 0];
    %
    % figure
    % colormap(map);
    % set(gcf,'Position',[0 100 850 600]);
    % subplot(1,2,1)
    % axis equal
    % patch('Faces',fu,'Vertices',v,'FaceVertexCData',Cmap,'EdgeColor','none','FaceColor','interp','FaceLighting','phong','backfacelight','unlit');
    % light('Position',[1,1,1]);
    % light('Position',[-1,-1,1]);
    % light('Position',[-1,-1,-1]);
    % light('Position',[1,1,-1]);
    % material dull;
    % colorbar
    % subplot(1,2,2)
    % axis equal
    % patch('Faces',fu,'Vertices',v,'FaceVertexCData',Cmap,'EdgeColor','none','FaceColor','interp','FaceLighting','phong','backfacelight','unlit');
    % colorbar
    %
    % figure
    % colormap(map);
    % set(gcf,'Position',[0 100 850 600]);
    % subplot(1,2,1)
    % axis equal
    % patch('Faces',fu,'Vertices',v_pos,'FaceVertexCData',Cmap_pos,'EdgeColor','none','FaceColor','interp','FaceLighting','phong','backfacelight','unlit');
    % light('Position',[1,1,1]);
    % light('Position',[-1,-1,1]);
    % light('Position',[-1,-1,-1]);
    % light('Position',[1,1,-1]);
    % material dull;
    % colorbar
    % subplot(1,2,2)
    % axis equal
    % patch('Faces',fu,'Vertices',v_neg,'FaceVertexCData',Cmap_neg,'EdgeColor','none','FaceColor','interp','FaceLighting','phong','backfacelight','unlit');
    % light('Position',[1,1,1]);
    % light('Position',[-1,-1,1]);
    % light('Position',[-1,-1,-1]);
    % light('Position',[1,1,-1]);
    % material dull;
    % set(gcf,'Position',[0 100 850 600]);
    % colorbar

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