headplot.m

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% headplot() - plot a spherically-splined EEG field map on a semi-realistic 
%              3-D head model. Rotate head using left mouse button.
% Example:
%   >> headplot example   - show an example spherical 'eloc_angles' file
%   >> headplot cartesian - show an example cartesian 'eloc_angles' file
%
% Setup usage (do once):
%   >> headplot('setup', elocs, splinefile, 'Param','Value',...);
%   (previous call format headplot('setup', elocs, splinefile, cooment, type)
%    is still supported)
%
% Inputs: 
%   elocs         - file of electrode locations (compatible with readlocs())
%                   or channel location structure. If the channel file extension
%                   is not standard, use readlocs() to load the data file, e.g.
%                   >> headplot('setup', readlocs('myfile', 'filetype', 'besa'), ...
%                      'splinefile');
%   splinefile    - name of spline file to save splining info into
%
% Optional Parameters:
%   'comment'     - ['string'] optional string vector containing info for spline 
%                   file.
%   'orilocs'     - ['off'|'on'] use original electrode location on the head
%                  default: 'off' (extrapolated to spherical). Note that 
%                  electrode location must be coregisted with the MRI head.
%   'meshfile'    - ['string'] Matlab files containing at least 2 variables
%                   POS    - vertices 3-D positions, x=left-right; y=back-front, 
%                            z=up-down
%                   TRI1   - faces on which the scalp map should be computed
%                   center (optional) - 3-D center of head mesh
%                   TRI2   (optional) - faces in skin color
%                   NORM   (optional) - normal for each vertex (better shades)
%
% General usage:
%   >> headplot(values,'spline_file','Param','Value',...)
%
% Inputs:
%   values        - vector containing value at each electrode position
%   'spline_file' - spline filename computed and saved by running 'setup'
%
% Optional Parameters:
%   'meshfile'   - [string] mesh file name. See file content in the setup
%                  description. By default uses the template EEGLAB file.
%   'electrodes' - ['on'|'off'] -> show electrode positions {default 'on'}
%   'title'      -  Plot title {default none}
%   'labels'     -  2 -> plot stored electrode labels;
%                   1 -> plot channel numbers; 0 -> no labels {default}
%   'cbar'       -  0 -> Plot colorbar {default: no colorbar}
%                   H -> Colorbar axis handle (e.g., choose location)
%   'view'       - Camera viewpoint in deg. [azimuth elevation]
%                  'back'|'b'=[  0 30]; 'front'|'f'=[180 30] 
%                  'left'|'l'=[-90 30]; 'right'|'r'=[ 90 30];
%                  'frontleft'|'bl','backright'|'br', etc.,
%                  'top'=[0 90]   {default [143 18]}
%   'orilocs'    - [channel structure or channel file name] Use original 
%                  channel locations instead of the one extrapolated from 
%                  spherical locations.
%   'maplimits'  - 'absmax' -> make limits +/- the absolute-max
%                  'maxmin' -> scale to data range
%                   [min,max] -> user-definined values
%                   {default = 'absmax'; red +, blue -, green 0}
%   'lights'     - (3,N) matrix whose rows give x,y,z pos. of 
%                   N lights {default: 4 lights at corners}
%   'lighting'   - 'off' = show wire frame {default 'on'} 
%   'colormap'   -  3-column colormap matrix {default jet(64)}
%   'verbose'    - 'off' -> no msgs, no rotate3d {default 'on'}
%
% Note: if an error is generated, headplot may close the current figure
%
% Authors: Arnaud Delorme, Colin Humphries, Scott Makeig, SCCN/INC/UCSD, 
%          La Jolla, 1998-

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Copyright (C) Arnaud Delorme, Colin Humphries and Scott Makeig, 
%               CNL / Salk Institute, Feb. 1998
%
% Spherical spline method: Perrin et al. (1989) Electroenceph clin Neurophys
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

% $Log: headplot.m,v $
% Revision 1.46  2004/07/26 21:05:22  arno
% remove index1
%
% Revision 1.45  2004/07/26 21:04:32  arno
% remove tri2
%
% Revision 1.44  2004/07/26 21:03:51  arno
% remove mheadtri2
%
% Revision 1.43  2004/07/26 18:59:37  arno
% nothing
%
% Revision 1.42  2004/07/09 16:10:04  arno
% debug
% cbar
%
% Revision 1.41  2004/07/01 22:17:37  arno
% rename mhead files
%
% Revision 1.40  2004/07/01 22:12:35  arno
% change default mesh
%
% Revision 1.39  2004/07/01 22:10:58  arno
% using julie's head
%
% Revision 1.5  2004/07/01 22:10:19  arno
% renormalize
%
% Revision 1.4  2004/07/01 18:03:24  arno
% fixing coordinate problem for 32 electrodes
%
% Revision 1.3  2004/06/04 20:40:57  arno
% default mesh problem
%
% Revision 1.2  2004/06/01 17:12:42  arno
% mhead.mat file
%
% Revision 1.1  2004/05/12 02:12:25  arno
% Initial revision
%
% Revision 1.34  2004/05/11 20:55:58  arno
% same
%
% Revision 1.33  2004/05/10 17:11:02  arno
% new decoding of arguments
%
% Revision 1.32  2004/03/25 23:09:29  arno
% adding mesh tag to head mesh
%
% Revision 1.31  2004/03/25 19:43:13  arno
% allowing to read custom mesh, fixed color bug
%
% Revision 1.30  2004/02/24 17:18:33  arno
% using readlocs to read file
%
% Revision 1.29  2004/02/24 16:08:41  arno
% removing spherical coords
%
% Revision 1.28  2004/02/24 15:39:03  arno
% header msg
%
% Revision 1.27  2004/02/09 19:39:53  scott
% returning to part-head view
%
% Revision 1.26  2004/02/08 16:32:46  scott
% same
%
% Revision 1.25  2004/02/08 16:31:41  scott
% trying newupper.mat again for 252 channels
%
% Revision 1.24  2004/02/08 15:31:36  scott
% try to plot whole head
%
% Revision 1.23  2003/12/17 23:02:42  scott
% remove output
%
% Revision 1.22  2003/12/17 23:00:24  scott
% return Wout
%
% Revision 1.21  2003/12/17 22:58:11  scott
% output TRI1
%
% Revision 1.20  2003/12/17 22:53:25  scott
% add W output
%
% Revision 1.19  2003/12/17 01:04:24  arno
% process empty coordinates
%
% Revision 1.18  2003/12/05 18:10:20  arno
% loading files differently for windows
%
% Revision 1.17  2003/08/02 00:24:10  scott
% nothing
%
% Revision 1.16  2002/11/26 19:42:24  arno
% /2 to sqrt in extentricity calculation (thanks to Tyler Lorig)
%
% Revision 1.15  2002/11/19 20:08:28  arno
% allowing ascii and binary read of mhead
%
% Revision 1.14  2002/11/19 19:45:09  arno
% back to original
%
% Revision 1.13  2002/11/19 19:34:00  arno
% mhead.dat -> mhead
%
% Revision 1.12  2002/11/19 19:30:37  arno
% mhead -> mhead.dat
%
% Revision 1.11  2002/11/19 19:29:59  arno
% mhead.mat -> mhead for windows compatibility
%
% Revision 1.10  2002/10/23 19:21:24  arno
% fixing division error
%
% Revision 1.9  2002/10/23 19:01:51  arno
% nothing
%
% Revision 1.8  2002/10/23 17:19:10  arno
% cleaning up, removing ls for windows
%
% Revision 1.7  2002/10/23 17:06:26  arno
% saving syntax change for windows
%
% Revision 1.6  2002/10/23 16:52:23  arno
% testing
%
% Revision 1.5  2002/08/27 00:35:39  arno
% closing current figure
%
% Revision 1.4  2002/08/14 16:48:54  arno
% remove ICADIR
%
% Revision 1.3  2002/07/25 18:24:08  arno
% debugging
%
% Revision 1.2  2002/04/17 20:56:14  arno
% changing XYZ coordinate transformation for eloc structure
%
% Revision 1.1  2002/04/05 17:36:45  jorn
% Initial revision
%

% 12-12-98 changed electrode label lines to MarkerColor -sm
% 12-12-98 added colorbar option -sm (still graphically marred by tan rect.)
% 12-13-98 implemented colorbar option using enhanced cbar -sm 
% 12-13-98 implemented 'setup' comment option -sm 
% 03-20-00 added cartesian electrode locations option -sm
% 07-14-00 fixed line in calgx() -sm from -ch
% 03-23-01 documented 'cartesian' locfile option -sm
% 01-25-02 reformated help & license, added links -ad 
% 03-21-02 added readlocs and the use of eloc input structure -ad 

function [] = headplot(values, arg1, varargin)

if nargin < 1
    help headplot
    return
end

%%%%%%%%%%%%%%%%%%%%%%%%%% Set Defaults %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

icadefs   % load definitions
set(gca,'Color',BACKCOLOR);
DEFAULT_MESH = ['mheadnew.mat'];      % upper head model file (987K)
%DEFAULT_MESH  = '/home/arno/matlab/juliehiresmesh.mat';
%DEFAULT_MESH  = ['/home/scott/matlab/old' '/newupper.mat']; 
                                 % whole head model file (183K)

DEFAULT_LIGHTS = [-125  125  80; ...
                  125  125  80; ...
                  125 -125 125; ...
                  -125 -125 125];    % default lights at four corners

HeadCenter = [0 0 30];
FaceColor  = [.8 .55 .35]*1.1; % ~= ruddy Caucasian - pick your complexion!
MAX_ELECTRODES = 1024;
ElectDFac  = 1.06;  % plot electrode marker dots out from head surface
NamesDFac  = 1.05;  % plot electrode names/numbers out from markers
NamesColor = 'k'; % 'r';
NamesSize  =  10;   % FontSize for electrode names
MarkerColor= 'k';

sqaxis     = 1;     % if non-zero, make head proportions anatomical
title_font = 18;
if isstr(values)
    values   = lower(values);
    if strcmp(values,'setup')
        
%
%%%%%%%%%%%%%%%%%%% Perform splining file setup %%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
    if nargin < 3
        help headplot;
        return;
    end;
    eloc_file = arg1;
    spline_file = varargin{1};
        
    g = finputcheck(varargin(2:end), { 'orilocs'   'string'  { 'on' 'off' }  'off';
                                       'meshfile'  'string'  []              DEFAULT_MESH;
                                       'comment'   'string'  []              '' });
    if isstr(g), 
        clear g; 
        g.comment   = varargin{2}; 
        g.orilocs   = 'off';
        g.meshfile  = DEFAULT_MESH;
    end;
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%
    % Open electrode file
    %%%%%%%%%%%%%%%%%%%%%%%%%%%
    [eloc_file labels Th Rd ind] = readlocs(eloc_file);
    fprintf('Headplot: using existing XYZ coordinates\n');
    %for index = 1:length(eloc_file)
    %    eloc_file(index).radius     = eloc_file(index).radius*1.4;
    %    eloc_file(index).sph_radius = 1;
    %end;
    %eloc_file = convertlocs(eloc_file, 'topo2all');
    tmpX = { eloc_file.X };
    tmpY = { eloc_file.Y };
    tmpZ = { eloc_file.Z };
    indices = find(~cellfun('isempty', tmpX));
    ElectrodeNames = strvcat({ eloc_file.labels });
    ElectrodeNames = ElectrodeNames(indices,:);
    Xe = cell2mat( tmpX(indices) )';
    Ye = cell2mat( tmpY(indices) )';
    Ze = cell2mat( tmpZ(indices) )';
    dists = sqrt(Xe.^2+Ye.^2+Ze.^2);
    Xe = Xe./dists;
    Ye = Ye./dists;
    Ze = Ze./dists;
    newcoords = [ Ye Xe Ze ];
    newcoords = transformcoords( [ Xe Ye Ze ], [0 -pi/16 0], 100, [6 0 46]);
    % original center was [6 0 16] but the center of the sphere is [0 0 30] 
    % which compensate (see variable Headcenter)
    %newcoords = transformcoords( [ Xe Ye Ze ], [0 0 -pi/6]);
    Xe = newcoords(:,1);
    Ye = newcoords(:,2);
    Ze = newcoords(:,3);
    dists = sqrt(Xe.^2+Ye.^2+Ze.^2);
    Xe = Xe./dists;
    Ye = Ye./dists;
    Ze = Ze./dists;
    Xetmp = Xe;
    Xe = -Ye;
    Ye = Xetmp;

    Xe = Xe(:);
    Ye = Ye(:);
    Ze = Ze(:);
    %plotchans3d([ Xe Ye Ze], cellstr(ElectrodeNames)); return;
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % Calculate g(x) for electrodes 
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    fprintf('Setting up splining matrix.\n');
    enum = length(Xe);
    onemat = ones(enum,1);
    G = zeros(enum,enum);
    for i = 1:enum
        ei = onemat-sqrt((Xe(i)*onemat-Xe).^2 + (Ye(i)*onemat-Ye).^2 + ...
                         (Ze(i)*onemat-Ze).^2); % default was /2 and no sqrt
        gx = zeros(1,enum);
        for j = 1:enum
            gx(j) = calcgx(ei(j));
        end
        G(i,:) = gx;
    end
    fprintf('Calculating splining matrix...\n')

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % Open mesh file - contains POS and index1
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    if ~exist(g.meshfile)
       error(sprintf('headplot(): mesh file "%s" not found\n',g.meshfile));
    end
    try, load(g.meshfile,'-mat');
    catch,
        POS  = load('mheadnewpos.txt', '-ascii');
        TRI1 = load('mheadnewtri1.txt', '-ascii'); % upper head
        %try, TRI2 = load('mheadnewtri2.txt', '-ascii'); catch, end; % lower head
        %index1 = load('mheadnewindex1.txt', '-ascii');
        center = load('mheadnewcenter.txt', '-ascii');
    end;
    if exist('index1') ~= 1, index1 = sort(unique(TRI1(:))); end;
    if exist('TRI2')   ~= 1, TRI2 = []; end;
    if exist('NORM')   ~= 1, NORM = []; end;
    if exist('TRI1')   ~= 1, error('Variable ''TRI1'' not defined in mesh file'); end;
    if exist('POS')    ~= 1, error('Variable ''POS'' not defined in mesh file'); end;
    if exist('center') ~= 1, center = [0 0 0]; disp('Using [0 0 0] for center of head mesh'); end;
    
    fprintf('Loaded mesh file %s\n',g.meshfile);
    newPOS = POS(index1,:);
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % Project head vertices onto unit sphere
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    nPOS = newPOS-ones(size(newPOS,1),1)*HeadCenter;
    spherePOS = sqrt(ones./(sum((nPOS.*nPOS)')))'*ones(1,3).*nPOS;
    x = spherePOS(:,1);
    y = spherePOS(:,2);
    z = spherePOS(:,3);
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % Calculate new electrode positions