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brainmovie3d.m
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brainmovie3d.m
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% brainmovie3d() - generate a sequence of images showing event-related coherence,
% event-related spectral perturbations, and inter-trial coherence
% of localized EEG waveforms. Uses outputs of timef() and cross().
% Usage:
% >> brainmovie3d(ersps,itcs,crossfs_amp,crossfs_phase,times,freqs,selected,...
% 'keyword1',value1,...); % creates files image0001.eps, etc.
%
% Inputs:
% ersps - Cell array (components,conditions) of ERSP arrays (freqs,times)
% ERSP = event-related spectral perturbation; returned by timef()
% itcs - Cell array (components,conditions) of ITC arrays (freqs,times)
% ITC = inter-trial coherence; returned by timef()
% crossfs_amp - Cell array (components,components,conditions) of crossf()
% amplitude output arrays of size (freqs,times).
% crossfs_phase - Cell array (components,components,conditions) of crossf() phase
% output arrays of size (freqs,times). (Only the upper diagonal part
% of the matrix is taken into account).
% times - Array of times returned by timef() or crossf()
% freqs - Indices into the array of freqs returned by timef() or crossf()
% (e.g., [1:2] means plot the mean of the first two frequencies).
% These indexes determine for which freqs plotting will be performed.
% selected - Component indices to plot (default all)
%
% Optional 'keyword' parameters:
% 'latency' - plot only a subset of latencies. The time point closest to the
% latency given are plotted. Default = empty, all latencies.
% 'frames' - vector of frame indices to compute. [1:2] only computes the
% first two frames.
% 'envelope' - (2,points,conditions) envelopes of the average data (ERP) in each condition
% (envelope = min and max traces of each ERP across all channels and times)
% 'rt' - cell array of vector containing reaction times of the subject in
% each conditions. This will plot a small bar which height will vary
% based on the probability of response (default {} -> ignored)
% 'flashes' - vector of time indices at which the background flashes. Specify the color
% of the flash with a cell array of [1,2] cell arrays.
% Ex. { { 200 'y' } { 1500 '5' }} will generate two flashes,
% yellow at 200 ms and red at 1500 ms
%
% Movie ITC, Power and Crossf options:
% 'power' - ['on'|'off'] vary the size of the component disks according to spectral power
% {default: on}
% 'itc' - ['on'|'off'] vary component disk colors according to inter-trial coherence
% {default: on}
% 'crossf' - ['on'|'off'] plot | do not plot coherence {default: on}
% 'crossfcoh' - ['on'|'off'] vary the width of the connecting arc
% according to cross-coherence magnitude {def: on}
% 'crossfphasecolor' -['on'|'off'] vary the arc color according to coherence {default: on}
% 'crossfphasespeed' - ['on'|'off'] vary the arc speed according to
% cross-coherence phase {def: off}
% 'crossfphaseunit' - ['degree'|'radian']. Coherence phase angle unit {Default is degree}.
% 'colmapcrossf' - colormap array for arcs {default: hsv(64) with green as 0}
% 'colmapcoh' - colormap array for disks (according to inter-trial coherence)
% {default: hot(64)}
% 'scalepower' - [min max] dB range for power (and disk size) variation {default: [-5 5]}
% 'scalecoher' - [min max] coherence range {default: [0 1]}
% 'scaleitc' - [absmax] maximum itc {Default: 1}
% 'polarity' - ['pos'|'posneg'] polarity for ITC and crossf. 'pos' = only positive values
% 'posneg' = positive and negative values.
%
% Movie coordinates and axis options:
% 'magnify' - integer magnification factor for graphics. Default is 1.
% 'diskscale' - numeric value that scales the size of disks {default: [1.0]}
% 'xlimaxes' - x-axis limits axis for the component locations {default: [-1 1]}
% 'ylimaxes' - y-axis limits axis for the component locations {default: [-1 to 1]}
% 'coordinates' - 2-column array of [x y] coordinates of the selected components
% {default: spaced evenly around the head circle boundary}
% 'square' - ['on'|'off'] re-square all coordinates (so X and Y width is the same)
% default is 'on';
% 'project3d' - ['on'|'off'] project disks on each 3-D axis. Default is 'off'.
% 'circfactor' - (ncomps,ncomps) array of arc curvatures (0=straight; 1=half-round,
% positive or negative values give the sense of rotation) {def: 0s}
% 'envylabel' - ordinate label for envelope. {Default 'Potential \muV'}
% 'envvert' - cell array of time indices at which to draw vertical lines.
% Can also be a cell array of cell to specify line aspect. For instance
% { { 0 'color' 'b' 'linewidth' 2 } {1000 'color' 'r' }} would draw two
% lines, one blue thick line at latency 0 and one thin red line at latency 1000.
% 'rthistloc' - location and size of rt histograms in individual axes.
% [abscissa ordinate width maxheight].
% 'title' - (string) main movie title
% 'condtitle' - (string array) condition titles (one condition title per row)
% 'condtitleformat' - list of title properties. Ex: { 'fontize', 12, 'fontweight', 'bold' }
% 'plotorder' - [integer vector] component plot order from 1 to the number of selected
% components.
% 'backcolor' - [float array] background color. Default is [1 1 1] (white).
%
% Picture and movie output options:
% 'moviename' - ['string'] Movie file name. Default is "output.avi".
% 'movieopts' - [cell] Movie options for avifile function. See "help avifile".
% 'framesout' - ['eps'|'ppm'|'fig'|'tiff'|'none'] Default format for saving frames on disk.
% Default is 'tiff'.
% 'framefolder' - [string] frames output folder. Default uses current directory.
% the directory is created if it does not exist.
% 'visible' - ['on'|'off'] show the images on the screen or keep them hidden {default 'on'}
% 'size' - [widthcond height] output image size {default [400,400]}
% widthcond is the width of a single condition plot (in pixels)
% 'view' - 3D static starting view. See help view. Default is [1 0 0].
% 'path3d' - ['on'|'off'|[thetafact phifact]] 'on' activate automatic rotation in 3-D. Use
% [exttheta extphi] to specify theta and phi multiplicative factor (default is
% [1 0.75]. Use parameter 'view' to specify starting view point. Default is
% 'stereo' - [Real] Create a stereo movie. The figure should contain a [left right]
% display of two identical 3-D plots. The left plot view will follow the
% given 'path' (see above). The right plot axis will be 3-D rotated by an
% additional horizontal disparity angle specified by the 'stereo' argument:
% 6 (degrees) suggested. Default is [] = mono display.
% 'off'.
%Outputs to disk:
% imageX - brainmovie3d() saves an output.avi movie (see 'moviename' option above)
% and a sequence of image files to disk (image0001.eps, as define in the
% 'framesout' option).
%Example:
%
% % Given ICA activations in array icaact (size ncomps,nframes,ntrials), animate (here)
% % activity at/between two components at 176 points per epoch (from -100 ms to 600 ms
% % re stimulus onset) assuming a 250-Hz sampling rate and 100 output frames
%
% [ersps{1,1},itcs{1,1},powbase,times,freqs] = ...
% newtimef(EEG.icaact(1,:),EEG.pnts,[EEG.xmin EEG.xmax]*1000,EEG.srate); % 1st comp
% [ersps{2,1},itcs{2,1},powbase,times,freqs] = ...
% newtimef(EEG.icaact(2,:),EEG.pnts,[EEG.xmin EEG.xmax]*1000,EEG.srate); % 2nd comp
% [crossfs_amp{1,2},mcoh,times,freqs,cohboot,crossfs_phase{1,2}] = ... % crossf for
% newcrossf(EEG.icaact(1,:),EEG.icaact(2,:),EEG.pnts,[EEG.xmin EEG.xmax]*1000,EEG.srate); % both
%
% brainmovie3d( ersps, itcs, crossfs_amp, crossfs_phase, times, freqs, [1:2], 'coordinates', [ EEG.dipfit.model(1).posxyz; EEG.dipfit.model(2).posxyz ] );
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, 30 Mai 2003
%
% Note: Better resolution movies can be generated by .eps -> .ppm -> .avi,
% (or, under a planned upgrade to brainmovie3d, from Matlab6 to .avi directly).
% >> !/usr/local/bin/convert images*.eps movie.mpg % ImageMagic 'convert' may be
% % used to generate the movie.
% arno@salk.edu, Arnaud Delorme, CNL / Salk Institute, 2003
% This program is free software; you can redistribute it and/or
% modify it.
% 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.
function [alltimepoints, mov] = brainmovie3d(ALLERSP,ALLITC,ALLCROSSF,ALLCROSSFANGLE,times,FREQS,selected,varargin);
if nargin < 6
help brainmovie3d;
return;
end
% create structure for option if necessary
%-----------------------------------------
if ~isempty( varargin )
for index=1:length(varargin)
if iscell(varargin{index})
varargin{index} = { varargin{index}};
end
end
g=struct(varargin{:});
else
g= [];
end
if nargin < 7
selected = 1:size(ALLERSP, 1);
end
nbconditions = size(ALLERSP,2);
nbcomponents = size(ALLERSP,1);
% add defaults
%-------------
defmaxpow = 0;
defmaxitc = 0;
for i=1:length(ALLERSP)
defmaxpow = max(defmaxpow, max(abs(ALLERSP{ i}(:))));
defmaxitc = max(defmaxitc, max(abs(ALLITC{ i}(:))));
end
defmaxcoh = 0;
for i=1:length(ALLCROSSF(:))
tmpmax = max(abs(ALLCROSSF{i}(:)));
if ~isempty(tmpmax), defmaxcoh = max(defmaxcoh, tmpmax); end
end
defmaxpow = ceil(defmaxpow*100)/100;
defmaxitc = ceil(defmaxitc*100)/100;
defmaxcoh = ceil(defmaxcoh*100)/100;
try, g.head; catch, g.head=''; end
try, g.visible; catch, g.visible='on'; end
try, g.square; catch, g.square='on'; enddefmaxpow = ceil(defmaxpow*100)/100;
try, g.moviename; catch, g.moviename='output.avi'; end
try, g.movieopts; catch, g.movieopts={}; end
try, g.rt; catch, g.rt={}; end
try, g.power; catch, g.power='on'; end
try, g.latency; catch, g.latency=[]; end
try, g.itc; catch, g.itc='on'; end
try, g.magnify; catch, g.magnify=1; end
try, g.crossf; catch, g.crossf='on'; end
try, g.crossfcoh; catch, g.crossfcoh='on'; end
try, g.size; catch, g.size=[400 400]; end
try, g.crossfphasecolor;catch, g.crossfphasecolor='on'; end
try, g.crossfphasespeed;catch, g.crossfphasespeed='off'; end
try, g.crossfphaseunit; catch, g.crossfphaseunit='degree'; end
try, g.scalepower; catch, g.scalepower = [-defmaxpow defmaxpow]; end
try, g.scalecoher; catch, g.scalecoher = [0 defmaxcoh]; end
try, g.scaleitc; catch, g.scaleitc = defmaxitc; end
try, g.diskscale; catch, g.diskscale = 1; end
try, g.framefolder; catch, g.framefolder = ''; end
try, g.envelope; catch, g.envelope = []; end
try, g.caption; catch, g.caption = 'on'; end
try, g.frames; catch, g.frames = []; end
try, g.envvert; catch, g.envvert = {}; end
try, g.flashes; catch, g.flashes = []; end
try, g.polarity; catch, g.polarity = 'pos'; end
try, g.framesout; catch, g.framesout = 'none'; end
try, g.condtitle; catch, g.condtitle = []; end
try, g.condtitleformat; catch, g.condtitleformat = {'fontsize', 14', 'fontweight', 'bold' }; end
try, g.title; catch, g.title = []; end
try, g.envylabel; catch, g.envylabel = 'Potential \muV'; end
try, g.plotorder; catch, g.plotorder = selected; end
try, g.coordformat; catch, g.coordformat = 'spherical'; end
try, g.stereo; catch, g.stereo = []; end
try, g.backcolor; catch, g.backcolor = [0 0 0]; end
try, g.path3d; catch, g.path3d = 'off'; end
try, g.project3d; catch, g.project3d = 'off'; end
try, g.view; catch, g.view = [43.6650 30.4420]; end
try, g.colmapcoh; catch
colormtmp = hot(64);
colormtmp(end,3) = (colormtmp(end,3)+colormtmp(end-1,3))/2; % white does not come out when the
g.colmapcoh = colormtmp; % the figure is printed to ppm
g.colmapcoh(:,1) = colormtmp(:,2);
g.colmapcoh(:,2) = colormtmp(:,3);
g.colmapcoh(:,3) = colormtmp(:,1);
g.colmapcoh = [ g.colmapcoh; colormtmp(end:-1:1,:)];
g.colmapcoh = jet(64);
end
try, g.colmapcrossf; catch
g.colmapcrossf = jet(64);
%g.colmapcrossf = hsv(64);
%g.colmapcrossf = [ g.colmapcrossf(55:end,:);
%g.colmapcrossf(1:54,:)]; g.colmapcrossf = g.colmapcrossf(linspace(64, 1, 64),:); % reorganize the colormap
%g.colmapcrossf = hsv(64);
%g.colmapcrossf = [g.colmapcrossf(16:end,:); g.colmapcrossf(1:5,:)];
end
try, g.xlimaxes; catch, g.xlimaxes = [-1 1]; end
try, g.ylimaxes; catch, g.ylimaxes = [-1 1]; end
try, g.rthistloc; catch, g.rthistloc(1) = (g.xlimaxes(2)-g.xlimaxes(1))*0.74 + g.xlimaxes(1); % abscicia
g.rthistloc(3) = (g.xlimaxes(2)-g.xlimaxes(1))*0.1; % width
g.rthistloc(2) = (g.ylimaxes(2)-g.ylimaxes(1))*0.34 + g.ylimaxes(1); % ordinate
g.rthistloc(4) = (g.ylimaxes(2)-g.ylimaxes(1))*0.1; % max height
end
try, g.coordinates; catch,
% coordinates around a circle
g.coordinates = zeros( nbcomponents, 2 );
count = 0;
for index = selected
if length(selected) > 1
g.coordinates( index,:) = [ cos(count/length(selected)*2*pi) sin(count/length(selected)*2*pi) ] * 0.7;
else g.coordinates(index,:) = [ 0.01 0.01];
end
count = count + 1;
end
end
try, g.circfactor; catch, g.circfactor = ones( nbcomponents, nbcomponents )*0.01; end
if isempty(g.circfactor), g.circfactor = ones( nbcomponents, nbcomponents )*0.01; end
if isstr(g.path3d)
switch g.path3d
case 'on', g.path3d = [ 1 0.75];
case 'off', g.path3d = [];
end
else
if length(g.path3d) ~= 2, error('path3d length have to be a string or a 2 element vector'); end
end
% messages for defaults
% ---------------------
if g.scalepower(1) == -defmaxpow, fprintf('Power limits set to %1.2f to %1.2f dB\n', -defmaxpow, defmaxpow); end
if g.scaleitc(1) == defmaxitc, fprintf('ITC limits set to 0 to %1.2f\n', defmaxitc); end
if g.scalecoher(2) == defmaxcoh, fprintf('Coherence limits set to 0 to %1.2f\n', defmaxcoh); end
% check size of inputs
% --------------------
try
if ~all(size(ALLERSP) == size(ALLITC))
disp('Error: ERSP and ITC cells array must be the same size'); return;
end
if ~isempty(ALLCROSSF)
if ~all(size(ALLCROSSF) == size(ALLCROSSFANGLE))
disp('Error: Crossf amplitude and Crossf angle cells array must be the same size'); return;
end
if ~(size(ALLCROSSF,2) == size(ALLERSP,1))
disp('Error: number of components different in ERSP and Crossf arrays'); return;
end
if ~(size(ALLCROSSF,3) == size(ALLERSP,2))
disp('Error: number of conditions different in ERSP and Crossf arrays'); return;
end
if ~(size(ALLCROSSF{1,2,1},1) == size(ALLERSP{1,1},1))
disp('Error: number of frequencies (rows) different in ERSP and Crossf arrays'); return;
end
if ~(size(ALLCROSSFANGLE{1,2,1},2) == size(ALLITC{1,1},2))
disp('Error: number of time points (columns) different in ERSP and Crossf arrays'); return;
end
if ~(size(ALLCROSSF{1,2,1},2) == length(times))
disp('Error: number of time points (columns) different in times and Crossf arrays'); return;
end
end
try, tmp = ALLERSP{1,1}; tmp(FREQS,:); catch, disp('Error: unable to access the defined frequencies in ERSPs (out of bounds) '); return; end
try, ALLERSP{selected,1}; catch, disp('Error: unable to access the defined components in ERSPs (out of bounds)'); return; end
catch
disp('Error accessing one of the variable. Remember: Except for selected, freqs, times and circfactor, all vars are cell arrays. Check also: dimensions and content.'); return;
end
% check structure content
% -----------------------
if ~isempty(g.rt)
if length(g.rt) ~= nbconditions
disp('Error: Rt must be either an array of the size of the number of conditions (might be 0 for some conditions)'); return;
end
end
switch lower(g.visible)
case {'on', 'off'}
otherwise disp('Error: Visibility must be either ''on'' or ''off'''); return;
end
switch lower(g.square)
case {'on', 'off'}
otherwise disp('Error: Square must be either ''on'' or ''off'''); return;
end
switch lower(g.power)
case {'on', 'off'}
otherwise disp('Error: Power must be either ''on'' or ''off'''); return;
end
switch lower(g.itc)
case {'on', 'off'}
otherwise disp('Error: Itc must be either ''on'' or ''off'''); return;
end
switch lower(g.crossf)
case {'on', 'off'}
otherwise disp('Error: Crossf must be either ''on'' or ''off'''); return;
end
switch lower(g.crossfcoh)
case {'on', 'off'}
otherwise disp('Error: Crossfcoh must be either ''on'' or ''off'''); return;
end
switch lower(g.crossfphasecolor)
case {'on', 'off'}
otherwise disp('Error: Crossfphasecolor must be either ''on'' or ''off'''); return;
end
switch lower(g.crossfphasespeed)
case {'on', 'off'}
otherwise disp('Error: Crossfphasespeed must be either ''on'' or ''off'''); return;
end
switch lower(g.crossfphaseunit)
case {'degree', 'radian'}
otherwise disp('Error: Crossfphaseunit must be either ''degree'' or ''radian'''); return;
end
switch lower(g.caption)
case {'on', 'off'}
otherwise disp('Error: Caption must be either ''on'' or ''off'''); return;
end
switch lower(g.polarity)
case {'pos', 'posneg'}
otherwise disp('Error: Polarity must be either ''pos'' or ''posneg'''); return;
end
if ~isempty(g.envvert)
if ~iscell(g.envvert) && ~( isstruct(g.envvert{1}) || isnumeric(g.envvert{1}) )
disp('Error: Invalid type for Envvert.'); return;
end
end
if ~isempty(g.latency) && ~isnumeric(g.latency)
disp('Error: Latency must be a vector'); return;
end
if length(g.scalepower) ~= 2
disp('Error: Scalepower must be a 2-element array'); return;
end
if length(g.scalecoher) ~= 2
disp('Error: Scalecoher must be a 2-element array'); return;
end
if (length(g.diskscale) ~= 1 || g.diskscale < 0)
disp('Error: Diskscale must be a scalar value >= 0.'); return;
end
if size(g.colmapcoh,2) ~= 3
disp('Error: Colmapcoh must be a colormap (3 columns)'); return;
end
if size(g.colmapcrossf,2) ~= 3
disp('Error: Colmapcrossf must be a colormap (3 columns)'); return;
end
if size(g.circfactor,1) ~= size(g.circfactor,2)
disp('Error: Circfactor must be a square matrix'); return;
end
if ~iscell(g.coordinates) && ~isempty(g.circfactor)
if size(g.circfactor,1) ~= size(g.coordinates,1)
disp('Error: Circfactor must have the same number of rows as the number of rows of coordinates'); return;
end
if nbcomponents ~= size(g.coordinates,1)
disp('Error: The array of selected components must have length nrows of the array coordinates'); return;
end
end
if ~isstr(g.envylabel)
disp('Error: envelope label must be a string'); return;
end
if ~isempty(g.envelope)
if (size( g.envelope,1 ) ~=2) || (size( g.envelope,2 ) ~= length(times)) || (size( g.envelope,3 ) ~= nbconditions)
fprintf('Error: Enveloppe array does not have the right size (%s), i.e. 2 x %d (number of time points) x %d (number of conditions)\n', int2str(size( g.envelope)), length(times), nbconditions); return;
end
end
if ~isempty(g.condtitle)
if iscell(g.condtitle), g.condtitle = strvcat(g.condtitle{:}); end
if size( g.condtitle,1 ) ~= nbconditions
fprintf('Error: The number of rows in the title array(%d) must match the number of conditions (%d)\n', size(g.condtitle,1), nbconditions); return;
end
end
if length(g.plotorder) ~= length(selected)
error([ 'Error: ''plotorder'' must be the same size as the number of selected components:' int2str(length(selected)) ]);
end
if max(g.plotorder) > max(selected)
error([ 'Error: ''plotorder'' must be below the number of selected components:' int2str(max(selected)) ]);
end
if ~isempty(g.framefolder)
[tmp1 tmp2] = mkdir('/', g.framefolder(2:end) );
if g.framefolder(end) == '/', g.framefolder(end) = []; end
end
% create movie
% ------------
disp('A movie is being saved under output.avi (movie parameters shown below):');
mov = VideoWriter(g.moviename, g.movieopts{:});
open(mov);
% other variables
% ---------------
%limits: power -6 to 6
%limits: ITC 0-1
%limits: coherence 0-1
%limits: coherence angle -180 to 180
g.factproj = [-71 88 -71];
g.projcolor = [0.35 0.35 0.35];
g.rthistcolor = [1 1 1];
g.resmult = 1;
currentphase = zeros( length(selected), length(selected), nbconditions);
tmp = ALLERSP{1,1};
nwin = size(tmp,2);
%for index = 1:64
% circle(1+index,1, 0.5, g.colormaphsv(index, :));
%end
% optional resqure of all coordinates
% -----------------------------------
g.magnify = g.magnify/4;
% compute RT distribution
% -----------------------
if ~isempty(g.rt)
RTdist = zeros(nbconditions,nwin);
for index = 1:nbconditions
if ~isempty(g.rt{index})
timestep = (times(2)-times(1))/2;
for indeximage = 1:nwin
RTdist(index, indeximage) = length( intersect( find( g.rt{index} > times(indeximage)-timestep ) , ...
find( g.rt{index} <= times(indeximage)+timestep ) ) );
end
RTdist(index,:) = RTdist(index,:)/max(RTdist(index,:));
end
end
RTdist = RTdist/max(RTdist(:));
end
figure( 'position', [100, 100, ceil(nbconditions*g.size(1)/4)*4, ceil(g.size(2)/4)*4], ...
'PaperPositionMode', 'auto', 'papertype', 'A1', 'visible',g.visible); %'paperorientation', 'landscape' );
axis off
if strcmpi(g.framesout, 'ppm')
r = 0.8465;
pos = get(gcf,'position');
if floor(pos(3)/r)> 1280
fact = 1280/(pos(3)/r);
set(gcf, 'position', [ 0 0 1280 floor(pos(4)/r*fact) ]);
else
set(gcf, 'position', [ 0 0 floor(pos(3)/r), floor(pos(4)/r) ]);
end
end
pos = get(gca,'position');
q = [pos(1) pos(2) 0 0];
s = [pos(3) pos(4) pos(3) pos(4)];
% compute selected latency point
% ------------------------------
if ~isempty(g.latency)
alltimepoints = [];
for index = 1:length(g.latency)
[tmp tmptimepoint] = min(abs(g.latency(index)-times));
alltimepoints = [ alltimepoints tmptimepoint];
end
else
if isempty(g.frames)
alltimepoints = 1:nwin;
else
alltimepoints = g.frames;
end
end
% make black patch behind figure
% ------------------------------
hback = axes('position' , [0 0 1 1], 'xtick', [], 'ytick', [], 'box', 'off');
hpatch = patch([0 1 1 0], [0 0 1 1], g.backcolor); xlim([0 1]); ylim([0 1]);
set(hpatch, 'facecolor' , g.backcolor, 'edgecolor', 'none');
% compute flashes latency
% -----------------------
if ~isempty(g.flashes)
if iscell(g.flashes)
for index = 1:length(g.flashes)
flasheslat(index) = g.flashes{index}{1};
flashescol{index} = g.flashes{index}{2};
end
else
flasheslat = g.flashes;
for index = 1:length(g.flashes)
flashescol{index} = [0.5 0.5 0.5];
end
end
allflashes = [];
for index = 1:length(g.flashes)
[tmp tmptimepoint] = min(abs(flasheslat(index)-times));
allflashes = [ allflashes tmptimepoint];
end
%hpatch = patch([ 0.02 .11 .11 0.02], [0.05 0.05 0.925 0.925], [0.5 0.5 0.5]); lateral
%hpatch = patch([ 0 1 1 0], [0 0 1 1], [0.5 0.5 0.5]); full
%hpatch = patch([ 0.13 0.84 0.84 0.13 ], [0.92 0.92 1 1], [0.5 0.5 0.5]); %up
hpatch = patch([ 0.13 0.84 0.84 0.13 ], [0.8 0.8 0.93 0.93], [0.5 0.5 0.5]);
set(hpatch, 'facecolor', 'w', 'edgecolor', 'none');
xlim([0 1]); ylim([0 1]);
posf = 0; % used as a counter to preserve color
end
% draw axes and display images
% ----------------------------
ordinate = 0.2;
max_ordinate = 1-1.4*ordinate; % makes space at top for figure title
maxcoordx = 1.1-1/nbconditions/4;
coords = g.coordinates;
g.coordinates = {};
for i=1:nbconditions
% plot 3d head (*0.9 added for Nick - Arno).
% ------------
hh(i) = axes('position', [0+maxcoordx/nbconditions*(i-1), ordinate, maxcoordx/nbconditions*0.9, max_ordinate].*s+q );
gr = [ 0.3 0.3 0.3 ];
g.dipplotopt = { 'coordformat' g.coordformat 'gui', 'off', 'cornermri', 'on', 'color', { gr gr gr gr gr gr gr gr gr } };
if iscell(coords)
for index = 1:size(coords{1}, 1);
dipstruct(index).posxyz = coords{1}(index,:);
dipstruct(index).momxyz = [0 0 0];
dipstruct(index).component = index;
dipstruct(index).rv = 0.1;
end
else
for index = 1:size(coords, 1);
dipstruct(index).posxyz = coords(index,:);
dipstruct(index).momxyz = [0 0 0];
dipstruct(index).component = index;
dipstruct(index).rv = 0.1;
end
end
dipplot( dipstruct, 'view', g.view, g.dipplotopt{:}); axis off;
%g.maxc = 100;
%surface([-2 -2; -2 -2]*g.maxc, [-20 20; -20 20]*g.maxc,[-20 -20; 20 20]*g.maxc, repmat(reshape([0 0 0], 1, 1, 3), [2 2 1]), 'facelighting', 'none');
%surface([-20 20; -20 20]*g.maxc,[2 2; 2 2]*g.maxc, [-20 -20; 20 20]*g.maxc, repmat(reshape([0 0 0], 1, 1, 3), [2 2 1]), 'facelighting', 'none');
%camproj('perspective');
set(gca, 'cameraviewanglemode', 'manual'); % disable change size
axis vis3d % same as above (for security)
camlight left
camlight right
view(g.view)
%camzoom(1.2)
for index = 1:length(dipstruct)
htmp = findobj(gca, 'tag', [ 'dipole' int2str(index) ]);
for dipindex = 1:length(htmp)
tmpstruct = get(htmp(dipindex), 'userdata');
if isstruct(tmpstruct) % look for dipole location % THIS DOES NOT WORK
if isfield(tmpstruct, 'pos3d')
g.coordinates{i}(index, :) = tmpstruct.pos3d;
elseif isfield(tmpstruct, 'eleccoord')
g.coordinates{i}(index, :) = tmpstruct.eleccoord;
else
tmpstruct
error('Field not found in tmpstruct');
end
end
end
delete(htmp);
end
%h = plot3(g.coordinates{i}(:, 1), g.coordinates{i}(:, 2), g.coordinates{i}(:, 3), 'r.', 'markersize', 30);
%dsaf
xltmp = xlim;
yltmp = ylim;
g.dimratio = (xltmp(2) - xltmp(1)) / (yltmp(2) - yltmp(1));
axis off;
if ~isempty(g.condtitle)
h = title(g.condtitle(i,:));
if ~isempty(g.condtitleformat)
set(h, g.condtitleformat{:} );
end
end
% this axis is used for the enveloppe but
% also used to print current time (which is why it is always created
e(i) = axes('position', [0.1/nbconditions+maxcoordx/nbconditions*(i-1), 0, ...
maxcoordx/nbconditions-0.1/nbconditions, ordinate].*s+q,'visible', g.visible);
end
% draw captions if necessary
% --------------------------
countl = 1;
switch lower(g.caption)
case 'on' ,
xlimnorm = (1.1-maxcoordx)/(maxcoordx/nbconditions) * g.xlimaxes;
ylimnorm = 0.45/(1-ordinate) * g.ylimaxes;
switch g.power, case 'on',
c(countl) = axes('position', [maxcoordx, -0.1, (1.1-maxcoordx), 0.45].*s+q, 'xlim', xlimnorm, ...
'ylim', ylimnorm,'visible', g.visible, 'color', 'w' );
% draw 3 spheres
[xstmp ystmp zs] = sphere(15);
l=sqrt(xstmp.*xstmp+ystmp.*ystmp+zs.*zs);
normals = reshape([xstmp./l ystmp./l zs./l],[16 16 3]);
tmpsize = 0.5; xs1 = tmpsize*ystmp; ys1 = tmpsize*xstmp; zs1 = tmpsize*zs;
tmpsize = 0.9; xs2 = tmpsize*ystmp; ys2 = tmpsize*xstmp; zs2 = tmpsize*zs + 2;
tmpsize = 0.1; xs3 = tmpsize*ystmp; ys3 = tmpsize*xstmp; zs3 = tmpsize*zs - 1.5;
colorarray = repmat(reshape([1 1 1], 1,1,3), [size(zs,1) size(zs,2) 1]);
handles = surf(xs1, ys1, zs1, colorarray, 'tag', 'tmpmov', 'EdgeColor','none', 'VertexNormals', normals, ...
'backfacelighting', 'lit', 'facelighting', 'phong', 'facecolor', 'interp', 'ambientstrength', 0.3); hold on;
handles = surf(xs2, ys2, zs2, colorarray, 'tag', 'tmpmov', 'EdgeColor','none', 'VertexNormals', normals, ...
'backfacelighting', 'lit', 'facelighting', 'phong', 'facecolor', 'interp', 'ambientstrength', 0.3);
handles = surf(xs3, ys3, zs3, colorarray, 'tag', 'tmpmov', 'EdgeColor','none', 'VertexNormals', normals, ...
'backfacelighting', 'lit', 'facelighting', 'phong', 'facecolor', 'interp', 'ambientstrength', 0.3);
axis off;
camlight left
camlight right
view([1 0 0])
lightangle(45,0);
lighting phong;
material shiny;
axis equal;
set(gca, 'zlim', [-2 4]);
text(0, 1.3, 2, [ '+' num2str(g.scalepower(2),2) ], 'fontweight', 'bold');
text(0, 1, 0, '0', 'fontweight', 'bold');
text(0, 0.5, -1.5, [ num2str(g.scalepower(1),2) ' dB' ], 'fontweight', 'bold');
%scalepower(mean(xlimnorm), min(ylimnorm)+0.2, g); % see function at the end
%axis off;
%countl = countl + 1;
end
switch g.itc, case 'on',
c(countl) = axes('position', [maxcoordx+(1.1-maxcoordx)/2, 0.29 , (1.1-maxcoordx)/2, 0.14].*s+q, ...
'visible', g.visible, 'color', 'none' );
countl = countl + 1;
if strcmpi(g.polarity, 'posneg') % negative ITCs (difference only) ?
cbar( [-1 1], [-1 1], g.colmapcoh, 'vert', 'circle', g);
ylabel('ITC', 'fontweight', 'bold');
set(gca, 'ytick', [-1 0 1], 'yticklabel', [-1 0 1], 'xticklabel', [], 'box', 'off');
else
cbar( [0 1], [0 1], g.colmapcoh(length(g.colmapcoh)/2:end,:), 'vert', 'circle', g);
ylabel('ITC', 'fontweight', 'bold');
set(gca, 'ytick', [0 1], 'yticklabel', [0 1], 'xticklabel', [], 'box', 'off');
end
axis off;
text(-0.2, 0, '0', 'fontsize', 10);
text(-0.2, 1, num2str(g.scaleitc,2), 'fontsize', 10);
text(-0.8, 0.55, 'ITC', 'fontsize', 11, 'fontweight', 'bold');
end
switch g.crossf, case 'on',
c(countl) = axes('position', [maxcoordx+(1.1-maxcoordx)/2, 0.47 , (1.1-maxcoordx)/4, 0.14].*s+q, ...
'visible', g.visible, 'color', 'none' );
countl = countl + 1;
if strcmpi(g.polarity, 'posneg') % negative ITCs (difference only) ?
cbar( [-1 1], [-1 1], g.colmapcrossf, 'vert', '', g);
ylabel('Cross-Coh' , 'fontweight', 'bold');
set(gca, 'ytick', [-1 0 1], 'yticklabel', [g.scalecoher(1) 0 g.scalecoher(2)], 'xticklabel', []);
else
cbar( [0 1], [0 1], g.colmapcrossf(length(g.colmapcrossf)/2:end,:), 'vert', '', g);
ylabel('Cross-Coh' , 'fontweight', 'bold');
set(gca, 'ytick', [0 1], 'yticklabel', [g.scalecoher(1) g.scalecoher(2)], 'xticklabel', []);
end
switch g.crossfphasespeed, case 'on',
c(countl) = axes('position', [maxcoordx+(1.1-maxcoordx)/2, 0.69,(1.1-maxcoordx)/2, 0.25 ].*s+q, ...
'visible', g.visible );
countl = countl + 1;
scalecoher([0.02 1], [0.04 0.96], 5, g); % see function at the end
end
end
case 'off', maxcoordx = 1;
end
% draw white axis on envelop if flashes DOES NOT WORK WHEN PRINTING IN EPS
% -------------------------------------
%if ~isempty(g.flashes)
% if ~isempty(g.envelope) % draw axis for the envelope
% eflash = axes('position', [0 0 maxcoordx-0.1 ordinate].*s+q, ...
% 'xtick', [], 'ytick', [], 'box', 'off', 'visible', g.visible, 'color', 'none');
% hpatch2 = patch([ 0 1 1 0], [0 0 1 1], [0.5 0.5 0.5]); set(hpatch2, 'facecolor', 'w', 'edgecolor', 'none');
% end
%end
% scan time windows
% -----------------
set(gcf, 'renderer', 'zbuffer');
for indeximage = alltimepoints
fprintf('Processing image %d\n', indeximage);
% invert background if necessary
% ------------------------------
if ~isempty(g.flashes)
%axes(hback); set (gcf, 'visible', g.visible);
if ~isempty(find(indeximage == allflashes))
posf = find(indeximage == allflashes);
set(hpatch, 'facecolor', flashescol{posf});
elseif posf == 0 % allow the color to stay 2 images
set(hpatch, 'facecolor', 'w');
else
posf = 0;
end
end
for tmpcond=1:nbconditions
axes(hh(tmpcond)); set (gcf, 'visible', g.visible);
% clean images and update view
% ----------------------------
if ~isempty(g.path3d)
angle = (indeximage-1)/length(alltimepoints)*360;
camorbit( cos(angle/180*pi)*g.path3d(1), sin(angle/180*pi)*g.path3d(2) );
end
delete( findobj( hh(i), 'tag', 'tmpmov') );
set (gcf, 'visible', g.visible);
if ~isempty(g.title) & i == 1
t = textsc(g.title,'title');
set(t,'VerticalAlignment','top', 'fontsize', 15);
end
% draw correlations
% -----------------
switch lower(g.crossf), case 'on',
for index1 = selected
for index2 = selected
if index2 > index1
tmpcrossfpow = ALLCROSSF { index1, index2, tmpcond };
tmpcrossfang = ALLCROSSFANGLE { index1, index2, tmpcond };
tmppower = mean(tmpcrossfpow( FREQS, indeximage));
tmpangle = mean(tmpcrossfang( FREQS, indeximage));
if strcmp(lower(g.crossfphaseunit), 'radian'), tmpangle = tmpangle/pi*180; end
%fprintf('%d-%d -> power %1.1f\n', index1, index2, tmppower);
drawconnections( g.coordinates{tmpcond}( index1,: ), g.coordinates{tmpcond}( index2,: ), ...
tmppower, tmpangle, g.circfactor(index1, index2), g);
end
end
end
end
% draw circles
% ------------
for index1 = g.plotorder(:)'
tmptimef = ALLERSP{ index1, tmpcond};
tmppow = mean(tmptimef( FREQS, indeximage)); % size is power
tmptimef = ALLITC{ index1, tmpcond};
tmpitc = mean(abs(tmptimef( FREQS, indeximage))); % color is ITC
%index1, tmpitc, tmppow,
drawcircle( g.coordinates{tmpcond}( index1,: ), tmppow, tmpitc, g);
end
% draw a bar for time probability
% -------------------------------
if ~isempty(g.rt)
if ~isempty(g.rt{tmpcond})
ll = line([g.rthistloc(1)-g.rthistloc(3)/2 g.rthistloc(1)+g.rthistloc(3)/2], [g.rthistloc(2) g.rthistloc(2)]);
set(ll, 'linewidth', 2*g.resmult, 'color', 'k');
barheight = RTdist(tmpcond, indeximage)*g.rthistloc(4);
x1 = g.rthistloc(1)-0.65*g.rthistloc(3)/2;
x2 = g.rthistloc(1)+0.65*g.rthistloc(3)/2;
y1 = g.rthistloc(2);
y2 = g.rthistloc(2)-barheight;
ll = patch([x1 x1 x2 x2], [y1 y2 y2 y1], g.rthistcolor, 'linewidth', 2*g.resmult);
end
end
end
% draw the enveloppe of the signal if necessary
% ---------------------------------------------
axes(e(tmpcond)); cla; axis off; set (gcf, 'visible', g.visible);
if ~isempty( g.envelope )
minordinate = min(min(min(g.envelope)));
maxordinate = max(max(max(g.envelope)));
for tmpcond = 1:nbconditions
axes(e(tmpcond)); cla; axis on; set (gcf, 'visible', g.visible);
plot(times, g.envelope(:,:,tmpcond), 'k', 'linewidth', 2*g.resmult); hold on;
set(gca, 'ylim', [minordinate maxordinate]);
set(gca, 'xlim', [times(1) times(end)]);
plot([times(indeximage) times(indeximage)], [minordinate maxordinate], 'b', 'linewidth', 2*g.resmult);
xlabel('Time (ms)', 'fontweight', 'bold', 'fontsize', 12*g.resmult); set(gca, 'box', 'off');
set(gca, 'fontsize', 10*g.resmult);
if tmpcond == 1
ylabel(g.envylabel, 'fontweight', 'bold', 'fontsize', 12*g.resmult);
end
% draw vertical lines if needed
% -----------------------------
if ~isempty(g.envvert)
drawvert(g.envvert, tmpcond, [minordinate maxordinate]);
end
end
% put the time on the ERP axis
% ----------------------------
%coordx1 = (g.xlimaxes(2)-g.xlimaxes(1))*0.1 + g.xlimaxes(1);
%coordy1 = (g.ylimaxes(2)-g.ylimaxes(1))*0.87 + g.ylimaxes(1);
end
% put the time in the left bottom corner
% --------------------------------------
tt = text(-0.1, -0.25, sprintf('%d ms', round(times(indeximage))), 'unit', 'normalized');
set(tt, 'fontsize', 12*g.resmult, 'horizontalalignment', 'right', 'tag', 'tmpmov', 'color', 'w');
% last 3-D settings
% -----------------
lighting phong;
material shiny;
setfont(gcf, 'color', [0.99 0.99 0.99]); % warning, for some reasons white does not print
for index = 1:length(c)
axes(c(index)); % bring back legend to front
end
% save the file for a movie
% -------------------------
movframes = getframe(gcf);
writeVideo(mov,movframes);
if strcmpi(g.framesout, 'tiff')
command2 = sprintf('print -dtiff %s/image%4.4d.tiff', g.framefolder, indeximage);
eval(command2);
elseif strcmpi(g.framesout, 'eps')
command2 = sprintf('print -depsc -loose %s/image%4.4d.eps', g.framefolder, indeximage);
eval(command2);
elseif strcmpi(g.framesout, 'ppm')
command2 = sprintf('print -dppm -loose %s/image%4.4d.ppm', g.framefolder, indeximage);
eval(command2);
elseif strcmpi(g.framesout, 'fig') % fig format
hgsave(sprintf('%s/image%4.4d.fig', g.framefolder, indeximage));
if strcmp(g.visible, 'on')
drawnow;
end
end
end
close(mov);
return;
% function to draw circles
% ------------------------
function [tmpsize, tmpcolor, handles] = drawcircle( tmpcoord, tmpersp, tmpitc, g);
% tmpcoord coordinate of the circle
% tmpersp erps power -> radius
% tmpitc itc -> color
% g preference
switch lower(g.power)
case 'on', tmpsize = (tmpersp-g.scalepower(1))/(g.scalepower(2)-g.scalepower(1)); % in between 0 and 1
case 'off', tmpsize = 0.5;
end
tmpsize = 0.05 * tmpsize * (g.xlimaxes(2)-g.xlimaxes(1))+0.1;
if isnan(tmpitc), tmpitc = 0; end
switch lower(g.itc)
case 'on',
indexcolor = length(g.colmapcoh)/2+ceil((tmpitc/g.scaleitc)*length(g.colmapcoh)/2);
if indexcolor < 1 | indexcolor > length(g.colmapcoh)
error([ 'ITC ' num2str(tmpitc) 'out of bound, use ''scaleitc'' to increase maxitc' ] );
end
tmpcolor = g.colmapcoh( indexcolor,: );
case 'off', tmpcolor = g.colmapcoh( length(g.colmapcoh)/2,: );
%case 'on', tmpcolor = g.colmapcoh( 64-ceil((tmpitc+0.01)*63),: );
%case 'off', tmpcolor = g.colmapcoh( 64-ceil((0+0.01)*63),: );
end
if tmpersp == 0
dashed = 1;
else
dashed = 0;
end
tmpsize = g.diskscale*tmpsize*100;
if tmpsize > 0
if length(tmpcoord) > 2
[xstmp ystmp zs] = sphere(15);
l=sqrt(xstmp.*xstmp+ystmp.*ystmp+zs.*zs);
normals = reshape([xstmp./l ystmp./l zs./l],[16 16 3]);
xs = tmpcoord(1) + tmpsize*ystmp*g.dimratio;
ys = tmpcoord(2) + tmpsize*xstmp;
zs = tmpcoord(3) + tmpsize*zs;
if tmpitc ~= 0
colorarray = repmat(reshape(tmpcolor, 1,1,3), [size(zs,1) size(zs,2) 1]);
else colorarray = repmat(reshape([1 1 1], 1,1,3), [size(zs,1) size(zs,2) 1]);
end
%figure;gca; hold on;
handles = surf(xs, ys, zs, colorarray, 'tag', 'tmpmov', 'EdgeColor','none', 'VertexNormals', normals, ...
'backfacelighting', 'lit', 'facelighting', 'phong', 'facecolor', 'interp', 'ambientstrength', 0.3);
%axis off; axis equal; lighting phong; camlight left; rotate3d
if strcmpi(g.project3d, 'on')
colorarray = repmat(reshape(g.projcolor, 1,1,3), [size(zs,1) size(zs,2) 1]);
surf(xs, ys, g.factproj(3)*ones(size(zs)), colorarray, 'tag', 'tmpmov', 'edgecolor', 'none', 'facelighting', 'none');
surf(xs, g.factproj(2)*ones(size(ys)), zs, colorarray, 'tag', 'tmpmov', 'edgecolor', 'none', 'facelighting', 'none');
surf(g.factproj(1)*ones(size(xs)), ys, zs, colorarray, 'tag', 'tmpmov', 'edgecolor', 'none', 'facelighting', 'none');
end
else
circle( tmpcoord(1), tmpcoord(2), tmpsize, tmpcolor, 'k', 0, 360, dashed, fastif(dashed, 2, 1));
end
end
return;
% function to draw the lines
% --------------------------
function handles = drawconnections( pos1, pos2, crossfpower, crossfangle, circfact, g);
% pos1, pos2 position of the points
% crossfpower coherence power for width of the line
% crossfangle coherence angle for color and speed of the line
% cirfact curvature of the line
% g preference
% normalize values depending on scaling
% -------------------------------------
%g.scalecoher = 2 * g.scalecoher / (g.xlimaxes(2)-g.xlimaxes(1));
%g.scalepower = 2 * g.scalepower / (g.xlimaxes(2)-g.xlimaxes(1));
% if the two circle are too close and do not draw the line
% --------------------------------------------------------
distance = sqrt(sum((pos1-pos2).^2));
if distance < 0.05*(g.ylimaxes(2) - g.ylimaxes(1)), return;
end
crossfpowerabs = abs(crossfpower);
switch lower(g.crossfcoh)
case 'on', tmpthick = (crossfpowerabs-g.scalecoher(1))/(g.scalecoher(2)-g.scalecoher(1)); % determine thickness = coherence amplitude
case 'off', tmpthick = 0;
end
sizec = size( g.colmapcrossf,1 );
switch lower(g.crossfphasecolor)
case 'on', tmpcolor = g.colmapcrossf( sizec/2+ ceil(tmpthick*(sizec/2-1)+1)*sign(crossfpower), : ); % determine color = coherence phase
case 'off', tmpcolor = g.colmapcrossf( sizec/2, : );
end
%tmpthick = 30 * (tmpthick-0.1); % does not vary with the axis zoom
tmpthick = 30 * (tmpthick); % adjusted for Nick
% absolute value to 90 degree determine speed
switch lower(g.crossfphasespeed)
case 'on', curphase = (crossfangle+180)/360; % phase from 1 to 0
case 'off', curphase = 0.5;
end
if crossfpower == 0, tmpthick = 0; end
if tmpthick > 0
[xc yc zc] = cylinder( g.resmult*tmpthick/300*100, 10);
colorarray = repmat(reshape(tmpcolor, 1,1,3), [size(zc,1) size(zc,2) 1]);
handles = surf(xc, yc, zc, colorarray, 'tag', 'tmpmov', 'edgecolor', 'none', ...
'backfacelighting', 'lit', 'facecolor', 'interp', 'facelighting', 'phong', 'ambientstrength', 0.3);
[xc yc zc] = adjustcylinder2( handles, [pos1(1) pos1(2) pos1(3)], [pos2(1) pos2(2) pos2(3)] );
% compute cylinder normals (have to bias normal closer to sphere
% to get a specular point
cx = mean(xc,2); cx = [(3*cx(1)+cx(2))/4; (cx(1)+3*cx(2))/4];
cy = mean(yc,2); cy = [(3*cy(1)+cy(2))/4; (cy(1)+3*cy(2))/4];
cz = mean(zc,2); cz = [(3*cz(1)+cz(2))/4; (cz(1)+3*cz(2))/4];
tmpx = xc - repmat(cx, [1 11]);
tmpy = yc - repmat(cy, [1 11]);
tmpz = zc - repmat(cz, [1 11]);
l=sqrt(tmpx.^2+tmpy.^2+tmpz.^2);
normals = reshape([tmpx./l tmpy./l tmpz./l],[2 11 3]);
set( handles, 'vertexnormals', normals);
%figure
%axis off; axis equal; lighting phong; camlight left; rotate3d
if strcmpi(g.project3d, 'on')
colorarray = repmat(reshape(g.projcolor, 1,1,3), [size(zc,1) size(zc,2) 1]);
surf(xc, yc, g.factproj(3)*ones(size(zc)), colorarray, 'tag', 'tmpmov', 'edgecolor', 'none', 'facelighting', 'none');
surf(xc, g.factproj(2)*ones(size(yc)), zc, colorarray, 'tag', 'tmpmov', 'edgecolor', 'none', 'facelighting', 'none');
surf(g.factproj(1)*ones(size(xc)), yc, zc, colorarray, 'tag', 'tmpmov', 'edgecolor', 'none', 'facelighting', 'none');
end
%if round(tmpthick) == 7, asdf; end
end
return;
% ***************************************************************************************
% Caption and tests
% ***************************************************************************************
% function to draw circles at all power
% -------------------------------------
function scalepower(posx, posy, g);
NBCIRCLE = 3;
coordy = posy;