Khani_and_Gollisch_2021_RGC_spike_trains_chromatic_integration/Stimulation/Chromatic_Integration_Stimulus.m

function varargout = Chromatic_Integration_Stimulus(varargin)

%===================================================================================
% Parameter             Default                     Usage
%===================================================================================

% selecttextfile        false       Browse prompt to select the parameters text file
% stimduration          30          Stimulus presentation duration screen refresh rate unit (30 = 0.5 sec)
% preframes             120         Duration of background light presented in between the stimulus flashes
% maxcontrast           0.2         Maximum Weber contrast value (ranges from -1 to 1)
% mincontrast          -0.2         Minimum Weber contrast value (ranges from -1 to 1)
% contrastdiff          0.02        Contrast steps from mincontrast to maxcontrast e.g. -20 : 2 : 20
% seed                  -1000   	Starting value for random number generator (should be always negative)
% redmeanintensity        0     	Mean intensity for red gun of the screen
% greenmeanintensity	0.5         Mean intensity for green gun of the screen
% bluemeanintensity     0.5     	Mean intensity for blue gun of the screen
% screensize            864 x 480	Screen resolution, default value is the resolution of the lightcrafter projector
% refreshrate           60          Screen refresh rate in Hz
% fullscreen            false       Option to display the stimulus in full-screen mode
% help                  false       Option to check the list of available parameters
% lmargin               0           Margins from left side of the screen (not available for this stimulus)
% rmagin                0           Margins from right side of the screen (not available for this stimulus)
% tmargin               0           Margins from top of the screen (not available for this stimulus)
% bmargin               0           Margins from bottom of the screen (not available for this stimulus)
% coneisolating         false       Option to activate opsin-isolation (excluded for simplicity)
% 
%===================================================================================

para            =   read_stimulus_parameters(varargin{:});
if para.help, return; end

offcontrasts    =   fliplr(0:-para.contrastdiff:para.mincontrast);
oncontrasts     =   0:para.contrastdiff:para.maxcontrast;

greencontrasts  =   [offcontrasts,oncontrasts];
bluecontrasts   =   [oncontrasts,offcontrasts];

% convert to weber contrast (mean+(contrast*mean))
greencontrasts  =   para.greenmeanintensity + (greencontrasts * para.greenmeanintensity);
bluecontrasts   =   para.bluemeanintensity + (bluecontrasts * para.bluemeanintensity);

numcontrasts    =   size(greencontrasts,2);

% The darwing of the screen goes here
monitorsize =   get(0,'ScreenSize');
scpos       =   [monitorsize(3)/2-(para.screensize(1)/2), ...
                monitorsize(4)/2-(para.screensize(2)/2), para.screensize];
% make an screen like figure
fh          =   figure('Menu','none','ToolBar','none','Position',scpos,'Color',0.5*[1 1 1]);
fh.Name     =   'Example of Chromatic Integration Stimulus, from Khani and Gollisch (2021)';
fh.Colormap =   gray;
ah          =   axes('Units','Normalize','Position',[0 0 1 1]);
                axis(ah,[0, para.screensize(1),0, para.screensize(2)]);
                axis(ah,'off');

stimsize    =   [0+para.bmargin, 0+para.lmargin, para.screensize(1)-para.rmargin,...
                para.screensize(2)-para.tmargin];
framecounter=   0;
seed        =   para.seed;
collistorderout = [];

while ishandle(fh)
    
    if framecounter == 0
        % start with gray screen
        r= rectangle('pos',stimsize,'facecolor',[0.5 0.5 0.5],'edgecolor','none');
    end
    
    frameMod        =   mod(framecounter,para.stimduration + para.preframes);
    colorindexMod   =   floor(mod((framecounter)/(para.stimduration+para.preframes),numcontrasts));
    
    % resest the color order using Fisher-Yates random permutations
    if colorindexMod == 0 && frameMod == 0
        [col_order, seed]    =   fisher_Yates_shuffle_order(seed,1:numcontrasts);
        collistorderout = [collistorderout; col_order]; %#ok, not the most efficient way!
    end
    
    % show gray screen in between stimulus frames
    if frameMod < (para.preframes)
        r.FaceColor =   [0.5 0.5 0.5]; % gray screen during preframes
    else
        r.FaceColor =   [0, greencontrasts(col_order(colorindexMod+1)), bluecontrasts(col_order(colorindexMod+1))];
    end
    
    % this is to draw the frames relatively accurately.
    drawnow;
    java.lang.Thread.sleep(1/para.refreshrate*1e3);
    %pause(1/para.refreshrate);
    framecounter    =   framecounter+1;
end

% setting up output to get the stimulus order contrast orders
collistorderout     =   collistorderout';     % transposing to make vectorization (:) easier
collistorderout     =   collistorderout(:);
out.numberContrastsShown    =   floor((framecounter-1)/(para.stimduration+para.preframes));
collistorderout     =   collistorderout(1:out.numberContrastsShown);
out.stimulusOrder   =   transpose(collistorderout);
% to get contrasts between input values
greencontrasts      =   [offcontrasts,oncontrasts];
bluecontrasts       =   [oncontrasts,offcontrasts];
out.greenContrasts  =   greencontrasts(collistorderout);
out.blueContrasts   =   bluecontrasts(collistorderout);
out.frameCounter    =   framecounter -1 ;        % -1 for the last +1

varargout{1} = out;

end

%--------------------------------------------------------------------------------------------------%
%----------                               sub-functions                                  ----------%
%--------------------------------------------------------------------------------------------------%


function varargout = fisher_Yates_shuffle_order(seed,inputVec,varargin)
%
%%% fisher_Yates_shuffle_order %%%
%
%
% This function generate psudorandom permution similar to randperm in MATLAB
% but works with psudorandom number generator ran1. It also gives back the
% most recent seed value to continue the permuation in case of repeated trials.
% note that the direction of permutation is along x-axix or for columns of
% MATALB not for the rows.
%
%
% ===============================Inputs====================================
%
%   seed : seed value for random number generation.
%   inputVec : input vector used for permutation.
%
%================================Output====================================
%
%   testOrder : vector of permuted indices for the inputVec.
%   newSeed : the recent seed that used in the ran1 function.
%   outputVec : the permuted input vector along x-axis
%
% Note that the permution algorithem is based on Fisher-Yates shuffle
% algorithem identical to what is used in the stimulus program.
% for more info check :
% https://en.wikipedia.org/wiki/Fisher%E2%80%93Yates_shuffle
%
% written by Mohammad, 01.02.2016

newSeed         =   seed;
testOrder       =   zeros(1,size(inputVec,2));
testOrder(1)    =   1;

for i   =   2:length(inputVec)-1
    
    [randVal,newSeed] = ran1(newSeed);
    
    j               =   ceil(i*randVal);    % based on Fischer-Yates algorithem
    testOrder(i)    =   testOrder(j);
    testOrder(j)    =   i;
    
end

testOrder           =   [testOrder(end),testOrder(1:end-1)]+1;   % to match MATLAB indexing
varargout{1}        =   testOrder;
varargout{2}        =   newSeed;
for j   =   1:size(inputVec,1)
    varargout{3}(j,:)   =   inputVec(j,testOrder);
end

end

%--------------------------------------------------------------------------------------------------%

function paraout = read_stimulus_parameters(varargin)

% first parse the user inputs
p = inputParser();      % check the user options.
p.addParameter('selecttextfile', false,  @(x) islogical(x) || (isnumeric(x) && ismember(x,[0,1])));
p.addParameter('stimduration', 30, @isnumeric);
p.addParameter('preframes', 120, @isnumeric);
p.addParameter('contrastdiff', 0.02, @isnumeric);
p.addParameter('mincontrast',-0.2, @isnumeric);
p.addParameter('maxcontrast', 0.2, @isnumeric);
p.addParameter('seed', -1000, @isnumeric);
p.addParameter('redmeanintensity', 0, @isnumeric);
p.addParameter('greenmeanintensity', 0.5, @isnumeric);
p.addParameter('bluemeanintensity', 0.5, @isnumeric);
p.addParameter('lmargin',0, @isnumeric);
p.addParameter('rmargin', 0, @isnumeric);
p.addParameter('bmargin', 0, @isnumeric);
p.addParameter('tmargin', 0, @isnumeric);
p.addParameter('coneisolating', true,  @(x) islogical(x) || (isnumeric(x) && ismember(x,[0,1])));
p.addParameter('screensize', [864 480], @isnumeric);
p.addParameter('refreshrate', 60, @isnumeric);
p.addParameter('fullscreen', false,  @(x) islogical(x) || (isnumeric(x) && ismember(x,[0,1])));
p.addParameter('help', false,  @(x) islogical(x) || (isnumeric(x) && ismember(x,[0,1])));

p.parse(varargin{:});
% defualt parameters
defpara     =    p.Results;

if defpara.help
    help_info_for_parameters(defpara);
    paraout     =   defpara;
    return;
end

if defpara.selecttextfile
    % now read the text files
    [stimfile, stimpath] = uigetfile('*.txt','Select a chromatic integration stimulus parameter file','chromatic_integration.txt');
    
    fid     =   fopen([stimpath,filesep,stimfile]);
    tline   =   fgetl(fid);
    while ischar(tline)
        tline   =   fgetl(fid);
        if tline == -1, break; end
        fn      =   extractBefore(tline,' = ');
        if isempty(fn), continue; end
        val     =   extractAfter(tline,' = ');
        % to convert to double
        if ~isnan(str2double(val))
            val =   str2double(val);
        end
        % to convert to logical
        if strcmp(val,'true'),        val = true;       end
        if strcmp(val,'false'),       val = false;       end
        % store the values in a structure
        stimpara.(fn)   =   val;
    end
    fclose(fid);
    
    % compare the text file to the defualt values and fill the missing parameters
    fn      =       fieldnames(defpara);
    for ii  =   1:numel(fn)
        if isfield(stimpara,fn{ii})
            paraout.(fn{ii})    =       stimpara.(fn{ii});
        else
            paraout.(fn{ii})    =       defpara.(fn{ii});
        end
    end
else
    paraout     =       defpara;
end

if paraout.fullscreen
    monitorsize         =   get(0,'ScreenSize');
    paraout.screensize  =   monitorsize(3:4) ;
end

end

%--------------------------------------------------------------------------------------------------%

function help_info_for_parameters(defpara)

fn          =   fieldnames(defpara);
fprintf(['\n\n',repmat('==',1,50),'\r\n']);
fprintf([repmat(' ',1,35),'List of Stimulus Parameters\r\n']);
fprintf([repmat('==',1,50),'\r\n']);
maxtxtlen   =   max(cellfun(@numel,fn))+10;
for ii      =  1:numel(fn)
    g       =  repmat(' ',1,maxtxtlen - numel(fn{ii}));
   fprintf(['\t-- \t%s',g,':',repmat(' ',1,10),'%s\n'],fn{ii},num2str(defpara.(fn{ii}))); 
end
fprintf(['\n',repmat('==',1,50),'\r\n']);

end