fixed folder organization

Chromatic_Integration_Stimulus.m

@@ -1,265 +0,0 @@
-
-
-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