update doc and help sections

Author: Remi-Gau

README.md

@@ -98,9 +98,66 @@ press the keys necessary to start or abort the experiment.
 
 Using empty vectors (ie `[]`) or a negative value for those means that you will let PTB find and use the default device.
 
-## Structure and function details
+## Structure
+
+```matlab
+
+cfg.testingDevice = 'pc';
+
+% cfg.color
+cfg.keyboard.keyboard = [];
+cfg.keyboard.responseBox = [];
+cfg.keyboard.responseKey = {};
+cfg.keyboard.escapeKey = 'ESCAPE';
+
+% cfg.debug
+cfg.debug.do = true;
+cfg.debug.transpWin = true;
+cfg.debug.smallWin = true;
+
+% cfg.text
+cfg.text.font 
+cfg.text.size 
+cfg.text.style 
+
+% cfg.color
+cfg.color.background
+
+% cfg.screen
+cfg.screen.monitorWidth
+cfg.screen.monitorDistance
+cfg.screen.idx
+cfg.screen.win 
+cfg.screen.winRect 
+cfg.screen.winWidth 
+cfg.screen.winHeight 
+cfg.screen.center 
+cfg.screen.FOV
+cfg.screen.ppd 
+cfg.screen.ifi 
+cfg.screen.monRefresh 
+
+% cfg.audio
+cfg.audio.do
+cfg.audio.pahandle
+cfg.audio.devIdx
+cfg.audio.playbackMode
+cfg.audio.requestedLatency
+cfg.audio.fs
+cfg.audio.channels
+cfg.audio.initVolume
+cfg.audio.pushSize  
+cfg.audio.requestOffsetTime 
+cfg.audio.reqsSampleOffset
+
+% cfg.mri
+cfg.mri.repetitionTime
+cfg.mri.triggerNb
+cfg.mri.triggerKey
+```
+
+## function details
 
-<!-- ### setParameters -->
 
 ### initPTB
 

checkAbort.m

@@ -1,4 +1,6 @@
 function checkAbort(cfg, deviceNumber)
+    % checkAbort(cfg, deviceNumber)
+    %
     % Check for experiment abortion from operator
     % When no deviceNumber is set then it will check the default device
     % When an abort key s detected this will set a global variable and throw a

cleanUp.m

@@ -1,4 +1,6 @@
-function cleanUp
+function cleanUp()
+    % cleanUp()
+    %
     % A wrapper function to close all windows, ports, show mouse cursor, close keyboard queues
     % and give access back to the keyboards.
 

degToPix.m

@@ -1,4 +1,6 @@
 function structure = degToPix(fieldName, structure, cfg)
+    % structure = degToPix(fieldName, structure, cfg)
+    %
     % For a given field value in degrees of visual angle in the structure,
     % this computes its value in pixel using the pixel per degree value of the cfg structure
     % and returns a structure with an additional field with Pix suffix holding that new value.

eyeTracker.m

@@ -1,4 +1,7 @@
 function [el, edfFile] = eyeTracker(input, cfg, varargin)
+    % [el, edfFile] = eyeTracker(input, cfg, varargin)
+    %
+    %
 
     if ~cfg.eyeTracker.do
 

getResponse.m

@@ -1,4 +1,6 @@
 function responseEvents = getResponse(action, deviceNumber, cfg, getOnlyPress)
+    % responseEvents = getResponse(action, deviceNumber, cfg, getOnlyPress)
+    %
     % Wrapper function to use KbQueue
     %
     % The queue will be listening to key presses on a keyboard device:

initPTB.m

@@ -1,4 +1,6 @@
 function [cfg] = initPTB(cfg)
+    % [cfg] = initPTB(cfg)
+    %
     % This will initialize PsychToolBox
     % - screen
     % - the windon opened takes the whole screen unless
@@ -13,7 +15,8 @@
     % - hides cursor
     % - sound
     %
-    % OUTPUT:
+    % See the Readme for more details on the content of cfg
+    %
     %
     %
 

pressSpaceForMe.m

@@ -1,5 +1,8 @@
-function pressSpaceForMe
+function pressSpaceForMe()
+    % pressSpaceForMe()
+    %
     % Use that to stop your script and only restart when the space bar is pressed.
+    %
 
     fprintf('\nPress space to continue.\n');
 

testKeyboards.m

@@ -1,4 +1,6 @@
 function testKeyboards(cfg)
+    % testKeyboards(cfg)
+    %
     % Checks that the keyboards asked for properly connected.
     % If no key is pressed on the correct keyboard after the timeOut time this exits with an error.
 

waitForTrigger.m

@@ -1,4 +1,6 @@
 function waitForTrigger(cfg, deviceNumber)
+    % waitForTrigger(cfg, deviceNumber)
+    %
     % Counts a certain number of triggers coming from the scanner before returning.
     %
     % Will print the count down in the command line and on the PTB window if one is