clean doc and move fixation functions in a separate folder

Author: Remi-Gau

README.md

@@ -1,3 +1,14 @@
+[![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/CPP_PTB/actions)
+![](https://github.com/cpp-lln-lab/CPP_PTB/workflows/CI/badge.svg) 
+
+[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_BIDS.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_PTB)
+
+<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
+[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)
+<!-- ALL-CONTRIBUTORS-BADGE:END -->
+
+# CPP_PTB
+
 <!-- vscode-markdown-toc -->
 * 1. [Requirements](#Requirements)
 * 2. [Code guidestyle](#Codeguidestyle)
@@ -17,17 +28,13 @@
 	numbering=true
 	autoSave=true
 	/vscode-markdown-toc-config -->
-<!-- /vscode-markdown-toc --># CPP_PTB
+<!-- /vscode-markdown-toc -->
 
-<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)
-<!-- ALL-CONTRIBUTORS-BADGE:END -->
 
-This is List of Crossmodal Perception and Plasticity lab (CPP) PsychToolBox (PTB) toolbox.
+This is the Crossmodal Perception and Plasticity lab (CPP) PsychToolBox (PTB) toolbox.
 
 Those functions are mostly wrappers around some PTB functions to facilitate their use and to have a codebase to facilitate their reuse.
 
-
 ##  1. <a name='Requirements'></a>Requirements
 
 Make sure that the following toolboxes are installed and added to the matlab / octave path.

docs/functions_description.md

@@ -1,28 +1,31 @@
+# functions description
+
 <!-- vscode-markdown-toc -->
-* 1. [function details](#functiondetails)
+* 1. [ General functions](#Generalfunctions)
 	* 1.1. [initPTB](#initPTB)
-	* 1.2. [testKeyboards](#testKeyboards)
-	* 1.3. [cleanUp](#cleanUp)
-	* 1.4. [getExperimentStart](#getExperimentStart)
-	* 1.5. [getExperimentEnd](#getExperimentEnd)
-	* 1.6. [getResponse](#getResponse)
-	* 1.7. [deg2Pix](#deg2Pix)
-	* 1.8. [drawFixationCross](#drawFixationCross)
-	* 1.9. [eyeTracker](#eyeTracker)
-	* 1.10. [pressSpace4me](#pressSpace4me)
-	* 1.11. [standByScreen](#standByScreen)
-	* 1.12. [waitForTrigger](#waitForTrigger)
+	* 1.2. [cleanUp](#cleanUp)
+	* 1.3. [getExperimentStart](#getExperimentStart)
+	* 1.4. [getExperimentEnd](#getExperimentEnd)
+	* 1.5. [deg2Pix](#deg2Pix)
+	* 1.6. [eyeTracker](#eyeTracker)
+	* 1.7. [standByScreen](#standByScreen)
+	* 1.8. [waitForTrigger](#waitForTrigger)
+* 2. [Keyboard functions: response collection and aborting experiment](#Keyboardfunctions:responsecollectionandabortingexperiment)
+	* 2.1. [testKeyboards](#testKeyboards)
+	* 2.2. [getResponse](#getResponse)
+	* 2.3. [pressSpace4me](#pressSpace4me)
+* 3. [Fixations](#Fixations)
+	* 3.1. [drawFixationCross](#drawFixationCross)
+* 4. [Drawing dots](#Drawingdots)
+* 5. [Drawing apertures](#Drawingapertures)
 
 <!-- vscode-markdown-toc-config
 	numbering=true
 	autoSave=true
 	/vscode-markdown-toc-config -->
-<!-- /vscode-markdown-toc --># functions description
-
-
-
-##  1. <a name='functiondetails'></a>function details
+<!-- /vscode-markdown-toc -->
 
+##  1. <a name='Generalfunctions'></a> General functions
 
 ###  1.1. <a name='initPTB'></a>initPTB
 
@@ -38,26 +41,48 @@ This will initialize PsychToolBox
 -   keyboard
 -   sound
 
-###  1.2. <a name='testKeyboards'></a>testKeyboards
-
-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.
-
-###  1.3. <a name='cleanUp'></a>cleanUp
+###  1.2. <a name='cleanUp'></a>cleanUp
 
 A wrapper function to close all windows, ports, show mouse cursor, close keyboard queues
 and give access back to the keyboards.
 
-###  1.4. <a name='getExperimentStart'></a>getExperimentStart
+###  1.3. <a name='getExperimentStart'></a>getExperimentStart
 
 Wrapper function that will show a fixation cross and collect a start timestamp in `cfg.experimentStart`
 
-###  1.5. <a name='getExperimentEnd'></a>getExperimentEnd
+###  1.4. <a name='getExperimentEnd'></a>getExperimentEnd
 
 Wrapper function that will show a fixation cross and display in the console the whole experiment's duration in minutes and seconds  
 
-###  1.6. <a name='getResponse'></a>getResponse
+###  1.5. <a name='deg2Pix'></a>deg2Pix
+
+For a given field value in degrees of visual angle in the input `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.
+
+###  1.6. <a name='eyeTracker'></a>eyeTracker
+
+This will handle the Eye Tracker (EyeLink set up) and can be called to initialize the connection and start the calibration, start/stop eye(s) movement recordings and save the `*.edf` file (named with BIDS specification from cpp-lln-lab/CPP_BIDS).  
+
+###  1.7. <a name='standByScreen'></a>standByScreen
+
+It shows a basic one-page instruction stored in `cfg.task.instruction` and wait for `space` stroke.
+
+###  1.8. <a name='waitForTrigger'></a>waitForTrigger
+
+Counts a certain number of triggers coming from the mri/scanner before returning.
+Requires number of triggers to wait for.
+
+
+##  2. <a name='Keyboardfunctions:responsecollectionandabortingexperiment'></a>Keyboard functions: response collection and aborting experiment
+
+###  2.1. <a name='testKeyboards'></a>testKeyboards
+
+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.
+
+###  2.2. <a name='getResponse'></a>getResponse
 
 It is wrapper function to use `KbQueue` which is definitely what you should use to collect responses.
 
@@ -83,29 +108,16 @@ In brief, there are several actions you can execute with this function.
 -   stop: Stops buffering key presses. You can still restart by calling "start" again.
 -   release: Closes the buffer for good.
 
-###  1.7. <a name='deg2Pix'></a>deg2Pix
-
-For a given field value in degrees of visual angle in the input `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.
-
-###  1.8. <a name='drawFixationCross'></a>drawFixationCross
-
-Define the parameters of the fixation cross in `cfg` and `expParameters` and this does the rest.
-
-###  1.9. <a name='eyeTracker'></a>eyeTracker
-
-This will handle the Eye Tracker (EyeLink set up) and can be called to initialize the connection and start the calibration, start/stop eye(s) movement recordings and save the `*.edf` file (named with BIDS specification from cpp-lln-lab/CPP_BIDS).  
-
-###  1.10. <a name='pressSpace4me'></a>pressSpace4me
+###  2.3. <a name='pressSpace4me'></a>pressSpace4me
 
 Use that to stop your script and only restart when the space bar is pressed.
 
-###  1.11. <a name='standByScreen'></a>standByScreen
+##  3. <a name='Fixations'></a>Fixations
 
-It shows a basic one-page instruction stored in `cfg.task.instruction` and wait for `space` stroke.
+###  3.1. <a name='drawFixationCross'></a>drawFixationCross
 
-###  1.12. <a name='waitForTrigger'></a>waitForTrigger
+Define the parameters of the fixation cross in `cfg` and `expParameters` and this does the rest.
 
-Counts a certain number of triggers coming from the mri/scanner before returning.
-Requires number of triggers to wait for.
+##  4. <a name='Drawingdots'></a>Drawing dots
+
+##  5. <a name='Drawingapertures'></a>Drawing apertures