Merge pull request #44 from Remi-Gau/master

update README

Author: Remi-Gau

README.md

@@ -1,22 +1,25 @@
 [![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/localizer_visual_motion/actions)
-![](https://github.com/cpp-lln-lab/localizer_visual_motion/workflows/CI/badge.svg) 
+![](https://github.com/cpp-lln-lab/localizer_visual_motion/workflows/CI/badge.svg)
+
+[![codecov](https://codecov.io/gh/cpp-lln-lab/localizer_visual_motion/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/localizer_visual_motion)
 
 [![Build Status](https://travis-ci.com/cpp-lln-lab/localizer_visual_motion.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/localizer_visual_motion)
 
 <!-- vscode-markdown-toc -->
-* 1. [Requirements](#Requirements)
-* 2. [Installation](#Installation)
-* 3. [Structure and function details](#Structureandfunctiondetails)
-	* 3.1. [visualLocTranslational](#visualLocTranslational)
-	* 3.2. [setParameters](#setParameters)
-	* 3.3. [subfun/doDotMo](#subfundoDotMo)
-		* 3.3.1. [Input:](#Input:)
-		* 3.3.2. [Output:](#Output:)
-	* 3.4. [subfun/expDesign](#subfunexpDesign)
-		* 3.4.1. [EVENTS](#EVENTS)
-		* 3.4.2. [TARGETS:](#TARGETS:)
-		* 3.4.3. [Input:](#Input:-1)
-		* 3.4.4. [Output:](#Output:-1)
+
+- 1. [Requirements](#Requirements)
+- 2. [Installation](#Installation)
+- 3. [Structure and function details](#Structureandfunctiondetails)
+     _ 3.1. [visualLocTranslational](#visualLocTranslational)
+     _ 3.2. [setParameters](#setParameters)
+     _ 3.3. [subfun/doDotMo](#subfundoDotMo)
+     _ 3.3.1. [Input:](#Input:)
+     _ 3.3.2. [Output:](#Output:)
+     _ 3.4. [subfun/expDesign](#subfunexpDesign)
+     _ 3.4.1. [EVENTS](#EVENTS)
+     _ 3.4.2. [TARGETS:](#TARGETS:)
+     _ 3.4.3. [Input:](#Input:-1)
+     _ 3.4.4. [Output:](#Output:-1)
 
 <!-- vscode-markdown-toc-config
 	numbering=true
@@ -28,40 +31,40 @@
 
 # Translational Motion
 
-##  1. <a name='Requirements'></a>Requirements
+## 1. <a name='Requirements'></a>Requirements
 
 Make sure that the following toolboxes are installed and added to the matlab / octave path.
 
 For instructions see the following links:
 
 | Requirements                                             | Used version |
-|----------------------------------------------------------|--------------|
+| -------------------------------------------------------- | ------------ |
 | [CPP_BIDS](https://github.com/cpp-lln-lab/CPP_BIDS)      | ?            |
 | [CPP_PTB](https://github.com/cpp-lln-lab/CPP_PTB)        | ?            |
 | [PsychToolBox](http://psychtoolbox.org/)                 | >=3.0.14     |
 | [Matlab](https://www.mathworks.com/products/matlab.html) | >=2017       |
 | or [octave](https://www.gnu.org/software/octave/)        | >=4.?        |
 
-##  2. <a name='Installation'></a>Installation
+## 2. <a name='Installation'></a>Installation
 
 The CPP_BIDS and CPP_PTB dependencies are already set up as submodule to this repository.
-You can install it all with git by doing. 
+You can install it all with git by doing.
 
 ```bash
 git clone --recurse-submodules https://github.com/cpp-lln-lab/localizer_visual_motion.git
 ```
 
-##  3. <a name='Structureandfunctiondetails'></a>Structure and function details
+## 3. <a name='Structureandfunctiondetails'></a>Structure and function details
 
-###  3.1. <a name='visualLocTranslational'></a>visualLocTranslational
+### 3.1. <a name='visualLocTranslational'></a>visualLocTranslational
 
 Running this script will show blocks of motion dots (soon also moving gratings) and static dots. Motion blocks will show dots(/gratings) moving in one of four directions (up-, down-, left-, and right-ward)
 
 By default it is run in `Debug mode` meaning that it does not run care about subjID, run n., fMRI triggers, Eye Tracker, etc..
 
 Any details of the experiment can be changed in `setParameters.m` (e.g., experiment mode, motion stimuli details, exp. design, etc.)
 
-###  3.2. <a name='setParameters'></a>setParameters
+### 3.2. <a name='setParameters'></a>setParameters
 
 `setParameters.m` is the core engine of the experiment. It contains the following tweakable sections:
 
@@ -77,38 +80,44 @@ Any details of the experiment can be changed in `setParameters.m` (e.g., experim
   - Instructions
   - Task #1 parameters
 
-###  3.3. <a name='subfundoDotMo'></a>subfun/doDotMo
+### 3.3. <a name='subfundoDotMo'></a>subfun/doDotMo
+
+#### 3.3.1. <a name='Input:'></a>Input:
 
-####  3.3.1. <a name='Input:'></a>Input:
 - `cfg`: PTB/machine configurations returned by `setParameters` and `initPTB`
 - `expParameters`: parameters returned by `setParameters`
 - `logFile`: structure that stores the experiment logfile to be saved
 
-####  3.3.2. <a name='Output:'></a>Output:
+#### 3.3.2. <a name='Output:'></a>Output:
+
 - Event `onset`
 - Event `duration`
 
 The dots are drawn on a square that contains the round aperture, then any dots outside of the aperture is turned into a NaN so effectively the actual number of dots on the screen at any given time is not the one that you input but a smaller number (nDots / Area of aperture) on average.
 
-###  3.4. <a name='subfunexpDesign'></a>subfun/expDesign
+### 3.4. <a name='subfunexpDesign'></a>subfun/expDesign
+
 Creates the sequence of blocks and the events in them. The conditions are consecutive static and motion blocks (Gives better results than randomised). It can be run as a stand alone without inputs to display a visual example of possible design.
 
-####  3.4.1. <a name='EVENTS'></a>EVENTS
+#### 3.4.1. <a name='EVENTS'></a>EVENTS
+
 The `numEventsPerBlock` should be a multiple of the number of "base" listed in the `motionDirections` and `staticDirections` (4 at the moment).
 
-####  3.4.2. <a name='TARGETS:'></a>TARGETS:
+#### 3.4.2. <a name='TARGETS:'></a>TARGETS:
+
 - If there are 2 targets per block we make sure that they are at least 2 events apart.
 - Targets cannot be on the first or last event of a block
 
-####  3.4.3. <a name='Input:-1'></a>Input:
+#### 3.4.3. <a name='Input:-1'></a>Input:
+
 - `expParameters`: parameters returned by `setParameters`
 - `displayFigs`: a boolean to decide whether to show the basic design matrix of the design
 
-####  3.4.4. <a name='Output:-1'></a>Output:
+#### 3.4.4. <a name='Output:-1'></a>Output:
+
 - `expParameters.designBlockNames` is a cell array `(nr_blocks, 1)` with the name for each block
 - `expParameters.designDirections` is an array `(nr_blocks, numEventsPerBlock)` with the direction to present in a given block
   - `0 90 180 270` indicate the angle
   - `-1` indicates static
 - `expParameters.designSpeeds` is an array `(nr_blocks, numEventsPerBlock) * speedEvent`
 - `expParameters.designFixationTargets` is an array `(nr_blocks, numEventsPerBlock)` showing for each event if it should be accompanied by a target
-