fix CI and mh

Author: Remi-Gau

README.md

@@ -1,18 +1,46 @@
+[![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/localizer_auditory_motion/actions)
+![](https://github.com/cpp-lln-lab/localizer_auditory_motion/workflows/CI/badge.svg)
+
+[![codecov](https://codecov.io/gh/cpp-lln-lab/localizer_auditory_motion/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/localizer_auditory_motion)
+
+[![Build Status](https://travis-ci.com/cpp-lln-lab/localizer_auditory_motion.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/localizer_auditory_motion)
+
+
 # Auditory Translational Motion
 
-## Requirements
+<!-- vscode-markdown-toc -->
+
+- 1. [Requirements](#Requirements)
+- 2. [Installation](#Installation)
+- 3. [Structure and function details](#Structureandfunctiondetails)
+     _ 3.1. [audioLocTranslational](#audioLocTranslational)
+     _ 3.2. [setParameters](#setParameters)
+     _ 3.3. [subfun/expDesign](#subfunexpDesign)
+     _ 3.3.1. [EVENTS](#EVENTS)
+     _ 3.3.2. [TARGETS:](#TARGETS:)
+     _ 3.3.3. [Input:](#Input:)
+     _ 3.3.4. [Output:](#Output:)
+     _ 3.4. [subfun/eyeTracker](#subfuneyeTracker) \* 3.5. [subfun/wait4Trigger](#subfunwait4Trigger)
+
+<!-- vscode-markdown-toc-config
+	numbering=true
+	autoSave=true
+	/vscode-markdown-toc-config -->
+<!-- /vscode-markdown-toc -->
+
+## 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 |
-|----------------------------------------------------------|--------------|
+| -------------------------------------------------------- | ------------ |
 | [PsychToolBox](http://psychtoolbox.org/)                 | >=3.0.14     |
 | [Matlab](https://www.mathworks.com/products/matlab.html) | >=2017b      |
 | or [octave](https://www.gnu.org/software/octave/)        | >=4.?        |
 
-## 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.
@@ -21,18 +49,17 @@ You can install it all with git by doing.
 git clone --recurse-submodules https://github.com/cpp-lln-lab/localizer_auditory_motion.git
 ```
 
-## Structure and function details
-
+## 3. <a name='Structureandfunctiondetails'></a>Structure and function details
 
-### audioLocTranslational
+### 3.1. <a name='audioLocTranslational'></a>audioLocTranslational
 
 Running this script will play blocks of motion/static sounds. Motion blocks will play sounds 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 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.)
 
-### setParameters
+### 3.2. <a name='setParameters'></a>setParameters
 
 `setParameters.m` is the core engine of the experiment. It contains the following tweakable sections:
 
@@ -49,30 +76,37 @@ Any details of the experiment can be changed in `setParameters.m` (e.g., experim
   - Instructions
   - Task #1 parameters
 
-### subfun/expDesign
+### 3.3. <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 a possible design.
 
-#### EVENTS
+#### 3.3.1. <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).
 
-#### TARGETS:
+#### 3.3.2. <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
 
-#### Input:
+#### 3.3.3. <a name='Input:'></a>Input:
+
 - `expParameters`: parameters returned by `setParameters`
 - `displayFigs`: a boolean to decide whether to show the basic design matrix of the design
 
-#### Output:
+#### 3.3.4. <a name='Output:'></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
 
-### subfun/eyeTracker
+### 3.4. <a name='subfuneyeTracker'></a>subfun/eyeTracker
+
 Eyetracker script, still to be debugged. Will probably moved in the CPP_PTB package. It deals with the calibration (dufault or custom), eye movements recording and saving the files.
 
-### subfun/wait4Trigger
+### 3.5. <a name='subfunwait4Trigger'></a>subfun/wait4Trigger
+
 Simple functions that counts the triggers sent by the MRI computer to the stimulation computer to sync brain volume recordings and stimulation.

audioLocTranslational.m

@@ -40,14 +40,14 @@
     [cfg] = initPTB(cfg);
 
     [el] = eyeTracker('Calibration', cfg);
-    
+
     [cfg] = expDesign(cfg);
 
     % Prepare for the output logfiles with all
     logFile.extraColumns = cfg.extraColumns;
     logFile = saveEventsFile('open', cfg, logFile);
 
-%     disp(cfg);
+    %     disp(cfg);
 
     % Show experiment instruction
     standByScreen(cfg);
@@ -84,7 +84,7 @@
             thisEvent.direction = cfg.design.directions(iBlock, iEvent);
             % thisEvent.speed = cfg.design.speeds(iBlock, iEvent);
             thisEvent.target = cfg.design.fixationTargets(iBlock, iEvent);
-            
+
             % we wait for a trigger every 2 events
             if cfg.pacedByTriggers.do && mod(iEvent, 2) == 1
                 waitForTrigger( ...

setParameters.m

@@ -31,7 +31,7 @@
 
     % MRI settings
     cfg = setMRI(cfg);
-    
+
     cfg.pacedByTriggers.do = true;
 
     %% Experiment Design
@@ -41,7 +41,7 @@
     cfg.design.motionType = 'translation';
     cfg.design.names = {'static'; 'motion'};
     cfg.design.motionDirections = [-1 -1 1 1];
-    cfg.design.nbRepetitions = 14; 
+    cfg.design.nbRepetitions = 14;
     cfg.design.nbEventsPerBlock = 12;
 
     %% Timing
@@ -130,10 +130,10 @@
 
 function cfg = setKeyboards(cfg)
     cfg.keyboard.escapeKey = 'ESCAPE';
-    cfg.keyboard.responseKey = {...
+    cfg.keyboard.responseKey = { ...
         'r', 'g', 'y', 'b', ...
         'd', 'n', 'z', 'e', ...
-        't'}; %dnze rgyb
+        't'}; % dnze rgyb
     cfg.keyboard.keyboard = [];
     cfg.keyboard.responseBox = [];
 

subfun/doAuditoryMotion.m

@@ -1,5 +1,5 @@
 function [onset, duration] = doAuditoryMotion(cfg, thisEvent)
-    
+
     % Play the auditopry stimulation of moving in 4 directions or static noise bursts
     %
     % DIRECTIONS
@@ -14,15 +14,15 @@
     %     - onset in machine time
     %     - duration in seconds
     %
-    
+
     %% Get parameters
-    
+
     direction = thisEvent.direction(1);
     isTarget = thisEvent.target(1);
     targetDuration = cfg.target.duration;
-    
+
     soundData = cfg.soundData;
-    
+
     switch direction
         case -1
             fieldName = 'S';
@@ -35,18 +35,18 @@
         case 180
             fieldName = 'L';
     end
-    
+
     if isTarget == 1
         fieldName = [fieldName '_T'];
     end
-    
+
     sound = soundData.(fieldName);
-    
+
     % Start the sound presentation
     PsychPortAudio('FillBuffer', cfg.audio.pahandle, sound);
     PsychPortAudio('Start', cfg.audio.pahandle);
     onset = GetSecs;
-    
+
     % draw first fixation and get a first visual time stamp
     % ideally we would want to synch that first time stamp and the sound start
     thisFixation.fixation = cfg.fixation;
@@ -56,29 +56,29 @@
     end
     drawFixation(thisFixation);
     vbl = Screen('Flip', cfg.screen.win);
-    
+
     while 1
-        
+
         % set default cross cross color but update if target time is not
         % finished
         thisFixation.fixation.color = cfg.fixation.color;
         if GetSecs < (onset + targetDuration) && isTarget == 1
             thisFixation.fixation.color = cfg.fixation.colorTarget;
         end
-        
+
         drawFixation(thisFixation);
         vbl = Screen('Flip', cfg.screen.win, vbl + cfg.screen.ifi);
-        
+
         status = PsychPortAudio('GetStatus', cfg.audio.pahandle);
         if ~status.Active
-            break;
+            break
         end
-        
+
     end
-    
+
     % Get the end time
     waitForEndOfPlayback = 1; % hard coding that will need to be moved out
     [onset, ~, ~, estStopTime] = PsychPortAudio('Stop', cfg.audio.pahandle, ...
         waitForEndOfPlayback);
-    
+
     duration = estStopTime - onset;

subfun/expDesign.m

@@ -59,8 +59,8 @@
     if nargin < 1 || isempty(cfg)
         error('give me something to work with');
     end
-    
-    fprintf('\n\nCreating design.\n\n')
+
+    fprintf('\n\nCreating design.\n\n');
 
     [NB_BLOCKS, NB_REPETITIONS, NB_EVENTS_PER_BLOCK, MAX_TARGET_PER_BLOCK] = getInput(cfg);
     [~, STATIC_INDEX, MOTION_INDEX] = assignConditions(cfg);