Merge pull request #62 from cpp-lln-lab/dev

[REL] v0.2.4

Author: Remi-Gau

.github/workflows/miss_hit_quality.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - master
+      - dev
   pull_request:
     branches: ['*']
 

.github/workflows/miss_hit_style.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - master
+      - dev
   pull_request:
     branches: ['*']
 

.github/workflows/moxunit.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - master
+      - dev
   pull_request:
     branches: ['*']
 
@@ -15,17 +16,22 @@ jobs:
       with:
         submodules: true
         fetch-depth: 1
+
     - name: MOxUnit Action
-      uses: joergbrech/moxunit-action@v1.1
+      uses: joergbrech/moxunit-action@v1.2.0
       with:
         tests: tests
         src: subfun
+        # add CPP_PTB to the path but don't include it the coverage
+        ext: lib/CPP_PTB/src
+        # Octave packages needed
+        pkg: statistics
         with_coverage: true
         cover_xml_file: coverage.xml
+
     - name: Code coverage
       uses: codecov/codecov-action@v1
       with:
-       token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
        file:  coverage.xml # optional
        flags: unittests # optional
        name: codecov-umbrella # optional

.gitignore

@@ -6,6 +6,10 @@
 *.tsv
 *.mat
 
+% tests and coverage
+coverage*
+test_report.log
+
 output
 
 ## virtual env

.gitmodules

@@ -1,8 +1,8 @@
 [submodule "lib/CPP_PTB"]
 	path = lib/CPP_PTB
 	url = https://github.com/cpp-lln-lab/CPP_PTB.git
-	branch = master
+	branch = dev
 [submodule "lib/CPP_BIDS"]
 	path = lib/CPP_BIDS
 	url = https://github.com/cpp-lln-lab/CPP_BIDS.git
-	branch = master
+	branch = dev

README.md

@@ -1,39 +1,38 @@
 [![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/localizer_auditory_motion/actions)
-<!-- 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 -->
 ![](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
 
-<!-- vscode-markdown-toc -->
+- [Auditory Translational Motion](#auditory-translational-motion)
+  - [`audioLocTranslational`](#audioloctranslational)
+    - [`setParameters`](#setparameters)
+  - [Requirements](#requirements)
+  - [Installation](#installation)
+  - [Contributors ✨](#contributors-)
+
+## `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)
 
-- 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)
+By default it is run in `Debug mode` meaning that it does not care about subjID,
+run n., fMRI triggers, Eye Tracker, etc..
 
-<!-- vscode-markdown-toc-config
-	numbering=true
-	autoSave=true
-	/vscode-markdown-toc-config -->
-<!-- /vscode-markdown-toc -->
+Any details of the experiment can be changed in `setParameters.m` (e.g.,
+experiment mode, motion stimuli details, exp. design, etc.)
 
-## 1. <a name='Requirements'></a>Requirements
+### `setParameters`
 
-Make sure that the following toolboxes are installed and added to the matlab / octave path.
+`setParameters.m` is the core engine of the experiment. See
+[docs/configuration](.docs/../docs/configuration.md) for more information.
+
+## Requirements
+
+Make sure that the following toolboxes are installed and added to the matlab /
+octave path.
 
 For instructions see the following links:
 
@@ -43,99 +42,19 @@ For instructions see the following links:
 | [Matlab](https://www.mathworks.com/products/matlab.html) | >=2017b      |
 | or [octave](https://www.gnu.org/software/octave/)        | >=4.?        |
 
-## 2. <a name='Installation'></a>Installation
+## 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.
+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.
 
 ```bash
 git clone --recurse-submodules https://github.com/cpp-lln-lab/localizer_auditory_motion.git
 ```
 
-## 3. <a name='Structureandfunctiondetails'></a>Structure and function details
-
-### 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.)
-
-### 3.2. <a name='setParameters'></a>setParameters
-
-`setParameters.m` is the core engine of the experiment. It contains the following tweakable sections:
-
-- Debug mode setting
-- Engine parameters:
-  - Devices parameters
-  - Monitor parameters
-  - Keyboard parameters
-  - MRI parameters
-- Experiment Design
-- Timing
-- Auditory Stimulation
-- Task(s)
-  - Instructions
-  - Task #1 parameters
-
-#### Let the scanner pace the experiment
-
-Set `cfg.pacedByTriggers.do` to `true` and you can then set all the details in this `if` block
-
-```matlab
-% Time is here in in terms of number repetition time (i.e MRI volumes)
-if cfg.pacedByTriggers.do
-
-  cfg.pacedByTriggers.quietMode = true;
-  cfg.pacedByTriggers.nbTriggers = 1;
-
-  cfg.timing.eventDuration = cfg.mri.repetitionTime / 2 - 0.04; % second
-
-  % Time between blocs in secs
-  cfg.timing.IBI = 0;
-  % Time between events in secs
-  cfg.timing.ISI = 0;
-  % Number of seconds before the motion stimuli are presented
-  cfg.timing.onsetDelay = 0;
-  % Number of seconds after the end all the stimuli before ending the run
-  cfg.timing.endDelay = 2;
-
-end
-```
-
-### 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.
-
-#### 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).
-
-#### 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
-
-#### 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
-
-#### 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
-
-
-
 ## Contributors ✨
 
-Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
+Thanks goes to these wonderful people
+([emoji key](https://allcontributors.org/docs/en/emoji-key)):
 
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
 <!-- prettier-ignore-start -->
@@ -150,6 +69,9 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 
 <!-- markdownlint-enable -->
 <!-- prettier-ignore-end -->
+
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
-This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
+This project follows the
+[all-contributors](https://github.com/all-contributors/all-contributors)
+specification. Contributions of any kind welcome!

audioLocTranslational.m

@@ -88,10 +88,9 @@
 
             thisEvent.isStim = logFile.isStim;
 
-            % we wait for a trigger every 2 events
-            if cfg.pacedByTriggers.do && mod(iEvent, 2) == 1
-                waitForTrigger( ...
-                               cfg, ...
+            % we wait for a trigger every events
+            if cfg.pacedByTriggers.do
+                waitForTrigger(cfg, ...
                                cfg.keyboard.responseBox, ...
                                cfg.pacedByTriggers.quietMode, ...
                                cfg.pacedByTriggers.nbTriggers);
@@ -133,6 +132,15 @@
 
         waitFor(cfg, cfg.timing.IBI);
 
+        % IBI trigger paced
+        if cfg.pacedByTriggers.do
+            waitForTrigger( ...
+                           cfg, ...
+                           cfg.keyboard.responseBox, ...
+                           cfg.pacedByTriggers.quietMode, ...
+                           cfg.timing.triggerIBI);
+        end
+
         % trigger monitoring
         triggerEvents = getResponse('check', cfg.keyboard.responseBox, cfg, ...
                                     getOnlyPress);

docs/configuration.md

@@ -0,0 +1,82 @@
+## Structure and function details
+
+`setParameters.m` is the core engine of the experiment. It contains the
+following tweakable sections. See
+[docs/configuration](.docs/../docs/configuration.md) for more information.
+
+- Debug mode setting
+- Engine parameters:
+  - Devices parameters
+  - Monitor parameters
+  - Keyboard parameters
+  - MRI parameters
+- Experiment Design
+- Timing
+- Auditory Stimulation
+- Task(s)
+  - Instructions
+  - Task #1 parameters
+
+#### Let the scanner pace the experiment
+
+Set `cfg.pacedByTriggers.do` to `true` and you can then set all the details in
+this `if` block
+
+```matlab
+% Time is here in in terms of number repetition time (i.e MRI volumes)
+if cfg.pacedByTriggers.do
+
+  cfg.pacedByTriggers.quietMode = true;
+  cfg.pacedByTriggers.nbTriggers = 1;
+
+  cfg.timing.eventDuration = cfg.mri.repetitionTime / 2 - 0.04; % second
+
+  % Time between blocs in secs
+  cfg.timing.IBI = 0;
+  % Time between events in secs
+  cfg.timing.ISI = 0;
+  % Number of seconds before the motion stimuli are presented
+  cfg.timing.onsetDelay = 0;
+  % Number of seconds after the end all the stimuli before ending the run
+  cfg.timing.endDelay = 2;
+
+end
+```
+
+### 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
+
+The `numEventsPerBlock` should be a multiple of the number of "base" listed in
+the `motionDirections` and `staticDirections` (4 at the moment).
+
+#### 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
+
+- `expParameters`: parameters returned by `setParameters`
+- `displayFigs`: a boolean to decide whether to show the basic design matrix of
+  the design
+
+#### 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