Merge remote-tracking branch 'cpp-lln-lab/master'

Author: marcobarilari

.all-contributorsrc

@@ -59,13 +59,23 @@
         "bug",
         "userTesting"
       ]
+    },
+    {
+      "login": "iqrashahzad14",
+      "name": "iqrashahzad14",
+      "avatar_url": "https://avatars.githubusercontent.com/u/75671348?v=4",
+      "profile": "https://github.com/iqrashahzad14",
+      "contributions": [
+        "code",
+        "ideas"
+      ]
     }
   ],
   "contributorsPerLine": 7,
   "projectName": "localizer_visual_motion",
   "projectOwner": "cpp-lln-lab",
   "repoType": "github",
   "repoHost": "https://github.com",
-  "skipCi": false
-  "contributorsSortAlphabetically": true
+  "skipCi": false,
+  "contributorsSortAlphabetically": false
 }

.github/workflows/miss_hit_quality.yml

@@ -0,0 +1,38 @@
+name: miss_hit_quality
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - name: Set up Python 3.6
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.6
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip3 install -r requirements.txt
+
+    - name: MISS_HIT Metrics
+      run: |
+        mh_metric --ci
+
+    - name: MISS_HIT Bug finder
+      run: |
+        mh_lint

.github/workflows/miss_hit_style.yml

@@ -0,0 +1,34 @@
+name: miss_hit_style
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - name: Set up Python 3.6
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.6
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip3 install -r requirements.txt
+
+    - name: MISS_HIT Code style
+      run: |
+        mh_style

.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+repos:
+
+-   repo: local
+
+    hooks:
+
+    - id: mh_style
+      name: mh_style
+      entry: mh_style
+      args: [--process-slx, --fix]
+      files: ^(.*\.(m|slx))$
+      language: python
+      additional_dependencies: [miss_hit_core]
+
+    - id: mh_metric
+      name: mh_metric
+      entry: mh_metric
+      args: [--ci]
+      files: ^(.*\.(m|slx))$
+      language: python
+      additional_dependencies: [miss_hit_core]
+
+    - id: mh_lint
+      name: mh_lint
+      entry: mh_lint
+      files: ^(.*\.(m|slx))$
+      language: python
+      additional_dependencies: [miss_hit]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.0.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-added-large-files

.travis.yml

@@ -1,40 +1,37 @@
 [![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/localizer_visual_motion/actions)
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-4-orange.svg?style=flat-square)](#contributors-)
+[![All Contributors](https://img.shields.io/badge/all_contributors-5-orange.svg?style=flat-square)](#contributors-)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 ![](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)
-
-<!-- vscode-markdown-toc-config
-	numbering=true
-	autoSave=true
-	/vscode-markdown-toc-config -->
-<!-- /vscode-markdown-toc -->
+<!-- TOC -->
+- [fMRI localizers for visual motion](#fmri-localizers-for-visual-motion)
+  - [Translational Motion](#translational-motion)
+  - [Requirements](#requirements)
+  - [Installation](#installation)
+  - [Structure and function details](#structure-and-function-details)
+    - [visualLocTranslational](#visualloctranslational)
+    - [setParameters](#setparameters)
+      - [Let the scanner pace the experiment](#let-the-scanner-pace-the-experiment)
+    - [subfun/doDotMo](#subfundodotmo)
+      - [Input](#input)
+      - [Output](#output)
+    - [subfun/expDesign](#subfunexpdesign)
+      - [EVENTS](#events)
+      - [TARGETS](#targets)
+      - [Input](#input-1)
+      - [Output](#output-1)
+<!-- TOC -->
 
 # fMRI localizers for visual motion
 
-# Translational Motion
+## Translational Motion
 
-## 1. <a name='Requirements'></a>Requirements
+## Requirements
 
 Make sure that the following toolboxes are installed and added to the matlab / octave path.
 
@@ -48,7 +45,7 @@ For instructions see the following links:
 | [Matlab](https://www.mathworks.com/products/matlab.html) | >=2017       |
 | 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.
@@ -57,17 +54,17 @@ You can install it all with git by doing.
 git clone --recurse-submodules https://github.com/cpp-lln-lab/localizer_visual_motion.git
 ```
 
-## 3. <a name='Structureandfunctiondetails'></a>Structure and function details
+## Structure and function details
 
-### 3.1. <a name='visualLocTranslational'></a>visualLocTranslational
+### 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
+### setParameters
 
 `setParameters.m` is the core engine of the experiment. It contains the following tweakable sections:
 
@@ -108,40 +105,40 @@ if cfg.pacedByTriggers.do
 end
 ```
 
-### 3.3. <a name='subfundoDotMo'></a>subfun/doDotMo
+### subfun/doDotMo
 
-#### 3.3.1. <a name='Input:'></a>Input:
+#### 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:
+#### 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
+### 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
+#### 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:
+#### 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:
+#### 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:
+#### 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
@@ -159,15 +156,17 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 <!-- markdownlint-disable -->
 <table>
   <tr>
-    <td align="center"><a href="https://github.com/mohmdrezk"><img src="https://avatars2.githubusercontent.com/u/9597815?v=4" width="100px;" alt=""/><br /><sub><b>Mohamed Rezk</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/commits?author=mohmdrezk" title="Code">💻</a> <a href="#design-mohmdrezk" title="Design">🎨</a> <a href="#ideas-mohmdrezk" title="Ideas, Planning, & Feedback">🤔</a></td>
-    <td align="center"><a href="https://github.com/marcobarilari"><img src="https://avatars3.githubusercontent.com/u/38101692?v=4" width="100px;" alt=""/><br /><sub><b>marcobarilari</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/commits?author=marcobarilari" title="Code">💻</a> <a href="#design-marcobarilari" title="Design">🎨</a> <a href="#ideas-marcobarilari" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/issues?q=author%3Amarcobarilari" title="Bug reports">🐛</a> <a href="#userTesting-marcobarilari" title="User Testing">📓</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/pulls?q=is%3Apr+reviewed-by%3Amarcobarilari" title="Reviewed Pull Requests">👀</a> <a href="#question-marcobarilari" title="Answering Questions">💬</a> <a href="#infra-marcobarilari" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-marcobarilari" title="Maintenance">🚧</a></td>
-    <td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars3.githubusercontent.com/u/6961185?v=4" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/commits?author=Remi-Gau" title="Code">💻</a> <a href="#design-Remi-Gau" title="Design">🎨</a> <a href="#ideas-Remi-Gau" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/issues?q=author%3ARemi-Gau" title="Bug reports">🐛</a> <a href="#userTesting-Remi-Gau" title="User Testing">📓</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/pulls?q=is%3Apr+reviewed-by%3ARemi-Gau" title="Reviewed Pull Requests">👀</a> <a href="#question-Remi-Gau" title="Answering Questions">💬</a> <a href="#infra-Remi-Gau" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-Remi-Gau" title="Maintenance">🚧</a></td>
-    <td align="center"><a href="https://github.com/CerenB"><img src="https://avatars1.githubusercontent.com/u/10451654?v=4" width="100px;" alt=""/><br /><sub><b>CerenB</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/issues?q=author%3ACerenB" title="Bug reports">🐛</a> <a href="#userTesting-CerenB" title="User Testing">📓</a></td>
+    <td align="center"><a href="https://github.com/mohmdrezk"><img src="https://avatars2.githubusercontent.com/u/9597815?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Mohamed Rezk</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/commits?author=mohmdrezk" title="Code">💻</a> <a href="#design-mohmdrezk" title="Design">🎨</a> <a href="#ideas-mohmdrezk" title="Ideas, Planning, & Feedback">🤔</a></td>
+    <td align="center"><a href="https://github.com/marcobarilari"><img src="https://avatars3.githubusercontent.com/u/38101692?v=4?s=100" width="100px;" alt=""/><br /><sub><b>marcobarilari</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/commits?author=marcobarilari" title="Code">💻</a> <a href="#design-marcobarilari" title="Design">🎨</a> <a href="#ideas-marcobarilari" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/issues?q=author%3Amarcobarilari" title="Bug reports">🐛</a> <a href="#userTesting-marcobarilari" title="User Testing">📓</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/pulls?q=is%3Apr+reviewed-by%3Amarcobarilari" title="Reviewed Pull Requests">👀</a> <a href="#question-marcobarilari" title="Answering Questions">💬</a> <a href="#infra-marcobarilari" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-marcobarilari" title="Maintenance">🚧</a></td>
+    <td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars3.githubusercontent.com/u/6961185?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/commits?author=Remi-Gau" title="Code">💻</a> <a href="#design-Remi-Gau" title="Design">🎨</a> <a href="#ideas-Remi-Gau" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/issues?q=author%3ARemi-Gau" title="Bug reports">🐛</a> <a href="#userTesting-Remi-Gau" title="User Testing">📓</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/pulls?q=is%3Apr+reviewed-by%3ARemi-Gau" title="Reviewed Pull Requests">👀</a> <a href="#question-Remi-Gau" title="Answering Questions">💬</a> <a href="#infra-Remi-Gau" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-Remi-Gau" title="Maintenance">🚧</a></td>
+    <td align="center"><a href="https://github.com/CerenB"><img src="https://avatars1.githubusercontent.com/u/10451654?v=4?s=100" width="100px;" alt=""/><br /><sub><b>CerenB</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/issues?q=author%3ACerenB" title="Bug reports">🐛</a> <a href="#userTesting-CerenB" title="User Testing">📓</a></td>
+    <td align="center"><a href="https://github.com/iqrashahzad14"><img src="https://avatars.githubusercontent.com/u/75671348?v=4?s=100" width="100px;" alt=""/><br /><sub><b>iqrashahzad14</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/commits?author=iqrashahzad14" title="Code">💻</a> <a href="#ideas-iqrashahzad14" title="Ideas, Planning, & Feedback">🤔</a></td>
   </tr>
 </table>
 
-<!-- markdownlint-enable -->
+<!-- markdownlint-restore -->
 <!-- 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!

README.md

@@ -0,0 +1 @@
+# Documentation

docs/README.md

@@ -1,18 +1,19 @@
-%
-% 1 - Check if version requirements
-% are satisfied and the packages are
-% are installed/loaded:
-%   Octave > 4
-%       - image
-%       - optim
-%       - struct
-%       - statistics
-%
-%   MATLAB >= R2015b
-%
-% 2 - Add project to the O/M path
+% (C) Copyright 2020 Agah Karakuzu
+% (C) Copyright 2019 CPP visual motion localizer developpers
 
 function initEnv
+    % 1 - Check if version requirements
+    % are satisfied and the packages are
+    % are installed/loaded:
+    %   Octave > 4
+    %       - image
+    %       - optim
+    %       - struct
+    %       - statistics
+    %
+    %   MATLAB >= R2015b
+    %
+    % 2 - Add project to the O/M path
 
     octaveVersion = '4.0.3';
     matlabVersion = '8.6.0';
@@ -56,8 +57,8 @@
 
     if numel(dir(libDirectory)) <= 2 % Means that the external is empty
         error(['Git submodules are not cloned!', ...
-              'Try this in your terminal:', ...
-              ' git submodule update --recursive ']);
+               'Try this in your terminal:', ...
+               ' git submodule update --recursive ']);
     else
         addDependencies();
     end

initEnv.m

@@ -0,0 +1 @@
+# External libraries and dependencies

lib/README.md

@@ -0,0 +1,3 @@
+# This is here to keep pre-commit-ci from going ape and running on the content
+# of this folder.
+enable: false