add support for biosemi datasets

Author: Remi-Gau

README.md

@@ -1,150 +1,38 @@
-<!--
-
-When you have set up your repo
-
-**Unit tests and coverage**
-
-[![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/Remi-gau/template_matlab_analysis/actions)
-![](https://github.com/Remi-gau/template_matlab_analysis/workflows/CI/badge.svg)
-
-[![codecov](https://codecov.io/gh/Remi-gau/template_matlab_analysis/branch/master/graph/badge.svg)](https://codecov.io/gh/Remi-gau/template_matlab_analysis)
-
-**Miss_hit linter**
-
-[![Build Status](https://travis-ci.com/Remi-gau/template_matlab_analysis.svg?branch=master)](https://travis-ci.com/Remi-gau/template_matlab_analysis)
-
--->
-
 # Template repository for matlab analysis project
 
-## How to install and use this template
-
-### Install with Git
-
-1. Click the green button `Use this template`.
+## Requirements
 
-1. Give a name to the repository you want to create. Something short that
-   contains the name of your experiment: `analysis_my_study`.
+- Matlab - version >2017? (Possibly compatible with older versions ; Not tested
+  on Octave)
+- LetsWave - version 5 - 7
 
-1. Decide if you want this new repo to be public or private.
+- There is a bids-matlab "dependency" as a git sub-module that it will be
+  installed automatically if you use the `--recursive` flag when you clone the
+  repository (see the `install with git` section below).
 
-1. Click on `Create repository from template`
-
-You now have a copy of the template on your Github account. You can then
-download the code and the pre-set dependencies like this.
-
-1. Click on green `Download` button and copy the `URL_to_your_repo` that is
-   shown there.
+## Install with Git
 
 1. Open a terminal and type this:
 
 ```bash
-git clone --recurse-submodules URL_to_your_repo
-```
-
-This will set up everything automatically in your current directory.
-
-## Content
-
-```bash
-├── .git
-│   ├── COMMIT_EDITMSG
-│   ├── FETCH_HEAD
-│   ├── HEAD
-│   ├── ORIG_HEAD
-│   ├── branches
-│   ├── config
-│   ├── description
-│   ├── hooks
-│   │   ├── pre-commit.sample
-│   │   └── pre-push.sample
-│   ├── ...
-│   └── ...
-├── .github                # where you put anything github related
-│   └── workflows          # where you define your github actions
-│       └── moxunit.yml    # a yaml file that defines a github action
-├── lib                    # where you put the code from external libraries (mathworks website or other github repositories)
-│   └── README.md
-├── src                  # WHERE YOU PUT YOUR CODE
-│   ├── README.md
-│   └── miss_hit.cfg
-├── docs                 # where you write your documentation using sphinx
-│   ├── make.bat
-│   ├── Makefile
-│   ├── README.md
-│   ├── requirements.txt # to set up the python environment for the doc
-│   └── source           # the actual reStructured text file for your doc
-│       ├── conf.py
-│       ├── function_description.rst
-│       ├── index.rst
-│       ├── _static
-│       └── _templates
-├── tests               # where you put your unit tests
-|   ├── README.md
-|   └── miss_hit.cfg
-├── .travis.yml         # where you define the continuous integration done by Travis
-├── LICENSE
-├── README.md
-├── miss_hit.cfg        # configuration file for the matlab miss hit linter
-└── initEnv.m           # a .m file to set up your project (adds the right folder to the path)
-```
-
-## Keeping your code stylish: miss hit linter
-
-### Matlab code style guide and quality
-
-We use the [MISS_HIT linter](https://github.com/florianschanda/miss_hit/) to
-automatically enforce / fix some code style issues and check for code quality.
-
-The linter is a python package that can be installed with:
-
-```bash
-pip3 install --user miss_hit
-```
-
-The rules followed by MISS_HIT are in the
-[MISS_HIT configuration file](./miss_hit.cfg).
-
-To check the code style of the whole repository, you can can simply type:
-
-```bash
-mh_style .
-```
-
-Some styling issues can be automatically fixed by using the `--fix` flag. You
-might need to rerun this command several times if there are a lot of issues.
-
-```bash
-mh_style . --fix
+git clone --recurse-submodules https://github.com/cpp-lln-lab/letswave_bids_import.git
 ```
 
-Code quality can be checked with:
+## Usage
 
-```bash
-mh_metric .
-```
+### Add it to the Matlab path.
 
-To see only the issues that "break" the code quality rules set in the
-configuration file, type:
+You can do this by running the `init_env` that is in the root folder of the
+repository.
 
-```bash
-mh_metric . --ci
 ```
+this_dir = fileparts(mfilename('fullpath'));
 
-The code style and quality is also checked during the
-[continuous integration](.github/workflows/miss_hit.yml).
-
-For more information about MISS_HIT see its
-[documentation](https://florianschanda.github.io/miss_hit/).
-
-## Python environment
-
-More on this
-[here](https://the-turing-way.netlify.app/reproducible-research/renv/renv-package.html)
-
-## Testing your code
+% input and output directory
+cfg.bidsroot = pwd;
+cfg.out_path = fullfile(cfg.bidsroot, 'derivatives');
 
-The [MOxUnit testing framework](https://github.com/MOxUnit/MOxUnit) is set up to
-run tests automatically for any tests in the `tests` folder.
+initialize_letswave();
 
-## Continuous integration
+import_bids(cfg);
+```

init_env.m

@@ -12,6 +12,7 @@ function init_env()
     %   MATLAB >= R2015b
     %
     % 2 - Add project to the O/M path
+    %
     % (C) Copyright 2021 Remi Gau
 
     octaveVersion = '4.0.3';

lib/bids-matlab

@@ -1,4 +1,4 @@
-function import_bids(cfg)
+function importBids(cfg)
     %
     %
     %
@@ -15,6 +15,8 @@ function import_bids(cfg)
 
     cfg.filter = struct();
 
+    printCredits(cfg);
+
     BIDS = bids.layout(cfg.bidsroot);
 
     pipeline_name = 'letswave_bids_import';
@@ -51,12 +53,23 @@ function import_bids(cfg)
 
                 configuration.parameters.filenames = {files{iFile}};
 
-                [~, datasets] = LW_import_BDF('process', configuration);
+                [~, datasets] = LW_import_SET('process', configuration);
 
                 save_data(files{iFile}, datasets);
 
                 delete(files{iFile});
 
+            case '.bdf'                
+                configuration = LW_import_BDF('default');
+
+                configuration.parameters.filenames = {files{iFile}};
+
+                [~, datasets] = LW_import_BDF('process', configuration);
+
+                save_data(files{iFile}, datasets);
+
+                delete(files{iFile});
+                
             otherwise
                 % TODO
                 warning('FORMAT NOT YET SUPPORTED');

src/importBids.m

@@ -1,4 +1,4 @@
-function repoURL = printCredits(cfg)
+function printCredits(cfg)
     %
     % TODO: use the .zenodo.json to load contributors
     %

src/utils/printCredits.m

@@ -1,4 +1,4 @@
-function test_suite = test_import_bids %#ok<*STOUT>
+function test_suite = test_importBids %#ok<*STOUT>
     % (C) Copyright 2021 Remi Gau
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
@@ -7,24 +7,49 @@
     initTestSuite;
 end
 
-function test_import_bids_basic()
+function test_import_bids_eeglab()
 
-    clean_dir();
-
-    cfg.out_path = fullfile(this_dir(), 'output');
+    cfg.out_path = fullfile(this_dir(), 'output', 'eeglab');
+    
+    clean_dir(cfg.out_path);
 
     cfg.bidsroot = fullfile(return_test_data_dir(), 'eeglab');
 
     initialize_letswave();
     close all;
 
-    import_bids(cfg);
+    importBids(cfg);
+    
+    % TODO 
+    % add tests
+    
+%     clean_dir();
+
+end
+
+function test_import_bids_biosemi()
+
+    cfg.out_path = fullfile(this_dir(), 'output', 'biosemi');
+    
+    clean_dir(cfg.out_path);
+
+    cfg.bidsroot = fullfile(return_test_data_dir(), 'spm_multimodal');
+
+    initialize_letswave();
+    close all;
+
+    importBids(cfg);
+    
+    % TODO 
+    % add tests
+    
+%     clean_dir();
 
 end
 
-function clean_dir()
-    if exist(fullfile(this_dir(), 'output'), 'dir')
-        rmdir(fullfile(this_dir(), 'output'), 's');
+function clean_dir(this_dir)
+    if exist(this_dir, 'dir')
+        rmdir(this_dir, 's');
     end
 end