Merge pull request #82 from Remi-Gau/remi-eeg_beh

improve support for EEG, MEG, iEEG and eyetracking data

Author: Remi-Gau

.travis.yml

@@ -1,32 +1,39 @@
 # Travis CI (https://travis-ci.org/)
+# This will only work on your repo if you have an account on travis and you
+# have set it up to run continuous integration on this this repo
+
+# Linux distribution (bionic beaver)
+dist: bionic
+
+# Language and version
+language: python
+python:
+  - "3.6" # current default Python on Travis CI
 
-language: c
-dist: bionic # based on bionic beaver ubuntu distribution
 cache:
   apt: true # only works with Pro version
 
 env:
-  global: # define environment variables for bash
+  global: # Define environment variables for bash
     - OCTFLAGS="--no-gui --no-window-system --silent"
 
 before_install:
   - travis_retry sudo apt-get -y -qq update
-  # install octave
+  # Install octave
   - travis_retry sudo apt-get -y install octave
   - travis_retry sudo apt-get -y install liboctave-dev
-  # install javascript
+  # Install javascript node and node package manager necessary to run the validator
   - travis_retry sudo apt-get -y install nodejs
   - travis_retry sudo apt-get -y install npm
-  # install miss_hit linter
-  - cd .. && git clone https://github.com/florianschanda/miss_hit.git && export PATH=$PATH:`pwd`/miss_hit && cd CPP_BIDS
-
+  # Install BIDS-Validator
+  - sudo npm install -g bids-validator
+  # Install miss_hit linter
+  - pip3 install miss_hit
 
 install:
   # make octave file the JSONio submodule
   - cd lib/JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ../..
   - octave $OCTFLAGS --eval "addpath (pwd); savepath ();"
-  # Install BIDS-Validator
-  - sudo npm install -g bids-validator
 
 before_script:
   # Add to src functions to path
@@ -36,11 +43,9 @@ before_script:
 
 jobs:
   include:
-    - stage: "BIDS validator"
-      name: "Create and check dataset"
+    - name: "BIDS validator: create and check dataset"
       script: octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/rawdata/ --ignoreNiftiHeaders
-    - stage: "Linter"
-      name: "miss_hit"
-      script: cd .. && mh_style `pwd`
-      
-    
+    - name: "miss_hit: checking code quality"
+      script: mh_metric . --ci
+    - name: "miss_hit: checking code style"
+      script: mh_style .

README.md

@@ -76,6 +76,13 @@ Feel free to open issues to report a bug and ask for improvements.
 
 Here are the naming templates used.
 
+-   Behavior
+
+`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.tsv`
+`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.json`
+`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.tsv`
+`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.json`
+
 -   BOLD
 
 `sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]`
@@ -87,15 +94,37 @@ Here are the naming templates used.
 -   EEG
 
 `sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>`
+`sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.json`
+
+<!-- European data format (Each recording consisting of a .edf file)
+
+BrainVision Core Data Format (Each recording consisting of a .vhdr, .vmrk, .eeg file triplet)
+
+The format used by the MATLAB toolbox EEGLAB (Each recording consisting of a .set file with an optional .fdt file)
+
+Biosemi data format (Each recording consisting of a .bdf file) -->
+
+
 
 -   MEG
 
 ???
 
 -   Eyetracker
 
+current format
+`<matches>_recording-eyetracking_physio.tsv.gz`
+
+future BEP format in a dedicated eyetracker folder
 `sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>`
 
+-   Stim and physio
+
+`<matches>[_recording-<label>]_physio.tsv.gz`
+`<matches>[_recording-<label>]_physio.json`
+`<matches>[_recording-<label>]_stim.tsv.gz`
+`<matches>[_recording-<label>]_stim.json`
+
 ###  3.3. <a name='Contributors'></a>Contributors ✨
 
 Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):

manualTests/dummyData/.bidsignore

@@ -0,0 +1,11 @@
+*_beh.*
+*_eeg.*
+*_ieeg.*
+*_meg.*
+
+# *_beh.tsv
+# *_eeg.edf
+# *_ieeg.edf
+# *_meg.fif
+
+# *_bold.nii.gz

tests/test_createDatasetDescription.m renamed to manualTests/test_createDatasetDescription.m

@@ -1,12 +1,12 @@
-function test_suite = test_createBoldJson %#ok<*STOUT>
+function test_suite = test_createJson %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
     catch % no problem; early Matlab versions can use initTestSuite fine
     end
     initTestSuite;
 end
 
-function test_createBoldJsonExtra()
+function test_createJsonExtra()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
 
@@ -29,7 +29,7 @@ function test_createBoldJsonExtra()
 
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
 
-    createBoldJson(cfg, extraInfo);
+    createJson(cfg, extraInfo);
 
     %% check content
     fileName = strrep(cfg.fileName.events, '_events', '_bold');

manualTests/test_createBoldJson.m renamed to manualTests/test_createJson.m

@@ -22,6 +22,7 @@ function test_makeRawDataset()
     cfg.subject.runNb = 1;
 
     cfg.task.name = 'testtask';
+    cfg.task.instructions = 'do this';
 
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
@@ -30,7 +31,7 @@ function test_makeRawDataset()
     cfg = createFilename(cfg);
 
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
-    createBoldJson(cfg, extraInfo);
+    createJson(cfg, extraInfo);
 
     createDatasetDescription(cfg);
 
@@ -82,49 +83,165 @@ function test_makeRawDataset()
     saveEventsFile('save', cfg, stimLogFile);
     saveEventsFile('close', cfg, stimLogFile);
 
-    % add dummy functional data
-    funcDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001', 'func');
-    boldFilename = 'sub-001_ses-001_task-testtask_run-001_bold.nii.gz';
-
-    copyfile( ...
-        fullfile('dummyData', 'dummyData.nii.gz'), ...
-        fullfile(funcDir, boldFilename));
-
     %% MRI bold rest data and fancy suffixes
     clear cfg;
 
     cfg.dir.output = outputDir;
 
     cfg.testingDevice = 'mri';
 
-    cfg.subject.subjectNb = 2;
-    cfg.subject.sessionNb = 3;
-    cfg.subject.runNb = 4;
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
 
     % deal with MRI suffixes
-    cfg.mri.reconstruction = 'fast recon';
-    cfg.mri.contrastEnhancement = 'test';
-    cfg.mri.phaseEncodingDirection = 'y pos';
-    cfg.mri.echo = '1';
-    cfg.mri.acquisition = ' new tYpe';
+    cfg.suffix.reconstruction = 'fast recon';
+    cfg.suffix.contrastEnhancement = 'test';
+    cfg.suffix.phaseEncodingDirection = 'y pos';
+    cfg.suffix.echo = '1';
+    cfg.suffix.acquisition = ' new tYpe';
+
     cfg.mri.repetitionTime = 1.56;
 
     cfg.task.name = 'rest';
 
     cfg = createFilename(cfg);
 
-    createBoldJson(cfg);
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+    createJson(cfg, extraInfo);
+
+    %% EEG data and fancy suffixes
+    clear cfg;
+
+    cfg.dir.output = outputDir;
+
+    cfg.testingDevice = 'eeg';
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'target practice';
+    cfg.task.instructions = 'do this';
+
+    cfg.bids.eeg.EEGReference = 'Cz';
+    cfg.bids.eeg.SamplingFrequency = 2400;
+    cfg.bids.eeg.PowerLineFrequency = 50;
+    cfg.bids.eeg.SoftwareFilters = 'n/a';
+
+    cfg = createFilename(cfg);
+
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+    createJson(cfg, extraInfo);
+
+    %% iEEG data and fancy suffixes
+    clear cfg;
+
+    cfg.dir.output = outputDir;
+
+    cfg.testingDevice = 'ieeg';
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'implanted target practice';
+    cfg.task.instructions = 'do this';
+
+    cfg.bids.ieeg.iEEGReference = 'Cz';
+    cfg.bids.ieeg.SamplingFrequency = 2400;
+    cfg.bids.ieeg.PowerLineFrequency = 50;
+    cfg.bids.ieeg.SoftwareFilters = 'n/a';
+
+    cfg = createFilename(cfg);
+
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+    createJson(cfg, extraInfo);
+
+    %% MEG data and fancy suffixes
+    clear cfg;
+
+    cfg.dir.output = outputDir;
+
+    cfg.testingDevice = 'meg';
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'magnetic target practice';
+    cfg.task.instructions = 'do this';
+
+    cfg.bids.meg.SamplingFrequency = 2400;
+    cfg.bids.meg.PowerLineFrequency = 60;
+    cfg.bids.meg.DewarPosition = 'upright';
+    cfg.bids.meg.SoftwareFilters = 'n/a';
+    cfg.bids.meg.DigitizedLandmarks = false;
+    cfg.bids.meg.DigitizedHeadPoints = false;
+
+    cfg = createFilename(cfg);
+
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+    createJson(cfg, extraInfo);
+
+    %% beh data and fancy suffixes
+    clear cfg;
+
+    cfg.dir.output = outputDir;
+
+    cfg.testingDevice = 'pc';
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'easy target practice';
+    cfg.task.instructions = 'do this';
+
+    cfg = createFilename(cfg);
+
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+    createJson(cfg, extraInfo);
 
-    %% add dummy functional data
-    funcDir = fullfile(cfg.dir.output, 'source', 'sub-002', 'ses-003', 'func');
-    boldFilename = ['sub-002_ses-003_task-rest',  ...
+    %% add dummy data
+    subjectDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001');
+    funcDir = fullfile(subjectDir, 'func');
+
+    boldFilename = 'sub-001_ses-001_task-testtask_run-001_bold.nii.gz';
+
+    copyfile( ...
+        fullfile('dummyData', 'dummyData.nii.gz'), ...
+        fullfile(funcDir, boldFilename));
+
+    boldFilename = ['sub-001_ses-001_task-rest',  ...
         '_acq-newTYpe_ce-test_dir-yPos_rec-fastRecon', ...
-        '_run-004_echo-1_bold.nii.gz'];
+        '_run-001_echo-1_bold.nii.gz'];
 
     copyfile( ...
         fullfile('dummyData', 'dummyData.nii.gz'), ...
         fullfile(funcDir, boldFilename));
 
+    eegDir = fullfile(subjectDir, 'eeg');
+    megDir = fullfile(subjectDir, 'meg');
+    ieegDir = fullfile(subjectDir, 'ieeg');
+    behDir = fullfile(subjectDir, 'beh');
+
+    eegFilename = 'sub-001_ses-001_task-targetPractice_run-001_eeg.edf';
+    megFilename = 'sub-001_ses-001_task-magneticTargetPractice_run-001_meg.fif';
+    ieegFilename = 'sub-001_ses-001_task-implantedTargetPractice_run-001_ieeg.edf';
+    behFilename = 'sub-001_ses-001_task-easyTargetPractice_run-001_beh.tsv';
+
+    copyfile( ...
+        fullfile('dummyData', 'dummyData.nii.gz'), ...
+        fullfile(eegDir, eegFilename));
+
+    copyfile( ...
+        fullfile('dummyData', 'dummyData.nii.gz'), ...
+        fullfile(megDir, megFilename));
+
+    copyfile( ...
+        fullfile('dummyData', 'dummyData.nii.gz'), ...
+        fullfile(ieegDir, ieegFilename));
+
+    copyfile( ...
+        fullfile('dummyData', 'dummyData.nii.gz'), ...
+        fullfile(behDir, behFilename));
+
     %% actually do the conversion of the source data thus created
     clear;
 

manualTests/test_makeRawDataset.m

@@ -1,4 +1,11 @@
+# styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
 regex_function_name: "[a-z]+(([A-Z]){1}[A-Za-z]+)*"
 suppress_rule: "copyright_notice"
-exclude_dir: "lib"
+exclude_dir: "lib"
+
+# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
+metric "cnest": limit 4
+metric "file_length": limit 500
+metric "cyc": limit 15
+metric "parameters": limit 6