update to eyetracking filenaming

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 +94,43 @@ 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) -->
+
+
+EEGReference 	REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "Cz", "CMS"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the _channels.tsv file.
+SamplingFrequency 	REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400).
+PowerLineFrequency 	REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the EEG instrument (i.e., 50 or 60).
+SoftwareFilters 	REQUIRED. A JSON object of temporal software filters applied, or "n/a" if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., {"Anti-aliasing filter": {"half-amplitude cutoff (Hz)": 500, "Roll-off": "6dB/Octave"}}.
+
+
 
 -   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)):

miss_hit.cfg

@@ -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

src/createFilename.m

@@ -90,11 +90,7 @@
     [~, ~, ~] = mkdir(cfg.dir.output);
     [~, ~, ~] = mkdir(cfg.dir.outputSubject);
     [~, ~, ~] = mkdir(fullfile(cfg.dir.outputSubject, modality));
-
-    if cfg.eyeTracker.do
-        [~, ~, ~] = mkdir(fullfile(cfg.dir.outputSubject, 'eyetracker'));
-    end
-
+    
 end
 
 function cfg = setSuffixes(cfg)
@@ -190,7 +186,7 @@
     if cfg.eyeTracker.do
         cfg.fileName.eyetracker = ...
             [fileNameBase, acqSuffix, ...
-            runSuffix, '_eyetrack_date-' thisDate '.edf'];
+            runSuffix, '_recording-eyetracking_physio_date-' thisDate '.edf'];
     end
 
 end

tests/test_createFilename.m

@@ -23,8 +23,6 @@ function test_createFilenameBasic()
     %% data to test against
     behDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'beh');
 
-    eyetrackerDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'eyetracker');
-
     eventFilename = ['sub-001_ses-001_task-testTask_run-001_events_date-'...
         cfg.fileName.date '.tsv'];
 
@@ -36,9 +34,6 @@ function test_createFilenameBasic()
     % make sure the beh dir is created
     assertTrue(exist(behDir, 'dir') == 7);
 
-    % make sure the eyetracker dir is not created
-    assertTrue(exist(eyetrackerDir, 'dir') == 0);
-
     % make sure the events filename is created
     assertEqual(cfg.fileName.events, eventFilename);
 
@@ -70,14 +65,15 @@ function test_createFilenameMriEyetracker()
 
     funcDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'func');
 
-    eyetrackerDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'eyetracker');
+    eyetrackerDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'func');
 
     baseFilename = 'sub-ctrl002_ses-002_task-testTask';
 
     eventFilename = ['sub-ctrl002_ses-002_task-testTask_run-002_events_date-' ...
         cfg.fileName.date '.tsv'];
 
-    eyetrackerFilename =  ['sub-ctrl002_ses-002_task-testTask_run-002_eyetrack_date-' ...
+    eyetrackerFilename =  [...
+        'sub-ctrl002_ses-002_task-testTask_run-002_recording-eyetracking_physio_date-' ...
         cfg.fileName.date '.edf'];
 
     %% tests