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

Author: CerenB

.gitignore

@@ -10,3 +10,5 @@
 
 check_my_code_report.txt
 test_code_report.txt
+
+output/**

.gitmodules

@@ -0,0 +1,8 @@
+[submodule "lib/bids-matlab"]
+	path = lib/bids-matlab
+	url = https://github.com/bids-standard/bids-matlab.git
+	branch = master
+[submodule "lib/JSONio"]
+	path = lib/JSONio
+	url = https://github.com/gllmflndn/JSONio.git
+	branch = master

.travis.yml

@@ -13,29 +13,32 @@ before_install:
   - travis_retry sudo apt-get -y -qq update
   - travis_retry sudo apt-get -y install octave
   - travis_retry sudo apt-get -y install liboctave-dev
-  # - travis_retry sudo apt-get -y install nodejs
-  # - travis_retry sudo apt-get -y install npm
+  - travis_retry sudo apt-get -y install nodejs
+  - travis_retry sudo apt-get -y install npm
   - cd .. && git clone https://github.com/florianschanda/miss_hit.git && export PATH=$PATH:`pwd`/miss_hit && cd CPP_BIDS
 
 
 install:
-  # Install JSONio
-  #- travis_retry git clone git://github.com/gllmflndn/JSONio.git --depth 1
-  #- cd JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ..
-  #- octave $OCTFLAGS --eval "addpath (fullfile (pwd, 'JSONio')); savepath ();"
-  # Install BIDS-MATLAB
+  # make octave file for JSONio
+  - 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
+  - sudo npm install -g bids-validator
 
 before_script:
   # Change current directory
   - cd tests
 
 jobs:
   include:
-    - stage: "Tests and linter"
-      name: "Unit Tests" # names the first job
+    - stage: "Tests"
+      name: "Unit and integration Tests"
       script: octave $OCTFLAGS --eval "results = runTests; assert(all(~[results.Failed]))"
-    - script: cd .. && mh_style.py `pwd`
-      name: "miss_hit linter" # names the second job
+    - stage: "BIDS validator"
+      name: "Create and check dataset"
+      script: octave $OCTFLAGS --eval "testmanual_makeRawDataset" && bids-validator `pwd`/../output/rawdata/ --ignoreNiftiHeaders
+    - stage: "Linter"
+      name: "miss_hit"
+      script: cd .. && mh_style `pwd`
+      
+    

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 Crossmodal Perception and Plasticity laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -127,16 +127,17 @@ logFile.extraColumns = {'Speed', 'is_Fixation'};
 
 [cfg, expParameters] = createFilename(cfg, expParameters);
 
-% dummy call to initialize the logFile variable
-logFile = saveEventsFile('open', expParameters, logFile);
+% initialize the logFile variable
+[logFile] = saveEventsFile('init', expParameters, logFile);
 
 % set the real length we really want
 logFile.extraColumns.Speed.length = 12;
 
-% actual inititalization
+% open the file
 logFile = saveEventsFile('open', expParameters, logFile);
 ```
 
+
 ## Functions descriptions
 
 ### userInputs

checkCFG.m

@@ -1,75 +1,110 @@
 function [cfg, expParameters] = checkCFG(cfg, expParameters)
     % check that we have all the fields that we need in the experiment parameters
 
+    checkCppBidsDependencies();
+
+    if nargin < 1 || isempty(cfg)
+        cfg = struct();
+    end
+    if nargin < 2 || isempty(expParameters)
+        expParameters = struct();
+    end
+
     %% set the expParameters defaults
 
-    fieldsToSet.verbose = 0;
+    fieldsToSet.verbose = false;
     fieldsToSet.outputDir = fullfile( ...
         fileparts(mfilename('fullpath')), ...
         '..', ...
         'output');
 
-    fieldsToSet.subjectGrp = []; % in case no group was provided
+    fieldsToSet = mriDefaults(fieldsToSet);
+
+    fieldsToSet.subjectGrp = ''; % in case no group was provided
     fieldsToSet.sessionNb = 1; % in case no session was provided
     fieldsToSet.askGrpSess = [true true];
 
-    % BIDS
+    expParameters = setDefaultFields(expParameters, fieldsToSet);
 
-    % dataset description json
-    % required
-    fieldsToSet.bids.datasetDescription.json.Name = '';
-    fieldsToSet.bids.datasetDescription.json.BIDSVersion = '';
-    % recommended
-    fieldsToSet.bids.datasetDescription.json.License = '';
-    fieldsToSet.bids.datasetDescription.json.Authors = {''};
-    fieldsToSet.bids.datasetDescription.json.Acknowledgements = '';
-    fieldsToSet.bids.datasetDescription.json.HowToAcknowledge = '';
-    fieldsToSet.bids.datasetDescription.json.Funding = {''};
-    fieldsToSet.bids.datasetDescription.json.ReferencesAndLinks = {''};
-    fieldsToSet.bids.datasetDescription.json.DatasetDOI = '';
-
-    % mri
-    % for json
-    fieldsToSet.MRI.repetitionTime = [];
-    % for file naming
-    fieldsToSet.MRI.ce = [];
-    fieldsToSet.MRI.dir = []; % phase encoding direction of acquisition for fMRI
-    fieldsToSet.MRI.rec = []; % reconstruction of fMRI images
-    fieldsToSet.MRI.echo = []; % echo fMRI images
-    fieldsToSet.MRI.acq = []; % acquisition of fMRI images
+    %% BIDS
+    clear fieldsToSet;
+    fieldsToSet.bids = struct();
+    expParameters = setDefaultFields(expParameters, fieldsToSet);
+
+    clear fieldsToSet;
+    fieldsToSet.MRI = struct();
+    fieldsToSet.datasetDescription = struct();
+    expParameters.bids = setDefaultFields(expParameters.bids, fieldsToSet);
+
+    clear fieldsToSet;
+    fieldsToSet = datasetDescriptionDefaults();
+
+    expParameters.bids.datasetDescription = ...
+        setDefaultFields(expParameters.bids.datasetDescription, fieldsToSet);
+
+    clear fieldsToSet;
+    fieldsToSet = mriJsonDefaults();
+    if isfield(expParameters, 'task')
+        fieldsToSet.TaskName = expParameters.task;
+    end
+
+    expParameters.bids.MRI = ...
+        setDefaultFields(expParameters.bids.MRI, fieldsToSet);
 
-    expParameters = setDefaults(expParameters, fieldsToSet);
+    % sort fields alphabetically
+    expParameters = orderfields(expParameters);
 
     %% set the cfg defaults
 
     clear fieldsToSet;
+    fieldsToSet.verbose = false;
     fieldsToSet.testingDevice = 'pc';
     fieldsToSet.eyeTracker = false;
 
-    cfg = setDefaults(cfg, fieldsToSet);
+    cfg = setDefaultFields(cfg, fieldsToSet);
 
-end
+    % sort fields alphabetically
+    cfg = orderfields(cfg);
 
-function structure = setDefaults(structure, fieldsToSet)
-    % loop through the defaults fiels to set and update if they don't exist
+end
 
-    names = fieldnames(fieldsToSet);
+function fieldsToSet = mriDefaults(fieldsToSet)
 
-    for i = 1:numel(names)
+    % for file naming
+    fieldsToSet.MRI.ce = [];
+    fieldsToSet.MRI.dir = []; % phase encoding direction of acquisition for fMRI
+    fieldsToSet.MRI.rec = []; % reconstruction of fMRI images
+    fieldsToSet.MRI.echo = []; % echo fMRI images
+    fieldsToSet.MRI.acq = []; % acquisition of fMRI images
 
-        thisField = fieldsToSet.(names{i});
+end
 
-        structure = setFieldToIfNotPresent( ...
-            structure, ...
-            names{i}, ...
-            thisField);
+function fieldsToSet = datasetDescriptionDefaults()
+    % required
+    fieldsToSet.Name = '';
+    fieldsToSet.BIDSVersion = '';
+    % recommended
+    fieldsToSet.License = '';
+    fieldsToSet.Authors = {''};
+    fieldsToSet.Acknowledgements = '';
+    fieldsToSet.HowToAcknowledge = '';
+    fieldsToSet.Funding = {''};
+    fieldsToSet.ReferencesAndLinks = {''};
+    fieldsToSet.DatasetDOI = '';
+end
 
-    end
+function fieldsToSet = mriJsonDefaults()
 
-end
+    % for json for funcfional data
+    % required
+    fieldsToSet.RepetitionTime = [];
+    fieldsToSet.SliceTiming = [];
+    fieldsToSet.TaskName = [];
+    %     fieldsToSet.PhaseEncodingDirection = [];
+    %     fieldsToSet.EffectiveEchoSpacing = [];
+    %     fieldsToSet.EchoTime = [];
+    % recommended
+    fieldsToSet.Instructions = [];
+    fieldsToSet.TaskDescription = [];
 
-function structure = setFieldToIfNotPresent(structure, fieldName, value)
-    if ~isfield(structure, fieldName)
-        structure.(fieldName) = value;
-    end
 end

checkCppBidsDependencies.m

@@ -0,0 +1,25 @@
+function checkCppBidsDependencies
+
+    pth = fileparts(mfilename('fullpath'));
+    
+    checkSubmodule(fullfile(pth, 'lib', 'JSONio'))
+    checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'))
+    
+    addpath(fullfile(pth, 'lib', 'utils'));
+    addpath(fullfile(pth, 'subfun'));
+    
+    printCreditsCppBids();
+
+end
+
+function checkSubmodule(pth)
+    % If external dir is empty throw an exception
+    % and ask user to update submodules.
+    if numel(dir(pth)) <= 2 % Means that the external is empty
+        error(['Git submodules are not cloned!', ...
+              'Try this in your terminal:', ...
+              ' git submodule update --recursive ']);
+    else
+        addpath(pth);
+    end
+end

convertSourceToRaw.m

@@ -0,0 +1,69 @@
+function convertSourceToRaw(expParameters)
+
+    sourceDir = fullfile(expParameters.outputDir, 'source');
+    rawDir = fullfile(expParameters.outputDir, 'rawdata');
+
+    % add dummy readme and change file
+    copyfile(fullfile('..', 'dummyData', 'README'), sourceDir);
+    copyfile(fullfile('..', 'dummyData', 'CHANGES'), sourceDir);
+
+    copyfile(sourceDir, rawDir);
+
+    % list subjects
+    subjects = cellstr(file_utils('List', rawDir, 'dir', '^sub-.*$'));
+
+    if isequal(subjects, {''})
+        error('No subjects found in BIDS directory.');
+    end
+
+    for su = 1:numel(subjects)
+
+        sess = cellstr(file_utils('List', fullfile(rawDir, subjects{su}), 'dir', '^ses-.*$'));
+
+        for se = 1:numel(sess)
+            parseFunc(rawDir, subjects{su}, sess{se});
+        end
+
+    end
+
+end
+
+function parseFunc(rawDir, subjName, sesName)
+
+    subjectPath = fullfile(rawDir, subjName, sesName, 'func');
+
+    if exist(subjectPath, 'dir')
+
+        % do events
+        filenames = file_utils('List', subjectPath, ...
+            sprintf('^%s.*_task-.*_events_date-.*$', subjName));
+
+        removeDateSuffix(filenames, subjectPath);
+
+        % do bold
+        filenames = file_utils('List', subjectPath, ...
+            sprintf('^%s.*_task-.*_bold_date-.*$', subjName));
+
+        removeDateSuffix(filenames, subjectPath);
+
+    end
+end
+
+function removeDateSuffix(filenames, subjectPath)
+    if isempty(filenames)
+        filenames = {};
+    else
+        filenames = cellstr(filenames);
+    end
+
+    for i = 1:numel(filenames)
+
+        [~, name, ext] = fileparts(filenames{i});
+
+        [parts, ~] = regexp(name, '(?:_date-)+', 'split', 'match');
+
+        movefile(fullfile(subjectPath, filenames{i}), ...
+            fullfile(subjectPath, [parts{1} ext]));
+
+    end
+end

createBoldJson.m

@@ -0,0 +1,17 @@
+function createBoldJson(expParameters)
+
+    opts.Indent = '    ';
+
+    fileName = strrep(expParameters.fileName.events, '_events', '_bold');
+    fileName = strrep(fileName, '.tsv', '.json');
+
+    fileName = fullfile( ...
+        expParameters.subjectOutputDir, ...
+        expParameters.modality, ...
+        fileName);
+
+    jsonContent = expParameters.bids.MRI;
+
+    bids.util.jsonencode(fileName, jsonContent, opts);
+
+end