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Remi-GauRemi-Gau
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Merge pull request #47 from Remi-Gau/remi-JSON_output
generate json output and a valid BIDS data set
2 parents 0f968f8 + b227d42 commit b01eb2e

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‎.gitignore‎

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

‎.gitmodules‎

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[submodule "lib/bids-matlab"]
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path = lib/bids-matlab
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url = https://github.com/bids-standard/bids-matlab.git
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branch = master
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[submodule "lib/JSONio"]
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path = lib/JSONio
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url = https://github.com/gllmflndn/JSONio.git
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branch = master

‎.travis.yml‎

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@@ -13,29 +13,32 @@ before_install:
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- travis_retry sudo apt-get -y -qq update
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- travis_retry sudo apt-get -y install octave
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- travis_retry sudo apt-get -y install liboctave-dev
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# - travis_retry sudo apt-get -y install nodejs
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# - travis_retry sudo apt-get -y install npm
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- travis_retry sudo apt-get -y install nodejs
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- travis_retry sudo apt-get -y install npm
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- cd .. && git clone https://github.com/florianschanda/miss_hit.git && export PATH=$PATH:`pwd`/miss_hit && cd CPP_BIDS
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2020

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install:
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# Install JSONio
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#- travis_retry git clone git://github.com/gllmflndn/JSONio.git --depth 1
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#- cd JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ..
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#- octave $OCTFLAGS --eval "addpath (fullfile (pwd, 'JSONio')); savepath ();"
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# Install BIDS-MATLAB
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# make octave file for JSONio
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- cd lib/JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ../..
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- octave $OCTFLAGS --eval "addpath (pwd); savepath ();"
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# Install BIDS-Validator
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#- sudo npm install -g bids-validator
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- sudo npm install -g bids-validator
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before_script:
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# Change current directory
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- cd tests
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jobs:
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include:
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- stage: "Tests and linter"
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name: "Unit Tests" # names the first job
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- stage: "Tests"
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name: "Unit and integration Tests"
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script: octave $OCTFLAGS --eval "results = runTests; assert(all(~[results.Failed]))"
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- script: cd .. && mh_style.py `pwd`
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name: "miss_hit linter" # names the second job
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- stage: "BIDS validator"
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name: "Create and check dataset"
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script: octave $OCTFLAGS --eval "testmanual_makeRawDataset" && bids-validator `pwd`/../output/rawdata/ --ignoreNiftiHeaders
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- stage: "Linter"
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name: "miss_hit"
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script: cd .. && mh_style `pwd`
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‎README.md‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -127,16 +127,17 @@ logFile.extraColumns = {'Speed', 'is_Fixation'};
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[cfg, expParameters] = createFilename(cfg, expParameters);
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130-
% dummy call to initialize the logFile variable
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logFile = saveEventsFile('open', expParameters, logFile);
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% initialize the logFile variable
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[logFile] = saveEventsFile('init', expParameters, logFile);
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% set the real length we really want
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logFile.extraColumns.Speed.length = 12;
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% actual inititalization
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% open the file
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logFile = saveEventsFile('open', expParameters, logFile);
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```
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## Functions descriptions
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### userInputs

‎checkCFG.m‎

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@@ -1,6 +1,15 @@
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function [cfg, expParameters] = checkCFG(cfg, expParameters)
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% check that we have all the fields that we need in the experiment parameters
33

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checkCppBidsDependencies();
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if nargin < 1 || isempty(cfg)
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cfg = struct();
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end
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if nargin < 2 || isempty(expParameters)
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expParameters = struct();
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end
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%% set the expParameters defaults
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fieldsToSet.verbose = 0;
@@ -9,67 +18,92 @@
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'..', ...
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'output');
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12-
fieldsToSet.subjectGrp = []; % in case no group was provided
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fieldsToSet = mriDefaults(fieldsToSet);
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fieldsToSet.subjectGrp = ''; % in case no group was provided
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fieldsToSet.sessionNb = 1; % in case no session was provided
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fieldsToSet.askGrpSess = [true true];
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% BIDS
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expParameters = setDefaultFields(expParameters, fieldsToSet);
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% dataset description json
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% required
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fieldsToSet.bids.datasetDescription.json.Name = '';
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fieldsToSet.bids.datasetDescription.json.BIDSVersion = '';
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% recommended
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fieldsToSet.bids.datasetDescription.json.License = '';
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fieldsToSet.bids.datasetDescription.json.Authors = {''};
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fieldsToSet.bids.datasetDescription.json.Acknowledgements = '';
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fieldsToSet.bids.datasetDescription.json.HowToAcknowledge = '';
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fieldsToSet.bids.datasetDescription.json.Funding = {''};
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fieldsToSet.bids.datasetDescription.json.ReferencesAndLinks = {''};
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fieldsToSet.bids.datasetDescription.json.DatasetDOI = '';
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% mri
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% for json
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fieldsToSet.MRI.repetitionTime = [];
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% for file naming
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fieldsToSet.MRI.ce = [];
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fieldsToSet.MRI.dir = []; % phase encoding direction of acquisition for fMRI
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fieldsToSet.MRI.rec = []; % reconstruction of fMRI images
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fieldsToSet.MRI.echo = []; % echo fMRI images
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fieldsToSet.MRI.acq = []; % acquisition of fMRI images
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%% BIDS
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clear fieldsToSet;
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fieldsToSet.bids = struct();
32+
expParameters = setDefaultFields(expParameters, fieldsToSet);
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34+
clear fieldsToSet;
35+
fieldsToSet.MRI = struct();
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fieldsToSet.datasetDescription = struct();
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expParameters.bids = setDefaultFields(expParameters.bids, fieldsToSet);
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39+
clear fieldsToSet;
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fieldsToSet = datasetDescriptionDefaults();
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42+
expParameters.bids.datasetDescription = ...
43+
setDefaultFields(expParameters.bids.datasetDescription, fieldsToSet);
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clear fieldsToSet;
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fieldsToSet = mriJsonDefaults();
47+
if isfield(expParameters, 'task')
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fieldsToSet.TaskName = expParameters.task;
49+
end
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51+
expParameters.bids.MRI = ...
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setDefaultFields(expParameters.bids.MRI, fieldsToSet);
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41-
expParameters = setDefaults(expParameters, fieldsToSet);
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% sort fields alphabetically
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expParameters = orderfields(expParameters);
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%% set the cfg defaults
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4559
clear fieldsToSet;
4660
fieldsToSet.testingDevice = 'pc';
4761
fieldsToSet.eyeTracker = false;
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49-
cfg = setDefaults(cfg, fieldsToSet);
63+
cfg = setDefaultFields(cfg, fieldsToSet);
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51-
end
65+
% sort fields alphabetically
66+
cfg = orderfields(cfg);
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53-
function structure = setDefaults(structure, fieldsToSet)
54-
% loop through the defaults fiels to set and update if they don't exist
68+
end
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56-
names = fieldnames(fieldsToSet);
70+
function fieldsToSet = mriDefaults(fieldsToSet)
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58-
for i = 1:numel(names)
72+
% for file naming
73+
fieldsToSet.MRI.ce = [];
74+
fieldsToSet.MRI.dir = []; % phase encoding direction of acquisition for fMRI
75+
fieldsToSet.MRI.rec = []; % reconstruction of fMRI images
76+
fieldsToSet.MRI.echo = []; % echo fMRI images
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fieldsToSet.MRI.acq = []; % acquisition of fMRI images
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60-
thisField = fieldsToSet.(names{i});
79+
end
6180

62-
structure = setFieldToIfNotPresent( ...
63-
structure, ...
64-
names{i}, ...
65-
thisField);
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function fieldsToSet = datasetDescriptionDefaults()
82+
% required
83+
fieldsToSet.Name = '';
84+
fieldsToSet.BIDSVersion = '';
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% recommended
86+
fieldsToSet.License = '';
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fieldsToSet.Authors = {''};
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fieldsToSet.Acknowledgements = '';
89+
fieldsToSet.HowToAcknowledge = '';
90+
fieldsToSet.Funding = {''};
91+
fieldsToSet.ReferencesAndLinks = {''};
92+
fieldsToSet.DatasetDOI = '';
93+
end
6694

67-
end
95+
function fieldsToSet = mriJsonDefaults()
6896

69-
end
97+
% for json for funcfional data
98+
% required
99+
fieldsToSet.RepetitionTime = [];
100+
fieldsToSet.SliceTiming = [];
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fieldsToSet.TaskName = [];
102+
% fieldsToSet.PhaseEncodingDirection = [];
103+
% fieldsToSet.EffectiveEchoSpacing = [];
104+
% fieldsToSet.EchoTime = [];
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% recommended
106+
fieldsToSet.Instructions = [];
107+
fieldsToSet.TaskDescription = [];
70108

71-
function structure = setFieldToIfNotPresent(structure, fieldName, value)
72-
if ~isfield(structure, fieldName)
73-
structure.(fieldName) = value;
74-
end
75109
end

‎checkCppBidsDependencies.m‎

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function checkCppBidsDependencies
2+
3+
pth = fileparts(mfilename('fullpath'));
4+
addpath(fullfile(pth, 'lib', 'JSONio'));
5+
addpath(fullfile(pth, 'lib', 'bids-matlab'));
6+
addpath(fullfile(pth, 'lib', 'utils'));
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addpath(fullfile(pth, 'subfun'));
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9+
end

‎convertSourceToRaw.m‎

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function convertSourceToRaw(expParameters)
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3+
sourceDir = fullfile(expParameters.outputDir, 'source');
4+
rawDir = fullfile(expParameters.outputDir, 'rawdata');
5+
6+
% add dummy readme and change file
7+
copyfile(fullfile('..', 'dummyData', 'README'), sourceDir);
8+
copyfile(fullfile('..', 'dummyData', 'CHANGES'), sourceDir);
9+
10+
copyfile(sourceDir, rawDir);
11+
12+
% list subjects
13+
subjects = cellstr(file_utils('List', rawDir, 'dir', '^sub-.*$'));
14+
15+
if isequal(subjects, {''})
16+
error('No subjects found in BIDS directory.');
17+
end
18+
19+
for su = 1:numel(subjects)
20+
21+
sess = cellstr(file_utils('List', fullfile(rawDir, subjects{su}), 'dir', '^ses-.*$'));
22+
23+
for se = 1:numel(sess)
24+
parseFunc(rawDir, subjects{su}, sess{se});
25+
end
26+
27+
end
28+
29+
end
30+
31+
function parseFunc(rawDir, subjName, sesName)
32+
33+
subjectPath = fullfile(rawDir, subjName, sesName, 'func');
34+
35+
if exist(subjectPath, 'dir')
36+
37+
% do events
38+
filenames = file_utils('List', subjectPath, ...
39+
sprintf('^%s.*_task-.*_events_date-.*$', subjName));
40+
41+
removeDateSuffix(filenames, subjectPath);
42+
43+
% do bold
44+
filenames = file_utils('List', subjectPath, ...
45+
sprintf('^%s.*_task-.*_bold_date-.*$', subjName));
46+
47+
removeDateSuffix(filenames, subjectPath);
48+
49+
end
50+
end
51+
52+
function removeDateSuffix(filenames, subjectPath)
53+
if isempty(filenames)
54+
filenames = {};
55+
else
56+
filenames = cellstr(filenames);
57+
end
58+
59+
for i = 1:numel(filenames)
60+
61+
[~, name, ext] = fileparts(filenames{i});
62+
63+
[parts, ~] = regexp(name, '(?:_date-)+', 'split', 'match');
64+
65+
movefile(fullfile(subjectPath, filenames{i}), ...
66+
fullfile(subjectPath, [parts{1} ext]));
67+
68+
end
69+
end

‎createBoldJson.m‎

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function createBoldJson(expParameters)
2+
3+
opts.Indent = ' ';
4+
5+
fileName = strrep(expParameters.fileName.events, '_events', '_bold');
6+
fileName = strrep(fileName, '.tsv', '.json');
7+
8+
fileName = fullfile( ...
9+
expParameters.subjectOutputDir, ...
10+
expParameters.modality, ...
11+
fileName);
12+
13+
jsonContent = expParameters.bids.MRI;
14+
15+
bids.util.jsonencode(fileName, jsonContent, opts);
16+
17+
end

‎createDataDictionary.m‎

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function createDataDictionary(expParameters, logFile)
2+
3+
opts.Indent = ' ';
4+
5+
fileName = strrep(expParameters.fileName.events, '.tsv', '.json');
6+
7+
fileName = fullfile( ...
8+
expParameters.subjectOutputDir, ...
9+
expParameters.modality, ...
10+
fileName);
11+
12+
jsonContent = struct( ...
13+
'onset', struct( ...
14+
'Description', 'time elapsed since experiment start', ...
15+
'Unit', 's'), ...
16+
'trial_type', struct( ...
17+
'Description', 'types of trial', ...
18+
'Levels', ''), ...
19+
'duration', struct( ...
20+
'Description', 'duration of the event or the block', ...
21+
'Unit', 's') ...
22+
);
23+
24+
% transfer content of extra fields to json content
25+
namesExtraColumns = returnNamesExtraColumns(logFile);
26+
27+
for iExtraColumn = 1:numel(namesExtraColumns)
28+
29+
nbCol = returnNbColumns(logFile, namesExtraColumns{iExtraColumn});
30+
31+
for iCol = 1:nbCol
32+
33+
headerName = returnHeaderName(namesExtraColumns{iExtraColumn}, nbCol, iCol);
34+
35+
jsonContent.(headerName) = ...
36+
logFile(1).extraColumns.(namesExtraColumns{iExtraColumn}).bids;
37+
38+
end
39+
40+
end
41+
42+
bids.util.jsonencode(fileName, jsonContent, opts);
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44+
end

‎createDatasetDescription.m‎

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function createDatasetDescription(expParameters)
2+
3+
opts.Indent = ' ';
4+
5+
fileName = fullfile( ...
6+
expParameters.outputDir, 'source', ...
7+
'dataset_description.json');
8+
9+
jsonContent = expParameters.bids.datasetDescription;
10+
11+
bids.util.jsonencode(fileName, jsonContent, opts);
12+
13+
end

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