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Remi-GauRemi-Gau
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make createJson be able to handle EEG MEG iEEG BEH
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4 files changed

Lines changed: 266 additions & 78 deletions

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‎src/createBoldJson.m‎

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‎src/createJson.m‎

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function createJson(varargin)
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% createBoldJson(cfg, varargin)
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%
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% Creates the side car JSON file for a run.
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% This will only contain the minimum BIDS requirement and will likey be less
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% complete than the info you could from a proper conversion.
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%
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% USAGE
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%
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% createJson(cfg, modality)
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%
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% modality is string ('beh', 'func', 'eeg', 'ieeg', 'meg') to specify which
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% JSON to save
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%
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%
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% createJson(cfg, extraInfo)
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%
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% extraInfo is a strcuture to add axtra content can be added to the JSON file
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%
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%
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% createJson(cfg, modality, extraInfo)
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%
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% both are possible
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%
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%
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[cfg, modality, extraInfo] = checkInput(varargin);
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if strcmp(modality, 'func')
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fileName = strrep(cfg.fileName.events, '_events', '_bold');
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jsonContent = cfg.bids.mri;
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else
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fileName = strrep(cfg.fileName.events, '_events', ['_' modality]);
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jsonContent = cfg.bids.(modality);
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end
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fileName = strrep(fileName, '.tsv', '.json');
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fileName = fullfile( ...
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cfg.dir.outputSubject, ...
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modality, ...
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fileName);
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%% add content of extraInfo to the JSON content
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fieldList = fieldnames(extraInfo);
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for iField = 1:numel(fieldList)
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jsonContent.(fieldList{iField}) = extraInfo.(fieldList{iField});
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end
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%% save
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opts.Indent = ' ';
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bids.util.jsonencode(fileName, jsonContent, opts);
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end
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function [cfg, modality, extraInfo] = checkInput(varargin)
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% trying to parse inputs
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% modality is either given as a string by user or guessed from cfg.fileName
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% extraInfo must be a structure
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input = varargin{1};
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modality = '';
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extraInfo = struct();
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switch numel(input)
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case 0
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errorCreateJson('notEnoughInput');
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case 1
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cfg = input{1};
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if isfield(cfg.fileName, 'modality')
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modality = cfg.fileName.modality;
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end
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case 2
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cfg = input{1};
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if ischar(input{2})
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modality = varargin{2};
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elseif isstruct(input{2})
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extraInfo = varargin{2};
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else
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errorCreateJson('wrongInputType');
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end
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otherwise
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cfg = input{1};
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modality = varargin{2};
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extraInfo = varargin{3};
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end
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if ~ischar(modality) || ...
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all(~strcmpi(modality, {'beh', 'func', 'eeg', 'ieeg', 'meg'}))
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errorCreateJson('wrongModalityInput', modality);
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end
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if ~isstruct(extraInfo)
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warning('Additional info added to a json file must be a structure.');
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end
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end
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function errorCreateJson(identifier, varargin)
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switch identifier
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case 'notEnoughInput'
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errorStruct.message = 'First input must be a valid cfg structure.';
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case 'wrongInputType'
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errorStruct.message = ['The second input must be a string (modality)' ...
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'or a structure (extraInfo)'];
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case 'wrongModalityInput'
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errorStruct.message = sprintf(['The given modality is not valid: %s.\n', ...
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'Only the following string are accepted: beh, func, eeg, ieeg, meg'], ...
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varargin{1});
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end
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errorStruct.identifier = ['createJson:' identifier];
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error(errorStruct);
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end

‎tests/test_createBoldJson.m‎

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‎tests/test_createJson.m‎

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function test_suite = test_createJson %#ok<*STOUT>
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try % assignment of 'localfunctions' is necessary in Matlab >= 2016
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test_functions = localfunctions(); %#ok<*NASGU>
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catch % no problem; early Matlab versions can use initTestSuite fine
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end
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initTestSuite;
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end
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function test_createJsonFunc()
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%% set up
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cfg = setUp();
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cfg.testingDevice = 'mri';
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cfg = createFilename(cfg);
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logFile = saveEventsFile('init', cfg); %#ok<*NASGU>
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createJson(cfg);
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%% data to test against
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funcDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001', 'func');
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eventFilename = ['sub-001_ses-001_task-testtask_run-001_bold_date-' ...
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cfg.fileName.date '.json'];
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%% test
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assertTrue(exist(fullfile(funcDir, eventFilename), 'file') == 2);
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end
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function test_createJsonBeh()
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%% set up
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cfg = setUp();
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cfg.testingDevice = 'pc';
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cfg = createFilename(cfg);
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logFile = saveEventsFile('init', cfg); %#ok<*NASGU>
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createJson(cfg);
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%% data to test against
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funcDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001', 'beh');
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eventFilename = ['sub-001_ses-001_task-testtask_run-001_beh_date-' ...
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cfg.fileName.date '.json'];
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%% test
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assertTrue(exist(fullfile(funcDir, eventFilename), 'file') == 2);
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end
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function test_createJsonEeg()
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%% set up
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cfg = setUp();
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cfg.testingDevice = 'eeg';
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cfg = createFilename(cfg);
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logFile = saveEventsFile('init', cfg); %#ok<*NASGU>
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createJson(cfg);
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%% data to test against
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funcDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001', 'eeg');
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eventFilename = ['sub-001_ses-001_task-testtask_run-001_eeg_date-' ...
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cfg.fileName.date '.json'];
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%% test
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assertTrue(exist(fullfile(funcDir, eventFilename), 'file') == 2);
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end
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function test_createJsonMeg()
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%% set up
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cfg = setUp();
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cfg.testingDevice = 'meg';
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cfg = createFilename(cfg);
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logFile = saveEventsFile('init', cfg); %#ok<*NASGU>
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createJson(cfg);
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%% data to test against
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funcDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001', 'meg');
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eventFilename = ['sub-001_ses-001_task-testtask_run-001_meg_date-' ...
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cfg.fileName.date '.json'];
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%% test
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assertTrue(exist(fullfile(funcDir, eventFilename), 'file') == 2);
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end
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function test_createJsonIeeg()
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%% set up
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cfg = setUp();
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cfg.testingDevice = 'ieeg';
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cfg = createFilename(cfg);
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logFile = saveEventsFile('init', cfg); %#ok<*NASGU>
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createJson(cfg);
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%% data to test against
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funcDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001', 'ieeg');
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eventFilename = ['sub-001_ses-001_task-testtask_run-001_ieeg_date-' ...
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cfg.fileName.date '.json'];
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%% test
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assertTrue(exist(fullfile(funcDir, eventFilename), 'file') == 2);
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end
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function cfg = setUp()
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cfg.verbose = false;
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cfg.subject.subjectNb = 1;
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cfg.subject.runNb = 1;
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cfg.task.name = 'testtask';
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cfg.dir.output = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
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end

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