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fix wrong stim.json save #99

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Merged
merged 2 commits into from
Sep 23, 2020
Merged

fix wrong stim.json save #99

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5a964cf
fix wrong stim.json save
Remi-Gau Sep 23, 2020
942a08a
mh fix
Remi-Gau Sep 23, 2020
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4 changes: 2 additions & 2 deletions manualTests/test_createDataDictionary.m
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ function test_createDataDictionaryBasic()
funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');

jsonFilename = ['sub-001_ses-001_task-testtask_run-001_events_date-' ...
cfg.fileName.date '.json'];
cfg.fileName.date '.json'];

% test
assertTrue(exist(fullfile(funcDir, jsonFilename), 'file') == 2);
Expand All @@ -47,7 +47,7 @@ function test_createDataDictionaryBasic()

% data to test against
expectedStruct = bids.util.jsondecode( ...
fullfile(pwd, 'testData', 'eventsDataDictionary.json'));
fullfile(pwd, 'testData', 'eventsDataDictionary.json'));

% test
assertTrue(isequal(expectedStruct, actualStruct));
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8 changes: 4 additions & 4 deletions manualTests/test_createJson.m
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Expand Up @@ -36,13 +36,13 @@ function test_createJsonExtra()
fileName = strrep(fileName, '.tsv', '.json');

actualStruct = bids.util.jsondecode(fullfile( ...
cfg.dir.outputSubject, ...
cfg.fileName.modality, ...
fileName));
cfg.dir.outputSubject, ...
cfg.fileName.modality, ...
fileName));

% data to test against
expectedStruct = bids.util.jsondecode( ...
fullfile(pwd, 'testData', 'extra_bold.json'));
fullfile(pwd, 'testData', 'extra_bold.json'));

% test
assertEqual(expectedStruct, actualStruct);
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28 changes: 14 additions & 14 deletions manualTests/test_makeRawDataset.m
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Expand Up @@ -205,16 +205,16 @@ function test_makeRawDataset()
boldFilename = 'sub-001_ses-001_task-testtask_run-001_bold.nii.gz';

copyfile( ...
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(funcDir, boldFilename));
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(funcDir, boldFilename));

boldFilename = ['sub-001_ses-001_task-rest', ...
'_acq-newTYpe_ce-test_dir-yPos_rec-fastRecon', ...
'_run-001_echo-1_bold.nii.gz'];
'_acq-newTYpe_ce-test_dir-yPos_rec-fastRecon', ...
'_run-001_echo-1_bold.nii.gz'];

copyfile( ...
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(funcDir, boldFilename));
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(funcDir, boldFilename));

eegDir = fullfile(subjectDir, 'eeg');
megDir = fullfile(subjectDir, 'meg');
Expand All @@ -227,20 +227,20 @@ function test_makeRawDataset()
behFilename = 'sub-001_ses-001_task-easyTargetPractice_run-001_beh.tsv';

copyfile( ...
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(eegDir, eegFilename));
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(eegDir, eegFilename));

copyfile( ...
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(megDir, megFilename));
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(megDir, megFilename));

copyfile( ...
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(ieegDir, ieegFilename));
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(ieegDir, ieegFilename));

copyfile( ...
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(behDir, behFilename));
fullfile('dummyData', 'dummyData.nii.gz'), ...
fullfile(behDir, behFilename));

%% actually do the conversion of the source data thus created
clear;
Expand Down
6 changes: 3 additions & 3 deletions src/checkCFG.m
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Expand Up @@ -23,9 +23,9 @@
fieldsToSet.fileName.dateFormat = 'yyyymmddHHMM';

fieldsToSet.dir.output = fullfile( ...
fileparts(mfilename('fullpath')), ...
'..', ...
'output');
fileparts(mfilename('fullpath')), ...
'..', ...
'output');

fieldsToSet.subject.askGrpSess = [true true];
fieldsToSet.subject.sessionNb = 1; % in case no session was provided
Expand Down
12 changes: 6 additions & 6 deletions src/convertSourceToRaw.m
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Expand Up @@ -16,14 +16,14 @@ function convertSourceToRaw(cfg)

% add dummy README and CHANGE file
copyfile(fullfile( ...
fileparts(mfilename('fullpath')), '..', 'manualTests', 'dummyData', 'README'), ...
sourceDir);
fileparts(mfilename('fullpath')), '..', 'manualTests', 'dummyData', 'README'), ...
sourceDir);
copyfile(fullfile( ...
fileparts(mfilename('fullpath')), '..', 'manualTests', 'dummyData', 'CHANGES'), ...
sourceDir);
fileparts(mfilename('fullpath')), '..', 'manualTests', 'dummyData', 'CHANGES'), ...
sourceDir);
copyfile(fullfile( ...
fileparts(mfilename('fullpath')), '..', 'manualTests', 'dummyData', '.bidsignore'), ...
sourceDir);
fileparts(mfilename('fullpath')), '..', 'manualTests', 'dummyData', '.bidsignore'), ...
sourceDir);

copyfile(sourceDir, rawDir);

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28 changes: 14 additions & 14 deletions src/createDataDictionary.m
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Expand Up @@ -9,24 +9,24 @@ function createDataDictionary(cfg, logFile)

opts.Indent = ' ';

fileName = strrep(cfg.fileName.events, '.tsv', '.json');
fileName = strrep(logFile.filename, '.tsv', '.json');

fileName = fullfile( ...
cfg.dir.outputSubject, ...
cfg.fileName.modality, ...
fileName);
cfg.dir.outputSubject, ...
cfg.fileName.modality, ...
fileName);

jsonContent = struct( ...
'onset', struct( ...
'Description', 'time elapsed since experiment start', ...
'Unit', 's'), ...
'trial_type', struct( ...
'Description', 'types of trial', ...
'Levels', ''), ...
'duration', struct( ...
'Description', 'duration of the event or the block', ...
'Unit', 's') ...
);
'onset', struct( ...
'Description', 'time elapsed since experiment start', ...
'Unit', 's'), ...
'trial_type', struct( ...
'Description', 'types of trial', ...
'Levels', ''), ...
'duration', struct( ...
'Description', 'duration of the event or the block', ...
'Unit', 's') ...
);

% transfer content of extra fields to json content
namesExtraColumns = returnNamesExtraColumns(logFile);
Expand Down
4 changes: 2 additions & 2 deletions src/createDatasetDescription.m
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Expand Up @@ -9,8 +9,8 @@ function createDatasetDescription(cfg)
opts.Indent = ' ';

fileName = fullfile( ...
cfg.dir.output, 'source', ...
'dataset_description.json');
cfg.dir.output, 'source', ...
'dataset_description.json');

jsonContent = cfg.bids.datasetDescription;

Expand Down
62 changes: 31 additions & 31 deletions src/createFilename.m
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Expand Up @@ -84,10 +84,10 @@

% output dir
cfg.dir.outputSubject = fullfile ( ...
cfg.dir.output, ...
'source', ...
['sub-' subjectGrp, sprintf(pattern, subjectNb)], ...
['ses-', sprintf(pattern, sessionNb)]);
cfg.dir.output, ...
'source', ...
['sub-' subjectGrp, sprintf(pattern, subjectNb)], ...
['ses-', sprintf(pattern, sessionNb)]);

[~, ~, ~] = mkdir(cfg.dir.output);
[~, ~, ~] = mkdir(cfg.dir.outputSubject);
Expand All @@ -102,22 +102,22 @@
%% MRI
% set values for the suffixes for the different fields in the BIDS name
fields2Check = { ...
'acquisition', ...
'contrastEnhancement', ...
'echo', ...
'phaseEncodingDirection', ...
'reconstruction', ...
'recording' ...
};
'acquisition', ...
'contrastEnhancement', ...
'echo', ...
'phaseEncodingDirection', ...
'reconstruction', ...
'recording' ...
};

targetFields = { ...
'acq', ...
'ce', ...
'echo', ...
'dir', ...
'rec', ...
'recording' ...
};
'acq', ...
'ce', ...
'echo', ...
'dir', ...
'rec', ...
'recording' ...
};

for iField = 1:numel(fields2Check)

Expand Down Expand Up @@ -158,31 +158,31 @@
thisDate = cfg.fileName.date;

cfg.fileName.datasetDescription = fullfile ( ...
cfg.dir.output, ...
'dataset_description.json');
cfg.dir.output, ...
'dataset_description.json');

% create base fileName
fileNameBase = ...
['sub-', subjectGrp, sprintf(pattern, subjectNb), ...
'_ses-', sprintf(pattern, sessionNb), ...
'_task-', taskName];
'_ses-', sprintf(pattern, sessionNb), ...
'_task-', taskName];
cfg.fileName.base = fileNameBase;

switch modality

case 'func'

basename = [fileNameBase, ...
acqSuffix, ceSuffix, ...
dirSuffix, recSuffix, ...
runSuffix, echoSuffix];
acqSuffix, ceSuffix, ...
dirSuffix, recSuffix, ...
runSuffix, echoSuffix];

case 'beh'

basename = ...
[fileNameBase, ...
acqSuffix, ...
runSuffix];
acqSuffix, ...
runSuffix];

otherwise

Expand All @@ -206,18 +206,18 @@ function talkToMe(cfg)
if cfg.verbose > 0

fprintf(1, '\nData will be saved in this directory:\n\t%s\n', ...
fullfile(cfg.dir.outputSubject, cfg.fileName.modality));
fullfile(cfg.dir.outputSubject, cfg.fileName.modality));

fprintf(1, '\nData will be saved in this file:\n\t%s\n', ...
cfg.fileName.events);
cfg.fileName.events);

if cfg.eyeTracker.do

fprintf(1, '\nEyetracking data will be saved in this directory:\n\t%s\n', ...
fullfile(cfg.dir.outputSubject, 'eyetracker'));
fullfile(cfg.dir.outputSubject, 'eyetracker'));

fprintf(1, '\nEyetracking data will be saved in this file:\n\t%s\n', ...
cfg.fileName.eyetracker);
cfg.fileName.eyetracker);

end

Expand Down
12 changes: 6 additions & 6 deletions src/createJson.m
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Expand Up @@ -39,9 +39,9 @@ function createJson(varargin)
fileName = strrep(fileName, '.tsv', '.json');

fileName = fullfile( ...
cfg.dir.outputSubject, ...
modality, ...
fileName);
cfg.dir.outputSubject, ...
modality, ...
fileName);

%% add content of extraInfo to the JSON content

Expand Down Expand Up @@ -115,11 +115,11 @@ function errorCreateJson(identifier, varargin)

case 'wrongInputType'
errorStruct.message = ['The second input must be a string (modality)' ...
'or a structure (extraInfo)'];
'or a structure (extraInfo)'];
case 'wrongModalityInput'
errorStruct.message = sprintf(['The given modality is not valid: %s.\n', ...
'Only the following string are accepted: beh, func, eeg, ieeg, meg'], ...
varargin{1});
'Only the following string are accepted: beh, func, eeg, ieeg, meg'], ...
varargin{1});

end

Expand Down
28 changes: 14 additions & 14 deletions src/saveEventsFile.m
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Expand Up @@ -154,11 +154,11 @@
% Initialize txt logfiles and empty fields for the standard BIDS
% event file
logFile(1).fileID = fopen( ...
fullfile( ...
cfg.dir.outputSubject, ...
cfg.fileName.modality, ...
logFile.filename), ...
'w');
fullfile( ...
cfg.dir.outputSubject, ...
cfg.fileName.modality, ...
logFile.filename), ...
'w');

% print the basic BIDS columns
fprintf(logFile(1).fileID, '%s\t%s\t%s', 'onset', 'duration', 'trial_type');
Expand Down Expand Up @@ -219,7 +219,7 @@ function printHeaderExtraColumns(logFile)

if ~ischar(data) && any(isnan(data))
warning('saveEventsFile:missingData', ...
'Missing some %s data for this event.', namesExtraColumns{iExtraColumn});
'Missing some %s data for this event.', namesExtraColumns{iExtraColumn});

if cfg.verbose > 1
disp(logFile(iEvent));
Expand Down Expand Up @@ -269,7 +269,7 @@ function printHeaderExtraColumns(logFile)
data(end + 1:end + padding) = nan(1, padding);
elseif ~isempty(expectedLength) && isnumeric(data) && max(size(data)) > expectedLength
warning('saveEventsFile:arrayTooLong', ...
'A field for this event is longer than expected. Truncating the extra values.');
'A field for this event is longer than expected. Truncating the extra values.');
data = data(1:expectedLength);
end

Expand All @@ -293,9 +293,9 @@ function printHeaderExtraColumns(logFile)
any(isempty({onset duration}))

warning('saveEventsFile:emptyEvent', ...
'\nSkipping saving this event.\n onset: %s \n duration: %s\n', ...
onset, ...
duration);
'\nSkipping saving this event.\n onset: %s \n duration: %s\n', ...
onset, ...
duration);

else

Expand Down Expand Up @@ -395,10 +395,10 @@ function talkToMe(cfg, logFile)
if cfg.verbose > 0

fprintf(1, '\nData were saved in this file:\n\n%s\n\n', ...
fullfile( ...
cfg.dir.outputSubject, ...
cfg.fileName.modality, ...
logFile.filename));
fullfile( ...
cfg.dir.outputSubject, ...
cfg.fileName.modality, ...
logFile.filename));

end

Expand Down
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