From 9382cd7156e86ea16679836e3e466b100786c689 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 27 May 2020 11:57:52 +0200
Subject: [PATCH 1/3] update unit tests

---
 createFilename.m~           | 132 ------------------------------------
 tests/test_createFilename.m |  32 ++++-----
 tests/test_saveEventsFile.m |   3 +
 3 files changed, 16 insertions(+), 151 deletions(-)
 delete mode 100644 createFilename.m~

diff --git a/createFilename.m~ b/createFilename.m~
deleted file mode 100644
index 8f6f0977..00000000
--- a/createFilename.m~
+++ /dev/null
@@ -1,132 +0,0 @@
-function expParameters = createFilename(expParameters, cfg)
-% create the BIDS compliant directories and filenames for the behavioral output for this subject /
-% session / run.
-% Will also create the right filename for the eyetracking data file.
-%
-% For the moment the date of acquisition is appreneded to the filename
-%
-% can work for behavioral experiment if cfg.device is set to 'PC'
-% can work for fMRI experiment if cfg.device is set to 'scanner'
-% can work for simple eyetracking data if cfg.eyeTracker is set to 1
-%
-% BOLD
-% sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
-%
-% iEEG
-% sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json
-%
-% EEG
-% sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>
-%
-% EYETRACKER
-% sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>
-
-zeroPadding = 3;
-pattern = ['%0' num2str(zeroPadding) '.0f'];
-
-dateFormat = 'yyyymmdd_HHMM';
-
-% Setting some defaults: no need to change things here
-expParameters = checkCFG(expParameters);
-
-% extract input
-subjectGrp = expParameters.subjectGrp;
-subjectNb = expParameters.subjectNb;
-sessionNb = expParameters.sessionNb;
-runNb = expParameters.runNb;
-
-expParameters.date = datestr(now, dateFormat);
-
-% output dir
-expParameters.outputDir = fullfile (...
-    expParameters.outputDir, ...
-    'source', ...
-    ['sub-' subjectGrp, sprintf(pattern, subjectNb)], ...
-    ['ses-', sprintf(pattern, sessionNb)]);
-
-% create base filename
-expParameters.fileName.base = ...
-    ['sub-', subjectGrp, sprintf(pattern, subjectNb), ...
-    '_ses-', sprintf(pattern, sessionNb) , ...
-    '_task-', expParameters.task];
-
-runSuffix = ['_run-' sprintf(pattern, runNb)];
-
-
-switch lower(cfg.device)
-    case 'pc'
-        modality = 'beh';
-    case 'scanner'
-        modality = 'func';
-    otherwise
-        modality = 'beh';
-end
-
-expParameters.modality = modality;
-
-
-% set values for the suffixes for the different fields in the BIDS name
-fields2Check = { ...
-    'ce', ...
-    'dir', ...  % For BIDS file naming: phase encoding direction of acquisition for fMRI
-    'rec', ...  % For BIDS file naming: reconstruction of fMRI images
-    'echo', ... % For BIDS file naming: echo fMRI images
-    'acq'       % For BIDS file naming: acquisition of fMRI images
-    };
-
-for iField = 1:numel(fields2Check)
-    if isempty (getfield(expParameters, fields2Check{iField}) ) %#ok<*GFLD>
-        expParameters = setfield(expParameters, [fields2Check{iField} 'Suffix'], ...
-            ''); %#ok<*SFLD>
-    else
-        expParameters = setfield(expParameters, [fields2Check{iField} 'Suffix'], ...
-            ['_' fields2Check{iField} '-' getfield(expParameters, fields2Check{iField})]);
-    end
-end
-
-
-%% create directories
-[~, ~, ~] = mkdir(expParameters.outputDir);
-[~, ~, ~] = mkdir(fullfile(expParameters.outputDir, modality));
-
-if cfg.eyeTracker
-    [~, ~, ~] = mkdir(fullfile(expParameters.outputDir, 'eyetracker'));
-end
-
-
-%% create filenames
-
-switch modality
-    
-    case 'beh'
-        
-        expParameters.fileName.events = ...
-            [expParameters.fileName.base, runSuffix, '_events_date-' expParameters.date '.tsv'];
-        
-    case 'func'
-        
-        expParameters.fileName.events = ...
-            [expParameters.fileName.base, ...
-            expParameters.acqSuffix, expParameters.ceSuffix, ...
-            expParameters.dirSuffix, expParameters.recSuffix, ...
-            runSuffix, expParameters.echoSuffix, ...
-            '_events_date-' expParameters.date '.tsv'];
-        
-end
-
-if cfg.eyeTracker
-    
-    expParameters.fileName.eyetracker = ...
-        [expParameters.fileName.base, expParameters.acqSuffix, ...
-        runSuffix, '_eyetrack_date-' expParameters.date '.edf'];
-    
-end
-
-if expParameters.verbose
-    fprintf(1,'\nData will be saved in this directory:\n\n%s\')
-    expParameters.outputDir
-    expParameters.fileName
-end
-
-
-end
\ No newline at end of file
diff --git a/tests/test_createFilename.m b/tests/test_createFilename.m
index 150af69d..8c8061da 100644
--- a/tests/test_createFilename.m
+++ b/tests/test_createFilename.m
@@ -14,19 +14,17 @@ function test_createFilename()
 cfg.eyeTracker = true;
 cfg.device = 'PC';
 
-expParameters = checkCFG(cfg,expParameters);
-expParameters = createFilename(cfg,expParameters);
+outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-outputDir = fullfile(pwd, ...
-    '..', '..', ...
-    'output', 'source', 'sub-001', 'ses-001', 'beh');
+behDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'beh');
+eyetrackerDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'eyetracker');
 
-eyetrackerDir = fullfile(pwd, ...
-    '..', '..', ...
-    'output', 'source', 'sub-001', 'ses-001', 'eyetracker');
+expParameters.outputDir = outputDir;
+expParameters = checkCFG(cfg,expParameters);
 
+expParameters = createFilename(cfg,expParameters);
 
-assert(exist(outputDir, 'dir')==7)
+assert(exist(behDir, 'dir')==7)
 assert(exist(eyetrackerDir, 'dir')==7)
 assert(strcmp(...
               expParameters.fileName.events, ...
@@ -49,19 +47,15 @@ function test_createFilename()
 cfg.eyeTracker = false;
 cfg.device = 'scanner';
 
-expParameters = checkCFG(cfg,expParameters);
-expParameters = createFilename(cfg,expParameters);
-
-outputDir = fullfile(pwd, ...
-    '..', '..', ...
-    'output', 'source', 'sub-ctrl002', 'ses-002', 'func');
+outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-eyetrackerDir = fullfile(pwd, ...
-    '..', '..', ...
-    'output', 'source', 'sub-ctrl002', 'ses-002', 'eyetracker');
+funcDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'func');
 
+expParameters.outputDir = outputDir;
+expParameters = checkCFG(cfg,expParameters);
+expParameters = createFilename(cfg,expParameters);
 
-assert(exist(outputDir, 'dir')==7)
+assert(exist(funcDir, 'dir')==7)
 assert(strcmp(expParameters.fileName.base, 'sub-ctrl002_ses-002_task-testtask'))
 assert(strcmp(...
               expParameters.fileName.events, ...
diff --git a/tests/test_saveEventsFile.m b/tests/test_saveEventsFile.m
index a84fa2b2..9e77131e 100644
--- a/tests/test_saveEventsFile.m
+++ b/tests/test_saveEventsFile.m
@@ -13,6 +13,9 @@ function test_saveEventsFile()
 cfg.eyeTracker = false;
 cfg.device = 'scanner';
 
+outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
+
+expParameters.outputDir = outputDir;
 expParameters = checkCFG(cfg,expParameters);
 expParameters = createFilename(cfg,expParameters);
 

From 9b522ff413e20af723855dd1e667cc28ade3b457 Mon Sep 17 00:00:00 2001
From: Ceren Battal <battal.ceren@gmail.com>
Date: Wed, 27 May 2020 16:30:33 +0200
Subject: [PATCH 2/3] gitignore

---
 saveEventsFile.m~ | 79 -----------------------------------------------
 1 file changed, 79 deletions(-)
 delete mode 100644 saveEventsFile.m~

diff --git a/saveEventsFile.m~ b/saveEventsFile.m~
deleted file mode 100644
index 5cf4b895..00000000
--- a/saveEventsFile.m~
+++ /dev/null
@@ -1,79 +0,0 @@
-function [ logFile ] = saveEventsFile(input, expParameters, logFile, varargin)
-
-if nargin<3 || isempty(logFile)
-    logFile = struct();
-end
-
-switch input
-    
-    case 'open'
-        
-        logFile = struct();
-        
-        % Initialize txt logfiles and empty fields for the standard BIDS
-        %  event file
-        logFile.eventLogFile = fopen(...
-            fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.events), ...
-            'w');
-        
-        % print the basic BIDS columns
-        fprintf(logFile.eventLogFile, '%s\t%s\t%s\t', 'onset', 'trial_type', 'duration');
-        
-        % print any extra column specified by the user
-        %  also prepare an empty field in the structure to collect data
-        %  for those
-        for iExtraColumn = 1:numel(varargin)
-            fprintf(logFile.eventLogFile,'%s\t', lower(varargin{iExtraColumn}));
-        end
-        
-        % next line so we start printing at the right place
-        fprintf(logFile.eventLogFile, '\n');
-        
-        
-    case 'save'
-        
-        % appends to the logfile all the data stored in the structure
-        % first with the standard BIDS data and then any extra things
-        for iEvent = 1:size(logFile,1)
-            
-            fprintf(logFile(1).eventLogFile,'%f\t%s\t%f\t',...
-                logFile(iEvent).onset, ...
-                logFile(iEvent).trial_type, ...
-                logFile(iEvent).duration);
-            
-            for iExtraColumn = 1:numel(varargin)
-                
-                % if the field we are looking for does not exist or is empty in the
-                % input logFile structure we will write a NaN otherwise we
-                % write its content
-                
-                if ~isfield(logFile, varargin{iExtraColumn})
-                    data = [];
-                else
-                    data = getfield(logFile(iEvent), varargin{iExtraColumn});
-                end
-                
-                if isempty(data)
-                    data = NaN;
-                end
-                
-                if ischar(data)
-                    fprintf(logFile(1).eventLogFile, '%s\t', data);
-                else
-                    fprintf(logFile(1).eventLogFile, '%f\t', data);
-                end
-                
-            end
-            
-            fprintf(logFile(1).eventLogFile, '\n');
-        end
-        
-    case 'close'
-        
-        % close txt log file
-        fclose(logFile(1).eventLogFile);
-        
-        if expParameters.verbose
-        fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.events)
-        
-end
\ No newline at end of file

From e25ec42ed2887bc18f41fb9f1836dc39250067a2 Mon Sep 17 00:00:00 2001
From: Ceren <battal.ceren@gmail.com>
Date: Tue, 21 Jul 2020 18:11:01 +0200
Subject: [PATCH 3/3] function name camelCase fix

---
 tests/runTests.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/runTests.m b/tests/runTests.m
index 6facd137..3c9e3a38 100644
--- a/tests/runTests.m
+++ b/tests/runTests.m
@@ -1,4 +1,4 @@
-function results = runtests(pth)
+function results = runTests(pth)
     % Run tests
     % List all the 'test_*.m' files located in the same directory as this
     % function, run them and keep track of how many passed, failed or are