Merge pull request #31 from Remi-Gau/remi-doc

update doc

Author: Remi-Gau

.gitignore

@@ -8,3 +8,4 @@
 *.tsv
 *.mat
 
+check_my_code_report.txt

.travis.yml

@@ -13,8 +13,8 @@ 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
 
 install:
   # Install JSONio

README.md

@@ -66,6 +66,9 @@ expParameters = createFilename(cfg, expParameters);
 % and add some more in this case (Speed and is_Fixation)
 logFile = saveEventsFile('open', expParameters, [], 'Speed', 'is_Fixation');
 
+% to initialize a stim file in case you want to store the info about the stimuli in it
+stimFile = saveEventsFile('open_stim', expParameters, []);
+
 % create the information about 2 events that we want to save
 logFile(1,1).onset = 2;
 logFile(1,1).trial_type = 'motion_up';
@@ -184,3 +187,24 @@ Here are the naming templates used.
 -   Eyetracker
 
 `sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>`
+
+### Contributors ✨
+
+Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
+
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
+<table>
+  <tr>
+    <td align="center"><a href="https://github.com/CerenB"><img src="https://avatars1.githubusercontent.com/u/10451654?v=4" width="100px;" alt=""/><br /><sub><b>CerenB</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=CerenB" title="Code">💻</a> <a href="#design-CerenB" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=CerenB" title="Documentation">📖</a></td>
+    <td align="center"><a href="https://github.com/marcobarilari"><img src="https://avatars3.githubusercontent.com/u/38101692?v=4" width="100px;" alt=""/><br /><sub><b>marcobarilari</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=marcobarilari" title="Code">💻</a> <a href="#design-marcobarilari" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=marcobarilari" title="Documentation">📖</a></td>
+    <td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars3.githubusercontent.com/u/6961185?v=4" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=Remi-Gau" title="Code">💻</a> <a href="#design-Remi-Gau" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=Remi-Gau" title="Documentation">📖</a></td>
+  </tr>
+</table>
+
+<!-- markdownlint-enable -->
+<!-- prettier-ignore-end -->
+<!-- ALL-CONTRIBUTORS-LIST:END -->
+
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!

checkCFG.m

@@ -14,17 +14,26 @@
 end
 
 % set empty values for a series of field if they have not been specified
+% '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
+% 'subjectGrp' in case no group was provided
+% 'sessionNb'  in case no session was provided
+
 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
-    };
+    'dir', ...  
+    'rec', ...  
+    'echo', ... 
+    'acq', ...  
+    'subjectGrp', ... 
+    'sessionNb'};
 
 fields2CheckFalse = { ...
     'eyeTracker'
-    }
+    };
 
 for iField = 1:numel(fields2Check)
     if ~isfield(expParameters, fields2Check{iField})

tests/test_createFilename.m

@@ -1,9 +1,10 @@
 function test_createFilename()
-
 % test for filename creation and their directories
 
 %% check directory and filename creation (PC)
 
+%%% set up part
+
 expParameters.subjectGrp = '';
 expParameters.subjectNb = 1;
 expParameters.sessionNb = 1;
@@ -14,32 +15,40 @@ function test_createFilename()
 cfg.eyeTracker = false;
 cfg.device = 'PC';
 
+% set up the output directories
 outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
+expParameters.outputDir = outputDir;
 
 behDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'beh');
 eyetrackerDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'eyetracker');
 
-expParameters.outputDir = outputDir;
 expParameters = checkCFG(cfg,expParameters);
-
 expParameters = createFilename(cfg,expParameters);
 
+%%% test part
+
+% make sure the beh dir is created
 assert(exist(behDir, 'dir')==7)
 
 % make sure the eyetracker dir is not created
-assert(exist(eyetrackerDir, 'dir')==0) 
+assert(exist(eyetrackerDir, 'dir')==0)
 
+% make sure the events filename is created
 assert(strcmp(...
-              expParameters.fileName.events, ...
-              ['sub-001_ses-001_task-testtask_run-001_events_date-' expParameters.date '.tsv']));
+    expParameters.fileName.events, ...
+    ['sub-001_ses-001_task-testtask_run-001_events_date-' expParameters.date '.tsv']));
+
+% make sure the stim filename is created
 assert(strcmp(...
-              expParameters.fileName.stim, ...
-              ['sub-001_ses-001_task-testtask_run-001_stim_date-' expParameters.date '.tsv']));
-          
+    expParameters.fileName.stim, ...
+    ['sub-001_ses-001_task-testtask_run-001_stim_date-' expParameters.date '.tsv']));
+
 %% check directory and filename creation (fMRI and eye tracker)
 
 clear
 
+%%% set up part
+
 expParameters.subjectGrp = 'ctrl';
 expParameters.subjectNb = 2;
 expParameters.sessionNb = 2;
@@ -58,13 +67,21 @@ function test_createFilename()
 expParameters = checkCFG(cfg,expParameters);
 expParameters = createFilename(cfg,expParameters);
 
+%%% test part
+
+% make sure the func dir is created
 assert(exist(funcDir, 'dir')==7)
+
+% make sure the eyetracker dir is created
 assert(exist(eyetrackerDir, 'dir')==7)
+
+% make sure the events filename is created
 assert(strcmp(expParameters.fileName.base, 'sub-ctrl002_ses-002_task-testtask'))
 assert(strcmp(...
-              expParameters.fileName.events, ...
-              ['sub-ctrl002_ses-002_task-testtask_run-002_events_date-' expParameters.date '.tsv']));
-          
+    expParameters.fileName.events, ...
+    ['sub-ctrl002_ses-002_task-testtask_run-002_events_date-' expParameters.date '.tsv']));
+
+% make sure the eyetracker filename is created
 assert(strcmp(...
-              expParameters.fileName.eyetracker, ...
-              ['sub-ctrl002_ses-002_task-testtask_run-002_eyetrack_date-' expParameters.date '.edf']));
+    expParameters.fileName.eyetracker, ...
+    ['sub-ctrl002_ses-002_task-testtask_run-002_eyetrack_date-' expParameters.date '.edf']));

tests/test_saveEventsFile.m

@@ -19,15 +19,13 @@ function test_saveEventsFile()
 expParameters = checkCFG(cfg,expParameters);
 expParameters = createFilename(cfg,expParameters);
 
-
-
 %% create the events and stim files
 
 logFile = saveEventsFile('open', expParameters, [], 'Speed', 'is_Fixation');
 
 stimFile = saveEventsFile('open_stim', expParameters, []);
 
-% ---- test section
+%%% test section
 
 fileName = fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.events);
 stimFileName = fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.stim);
@@ -60,23 +58,27 @@ function test_saveEventsFile()
 
 saveEventsFile('save', expParameters, logFile, 'speed', 'is_fixation');
 
-
 % close the file
 saveEventsFile('close', expParameters, logFile);
 
-
-% ---- test section
+%%% test section
 
 % check the extra columns of the header and some of the content
 
 FID = fopen(fileName, 'r');
 C = textscan(FID,'%s%s%s%s%s','Delimiter', '\t', 'EndOfLine', '\n');
 
-assert(isequal(C{4}{1}, 'speed')); % check header
+% check header
+assert(isequal(C{4}{1}, 'speed')); 
+
+% check that empty values are entered as NaN
+assert(isequal(C{4}{2}, 'NaN')); 
 
-assert(isequal(C{4}{2}, 'NaN')); % check that empty values are entered as NaN
-assert(isequal(C{4}{4}, 'NaN')); % check that missing fields are entered as NaN
+% check that missing fields are entered as NaN
+assert(isequal(C{4}{4}, 'NaN')); 
 
-assert(isequal(str2double(C{4}{3}), 2)); % check values entered properly
+% check values entered properly
+assert(isequal(str2double(C{4}{3}), 2)); 
 
-assert(isequal(str2double(C{5}{4}), 3)); % check values entered properly
+% check values entered properly
+assert(isequal(str2double(C{5}{4}), 3)); 

userInputs.m

@@ -1,54 +1,65 @@
-function [expParameters] = userInputs(cfg, expParameters)
+function [expParameters] = userInputs(cfg, expParameters, askGrpSess)
 % Get subject, run and session number and make sure they are
 % positive integer values
+%
+% skipGrpSess
+% a 1 X 2 array of booleans (default is [true true] ):
+%    - the first value set to false will skip asking for the participants
+%    group
+%    - the second value set to false will skip asking for the session
 
 if nargin<1
     cfg.debug = false;
 end
-
 if nargin<2
     expParameters = [];
 end
+if nargin<3
+    askGrpSess = [true true];
+end
 
 
+% When in debug more this function returns some dummy values
 if cfg.debug
-
     subjectGrp = 'ctrl';
     subjectNb = 666;
     runNb = 666;
     sessionNb = 666;
-
+    
+    % Otherwise it prompts the user for some information
 else
-
-    subjectGrp = lower(input('Enter subject group (leave empty if none): ', 's'));
-
+    
+    % subject group
+    if askGrpSess(1)
+        subjectGrp = lower(input('Enter subject group (leave empty if none): ', 's'));
+    end
+    
+    % the subject number
     subjectNb = str2double(input('Enter subject number (1-999): ', 's') );
     subjectNb = checkInput(subjectNb);
-
-    sessionNb = str2double(input('Enter the session (i.e day - 1-999)) number: ', 's'));
-    sessionNb = checkInput(sessionNb);
-
+    
+    % the session number
+    if askGrpSess(2)
+        sessionNb = str2double(input('Enter the session (i.e day - 1-999)) number: ', 's'));
+        sessionNb = checkInput(sessionNb);
+    end
+    
+    % the run number
     runNb = str2double(input('Enter the run number (1-999): ', 's'));
     runNb = checkInput(runNb);
-
+    
 end
 
-
 expParameters.subjectGrp = subjectGrp;
 expParameters.subjectNb = subjectNb;
 expParameters.sessionNb = sessionNb;
 expParameters.runNb = runNb;
 
-
 end
 
-
 function input2check = checkInput(input2check)
-
-
+% this function checks the input to makes sure the user enters a positive integer
 while isnan(input2check) || fix(input2check) ~= input2check || input2check<0
     input2check = str2double(input('Please enter a positive integer: ', 's'));
 end
-
-
 end