Merge pull request #20 from Remi-Gau/remi-randomize_trigger_paced

apply randomization, pacing by trigger from visual localizer and do some refactoring

Author: Remi-Gau

.github/workflows/moxunit.yml

@@ -0,0 +1,32 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+    - name: MOxUnit Action
+      uses: joergbrech/[email protected]
+      with:
+        tests: tests
+        src: subfun
+        with_coverage: true
+        cover_xml_file: coverage.xml
+    - name: Code coverage
+      uses: codecov/codecov-action@v1
+      with:
+       token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
+       file:  coverage.xml # optional
+       flags: unittests # optional
+       name: codecov-umbrella # optional
+       fail_ci_if_error: true # optional (default = false)

audioLocTranslational.m

@@ -40,14 +40,8 @@
     [cfg] = initPTB(cfg);
 
     [el] = eyeTracker('Calibration', cfg);
-
-    % % % REFACTOR THIS FUNCTION % % %
-
-    [cfg] = expDesign(cfg);
 
-    cfg.design.blockNames
-
-    % % % REFACTOR THIS FUNCTION % % %
+    [cfg] = expDesign(cfg);
 
     % Prepare for the output logfiles with all
     logFile.extraColumns = cfg.extraColumns;
@@ -69,7 +63,7 @@
 
     getResponse('start', cfg.keyboard.responseBox);
 
-    WaitSecs(cfg.timing.onsetDelay);
+    waitFor(cfg, cfg.timing.onsetDelay);
 
     %% For Each Block
 
@@ -90,13 +84,19 @@
             thisEvent.direction = cfg.design.directions(iBlock, iEvent);
             % thisEvent.speed = cfg.design.speeds(iBlock, iEvent);
             thisEvent.target = cfg.design.fixationTargets(iBlock, iEvent);
+            
+            % we wait for a trigger every 2 events
+            if cfg.pacedByTriggers.do && mod(iEvent, 2) == 1
+                waitForTrigger( ...
+                    cfg, ...
+                    cfg.keyboard.responseBox, ...
+                    cfg.pacedByTriggers.quietMode, ...
+                    cfg.pacedByTriggers.nbTriggers);
+            end
 
             % % % REFACTOR THIS FUNCTION % % %
-
             % play the sounds and collect onset and duration of the event
-            [onset, duration] = doAudMot(cfg, thisEvent);
-
-            % % % REFACTOR THIS FUNCTION % % %
+            [onset, duration] = doAuditoryMotion(cfg, thisEvent);
 
             thisEvent.event = iEvent;
             thisEvent.block = iBlock;
@@ -122,13 +122,13 @@
             saveResponsesAndTriggers(responseEvents, cfg, logFile, triggerString);
 
             % wait for the inter-stimulus interval
-            WaitSecs(cfg.timing.ISI);
+            waitFor(cfg, cfg.timing.ISI);
 
         end
 
         eyeTracker('StopRecordings', cfg);
 
-        WaitSecs(cfg.timing.IBI);
+        waitFor(cfg, cfg.timing.IBI);
 
         % trigger monitoring
         triggerEvents = getResponse('check', cfg.keyboard.responseBox, cfg, ...
@@ -140,7 +140,7 @@
     end
 
     % End of the run for the BOLD to go down
-    WaitSecs(cfg.timing.endDelay);
+    waitFor(cfg, cfg.timing.endDelay);
 
     cfg = getExperimentEnd(cfg);
 

initEnv.m

@@ -8,7 +8,7 @@
 %       - struct
 %       - statistics
 %
-%   MATLAB > R2017a
+%   MATLAB >= R2015b
 %
 % 2 - Add project to the O/M path
 
@@ -17,34 +17,28 @@
     octaveVersion = '4.0.3';
     matlabVersion = '8.6.0';
 
+    installlist = {'io', 'statistics', 'image'};
+
     if isOctave
 
         % Exit if min version is not satisfied
         if ~compare_versions(OCTAVE_VERSION, octaveVersion, '>=')
             error('Minimum required Octave version: %s', octaveVersion);
         end
 
-        installlist = {'statistics', 'image'};
         for ii = 1:length(installlist)
+
+            packageName = installlist{ii};
+
             try
                 % Try loading Octave packages
-                disp(['loading ' installlist{ii}]);
-                pkg('load', installlist{ii});
+                disp(['loading ' packageName]);
+                pkg('load', packageName);
 
             catch
-                errorcount = 1;
-                while errorcount % Attempt twice in case installation fails
-                    try
-                        pkg('install', '-forge', installlist{ii});
-                        pkg('load', installlist{ii});
-                        errorcount = 0;
-                    catch err
-                        errorcount = errorcount + 1;
-                        if errorcount > 2
-                            error(err.message);
-                        end
-                    end
-                end
+
+                tryInstallFromForge(packageName);
+
             end
         end
 
@@ -58,7 +52,9 @@
 
     % If external dir is empty throw an exception
     % and ask user to update submodules.
-    if numel(dir('lib')) <= 2 % Means that the external is empty
+    libDirectory = fullfile(fileparts(mfilename('fullpath')), 'lib');
+
+    if numel(dir(libDirectory)) <= 2 % Means that the external is empty
         error(['Git submodules are not cloned!', ...
               'Try this in your terminal:', ...
               ' git submodule update --recursive ']);
@@ -70,25 +66,41 @@
 
 end
 
-%%
-%% Return: true if the environment is Octave.
-%%
 function retval = isOctave
+    % Return: true if the environment is Octave.
     persistent cacheval   % speeds up repeated calls
 
     if isempty (cacheval)
         cacheval = (exist ('OCTAVE_VERSION', 'builtin') > 0);
     end
 
     retval = cacheval;
+
+end
+
+function tryInstallFromForge(packageName)
+
+    errorcount = 1;
+    while errorcount % Attempt twice in case installation fails
+        try
+            pkg('install', '-forge', packageName);
+            pkg('load', packageName);
+            errorcount = 0;
+        catch err
+            errorcount = errorcount + 1;
+            if errorcount > 2
+                error(err.message);
+            end
+        end
+    end
+
 end
 
 function addDependencies()
 
     pth = fileparts(mfilename('fullpath'));
     addpath(genpath(fullfile(pth, 'lib', 'CPP_BIDS', 'src')));
-    addpath(fullfile(pth, 'lib', 'CPP_PTB'));
+    addpath(genpath(fullfile(pth, 'lib', 'CPP_PTB', 'src')));
     addpath(fullfile(pth, 'subfun'));
-    addpath(fullfile(pth, 'input'));
 
 end

lib/CPP_BIDS

@@ -31,16 +31,17 @@
 
     % MRI settings
     cfg = setMRI(cfg);
+    
+    cfg.pacedByTriggers.do = true;
 
     %% Experiment Design
 
     %     cfg.design.motionType = 'translation';
     %     cfg.design.motionType = 'radial';
     cfg.design.motionType = 'translation';
     cfg.design.names = {'static'; 'motion'};
-    cfg.design.possibleDirections = [-1 1]; % 1 motion , -1 static %NOT IN USE AT THE MOMENT
-%     cfg.design.nbBlocks = size(cfg.design.names, 2); % TO CHECK
-    cfg.design.nbRepetitions = 14;  % AT THE MOMENT IT IS NOT SET IN THE MAIN SCRIPT
+    cfg.design.motionDirections = [-1 -1 1 1];
+    cfg.design.nbRepetitions = 14; 
     cfg.design.nbEventsPerBlock = 12;
 
     %% Timing
@@ -51,15 +52,35 @@
     % IBI
     % block length = (cfg.eventDuration + cfg.ISI) * cfg.design.nbEventsPerBlock
 
+    cfg.timing.eventDuration = 0.850; % second
+
     % Time between blocs in secs
-    cfg.timing.IBI = 1.8; % 8;
+    cfg.timing.IBI = 1.8;
     % Time between events in secs
     cfg.timing.ISI = 0;
     % Number of seconds before the motion stimuli are presented
-    cfg.timing.onsetDelay = .1;
+    cfg.timing.onsetDelay = 0;
     % Number of seconds after the end all the stimuli before ending the run
     cfg.timing.endDelay = 3.6;
 
+    % reexpress those in terms of repetition time
+    if cfg.pacedByTriggers.do
+
+        cfg.pacedByTriggers.quietMode = true;
+        cfg.pacedByTriggers.nbTriggers = 1;
+
+        cfg.timing.eventDuration = cfg.mri.repetitionTime / 2 - 0.04; % second
+
+        % Time between blocs in secs
+        cfg.timing.IBI = 1;
+        % Time between events in secs
+        cfg.timing.ISI = 0;
+        % Number of seconds before the motion stimuli are presented
+        cfg.timing.onsetDelay = 0;
+        % Number of seconds after the end all the stimuli before ending the run
+        cfg.timing.endDelay = 2;
+    end
+
     %% Auditory Stimulation
 
     cfg.audio.channels = 2;
@@ -80,7 +101,7 @@
     cfg.fixation.xDisplacement = 0;
     cfg.fixation.yDisplacement = 0;
 
-    cfg.target.maxNbPerBlock = 0;
+    cfg.target.maxNbPerBlock = 2;
     cfg.target.duration = 0.5; % In secs
 
     cfg.extraColumns = {'direction', 'speed', 'target', 'event', 'block', 'keyName'};

lib/CPP_PTB

@@ -1,4 +1,4 @@
-function [onset, duration] = doAudMot(cfg, thisEvent)
+function [onset, duration] = doAuditoryMotion(cfg, thisEvent)
 
     % Play the auditopry stimulation of moving in 4 directions or static noise bursts
     %
@@ -11,48 +11,36 @@
     %   - thisEvent: structure that the parameters regarding the event to present
     %
     % Output:
-    %     -
+    %     - onset in machine time
+    %     - duration in seconds
     %
 
     %% Get parameters
 
-    sound = [];
-    
     direction = thisEvent.direction(1);
     isTarget = thisEvent.target(1);
     targetDuration = cfg.target.duration;
 
     soundData = cfg.soundData;
 
-    % if isTarget == 0
+    switch direction
+        case -1
+            fieldName = 'S';
+        case 90
+            fieldName = 'U';
+        case 270
+            fieldName = 'D';
+        case 0
+            fieldName = 'R';
+        case 180
+            fieldName = 'L';
+    end
 
-    if direction == -1
-        sound = soundData.S;
-    elseif direction == 90
-        sound = soundData.U;
-    elseif direction == 270
-        sound = soundData.D;
-    elseif direction == 0
-        sound = soundData.R;
-    elseif direction == 180
-        sound = soundData.L;
+    if isTarget == 1
+        fieldName = [fieldName '_T'];
     end
 
-    % elseif isTarget == 1
-    %
-    %   if direction == -1
-    %     sound = soundData.S_T;
-    %   elseif direction == 90
-    %     sound = soundData.U_T;
-    %   elseif direction == 270
-    %     sound = soundData.D_T;
-    %   elseif direction == 0
-    %     sound = soundData.R_T;
-    %   elseif direction == 180
-    %     sound = soundData.L_T;
-    %   end
-    %
-    % end
+    sound = soundData.(fieldName);
 
     % Start the sound presentation
     PsychPortAudio('FillBuffer', cfg.audio.pahandle, sound);