update randomization

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;

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

@@ -38,9 +38,8 @@
     %     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
@@ -80,7 +79,7 @@
     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

@@ -57,23 +57,16 @@
 
     % Set variables here for a dummy test of this function
     if nargin < 1 || isempty(cfg)
-        %         cfg.design.motionType = 'translation';
-        cfg.design.motionType = 'translation';
-        cfg.design.names = {'static'; 'motion'};
-        cfg.design.nbRepetitions = 16;
-        cfg.design.nbEventsPerBlock = 12;
-        cfg.target.maxNbPerBlock = 0;
-        displayFigs = 1;
+        error('give me something to work with');
     end
 
     fprintf('\n\nCreating design.\n\n')
 
-
     [NB_BLOCKS, NB_REPETITIONS, NB_EVENTS_PER_BLOCK, MAX_TARGET_PER_BLOCK] = getInput(cfg);
     [~, STATIC_INDEX, MOTION_INDEX] = assignConditions(cfg);
 
-    RANGE_TARGETS = [1 MAX_TARGET_PER_BLOCK];
-    targetPerCondition = repmat(RANGE_TARGETS, 1, NB_REPETITIONS / 2);
+    RANGE_TARGETS = 1:MAX_TARGET_PER_BLOCK;
+    targetPerCondition = repmat(RANGE_TARGETS, 1, NB_REPETITIONS / MAX_TARGET_PER_BLOCK);
 
     numTargetsForEachBlock = zeros(1, NB_BLOCKS);
     numTargetsForEachBlock(STATIC_INDEX) = shuffle(targetPerCondition);
@@ -92,33 +85,19 @@
             % - targets cannot be on the first or last event of a block
             % - no more than 2 target in the same event order
 
-            chosenTarget = [];
-
-            tmpTarget = numTargetsForEachBlock(iBlock);
-
-            switch tmpTarget
-
-                case 1
-
-                    chosenTarget = randsample(2:NB_EVENTS_PER_BLOCK - 1, tmpTarget, false);
+            nbTarget = numTargetsForEachBlock(iBlock);
 
-                case 2
+            chosenPosition = setTargetPositionInSequence( ...
+                NB_EVENTS_PER_BLOCK, ...
+                nbTarget, ...
+                [1 NB_EVENTS_PER_BLOCK]);
 
-                    targetDifference = 0;
-
-                    while any(targetDifference <= 2)
-                        chosenTarget = randsample(2:NB_EVENTS_PER_BLOCK - 1, tmpTarget, false);
-                        targetDifference = diff(chosenTarget);
-                    end
-
-            end
-
-            fixationTargets(iBlock, chosenTarget) = 1;
+            fixationTargets(iBlock, chosenPosition) = 1;
 
         end
 
         % Check rule 3
-        if max(sum(fixationTargets)) < 3
+        if max(sum(fixationTargets)) < NB_REPETITIONS - 1
             break
         end
 
@@ -154,26 +133,17 @@
     directions = zeros(NB_BLOCKS, NB_EVENTS_PER_BLOCK);
 
     % Create a vector for the static condition
+    NB_REPEATS_BASE_VECTOR = NB_EVENTS_PER_BLOCK / length(STATIC_DIRECTIONS);
+
     static_directions = repmat( ...
         STATIC_DIRECTIONS, ...
-        1, NB_EVENTS_PER_BLOCK / length(STATIC_DIRECTIONS));
+        1, NB_REPEATS_BASE_VECTOR);
 
     for iMotionBlock = 1:NB_REPETITIONS
 
-        % Check that we never have twice the same direction
-        while 1
-            tmp = [ ...
-                shuffle(MOTION_DIRECTIONS), ...
-                shuffle(MOTION_DIRECTIONS), ...
-                shuffle(MOTION_DIRECTIONS)];
-
-            if ~any(diff(tmp, [], 2) == 0)
-                break
-            end
-        end
-
         % Set motion direction and static order
-        directions(MOTION_INDEX(iMotionBlock), :) = tmp;
+        directions(MOTION_INDEX(iMotionBlock), :) = ...
+            repeatShuffleConditions(MOTION_DIRECTIONS, NB_REPEATS_BASE_VECTOR);
         directions(STATIC_INDEX(iMotionBlock), :) = static_directions;
 
     end
@@ -187,15 +157,8 @@
     % CONSTANTS
     % Set directions for static and motion condition
 
-    STATIC_DIRECTIONS = [-1 -1 -1 -1];
-
-    switch cfg.design.motionType
-        case 'translation'
-            MOTION_DIRECTIONS = [0 0 180 180];
-        case 'radial'
-            STATIC_DIRECTIONS = [666 -666 666 -666];
-            MOTION_DIRECTIONS = [666 -666 666 -666];
-    end
+    MOTION_DIRECTIONS = cfg.design.motionDirections;
+    STATIC_DIRECTIONS = repmat(-1, size(MOTION_DIRECTIONS));
 
 end
 
@@ -206,25 +169,16 @@
     nbBlocks = length(cfg.design.names) * nbRepet;
 end
 
-function [condition, STATIC_INDEX, MOTION_INDEX] = assignConditions(cfg)
+function [conditionNamesVector, STATIC_INDEX, MOTION_INDEX] = assignConditions(cfg)
 
     [~, nbRepet] = getInput(cfg);
 
-    condition = repmat(cfg.design.names, nbRepet, 1);
+    conditionNamesVector = repmat(cfg.design.names, nbRepet, 1);
 
     % Get the index of each condition
-    STATIC_INDEX = find(strcmp(condition, 'static'));
-    MOTION_INDEX = find(strcmp(condition, 'motion'));
-
-end
+    STATIC_INDEX = find(strcmp(conditionNamesVector, 'static'));
+    MOTION_INDEX = find(strcmp(conditionNamesVector, 'motion'));
 
-function shuffled = shuffle(unshuffled)
-    % in case PTB is not in the path
-    try
-        shuffled = Shuffle(unshuffled);
-    catch
-        shuffled = unshuffled(randperm(length(unshuffled)));
-    end
 end
 
 function diplayDesign(cfg, displayFigs)

setParameters.m

@@ -0,0 +1,10 @@
+# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
+line_length: 100
+regex_function_name: "((test_[a-z]+)|[a-z]+)(([A-Z]){1}[A-Za-z]+)*"
+suppress_rule: "copyright_notice"
+
+# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
+metric "cnest": limit 4
+metric "file_length": limit 500
+metric "cyc": limit 15
+metric "parameters": limit 5