Merge pull request #38 from Remi-Gau/remi-fix_randomize

fix randomize

Author: Remi-Gau

.github/workflows/moxunit.yml

@@ -19,7 +19,7 @@ jobs:
       uses: joergbrech/[email protected]
       with:
         tests: tests
-        src: src
+        src: subfun
         with_coverage: true
         cover_xml_file: coverage.xml
     - name: Code coverage

README.md

@@ -1,8 +1,34 @@
+[![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/localizer_visual_motion/actions)
+![](https://github.com/cpp-lln-lab/localizer_visual_motion/workflows/CI/badge.svg) 
+
+[![Build Status](https://travis-ci.com/cpp-lln-lab/localizer_visual_motion.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/localizer_visual_motion)
+
+<!-- vscode-markdown-toc -->
+* 1. [Requirements](#Requirements)
+* 2. [Installation](#Installation)
+* 3. [Structure and function details](#Structureandfunctiondetails)
+	* 3.1. [visualLocTranslational](#visualLocTranslational)
+	* 3.2. [setParameters](#setParameters)
+	* 3.3. [subfun/doDotMo](#subfundoDotMo)
+		* 3.3.1. [Input:](#Input:)
+		* 3.3.2. [Output:](#Output:)
+	* 3.4. [subfun/expDesign](#subfunexpDesign)
+		* 3.4.1. [EVENTS](#EVENTS)
+		* 3.4.2. [TARGETS:](#TARGETS:)
+		* 3.4.3. [Input:](#Input:-1)
+		* 3.4.4. [Output:](#Output:-1)
+
+<!-- vscode-markdown-toc-config
+	numbering=true
+	autoSave=true
+	/vscode-markdown-toc-config -->
+<!-- /vscode-markdown-toc -->
+
 # fMRI localizers for visual motion
 
 # Translational Motion
 
-## Requirements
+##  1. <a name='Requirements'></a>Requirements
 
 Make sure that the following toolboxes are installed and added to the matlab / octave path.
 
@@ -16,7 +42,7 @@ For instructions see the following links:
 | [Matlab](https://www.mathworks.com/products/matlab.html) | >=2017       |
 | or [octave](https://www.gnu.org/software/octave/)        | >=4.?        |
 
-## Installation
+##  2. <a name='Installation'></a>Installation
 
 The CPP_BIDS and CPP_PTB dependencies are already set up as submodule to this repository.
 You can install it all with git by doing. 
@@ -25,17 +51,17 @@ You can install it all with git by doing.
 git clone --recurse-submodules https://github.com/cpp-lln-lab/localizer_visual_motion.git
 ```
 
-## Structure and function details
+##  3. <a name='Structureandfunctiondetails'></a>Structure and function details
 
-### visualLocTranslational
+###  3.1. <a name='visualLocTranslational'></a>visualLocTranslational
 
 Running this script will show blocks of motion dots (soon also moving gratings) and static dots. Motion blocks will show dots(/gratings) moving in one of four directions (up-, down-, left-, and right-ward)
 
 By default it is run in `Debug mode` meaning that it does not run care about subjID, run n., fMRI triggers, Eye Tracker, etc..
 
 Any details of the experiment can be changed in `setParameters.m` (e.g., experiment mode, motion stimuli details, exp. design, etc.)
 
-### setParameters
+###  3.2. <a name='setParameters'></a>setParameters
 
 `setParameters.m` is the core engine of the experiment. It contains the following tweakable sections:
 
@@ -51,34 +77,34 @@ Any details of the experiment can be changed in `setParameters.m` (e.g., experim
   - Instructions
   - Task #1 parameters
 
-### subfun/doDotMo
+###  3.3. <a name='subfundoDotMo'></a>subfun/doDotMo
 
-#### Input:
+####  3.3.1. <a name='Input:'></a>Input:
 - `cfg`: PTB/machine configurations returned by `setParameters` and `initPTB`
 - `expParameters`: parameters returned by `setParameters`
 - `logFile`: structure that stores the experiment logfile to be saved
 
-#### Output:
+####  3.3.2. <a name='Output:'></a>Output:
 - Event `onset`
 - Event `duration`
 
 The dots are drawn on a square that contains the round aperture, then any dots outside of the aperture is turned into a NaN so effectively the actual number of dots on the screen at any given time is not the one that you input but a smaller number (nDots / Area of aperture) on average.
 
-### subfun/expDesign
+###  3.4. <a name='subfunexpDesign'></a>subfun/expDesign
 Creates the sequence of blocks and the events in them. The conditions are consecutive static and motion blocks (Gives better results than randomised). It can be run as a stand alone without inputs to display a visual example of possible design.
 
-#### EVENTS
+####  3.4.1. <a name='EVENTS'></a>EVENTS
 The `numEventsPerBlock` should be a multiple of the number of "base" listed in the `motionDirections` and `staticDirections` (4 at the moment).
 
-#### TARGETS:
+####  3.4.2. <a name='TARGETS:'></a>TARGETS:
 - If there are 2 targets per block we make sure that they are at least 2 events apart.
 - Targets cannot be on the first or last event of a block
 
-#### Input:
+####  3.4.3. <a name='Input:-1'></a>Input:
 - `expParameters`: parameters returned by `setParameters`
 - `displayFigs`: a boolean to decide whether to show the basic design matrix of the design
 
-#### Output:
+####  3.4.4. <a name='Output:-1'></a>Output:
 - `expParameters.designBlockNames` is a cell array `(nr_blocks, 1)` with the name for each block
 - `expParameters.designDirections` is an array `(nr_blocks, numEventsPerBlock)` with the direction to present in a given block
   - `0 90 180 270` indicate the angle

initEnv.m

@@ -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
 
@@ -72,17 +66,34 @@
 
 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()

lib/CPP_BIDS

@@ -1,5 +1,11 @@
+# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
 regex_function_name: "[a-z]+(([A-Z]){1}[A-Za-z]+)*"
 suppress_rule: "copyright_notice"
 exclude_dir: "lib"
-exclude_dir: "Visual-loc_radial"
+
+# 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

lib/CPP_PTB

@@ -39,6 +39,7 @@
     %     cfg.design.motionType = 'translation';
     %     cfg.design.motionType = 'radial';
     cfg.design.motionType = 'translation';
+    cfg.design.motionDirections = [0 0 180 180];
     cfg.design.names = {'static'; 'motion'};
     cfg.design.nbRepetitions = 10;
     cfg.design.nbEventsPerBlock = 12; % DO NOT CHANGE

miss_hit.cfg

@@ -22,10 +22,10 @@
     % TARGETS
     %
     % Pseudorandomization rules:
-    % (1) If there are 2 targets per block we make sure that they are at least 2
+    % (1) If there are more than 1 target per block we make sure that they are at least 2
     % events apart.
     % (2) Targets cannot be on the first or last event of a block.
-    % (3) Targets can not be present more than 2 times in the same event
+    % (3) Targets can not be present more than NB_REPETITIONS - 1 times in the same event
     % position across blocks.
     %
     % Input:
@@ -57,16 +57,20 @@
 
     % Set variables here for a dummy test of this function
     if nargin < 1 || isempty(cfg)
-        error('give me something to work with')
+        error('give me something to work with');
     end
-    
-    fprintf('\n\nCreating design.\n\n')
+
+    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);
+    if mod(NB_REPETITIONS, MAX_TARGET_PER_BLOCK) ~= 0
+        error('number of repetitions must be a multiple of max number of targets');
+    end
+
+    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);
@@ -85,33 +89,19 @@
             % - 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);
-
-                case 2
-
-                    targetDifference = 0;
-
-                    while abs(targetDifference) <= 2
-                        chosenTarget = randsample(2:NB_EVENTS_PER_BLOCK - 1, tmpTarget, false);
-                        targetDifference = diff(chosenTarget);
-                    end
+            nbTarget = numTargetsForEachBlock(iBlock);
 
-            end
+            chosenPosition = setTargetPositionInSequence( ...
+                NB_EVENTS_PER_BLOCK, ...
+                nbTarget, ...
+                [1 NB_EVENTS_PER_BLOCK]);
 
-            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
 
@@ -150,26 +140,17 @@
     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
@@ -183,15 +164,8 @@
     % 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
 
@@ -202,25 +176,16 @@
     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)