From 2b20116a872c7682ecf00b941c2155c1567a9221 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 23 Sep 2020 10:52:19 +0200
Subject: [PATCH 01/15] add function for pix to degree conversion

---
 src/utils/degToPix.m  | 13 +++++++++++++
 src/utils/pixToDeg.m  | 29 +++++++++++++++++++++++++++++
 tests/test_pixToDeg.m | 21 +++++++++++++++++++++
 3 files changed, 63 insertions(+)
 create mode 100644 src/utils/pixToDeg.m
 create mode 100644 tests/test_pixToDeg.m

diff --git a/src/utils/degToPix.m b/src/utils/degToPix.m
index 9780d02..5a38b38 100644
--- a/src/utils/degToPix.m
+++ b/src/utils/degToPix.m
@@ -4,6 +4,19 @@
     % For a given field value in degrees of visual angle in the structure,
     % this computes its value in pixel using the pixel per degree value of the cfg structure
     % and returns a structure with an additional field with Pix suffix holding that new value.
+    %
+    %
+    % USAGE:
+    % ------
+    % fixation.width = 2;
+    % cfg.screen.ppd = 10;
+    % 
+    % fixation = degToPix('width', fixation, cfg);
+    %
+    % Returns:
+    % ------- 
+    % fixation.widthPix = 20;
+    %
 
     deg = getfield(structure, fieldName); %#ok<GFLD>
 
diff --git a/src/utils/pixToDeg.m b/src/utils/pixToDeg.m
new file mode 100644
index 0000000..0d6b9e1
--- /dev/null
+++ b/src/utils/pixToDeg.m
@@ -0,0 +1,29 @@
+% 2020 CPP BIDS SPM-pipeline developpers 
+
+function structure = pixToDeg(fieldName, structure, cfg)
+    % structure = pixToDeg(fieldName, structure, cfg)
+    %
+    % For a given field value in pixel in the structure,
+    % this computes its value in degrees of viual angle using the pixel per 
+    % degree value of the cfg structure and returns a structure with an 
+    % additional field holding that new value and with a fieldname with any 
+    % 'Pix' suffix removed and replaced with the 'DegVA' suffix .
+    %
+    % USAGE:
+    % ------
+    % fixation.widthPix = 20;
+    % cfg.screen.ppd = 10;
+    % 
+    % fixation = degToPix('widthPix', fixation, cfg);
+    %
+    % Returns:
+    % ------- 
+    % fixation.widthDegVA = 2;
+    %
+
+    pix = getfield(structure, fieldName); %#ok<GFLD>
+
+    structure = setfield(structure, [strrep(fieldName, 'Pix', '') 'DegVA'], ...
+        floor(pix / cfg.screen.ppd)); %#ok<SFLD>
+
+end
\ No newline at end of file
diff --git a/tests/test_pixToDeg.m b/tests/test_pixToDeg.m
new file mode 100644
index 0000000..847b233
--- /dev/null
+++ b/tests/test_pixToDeg.m
@@ -0,0 +1,21 @@
+function test_suite = test_pixToDeg %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
+
+function test_pixToDegBasic()
+
+    fixation.widthPix = 20;
+    cfg.screen.ppd = 10;
+
+    fixation = pixToDeg('widthPix', fixation, cfg);
+
+    expectedStruct.widthDegVA = 2;
+    expectedStruct.widthPix = 20;
+
+    assertEqual(expectedStruct, fixation);
+
+end

From 17107b77df857fbb756b70f97db41ad5a86b71c9 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 23 Sep 2020 11:17:13 +0200
Subject: [PATCH 02/15] mh fix

---
 src/utils/degToPix.m |  4 ++--
 src/utils/pixToDeg.m | 14 +++++++-------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/utils/degToPix.m b/src/utils/degToPix.m
index 5a38b38..bb5fac5 100644
--- a/src/utils/degToPix.m
+++ b/src/utils/degToPix.m
@@ -10,11 +10,11 @@
     % ------
     % fixation.width = 2;
     % cfg.screen.ppd = 10;
-    % 
+    %
     % fixation = degToPix('width', fixation, cfg);
     %
     % Returns:
-    % ------- 
+    % -------
     % fixation.widthPix = 20;
     %
 
diff --git a/src/utils/pixToDeg.m b/src/utils/pixToDeg.m
index 0d6b9e1..5efcba5 100644
--- a/src/utils/pixToDeg.m
+++ b/src/utils/pixToDeg.m
@@ -1,23 +1,23 @@
-% 2020 CPP BIDS SPM-pipeline developpers 
+% 2020 CPP BIDS SPM-pipeline developpers
 
 function structure = pixToDeg(fieldName, structure, cfg)
     % structure = pixToDeg(fieldName, structure, cfg)
     %
     % For a given field value in pixel in the structure,
-    % this computes its value in degrees of viual angle using the pixel per 
-    % degree value of the cfg structure and returns a structure with an 
-    % additional field holding that new value and with a fieldname with any 
+    % this computes its value in degrees of viual angle using the pixel per
+    % degree value of the cfg structure and returns a structure with an
+    % additional field holding that new value and with a fieldname with any
     % 'Pix' suffix removed and replaced with the 'DegVA' suffix .
     %
     % USAGE:
     % ------
     % fixation.widthPix = 20;
     % cfg.screen.ppd = 10;
-    % 
+    %
     % fixation = degToPix('widthPix', fixation, cfg);
     %
     % Returns:
-    % ------- 
+    % -------
     % fixation.widthDegVA = 2;
     %
 
@@ -26,4 +26,4 @@
     structure = setfield(structure, [strrep(fieldName, 'Pix', '') 'DegVA'], ...
         floor(pix / cfg.screen.ppd)); %#ok<SFLD>
 
-end
\ No newline at end of file
+end

From ba72db41bb8c6731af7dadd29ac992202536982f Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 25 Sep 2020 17:05:59 +0200
Subject: [PATCH 03/15] refactor dot functions

refactor reseedDots function


refactor dot functions
---
 src/dot/computeCartCoord.m             |  7 ++--
 src/dot/computeRadialMotionDirection.m |  4 +-
 src/dot/dotTexture.m                   |  3 +-
 src/dot/generateNewDotPositions.m      |  4 +-
 src/dot/initDots.m                     | 41 +++++---------------
 src/dot/reseedDots.m                   | 19 +++++----
 src/dot/seedDots.m                     | 23 +++++++++++
 src/dot/setDotDirection.m              | 53 ++++++++++++++------------
 tests/test_generateNewDotPositions.m   |  4 +-
 tests/test_initDots.m                  |  6 +--
 tests/test_reseedDots.m                | 40 +++++++++----------
 tests/test_seedDots.m                  | 38 ++++++++++++++++++
 tests/test_setDotDirection.m           | 50 +++++++++++++++++++-----
 13 files changed, 183 insertions(+), 109 deletions(-)
 create mode 100644 src/dot/seedDots.m
 create mode 100644 tests/test_seedDots.m

diff --git a/src/dot/computeCartCoord.m b/src/dot/computeCartCoord.m
index 063944d..7224254 100644
--- a/src/dot/computeCartCoord.m
+++ b/src/dot/computeCartCoord.m
@@ -1,7 +1,8 @@
-function cartesianCoordinates = computeCartCoord(positions, cfg)
+function cartesianCoordinates = computeCartCoord(positions, dotMatrixWidth)
+    
     cartesianCoordinates = ...
-        [positions(:, 1) - cfg.dot.matrixWidth / 2, ... % x coordinate
-         positions(:, 2) - cfg.dot.matrixWidth / 2]; % y coordinate
+        [positions(:, 1) - dotMatrixWidth / 2, ... % x coordinate
+         positions(:, 2) - dotMatrixWidth / 2]; % y coordinate
 
     %         cartesianCoordinates = positions;
 end
diff --git a/src/dot/computeRadialMotionDirection.m b/src/dot/computeRadialMotionDirection.m
index ef47ed8..0c5f7bf 100644
--- a/src/dot/computeRadialMotionDirection.m
+++ b/src/dot/computeRadialMotionDirection.m
@@ -1,6 +1,6 @@
-function angleMotion = computeRadialMotionDirection(cfg, dots)
+function angleMotion = computeRadialMotionDirection(positions, dotMatrixWidth, dots)
 
-    cartesianCoordinates = computeCartCoord(dots.positions, cfg);
+    cartesianCoordinates = computeCartCoord(positions, dotMatrixWidth);
 
     [angleMotion, ~] = cart2pol(cartesianCoordinates(:, 1), cartesianCoordinates(:, 2));
     angleMotion = angleMotion / pi * 180;
diff --git a/src/dot/dotTexture.m b/src/dot/dotTexture.m
index c775a03..b4036bf 100644
--- a/src/dot/dotTexture.m
+++ b/src/dot/dotTexture.m
@@ -4,7 +4,8 @@
 
         case 'init'
             cfg.dot.texture = Screen('MakeTexture', cfg.screen.win, ...
-                                     cfg.color.background(1) * ones(cfg.screen.winRect([4 3])));
+                                     cfg.color.background(1) * ...
+                                     ones(cfg.screen.winRect([4 3])));
 
         case 'make'
 
diff --git a/src/dot/generateNewDotPositions.m b/src/dot/generateNewDotPositions.m
index 92bf28f..d59bb04 100644
--- a/src/dot/generateNewDotPositions.m
+++ b/src/dot/generateNewDotPositions.m
@@ -1,5 +1,5 @@
-function newPositions = generateNewDotPositions(cfg, dotNumber)
+function newPositions = generateNewDotPositions(dotMatrixWidth, nbDots)
 
-    newPositions = rand(dotNumber, 2) * cfg.dot.matrixWidth;
+    newPositions = rand(nbDots, 2) * dotMatrixWidth;
 
 end
diff --git a/src/dot/initDots.m b/src/dot/initDots.m
index 2c247cd..5ade937 100644
--- a/src/dot/initDots.m
+++ b/src/dot/initDots.m
@@ -24,47 +24,26 @@
 
     dots.direction = thisEvent.direction(1);
 
-    speedPixPerFrame = thisEvent.speed(1);
-
-    lifeTime = cfg.dot.lifeTime;
-
     % decide which dots are signal dots (1) and those are noise dots (0)
     dots.isSignal = rand(cfg.dot.number, 1) < cfg.dot.coherence;
+    
+    dots.speedPixPerFrame = thisEvent.speed(1);
+    lifeTime = cfg.dot.lifeTime;
 
     % for static dots
     if dots.direction == -1
-        speedPixPerFrame = 0;
-        lifeTime = Inf;
         dots.isSignal = true(cfg.dot.number, 1);
+        dots.speedPixPerFrame = 0;
+        lifeTime = Inf;
     end
 
-    %% Set an array of dot positions [xposition, yposition]
-    % These can never be bigger than 1 or lower than 0
-    % [0,0] is the top / left of the square
-    % [1,1] is the bottom / right of the square
-    dots.positions = generateNewDotPositions(cfg, cfg.dot.number);
-
-    %% Set vertical and horizontal speed for all dots
-    dots = setDotDirection(cfg, dots);
-
-    [horVector, vertVector] = decomposeMotion(dots.directionAllDots);
-    speeds = [horVector, vertVector];
-
-    % we were working with unit vectors. we now switch to pixels
-    speeds = speeds * speedPixPerFrame;
-
-    %% Create a vector to update to dotlife time of each dot
-    % Not all set to 1 so the dots will die at different times
-    % The maximum value is the duraion of the event in frames
-    time = floor(rand(cfg.dot.number, 1) * cfg.timing.eventDuration / cfg.screen.ifi);
+    % set position and directions fo the dots
+    [dots.positions, dots.speeds, dots.time] = ...
+        seedDots(dots, cfg, dots.isSignal);
 
     %% Convert from seconds to frames
     lifeTime = ceil(lifeTime / cfg.screen.ifi);
-
-    %%
     dots.lifeTime = lifeTime;
-    dots.time = time;
-    dots.speeds = speeds;
-    dots.speedPixPerFrame = speedPixPerFrame;
-
+    
+ 
 end
diff --git a/src/dot/reseedDots.m b/src/dot/reseedDots.m
index 7c2c750..1e9ec05 100644
--- a/src/dot/reseedDots.m
+++ b/src/dot/reseedDots.m
@@ -5,7 +5,7 @@
         fixationWidthPix = cfg.fixation.widthPix;
     end
 
-    cartesianCoordinates = computeCartCoord(dots.positions, cfg);
+    cartesianCoordinates = computeCartCoord(dots.positions, cfg.dot.matrixWidth);
     [~, radius] = cart2pol(cartesianCoordinates(:, 1), cartesianCoordinates(:, 2));
 
     % Create a logical vector to detect any dot that has:
@@ -26,15 +26,14 @@
     % If there is any such dot we relocate it to a new random position
     % and change its lifetime to 1
     if any(N)
-
-        dots.positions(N, :) = generateNewDotPositions(cfg, sum(N));
-
-        dots = setDotDirection(cfg, dots);
-
-        [horVector, vertVector] = decomposeMotion(dots.directionAllDots);
-        dots.speeds = [horVector, vertVector] * dots.speedPixPerFrame;
-
-        dots.time(N, 1) = 1;
+        
+        isSignal = dots.isSignal(N);
+        
+        [positions, speeds, time] = seedDots(dots, cfg, isSignal);
+
+        dots.positions(N, :) = positions;
+        dots.speeds(N, :) = speeds;
+        dots.time(N, 1) = time;
 
     end
 
diff --git a/src/dot/seedDots.m b/src/dot/seedDots.m
new file mode 100644
index 0000000..b835ec8
--- /dev/null
+++ b/src/dot/seedDots.m
@@ -0,0 +1,23 @@
+function [positions, speeds, time] = seedDots(dots, cfg, isSignal)
+    
+    nbDots = numel(isSignal);
+    
+    %% Set an array of dot positions [xposition, yposition]
+    % These can never be bigger than 1 or lower than 0
+    % [0,0] is the top / left of the square
+    % [1,1] is the bottom / right of the square
+    positions = generateNewDotPositions(cfg.dot.matrixWidth, nbDots);
+
+    %% Set vertical and horizontal speed for all dots
+    directionAllDots = setDotDirection(positions, cfg, dots, isSignal);
+    [horVector, vertVector] = decomposeMotion(directionAllDots);
+    
+    % we were working with unit vectors. we now switch to pixels
+    speeds = [horVector, vertVector] * dots.speedPixPerFrame;
+
+    %% Create a vector to update to dotlife time of each dot
+    % Not all set to 1 so the dots will die at different times
+    % The maximum value is the duraion of the event in frames
+    time = floor(rand(nbDots, 1) * cfg.timing.eventDuration / cfg.screen.ifi);
+    
+end
\ No newline at end of file
diff --git a/src/dot/setDotDirection.m b/src/dot/setDotDirection.m
index 0df6fe0..a9f08df 100644
--- a/src/dot/setDotDirection.m
+++ b/src/dot/setDotDirection.m
@@ -1,4 +1,4 @@
-function dots = setDotDirection(cfg, dots)
+function directionAllDots = setDotDirection(positions, cfg, dots, isSignal)
     % dots = setDotDirection(cfg, dots)
     %
     % creates some new direction for the dots
@@ -9,30 +9,35 @@
     % all the other dots get a random value between 0 and 360.
     %
     % all directions are in end expressed between 0 and 360
-
-    directionAllDots = nan(cfg.dot.number, 1);
-
-    % Coherent dots
-
-    if numel(dots.direction) == 1
-        dots.direction = ones(sum(dots.isSignal), 1) * dots.direction;
-    elseif numel(dots.direction) ~= sum(dots.isSignal)
-        error(['dots.direction must have one element' ...
-               'or as many element as there are coherent dots']);
+    
+    directionAllDots = dots.direction;
+    
+    % when we initialiaze the direction for all the dots
+    % after that dots.direction will be a vector
+    if numel(directionAllDots) == 1
+        
+        directionAllDots(isSignal) = ones(sum(isSignal), 1) * dots.direction;
+        
     end
-
-    directionAllDots(dots.isSignal) = dots.direction;
-
+    
+    %% Coherent dots
     if strcmp(cfg.design.motionType, 'radial')
-        angleMotion = computeRadialMotionDirection(cfg, dots);
-        directionAllDots(dots.isSignal) = angleMotion;
-    end
-
-    % Random direction for the non coherent dots
-
-    directionAllDots(~dots.isSignal) = rand(sum(~dots.isSignal), 1) * 360;
-    directionAllDots = rem(directionAllDots, 360);
-
-    dots.directionAllDots = directionAllDots;
+        
+        angleMotion = computeRadialMotionDirection(positions, cfg.dot.matrixWidth, dots);
+        
+        directionAllDots(isSignal) = angleMotion;
 
+    end
+    
+    %% Random direction for the non coherent dots
+    directionAllDots(~isSignal) = rand(sum(~isSignal), 1) * 360;
+    
+    %% Express the direction in the 0 to 360 range
+    directionAllDots = mod(directionAllDots, 360);
+    
+    % ensure we return a colum vector
+    if size(directionAllDots, 1)==1
+        directionAllDots = directionAllDots';
+    end
+    
 end
diff --git a/tests/test_generateNewDotPositions.m b/tests/test_generateNewDotPositions.m
index f6a2721..d47e285 100644
--- a/tests/test_generateNewDotPositions.m
+++ b/tests/test_generateNewDotPositions.m
@@ -8,10 +8,10 @@
 
 function test_generateNewDotPositionsBasic()
 
-    cfg.dot.matrixWidth = 400;
+    dotMatrixWidth = 400;
     dotNumber = 200;
 
-    newPositions = generateNewDotPositions(cfg, dotNumber);
+    newPositions = generateNewDotPositions(dotMatrixWidth, dotNumber);
 
     assertEqual([200, 2], size(newPositions));
 
diff --git a/tests/test_initDots.m b/tests/test_initDots.m
index 7f92d6e..991c76b 100644
--- a/tests/test_initDots.m
+++ b/tests/test_initDots.m
@@ -47,8 +47,7 @@ function test_initDotsBasic()
     expectedStructure.isSignal = ones(10, 1);
     expectedStructure.speeds = repmat([1 0], 10, 1) * 10;
     expectedStructure.speedPixPerFrame = 10;
-    expectedStructure.direction = zeros(10, 1);
-    expectedStructure.directionAllDots = zeros(10, 1);
+    expectedStructure.direction = 0;
 
     % remove undeterministic output
     dots = rmfield(dots, 'time');
@@ -84,8 +83,7 @@ function test_initDotsStatic()
     expectedStructure.isSignal = ones(10, 1);
     expectedStructure.speeds = zeros(10, 2);
     expectedStructure.speedPixPerFrame = 0;
-    expectedStructure.direction = -1 * ones(10, 1);
-    expectedStructure.directionAllDots = -1 * ones(10, 1);
+    expectedStructure.direction = -1;
 
     %% test
     assertEqual(expectedStructure, dots);
diff --git a/tests/test_reseedDots.m b/tests/test_reseedDots.m
index 6f3da93..7ed3abf 100644
--- a/tests/test_reseedDots.m
+++ b/tests/test_reseedDots.m
@@ -7,47 +7,45 @@
 end
 
 function test_reseedDotsBasic()
+    
+    dotNb = 5;
 
-    cfg.screen.winWidth = 2000;
+    cfg.design.motionType = 'translation';
+    cfg.timing.eventDuration = 1; % in seconds
+    cfg.screen.ifi = 0.01; % in seconds
 
-    cfg.design.motionType = 'radial';
-
-    cfg.dot.matrixWidth = 50; % in pixels
-    cfg.dot.number = 5;
+    cfg.dot.matrixWidth = 1000; % in pixels
+    cfg.dot.number = dotNb;
     cfg.dot.sizePix = 20;
     cfg.dot.proportionKilledPerFrame = 0;
 
-    cfg.fixation.widthPix = 20;
+    cfg.fixation.widthPix = 5;
 
     dots.lifeTime = 100;
     dots.speedPixPerFrame = 3;
     dots.direction = 90;
-    dots.isSignal = true(5, 1);
+    dots.isSignal = true(dotNb, 1);
+    dots.speeds = ones(dotNb, 2);
 
     dots.positions = [ ...
-                      49, 1  % OK
-                      490, 2043  % out of frame
-                      -104, 392  % out of frame
-                      492, 402  % OK
-                      1000, 1000  % on the fixation cross
+                      300, 10  % OK
+                      750, 1010  % out of frame
+                      -1040, 50  % out of frame
+                      300, 300  % OK
+                      500, 500  % on the fixation cross
                      ];
 
-    dots.time = [ ...
+    originalTime = [ ...
                  6; ... OK
                  4; ... OK
                  56; ... OK
                  300; ... % exceeded its life time
                  50]; % OK
+    dots.time = originalTime;
 
     dots = reseedDots(dots, cfg);
 
-    reseeded = [ ...
-                6
-                1
-                1
-                1
-                1];
-
-    assertEqual(reseeded, dots.time);
+    assertEqual(dots.time(1), originalTime(1));
+    assertTrue(all(dots.time(2:end) ~= originalTime(2:end)));
 
 end
diff --git a/tests/test_seedDots.m b/tests/test_seedDots.m
new file mode 100644
index 0000000..56ac733
--- /dev/null
+++ b/tests/test_seedDots.m
@@ -0,0 +1,38 @@
+function test_suite = test_seedDots %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
+
+function test_seedDotsBasic()
+
+    %% set up
+
+    cfg.dot.matrixWidth = 400;
+    cfg.design.motionType = 'translation';
+    cfg.timing.eventDuration = 1; % in seconds
+    cfg.screen.ifi = 0.01; % in seconds
+    
+    nbDots = 10;
+    isSignal = [true(5, 1); false(nbDots - 5, 1)];
+    
+    dots.direction = 0;
+    dots.speedPixPerFrame = 10;
+
+    [positions, speeds, time] = seedDots(dots, cfg, isSignal);
+
+    %% Deterministic output
+    assertEqual(size(positions), [nbDots, 2]);
+    assertTrue(all(all([...
+        positions(:) <= cfg.dot.matrixWidth, ...
+        positions(:) >= 0])));
+    
+    assertTrue(all(time(:) >= 0));
+    assertTrue(all(time(:) <= 1 / 0.01));
+    
+    assertEqual(speeds(1:5,:), repmat([10 0], 5, 1));
+
+end
+
diff --git a/tests/test_setDotDirection.m b/tests/test_setDotDirection.m
index f68fdd1..790bbe1 100644
--- a/tests/test_setDotDirection.m
+++ b/tests/test_setDotDirection.m
@@ -6,21 +6,53 @@
     initTestSuite;
 end
 
-function test_setDotDirectionBasic()
+function test_setDotDirectionInit()
     % create 5 coherent dots with direction == 362 (that should give 2 in the
     % end)
-    % also creates 955 additonal dots with random direction between 0 and 360
-
-    cfg.dot.number = 1000;
+    % also creates additonal dots with random direction between 0 and 360
+    
+    nbDots = 10;
+    
+    cfg.dot.matrixWidth = 400;
     cfg.design.motionType = 'translation';
+    
     dots.direction = 362;
+    dots.isSignal = [true(5, 1); false(nbDots - 5, 1)];
+    
+    
+    positions = generateNewDotPositions(cfg.dot.matrixWidth, numel(dots.isSignal));
+    
+    directionAllDots = setDotDirection(positions, cfg, dots, dots.isSignal);
+
+    assertEqual(directionAllDots(1:5), 2 * ones(5, 1));
+    assertGreaterThan(directionAllDots, zeros(size(directionAllDots)) );
+    assertLessThan(directionAllDots, 360 * ones(size(directionAllDots)));
 
-    dots.isSignal = [true(5, 1); false(1000 - 5, 1)];
+end
 
-    dots = setDotDirection(cfg, dots);
+function test_setDotDirectionReturn()
+    % make sure that if the directions are already set it only changes that of
+    % the noise dots
+    % input has 4 signal dots with set directions also has additonal noise dots with negative direction
+    
+    nbDots = 8;
+    
+    cfg.dot.matrixWidth = 400;
+    cfg.design.motionType = 'translation';
+    
+    dots.direction = [...
+        [362; 2; -362; -2];  ...
+        -20 * ones(4, 1)];
+    dots.isSignal = [true(4, 1); false(nbDots - 4, 1)];
+    
+    
+    positions = generateNewDotPositions(cfg.dot.matrixWidth, numel(dots.isSignal));
+    
+    directionAllDots = setDotDirection(positions, cfg, dots, dots.isSignal);
 
-    assertTrue(all(dots.directionAllDots(1:5) == 2 * ones(5, 1)));
-    assertTrue(all(dots.directionAllDots >= 0));
-    assertTrue(all(dots.directionAllDots <= 360));
+    assertEqual(directionAllDots(1:4), [2 2 358 358]');
+    assertGreaterThan(directionAllDots, zeros(size(directionAllDots)) );
+    assertLessThan(directionAllDots, 360 * ones(size(directionAllDots)));
+    assertTrue(all(directionAllDots(5:end) ~= -20 * ones(4,1)))
 
 end

From 619240538843c893b49a94e830254deb415d1b6c Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 25 Sep 2020 19:28:23 +0200
Subject: [PATCH 04/15] create a dot motion simulation

---
 src/dot/dotMotionSimulation.m | 104 ++++++++++++++++++++++++++++++++++
 tests/test_initDots.m         |   1 -
 2 files changed, 104 insertions(+), 1 deletion(-)
 create mode 100644 src/dot/dotMotionSimulation.m

diff --git a/src/dot/dotMotionSimulation.m b/src/dot/dotMotionSimulation.m
new file mode 100644
index 0000000..4e88f1e
--- /dev/null
+++ b/src/dot/dotMotionSimulation.m
@@ -0,0 +1,104 @@
+function relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, doPlot)
+    % to simulate where the dots are more dense on the screen
+    % relativeDensityContrast : hard to get it below 0.10
+    
+    close all
+    
+    if nargin<3
+        
+        doPlot=1;
+        
+    end
+    
+    
+    if nargin<2
+        
+        thisEvent.direction = 0; % degrees
+        thisEvent.speed = 1; % pix per frame
+        
+    end
+    
+    if nargin<1
+        
+        cfg.design.motionType = 'translation';
+        
+        cfg.dot.coherence = 1; % proportion
+        
+        cfg.dot.lifeTime = 10; % in seconds
+        
+        cfg.dot.matrixWidth = 250; % in pixels
+        
+        cfg.dot.proportionKilledPerFrame = 0;
+        
+        cfg.timing.eventDuration = 500; % in seconds
+
+    end
+    
+    % interframe interval
+    cfg.screen.ifi = 0.016; % in seconds
+    
+    % size of the fixation is 1% of screen width
+    cfg.fixation.widthPix = ceil(cfg.dot.matrixWidth * 1 / 100);
+    
+    % dot size
+    cfg.dot.sizePix = 1;
+    
+    % We fill 25% of the screen with dots
+    cfg.dot.number = round(cfg.dot.matrixWidth^2 * 25 / 100);
+    
+    fprintf(1, '\n\nDot motion simulation:')
+    
+    nbFrames = ceil(cfg.timing.eventDuration/cfg.screen.ifi);
+    frameToReport = round(linspace(1, nbFrames, 20));
+    
+    % to keep track of where the dots have been
+    dotDensity = zeros(cfg.dot.matrixWidth);
+    
+    [dots] = initDots(cfg, thisEvent);
+    dotDensity = updateDotDensity(dotDensity, dots);
+
+    for iFrame = 1:nbFrames
+        
+        if any(frameToReport==iFrame)
+            fprintf(1, '.')
+        end
+        
+        [dots] = updateDots(dots, cfg);
+        
+        dotDensity = updateDotDensity(dotDensity, dots);
+        
+    end
+    
+    %% Post sim
+    % trim the edges (to avoid super high/low values
+    dotDensity = dotDensity(2:end-1, 2:end-1);
+    
+    relativeDensityContrast = (max(dotDensity(:)) - min(dotDensity(:))) / max(dotDensity(:));
+    
+    if doPlot
+        imagesc(dotDensity)
+        axis square
+        title('dot density')
+    end
+    
+end
+
+
+function dotDensity = updateDotDensity(dotDensity, dots)
+    
+    x = round(dots.positions(:,1));
+    x = avoidEdgeValues(x, size(dotDensity, 2));
+    
+    y = round(dots.positions(:,2));
+    y = avoidEdgeValues(y, size(dotDensity, 1));
+    
+    ind = sub2ind(size(dotDensity), y, x);
+    
+    dotDensity(ind) = dotDensity(ind) + 1;
+    
+end
+
+function x = avoidEdgeValues(x, dim)
+    x(x<1) = 1;
+    x(x>dim) = dim;
+end
\ No newline at end of file
diff --git a/tests/test_initDots.m b/tests/test_initDots.m
index 991c76b..75a50d8 100644
--- a/tests/test_initDots.m
+++ b/tests/test_initDots.m
@@ -27,7 +27,6 @@ function test_initDotsBasic()
     cfg.dot.coherence = 1; % proportion
     cfg.dot.lifeTime = 0.250; % in seconds
     cfg.dot.matrixWidth = 50; % in pixels
-    cfg.screen.winWidth = 2000; % in pixels
     cfg.timing.eventDuration = 1; % in seconds
     cfg.screen.ifi = 0.01; % in seconds
 

From cea101ed2c4a9207dad766df50aa8beaa43c6d12 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 25 Sep 2020 19:31:18 +0200
Subject: [PATCH 05/15] mh fix

---
 src/dot/computeCartCoord.m    |   2 +-
 src/dot/dotMotionSimulation.m | 108 +++++++++++++++++-----------------
 src/dot/initDots.m            |   5 +-
 src/dot/reseedDots.m          |   4 +-
 src/dot/seedDots.m            |  14 +++--
 src/dot/setDotDirection.m     |  24 ++++----
 src/utils/pixToDeg.m          |   2 +-
 tests/test_reseedDots.m       |  12 ++--
 tests/test_seedDots.m         |  17 +++---
 tests/test_setDotDirection.m  |  37 ++++++------
 10 files changed, 111 insertions(+), 114 deletions(-)

diff --git a/src/dot/computeCartCoord.m b/src/dot/computeCartCoord.m
index 7224254..2982138 100644
--- a/src/dot/computeCartCoord.m
+++ b/src/dot/computeCartCoord.m
@@ -1,5 +1,5 @@
 function cartesianCoordinates = computeCartCoord(positions, dotMatrixWidth)
-    
+
     cartesianCoordinates = ...
         [positions(:, 1) - dotMatrixWidth / 2, ... % x coordinate
          positions(:, 2) - dotMatrixWidth / 2]; % y coordinate
diff --git a/src/dot/dotMotionSimulation.m b/src/dot/dotMotionSimulation.m
index 4e88f1e..4c82f2c 100644
--- a/src/dot/dotMotionSimulation.m
+++ b/src/dot/dotMotionSimulation.m
@@ -1,104 +1,102 @@
 function relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, doPlot)
     % to simulate where the dots are more dense on the screen
     % relativeDensityContrast : hard to get it below 0.10
-    
-    close all
-    
-    if nargin<3
-        
-        doPlot=1;
-        
+
+    close all;
+
+    if nargin < 3
+
+        doPlot = 1;
+
     end
-    
-    
-    if nargin<2
-        
+
+    if nargin < 2
+
         thisEvent.direction = 0; % degrees
         thisEvent.speed = 1; % pix per frame
-        
+
     end
-    
-    if nargin<1
-        
+
+    if nargin < 1
+
         cfg.design.motionType = 'translation';
-        
+
         cfg.dot.coherence = 1; % proportion
-        
+
         cfg.dot.lifeTime = 10; % in seconds
-        
+
         cfg.dot.matrixWidth = 250; % in pixels
-        
+
         cfg.dot.proportionKilledPerFrame = 0;
-        
+
         cfg.timing.eventDuration = 500; % in seconds
 
     end
-    
+
     % interframe interval
     cfg.screen.ifi = 0.016; % in seconds
-    
+
     % size of the fixation is 1% of screen width
     cfg.fixation.widthPix = ceil(cfg.dot.matrixWidth * 1 / 100);
-    
+
     % dot size
     cfg.dot.sizePix = 1;
-    
+
     % We fill 25% of the screen with dots
     cfg.dot.number = round(cfg.dot.matrixWidth^2 * 25 / 100);
-    
-    fprintf(1, '\n\nDot motion simulation:')
-    
-    nbFrames = ceil(cfg.timing.eventDuration/cfg.screen.ifi);
+
+    fprintf(1, '\n\nDot motion simulation:');
+
+    nbFrames = ceil(cfg.timing.eventDuration / cfg.screen.ifi);
     frameToReport = round(linspace(1, nbFrames, 20));
-    
+
     % to keep track of where the dots have been
     dotDensity = zeros(cfg.dot.matrixWidth);
-    
+
     [dots] = initDots(cfg, thisEvent);
     dotDensity = updateDotDensity(dotDensity, dots);
 
     for iFrame = 1:nbFrames
-        
-        if any(frameToReport==iFrame)
-            fprintf(1, '.')
+
+        if any(frameToReport == iFrame)
+            fprintf(1, '.');
         end
-        
+
         [dots] = updateDots(dots, cfg);
-        
+
         dotDensity = updateDotDensity(dotDensity, dots);
-        
+
     end
-    
+
     %% Post sim
     % trim the edges (to avoid super high/low values
-    dotDensity = dotDensity(2:end-1, 2:end-1);
-    
+    dotDensity = dotDensity(2:end - 1, 2:end - 1);
+
     relativeDensityContrast = (max(dotDensity(:)) - min(dotDensity(:))) / max(dotDensity(:));
-    
+
     if doPlot
-        imagesc(dotDensity)
-        axis square
-        title('dot density')
+        imagesc(dotDensity);
+        axis square;
+        title('dot density');
     end
-    
-end
 
+end
 
 function dotDensity = updateDotDensity(dotDensity, dots)
-    
-    x = round(dots.positions(:,1));
+
+    x = round(dots.positions(:, 1));
     x = avoidEdgeValues(x, size(dotDensity, 2));
-    
-    y = round(dots.positions(:,2));
+
+    y = round(dots.positions(:, 2));
     y = avoidEdgeValues(y, size(dotDensity, 1));
-    
+
     ind = sub2ind(size(dotDensity), y, x);
-    
+
     dotDensity(ind) = dotDensity(ind) + 1;
-    
+
 end
 
 function x = avoidEdgeValues(x, dim)
-    x(x<1) = 1;
-    x(x>dim) = dim;
-end
\ No newline at end of file
+    x(x < 1) = 1;
+    x(x > dim) = dim;
+end
diff --git a/src/dot/initDots.m b/src/dot/initDots.m
index 5ade937..94077b0 100644
--- a/src/dot/initDots.m
+++ b/src/dot/initDots.m
@@ -26,7 +26,7 @@
 
     % decide which dots are signal dots (1) and those are noise dots (0)
     dots.isSignal = rand(cfg.dot.number, 1) < cfg.dot.coherence;
-    
+
     dots.speedPixPerFrame = thisEvent.speed(1);
     lifeTime = cfg.dot.lifeTime;
 
@@ -44,6 +44,5 @@
     %% Convert from seconds to frames
     lifeTime = ceil(lifeTime / cfg.screen.ifi);
     dots.lifeTime = lifeTime;
-    
- 
+
 end
diff --git a/src/dot/reseedDots.m b/src/dot/reseedDots.m
index 1e9ec05..d30e7a9 100644
--- a/src/dot/reseedDots.m
+++ b/src/dot/reseedDots.m
@@ -26,9 +26,9 @@
     % If there is any such dot we relocate it to a new random position
     % and change its lifetime to 1
     if any(N)
-        
+
         isSignal = dots.isSignal(N);
-        
+
         [positions, speeds, time] = seedDots(dots, cfg, isSignal);
 
         dots.positions(N, :) = positions;
diff --git a/src/dot/seedDots.m b/src/dot/seedDots.m
index b835ec8..1e1fecb 100644
--- a/src/dot/seedDots.m
+++ b/src/dot/seedDots.m
@@ -1,7 +1,9 @@
-function [positions, speeds, time] = seedDots(dots, cfg, isSignal)
-    
+function [positions, speeds, time] = seedDots(varargin)
+
+    [dots, cfg, isSignal] = deal(varargin{:});
+
     nbDots = numel(isSignal);
-    
+
     %% Set an array of dot positions [xposition, yposition]
     % These can never be bigger than 1 or lower than 0
     % [0,0] is the top / left of the square
@@ -11,7 +13,7 @@
     %% Set vertical and horizontal speed for all dots
     directionAllDots = setDotDirection(positions, cfg, dots, isSignal);
     [horVector, vertVector] = decomposeMotion(directionAllDots);
-    
+
     % we were working with unit vectors. we now switch to pixels
     speeds = [horVector, vertVector] * dots.speedPixPerFrame;
 
@@ -19,5 +21,5 @@
     % Not all set to 1 so the dots will die at different times
     % The maximum value is the duraion of the event in frames
     time = floor(rand(nbDots, 1) * cfg.timing.eventDuration / cfg.screen.ifi);
-    
-end
\ No newline at end of file
+
+end
diff --git a/src/dot/setDotDirection.m b/src/dot/setDotDirection.m
index a9f08df..3d093b4 100644
--- a/src/dot/setDotDirection.m
+++ b/src/dot/setDotDirection.m
@@ -9,35 +9,35 @@
     % all the other dots get a random value between 0 and 360.
     %
     % all directions are in end expressed between 0 and 360
-    
+
     directionAllDots = dots.direction;
-    
+
     % when we initialiaze the direction for all the dots
     % after that dots.direction will be a vector
     if numel(directionAllDots) == 1
-        
+
         directionAllDots(isSignal) = ones(sum(isSignal), 1) * dots.direction;
-        
+
     end
-    
+
     %% Coherent dots
     if strcmp(cfg.design.motionType, 'radial')
-        
+
         angleMotion = computeRadialMotionDirection(positions, cfg.dot.matrixWidth, dots);
-        
+
         directionAllDots(isSignal) = angleMotion;
 
     end
-    
+
     %% Random direction for the non coherent dots
     directionAllDots(~isSignal) = rand(sum(~isSignal), 1) * 360;
-    
+
     %% Express the direction in the 0 to 360 range
     directionAllDots = mod(directionAllDots, 360);
-    
+
     % ensure we return a colum vector
-    if size(directionAllDots, 1)==1
+    if size(directionAllDots, 1) == 1
         directionAllDots = directionAllDots';
     end
-    
+
 end
diff --git a/src/utils/pixToDeg.m b/src/utils/pixToDeg.m
index 5efcba5..a55978c 100644
--- a/src/utils/pixToDeg.m
+++ b/src/utils/pixToDeg.m
@@ -24,6 +24,6 @@
     pix = getfield(structure, fieldName); %#ok<GFLD>
 
     structure = setfield(structure, [strrep(fieldName, 'Pix', '') 'DegVA'], ...
-        floor(pix / cfg.screen.ppd)); %#ok<SFLD>
+                         floor(pix / cfg.screen.ppd)); %#ok<SFLD>
 
 end
diff --git a/tests/test_reseedDots.m b/tests/test_reseedDots.m
index 7ed3abf..6097bf5 100644
--- a/tests/test_reseedDots.m
+++ b/tests/test_reseedDots.m
@@ -7,7 +7,7 @@
 end
 
 function test_reseedDotsBasic()
-    
+
     dotNb = 5;
 
     cfg.design.motionType = 'translation';
@@ -36,11 +36,11 @@ function test_reseedDotsBasic()
                      ];
 
     originalTime = [ ...
-                 6; ... OK
-                 4; ... OK
-                 56; ... OK
-                 300; ... % exceeded its life time
-                 50]; % OK
+                    6; ... OK
+                    4; ... OK
+                    56; ... OK
+                    300; ... % exceeded its life time
+                    50]; % OK
     dots.time = originalTime;
 
     dots = reseedDots(dots, cfg);
diff --git a/tests/test_seedDots.m b/tests/test_seedDots.m
index 56ac733..782b60d 100644
--- a/tests/test_seedDots.m
+++ b/tests/test_seedDots.m
@@ -14,10 +14,10 @@ function test_seedDotsBasic()
     cfg.design.motionType = 'translation';
     cfg.timing.eventDuration = 1; % in seconds
     cfg.screen.ifi = 0.01; % in seconds
-    
+
     nbDots = 10;
     isSignal = [true(5, 1); false(nbDots - 5, 1)];
-    
+
     dots.direction = 0;
     dots.speedPixPerFrame = 10;
 
@@ -25,14 +25,13 @@ function test_seedDotsBasic()
 
     %% Deterministic output
     assertEqual(size(positions), [nbDots, 2]);
-    assertTrue(all(all([...
-        positions(:) <= cfg.dot.matrixWidth, ...
-        positions(:) >= 0])));
-    
+    assertTrue(all(all([ ...
+                        positions(:) <= cfg.dot.matrixWidth, ...
+                        positions(:) >= 0])));
+
     assertTrue(all(time(:) >= 0));
     assertTrue(all(time(:) <= 1 / 0.01));
-    
-    assertEqual(speeds(1:5,:), repmat([10 0], 5, 1));
 
-end
+    assertEqual(speeds(1:5, :), repmat([10 0], 5, 1));
 
+end
diff --git a/tests/test_setDotDirection.m b/tests/test_setDotDirection.m
index 790bbe1..12a80b4 100644
--- a/tests/test_setDotDirection.m
+++ b/tests/test_setDotDirection.m
@@ -10,22 +10,21 @@ function test_setDotDirectionInit()
     % create 5 coherent dots with direction == 362 (that should give 2 in the
     % end)
     % also creates additonal dots with random direction between 0 and 360
-    
+
     nbDots = 10;
-    
+
     cfg.dot.matrixWidth = 400;
     cfg.design.motionType = 'translation';
-    
+
     dots.direction = 362;
     dots.isSignal = [true(5, 1); false(nbDots - 5, 1)];
-    
-    
+
     positions = generateNewDotPositions(cfg.dot.matrixWidth, numel(dots.isSignal));
-    
+
     directionAllDots = setDotDirection(positions, cfg, dots, dots.isSignal);
 
     assertEqual(directionAllDots(1:5), 2 * ones(5, 1));
-    assertGreaterThan(directionAllDots, zeros(size(directionAllDots)) );
+    assertGreaterThan(directionAllDots, zeros(size(directionAllDots)));
     assertLessThan(directionAllDots, 360 * ones(size(directionAllDots)));
 
 end
@@ -33,26 +32,26 @@ function test_setDotDirectionInit()
 function test_setDotDirectionReturn()
     % make sure that if the directions are already set it only changes that of
     % the noise dots
-    % input has 4 signal dots with set directions also has additonal noise dots with negative direction
-    
+    % input has 4 signal dots with set directions also has additonal noise dots
+    % with negative direction
+
     nbDots = 8;
-    
+
     cfg.dot.matrixWidth = 400;
     cfg.design.motionType = 'translation';
-    
-    dots.direction = [...
-        [362; 2; -362; -2];  ...
-        -20 * ones(4, 1)];
+
+    dots.direction = [ ...
+                      [362; 2; -362; -2];  ...
+                      -20 * ones(4, 1)];
     dots.isSignal = [true(4, 1); false(nbDots - 4, 1)];
-    
-    
+
     positions = generateNewDotPositions(cfg.dot.matrixWidth, numel(dots.isSignal));
-    
+
     directionAllDots = setDotDirection(positions, cfg, dots, dots.isSignal);
 
     assertEqual(directionAllDots(1:4), [2 2 358 358]');
-    assertGreaterThan(directionAllDots, zeros(size(directionAllDots)) );
+    assertGreaterThan(directionAllDots, zeros(size(directionAllDots)));
     assertLessThan(directionAllDots, 360 * ones(size(directionAllDots)));
-    assertTrue(all(directionAllDots(5:end) ~= -20 * ones(4,1)))
+    assertTrue(all(directionAllDots(5:end) ~= -20 * ones(4, 1)));
 
 end

From 053cf1529f01005b51a1ee8385ffde17a7ad497e Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 25 Sep 2020 20:06:43 +0200
Subject: [PATCH 06/15] add test for simulation

---
 src/dot/dotMotionSimulation.m    | 36 +++++++++++++-----------
 tests/test_dotMotionSimulation.m | 48 ++++++++++++++++++++++++++++++++
 2 files changed, 68 insertions(+), 16 deletions(-)
 create mode 100644 tests/test_dotMotionSimulation.m

diff --git a/src/dot/dotMotionSimulation.m b/src/dot/dotMotionSimulation.m
index 4c82f2c..25ca7ae 100644
--- a/src/dot/dotMotionSimulation.m
+++ b/src/dot/dotMotionSimulation.m
@@ -1,20 +1,20 @@
-function relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, doPlot)
+function relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, nbEvents, doPlot)
     % to simulate where the dots are more dense on the screen
     % relativeDensityContrast : hard to get it below 0.10
 
     close all;
 
-    if nargin < 3
-
+    if nargin < 4
         doPlot = 1;
+    end
 
+    if nargin < 3
+        nbEvents = 100;
     end
 
     if nargin < 2
-
         thisEvent.direction = 0; % degrees
         thisEvent.speed = 1; % pix per frame
-
     end
 
     if nargin < 1
@@ -23,13 +23,13 @@
 
         cfg.dot.coherence = 1; % proportion
 
-        cfg.dot.lifeTime = 10; % in seconds
+        cfg.dot.lifeTime = .1; % in seconds
 
         cfg.dot.matrixWidth = 250; % in pixels
 
         cfg.dot.proportionKilledPerFrame = 0;
 
-        cfg.timing.eventDuration = 500; % in seconds
+        cfg.timing.eventDuration = 1.8; % in seconds
 
     end
 
@@ -48,23 +48,27 @@
     fprintf(1, '\n\nDot motion simulation:');
 
     nbFrames = ceil(cfg.timing.eventDuration / cfg.screen.ifi);
-    frameToReport = round(linspace(1, nbFrames, 20));
+    %     frameToReport = round(linspace(1, nbFrames, 20));
 
     % to keep track of where the dots have been
     dotDensity = zeros(cfg.dot.matrixWidth);
 
-    [dots] = initDots(cfg, thisEvent);
-    dotDensity = updateDotDensity(dotDensity, dots);
+    for iEvent = 1:nbEvents
 
-    for iFrame = 1:nbFrames
+        [dots] = initDots(cfg, thisEvent);
+        dotDensity = updateDotDensity(dotDensity, dots);
 
-        if any(frameToReport == iFrame)
-            fprintf(1, '.');
-        end
+        for iFrame = 1:nbFrames
 
-        [dots] = updateDots(dots, cfg);
+            %         if any(frameToReport == iFrame)
+            %             fprintf(1, '.');
+            %         end
 
-        dotDensity = updateDotDensity(dotDensity, dots);
+            [dots] = updateDots(dots, cfg);
+
+            dotDensity = updateDotDensity(dotDensity, dots);
+
+        end
 
     end
 
diff --git a/tests/test_dotMotionSimulation.m b/tests/test_dotMotionSimulation.m
new file mode 100644
index 0000000..83e715e
--- /dev/null
+++ b/tests/test_dotMotionSimulation.m
@@ -0,0 +1,48 @@
+function test_suite = test_dotMotionSimulation %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
+
+function test_dotMotionSimulationStatic()
+
+    nbEvents = 1;
+    doPlot = false;
+
+    thisEvent.direction = -1; % degrees
+    thisEvent.speed = 1; % pix per frame
+
+    cfg.design.motionType = 'translation';
+    cfg.dot.coherence = 1; % proportion
+    cfg.dot.lifeTime = .5; % in seconds
+    cfg.dot.matrixWidth = 250; % in pixels
+    cfg.dot.proportionKilledPerFrame = 0;
+    cfg.timing.eventDuration = 1.8; % in seconds
+
+    relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, nbEvents, doPlot);
+
+end
+
+function test_dotMotionSimulationTranslation()
+    % ensure that dog homogenity is not too low when we kill dots often enough
+
+    nbEvents = 500;
+    doPlot = false;
+
+    thisEvent.direction = 0; % degrees
+    thisEvent.speed = 1; % pix per frame
+
+    cfg.design.motionType = 'translation';
+    cfg.dot.coherence = 1; % proportion
+    cfg.dot.lifeTime = .1; % in seconds
+    cfg.dot.matrixWidth = 250; % in pixels
+    cfg.dot.proportionKilledPerFrame = 0;
+    cfg.timing.eventDuration = 1.8; % in seconds
+
+    relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, nbEvents, doPlot);
+
+    assertLessThan(relativeDensityContrast, 0.5);
+
+end

From 472ef0559b1c72807791b7af6ea1be44def2c865 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 25 Sep 2020 20:17:57 +0200
Subject: [PATCH 07/15] markdown linting

---
 README.md                         |   8 +-
 docs/{00_index.md => 00-index.md} |   0
 docs/10-functions-description.md  | 214 ++++++++++++++++++++++++++++++
 docs/10_functions_description.md  |   6 -
 4 files changed, 216 insertions(+), 12 deletions(-)
 rename docs/{00_index.md => 00-index.md} (100%)
 create mode 100644 docs/10-functions-description.md

diff --git a/README.md b/README.md
index 1cf7da8..ec3fcf5 100644
--- a/README.md
+++ b/README.md
@@ -154,13 +154,9 @@ git submodule foreach --recursive 'git submodule update'
 
 Download the code. Unzip. And add to the matlab path.
 
-Pick a specific version:
+Pick a specific version from [here](https://github.com/cpp-lln-lab/CPP_PTB/releases).
 
-https://github.com/cpp-lln-lab/CPP_PTB/releases
-
-Or take the latest commit (NOT RECOMMENDED):
-
-https://github.com/cpp-lln-lab/CPP_PTB/archive/master.zip
+Or take [the latest commit](https://github.com/cpp-lln-lab/CPP_PTB/archive/master.zip) - NOT RECOMMENDED.
 
 ### Add CPP_PTB globally to the matlab path
 
diff --git a/docs/00_index.md b/docs/00-index.md
similarity index 100%
rename from docs/00_index.md
rename to docs/00-index.md
diff --git a/docs/10-functions-description.md b/docs/10-functions-description.md
new file mode 100644
index 0000000..ce76c4c
--- /dev/null
+++ b/docs/10-functions-description.md
@@ -0,0 +1,214 @@
+# functions description
+
+<!-- TOC -->
+
+-   [functions description](#functions-description)
+    -   [General functions](#general-functions)
+        -   [initPTB](#initptb)
+        -   [cleanUp](#cleanup)
+        -   [getExperimentStart](#getexperimentstart)
+        -   [getExperimentEnd](#getexperimentend)
+        -   [degToPix](#degtopix)
+        -   [computeFOV](#computefov)
+        -   [eyeTracker](#eyetracker)
+        -   [standByScreen](#standbyscreen)
+        -   [waitForTrigger](#waitfortrigger)
+        -   [waitFor](#waitfor)
+        -   [readAndFilterLogfile](#readandfilterlogfile)
+    -   [Keyboard functions: response collection and aborting experiment](#keyboard-functions-response-collection-and-aborting-experiment)
+        -   [testKeyboards](#testkeyboards)
+        -   [getResponse](#getresponse)
+        -   [pressSpaceForme](#pressspaceforme)
+        -   [checkAbort](#checkabort)
+    -   [Fixations](#fixations)
+        -   [drawFixationCross](#drawfixationcross)
+    -   [Drawing dots](#drawing-dots)
+    -   [Drawing apertures](#drawing-apertures)
+    -   [Randomization](#randomization)
+        -   [shuffle](#shuffle)
+        -   [setTargetPositionInSequence](#settargetpositioninsequence)
+        -   [repeatShuffleConditions](#repeatshuffleconditions)
+
+<!-- /TOC -->
+
+## General functions
+
+### initPTB
+
+This will initialize PsychToolBox.
+
+It is pretty much necessary to use this function to set up the stage for using
+any other functions of CPP_PTB.
+
+-   checks OS and PTB version
+-   set some defaults
+-   set the screen details
+    -   the window opened takes the whole screen by default
+    -   set in debug mode with window transparency if necessary
+    -   can skip synch test if you ask for it (nicely)
+    -   gets the flip interval
+    -   computes the pixel per degree of visual angle
+-   set fixation cross details
+-   set font details
+-   keyboard
+-   hides cursor
+-   sound
+
+### cleanUp
+
+A wrapper function to close all windows, ports, show mouse cursor, close
+keyboard queues and give you back access to the keyboards.
+
+### getExperimentStart
+
+Wrapper function that will show a fixation cross and collect a start timestamp
+in `cfg.experimentStart`
+
+### getExperimentEnd
+
+Wrapper function that will show a fixation cross and display in the console the
+whole experiment's duration in minutes and seconds
+
+### degToPix
+
+For a given field value in degrees of visual angle in the input `structure`,
+this computes its value in pixel using the pixel per degree value of the `cfg`
+structure and returns a structure with an additional field with Pix suffix
+holding that new value.
+
+### computeFOV
+
+Gives you the width of the field on view in degress of visual angle based on the
+screen width and distance to the screen in cm (taken from the `cfg`)
+
+### eyeTracker
+
+This will handle the Eye Tracker (EyeLink set up) and can be called to
+initialize the connection and start the calibration, start/stop eye(s) movement
+recordings and save the `*.edf` file (named with BIDS specification from
+cpp-lln-lab/CPP_BIDS).
+
+There are several actions to perform:
+
+-   Calibration: to initialize EyeLink and run calibration
+    -   'default calibration' (default) will run a calibration with 6 points
+    -   'custom calibration' (cfg.eyeTracker.defaultCalibration = 'false') will
+        run a calibration with 6 points but the experimenter can choose their
+        position on the screen
+-   StartRecording: to start eye movements recording
+-   Message: will add a tag (e.g. 'Block_n1') in the ET output file, the tag is
+    a string and it is input from `varargin`
+-   StopRecordings: to stop eye movements recornding
+-   Shutdown: to save the `.edf` file with BIDS compliant name, from
+    cpp-lln-lab/CPP_BIDS, in the output folder and shut the connection between
+    the stimulation computer and the EyeLink computer
+
+### standByScreen
+
+It shows a basic one-page instruction stored in `cfg.task.instruction` and wait
+for `space` stroke.
+
+### waitForTrigger
+
+Counts a certain number of triggers coming from the mri/scanner before
+returning. Requires number of triggers to wait for.
+
+This can also be used if you want to let the scanner pace the experiment and you
+want to synch stimulus presentation to the scanner trigger.
+
+### waitFor
+
+A generic function that you can use to for a certain amount of time or a number
+of triggers
+
+### readAndFilterLogfile
+
+Displays in the command window part of the `*events.tsv` file filtered by an
+element (e.g. 'trigger'). It can take the last output produced (through `cfg`)
+or any output BIDS compatible (through file path).
+
+## Keyboard functions: response collection and aborting experiment
+
+### testKeyboards
+
+Checks that the keyboards asked for are properly connected.
+
+If no key is pressed on the correct keyboard after the timeOut time this exits
+with an error.
+
+### getResponse
+
+It is wrapper function to use `KbQueue` which is definitely what you should use
+to collect responses.
+
+You can easily collect responses while running some other code at the same time.
+
+It will only take responses from one device which can simply be the "main
+keyboard" (the default device that PTB will find) or another keyboard connected
+to the computer or the response box that the participant is using.
+
+You can use it in a way so that it only takes responses from certain keys and
+ignore others (like the triggers from an MRI scanner).
+
+If you want to know more on how to use it check its help section and the
+`CPP_getResponseDemo.m`.
+
+In brief, there are several actions you can execute with this function.
+
+-   init: initialize the buffer for key presses on a given device (you can also
+    specify the keys of interest that should be listened to).
+-   start: start listening to the key presses (carefully insert into your
+    script - where do you want to start buffering the responses).
+-   check: till that point, it will check the buffer for all key presses. - It
+    only reports presses on the keys of interest mentioned at initialization. -
+    It **can** also check for presses on the escape key and abort if the escape
+    key is part of the keys of interest.
+-   flush: empties the buffer of key presses in case you want to discard any
+    previous key presses.
+-   stop: stops buffering key presses. You can still restart by calling "start"
+    again.
+-   release: closes the buffer for good.
+
+### pressSpaceForme
+
+Use that to stop your script and only restart when the space bar is pressed.
+
+This can be useful if as an experimenter you want to have one final check on
+some set up before giving the green light.
+
+### checkAbort
+
+A simple function that will quit your experiment if you press the key you have
+defined in `cfg.keyboard.escapeKey`.
+
+## Fixations
+
+### drawFixationCross
+
+Define the parameters of the fixation cross in `cfg` and `expParameters` and
+this does the rest.
+
+## Drawing dots
+
+## Drawing apertures
+
+## Randomization
+
+Functions that can be used to create random stimuli sequences.
+
+### shuffle
+
+Is just there to replace the Shuffle function from PTB in case it is not in the
+path. Can be useful for testing or for continuous integration.
+
+### setTargetPositionInSequence
+
+For a sequence of length `seqLength` where we want to insert `nbTarget` targets,
+this will return `nbTarget` random position in that sequence and make sure that
+they are not in consecutive positions.
+
+### repeatShuffleConditions
+
+Given `baseConditionVector`, a vector of conditions (coded as numbers), this
+will create a longer vector made of `nbRepeats` of this base vector and make
+sure that a given condition is not repeated one after the other.
diff --git a/docs/10_functions_description.md b/docs/10_functions_description.md
index f0bfa39..d1d50ab 100644
--- a/docs/10_functions_description.md
+++ b/docs/10_functions_description.md
@@ -26,7 +26,6 @@
     -   6.1. [shuffle](#shuffle)
     -   6.2. [setTargetPositionInSequence](#setTargetPositionInSequence)
     -   6.3. [repeatShuffleConditions](#repeatShuffleConditions)
-    -   6.4. [setUpRand](#setUprand)
 
 <!-- vscode-markdown-toc-config
 	numbering=true
@@ -215,8 +214,3 @@ they are not in consecutive positions.
 Given `baseConditionVector`, a vector of conditions (coded as numbers), this
 will create a longer vector made of `nbRepeats` of this base vector and make
 sure that a given condition is not repeated one after the other.
-
-### 6.4. <a name='setUpRand'></a>setUpRand
-
-Resets the seed of the random number generator. Will "adapt" depending on the matlab/octave version.
- It is of great importance to do this before anything else!

From 58a4e6b6aa77922f3ee25bb1c900078ba17b2beb Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 25 Sep 2020 20:33:30 +0200
Subject: [PATCH 08/15] fix function for computing radial motion

---
 src/dot/computeRadialMotionDirection.m    |  4 ++--
 tests/test_computeRadialMotionDirection.m | 10 ++++------
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/src/dot/computeRadialMotionDirection.m b/src/dot/computeRadialMotionDirection.m
index 0c5f7bf..1879f61 100644
--- a/src/dot/computeRadialMotionDirection.m
+++ b/src/dot/computeRadialMotionDirection.m
@@ -1,8 +1,8 @@
 function angleMotion = computeRadialMotionDirection(positions, dotMatrixWidth, dots)
 
-    cartesianCoordinates = computeCartCoord(positions, dotMatrixWidth);
+    positions = computeCartCoord(positions, dotMatrixWidth);
 
-    [angleMotion, ~] = cart2pol(cartesianCoordinates(:, 1), cartesianCoordinates(:, 2));
+    [angleMotion, ~] = cart2pol(positions(:, 1), positions(:, 2));
     angleMotion = angleMotion / pi * 180;
 
     if dots.direction == -666
diff --git a/tests/test_computeRadialMotionDirection.m b/tests/test_computeRadialMotionDirection.m
index 38083d6..d97767b 100644
--- a/tests/test_computeRadialMotionDirection.m
+++ b/tests/test_computeRadialMotionDirection.m
@@ -10,9 +10,7 @@ function test_computeRadialMotionDirectionBasic()
 
     %% set up
 
-    cfg.design.motionType = 'radial';
-    cfg.dot.matrixWidth = 50; % in pixels
-    cfg.screen.winWidth = 100; % in pixels
+    cfg.dot.matrixWidth = 100; % in pixels
     cfg.timing.eventDuration = 2;
 
     dots.direction = 666;
@@ -23,8 +21,8 @@ function test_computeRadialMotionDirectionBasic()
                       0, 100 / 2; ...
                       0, 0; ...
                       100 / 2, 0];
-
-    %     direction = computeRadialMotionDirection(cfg, positions, direction);
+    
+    angleMotion = computeRadialMotionDirection(dots.positions, cfg.dot.matrixWidth, dots);
 
     expectedDirection = [
                          0; ... right
@@ -36,6 +34,6 @@ function test_computeRadialMotionDirectionBasic()
 
     %% test
 
-    %     assertEqual(expectedDirection, direction);
+    assertEqual(angleMotion, expectedDirection);
 
 end

From 922b631abbeefbfd0aa46bfe1ec373f0f3a06d43 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 25 Sep 2020 21:14:50 +0200
Subject: [PATCH 09/15] do radial motion simulation

---
 manualTests/test_radialMotion.m | 24 ++++++++++++++++++++++++
 src/dot/computeCartCoord.m      |  1 -
 src/dot/dotMotionSimulation.m   | 18 +++++++++---------
 src/dot/seedDots.m              |  3 +++
 4 files changed, 36 insertions(+), 10 deletions(-)
 create mode 100644 manualTests/test_radialMotion.m

diff --git a/manualTests/test_radialMotion.m b/manualTests/test_radialMotion.m
new file mode 100644
index 0000000..c8135b1
--- /dev/null
+++ b/manualTests/test_radialMotion.m
@@ -0,0 +1,24 @@
+
+% ensure that dog homogenity is not too low when we kill dots often enough
+
+nbEvents = 1;
+doPlot = true;
+
+thisEvent.direction = -666; % degrees
+thisEvent.speed = 1; % pix per frame
+
+cfg.design.motionType = 'radial';
+
+cfg.dot.coherence = 1; % proportion
+cfg.dot.lifeTime = Inf; % in seconds
+cfg.dot.matrixWidth = 1000; % in pixels
+cfg.dot.proportionKilledPerFrame = 0;
+cfg.dot.number = 10;
+
+cfg.timing.eventDuration = 100; % in seconds
+
+
+relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, nbEvents, doPlot);
+
+
+
diff --git a/src/dot/computeCartCoord.m b/src/dot/computeCartCoord.m
index 2982138..a2c6f40 100644
--- a/src/dot/computeCartCoord.m
+++ b/src/dot/computeCartCoord.m
@@ -4,5 +4,4 @@
         [positions(:, 1) - dotMatrixWidth / 2, ... % x coordinate
          positions(:, 2) - dotMatrixWidth / 2]; % y coordinate
 
-    %         cartesianCoordinates = positions;
 end
diff --git a/src/dot/dotMotionSimulation.m b/src/dot/dotMotionSimulation.m
index 25ca7ae..72a4a99 100644
--- a/src/dot/dotMotionSimulation.m
+++ b/src/dot/dotMotionSimulation.m
@@ -13,7 +13,7 @@
     end
 
     if nargin < 2
-        thisEvent.direction = 0; % degrees
+        thisEvent.direction = 90; % degrees
         thisEvent.speed = 1; % pix per frame
     end
 
@@ -23,7 +23,7 @@
 
         cfg.dot.coherence = 1; % proportion
 
-        cfg.dot.lifeTime = .1; % in seconds
+        cfg.dot.lifeTime = Inf; % in seconds
 
         cfg.dot.matrixWidth = 250; % in pixels
 
@@ -42,13 +42,15 @@
     % dot size
     cfg.dot.sizePix = 1;
 
-    % We fill 25% of the screen with dots
-    cfg.dot.number = round(cfg.dot.matrixWidth^2 * 25 / 100);
+    
+    if ~isfield(cfg.dot, 'number')
+        % We fill 25% of the screen with dots
+        cfg.dot.number = round(cfg.dot.matrixWidth^2 * 25 / 100);
+    end
 
     fprintf(1, '\n\nDot motion simulation:');
 
     nbFrames = ceil(cfg.timing.eventDuration / cfg.screen.ifi);
-    %     frameToReport = round(linspace(1, nbFrames, 20));
 
     % to keep track of where the dots have been
     dotDensity = zeros(cfg.dot.matrixWidth);
@@ -60,10 +62,6 @@
 
         for iFrame = 1:nbFrames
 
-            %         if any(frameToReport == iFrame)
-            %             fprintf(1, '.');
-            %         end
-
             [dots] = updateDots(dots, cfg);
 
             dotDensity = updateDotDensity(dotDensity, dots);
@@ -83,6 +81,8 @@
         axis square;
         title('dot density');
     end
+    
+    fprintf(1, '\n');
 
 end
 
diff --git a/src/dot/seedDots.m b/src/dot/seedDots.m
index 1e1fecb..c219ea9 100644
--- a/src/dot/seedDots.m
+++ b/src/dot/seedDots.m
@@ -14,6 +14,9 @@
     directionAllDots = setDotDirection(positions, cfg, dots, isSignal);
     [horVector, vertVector] = decomposeMotion(directionAllDots);
 
+    if strcmp(cfg.design.motionType, 'radial')
+        vertVector = vertVector * -1;
+    end
     % we were working with unit vectors. we now switch to pixels
     speeds = [horVector, vertVector] * dots.speedPixPerFrame;
 

From 2a020472276bd9bef1f65b6b9cf93a0dd3252ae8 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 25 Sep 2020 21:24:01 +0200
Subject: [PATCH 10/15] mh fix

---
 manualTests/test_radialMotion.m           | 5 -----
 src/dot/dotMotionSimulation.m             | 3 +--
 tests/test_computeRadialMotionDirection.m | 2 +-
 3 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/manualTests/test_radialMotion.m b/manualTests/test_radialMotion.m
index c8135b1..2d56f36 100644
--- a/manualTests/test_radialMotion.m
+++ b/manualTests/test_radialMotion.m
@@ -1,4 +1,3 @@
-
 % ensure that dog homogenity is not too low when we kill dots often enough
 
 nbEvents = 1;
@@ -17,8 +16,4 @@
 
 cfg.timing.eventDuration = 100; % in seconds
 
-
 relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, nbEvents, doPlot);
-
-
-
diff --git a/src/dot/dotMotionSimulation.m b/src/dot/dotMotionSimulation.m
index 72a4a99..3d2819a 100644
--- a/src/dot/dotMotionSimulation.m
+++ b/src/dot/dotMotionSimulation.m
@@ -42,7 +42,6 @@
     % dot size
     cfg.dot.sizePix = 1;
 
-    
     if ~isfield(cfg.dot, 'number')
         % We fill 25% of the screen with dots
         cfg.dot.number = round(cfg.dot.matrixWidth^2 * 25 / 100);
@@ -81,7 +80,7 @@
         axis square;
         title('dot density');
     end
-    
+
     fprintf(1, '\n');
 
 end
diff --git a/tests/test_computeRadialMotionDirection.m b/tests/test_computeRadialMotionDirection.m
index d97767b..86f65fe 100644
--- a/tests/test_computeRadialMotionDirection.m
+++ b/tests/test_computeRadialMotionDirection.m
@@ -21,7 +21,7 @@ function test_computeRadialMotionDirectionBasic()
                       0, 100 / 2; ...
                       0, 0; ...
                       100 / 2, 0];
-    
+
     angleMotion = computeRadialMotionDirection(dots.positions, cfg.dot.matrixWidth, dots);
 
     expectedDirection = [

From 728967740549f8cd7319073d55932a5f3fc37d66 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 25 Sep 2020 22:18:22 +0200
Subject: [PATCH 11/15] MS / MST ready

---
 manualTests/test_radialMotion.m | 9 ++++-----
 src/aperture/apertureTexture.m  | 2 ++
 src/dot/dotTexture.m            | 5 ++++-
 3 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/manualTests/test_radialMotion.m b/manualTests/test_radialMotion.m
index 2d56f36..d8aa3bc 100644
--- a/manualTests/test_radialMotion.m
+++ b/manualTests/test_radialMotion.m
@@ -1,19 +1,18 @@
 % ensure that dog homogenity is not too low when we kill dots often enough
 
-nbEvents = 1;
+nbEvents = 10;
 doPlot = true;
 
-thisEvent.direction = -666; % degrees
+thisEvent.direction = 666; % degrees
 thisEvent.speed = 1; % pix per frame
 
 cfg.design.motionType = 'radial';
 
 cfg.dot.coherence = 1; % proportion
 cfg.dot.lifeTime = Inf; % in seconds
-cfg.dot.matrixWidth = 1000; % in pixels
+cfg.dot.matrixWidth = 250; % in pixels
 cfg.dot.proportionKilledPerFrame = 0;
-cfg.dot.number = 10;
 
-cfg.timing.eventDuration = 100; % in seconds
+cfg.timing.eventDuration = 10; % in seconds
 
 relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, nbEvents, doPlot);
diff --git a/src/aperture/apertureTexture.m b/src/aperture/apertureTexture.m
index 87a4f03..90b9307 100644
--- a/src/aperture/apertureTexture.m
+++ b/src/aperture/apertureTexture.m
@@ -106,6 +106,8 @@
 
         case 'circle'
 
+            Screen('Fillrect', cfg.aperture.texture, cfg.color.background);
+
             diameter = cfg.aperture.widthPix;
 
             if isfield(cfg.aperture, 'xPosPix')
diff --git a/src/dot/dotTexture.m b/src/dot/dotTexture.m
index b4036bf..50e287b 100644
--- a/src/dot/dotTexture.m
+++ b/src/dot/dotTexture.m
@@ -11,12 +11,15 @@
 
             dotType = 2;
 
+            xCenter = cfg.screen.center(1) + thisEvent.dotCenterXPosPix;
+            yCenter = cfg.screen.center(2);
+
             Screen('FillRect', cfg.dot.texture, cfg.color.background);
             Screen('DrawDots', cfg.dot.texture, ...
                    thisEvent.dot.positions, ...
                    cfg.dot.sizePix, ...
                    cfg.dot.color, ...
-                   cfg.screen.center, ...
+                   [xCenter yCenter], ...
                    dotType);
 
         case 'draw'

From cf420ac9d01d4ba9aa55b0a6fedcc7b54522a421 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 30 Sep 2020 17:49:26 +0200
Subject: [PATCH 12/15] add comments

---
 manualTests/test_radialMotion.m | 17 +++++++++++------
 src/dot/dotMotionSimulation.m   |  4 +++-
 2 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/manualTests/test_radialMotion.m b/manualTests/test_radialMotion.m
index d8aa3bc..86e4db3 100644
--- a/manualTests/test_radialMotion.m
+++ b/manualTests/test_radialMotion.m
@@ -1,18 +1,23 @@
-% ensure that dog homogenity is not too low when we kill dots often enough
+% ensure that dot density contrast is not too low when we kill dots often enough
 
-nbEvents = 10;
+% There is an actual official unit test in the tests folder so this here is more
+% to have the visualization turned on.
+
+nbEvents = 100;
 doPlot = true;
 
-thisEvent.direction = 666; % degrees
+thisEvent.direction = 0; % degrees
 thisEvent.speed = 1; % pix per frame
 
 cfg.design.motionType = 'radial';
 
 cfg.dot.coherence = 1; % proportion
-cfg.dot.lifeTime = Inf; % in seconds
+cfg.dot.lifeTime = .1; % in seconds
 cfg.dot.matrixWidth = 250; % in pixels
 cfg.dot.proportionKilledPerFrame = 0;
 
-cfg.timing.eventDuration = 10; % in seconds
+cfg.timing.eventDuration = 1.8; % in seconds
+
+relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, nbEvents, doPlot)
+
 
-relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, nbEvents, doPlot);
diff --git a/src/dot/dotMotionSimulation.m b/src/dot/dotMotionSimulation.m
index 3d2819a..f160fad 100644
--- a/src/dot/dotMotionSimulation.m
+++ b/src/dot/dotMotionSimulation.m
@@ -13,7 +13,7 @@
     end
 
     if nargin < 2
-        thisEvent.direction = 90; % degrees
+        thisEvent.direction = 0; % degrees
         thisEvent.speed = 1; % pix per frame
     end
 
@@ -73,6 +73,8 @@
     % trim the edges (to avoid super high/low values
     dotDensity = dotDensity(2:end - 1, 2:end - 1);
 
+    % computes the maximum difference in dot density over the all screen
+    % to be used for unit test
     relativeDensityContrast = (max(dotDensity(:)) - min(dotDensity(:))) / max(dotDensity(:));
 
     if doPlot

From 970743fb4d10b460b5c848058014a9b2470e2a45 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 30 Sep 2020 17:55:11 +0200
Subject: [PATCH 13/15] fix doc

---
 docs/00-index.md                 |   2 +-
 docs/10-functions-description.md |   5 +
 docs/10_functions_description.md | 216 -------------------------------
 3 files changed, 6 insertions(+), 217 deletions(-)
 delete mode 100644 docs/10_functions_description.md

diff --git a/docs/00-index.md b/docs/00-index.md
index e0ceec6..33c377c 100644
--- a/docs/00-index.md
+++ b/docs/00-index.md
@@ -193,7 +193,7 @@ let PTB find and use the default device.
 ## 3. <a name='functionsdescriptions'></a>functions descriptions
 
 The main functions of the toolbox are described
-[here](./10_functions_description.md).
+[here](./10-functions-description.md).
 
 ## 4. <a name='Annexes'></a>Annexes
 
diff --git a/docs/10-functions-description.md b/docs/10-functions-description.md
index ce76c4c..fb562ce 100644
--- a/docs/10-functions-description.md
+++ b/docs/10-functions-description.md
@@ -212,3 +212,8 @@ they are not in consecutive positions.
 Given `baseConditionVector`, a vector of conditions (coded as numbers), this
 will create a longer vector made of `nbRepeats` of this base vector and make
 sure that a given condition is not repeated one after the other.
+
+### 6.4. setUpRand
+
+Set up the randomizers for uniform and normal distributions. It is of great
+importance to do this before anything else!
diff --git a/docs/10_functions_description.md b/docs/10_functions_description.md
deleted file mode 100644
index d1d50ab..0000000
--- a/docs/10_functions_description.md
+++ /dev/null
@@ -1,216 +0,0 @@
-# functions description
-
-<!-- vscode-markdown-toc -->
-
--   1. [ General functions](#Generalfunctions)
-    -   1.1. [initPTB](#initPTB)
-    -   1.2. [cleanUp](#cleanUp)
-    -   1.3. [getExperimentStart](#getExperimentStart)
-    -   1.4. [getExperimentEnd](#getExperimentEnd)
-    -   1.5. [degToPix](#degToPix)
-    -   1.6. [computeFOV](#computeFOV)
-    -   1.7. [eyeTracker](#eyeTracker)
-    -   1.8. [standByScreen](#standByScreen)
-    -   1.9. [waitForTrigger](#waitForTrigger)
-    -   1.10. [waitFor](#waitFor)
-    -   1.11. [readAndFilterLogfile](#readAndFilterLogfile)
--   2. [Keyboard functions: response collection and aborting experiment](#Keyboardfunctions:responsecollectionandabortingexperiment)
-    -   2.1. [testKeyboards](#testKeyboards)
-    -   2.2. [getResponse](#getResponse)
-    -   2.3. [pressSpaceForme](#pressSpaceForme)
--   3. [Fixations](#Fixations)
-    -   3.1. [drawFixationCross](#drawFixationCross)
--   4. [Drawing dots](#Drawingdots)
--   5. [Drawing apertures](#Drawingapertures)
--   6. [Randomization](#Randomization)
-    -   6.1. [shuffle](#shuffle)
-    -   6.2. [setTargetPositionInSequence](#setTargetPositionInSequence)
-    -   6.3. [repeatShuffleConditions](#repeatShuffleConditions)
-
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-
-## 1. <a name='Generalfunctions'></a> General functions
-
-### 1.1. <a name='initPTB'></a>initPTB
-
-This will initialize PsychToolBox.
-
-It is pretty much necessary to use this function to set up the stage for using
-any other functions of CPP_PTB.
-
--   checks OS and PTB version
--   set some defaults
--   set the screen details
-    -   the window opened takes the whole screen by default
-    -   set in debug mode with window transparency if necessary
-    -   can skip synch test if you ask for it (nicely)
-    -   gets the flip interval
-    -   computes the pixel per degree of visual angle
--   set fixation cross details
--   set font details
--   keyboard
--   hides cursor
--   sound
-
-### 1.2. <a name='cleanUp'></a>cleanUp
-
-A wrapper function to close all windows, ports, show mouse cursor, close
-keyboard queues and give you back access to the keyboards.
-
-### 1.3. <a name='getExperimentStart'></a>getExperimentStart
-
-Wrapper function that will show a fixation cross and collect a start timestamp
-in `cfg.experimentStart`
-
-### 1.4. <a name='getExperimentEnd'></a>getExperimentEnd
-
-Wrapper function that will show a fixation cross and display in the console the
-whole experiment's duration in minutes and seconds
-
-### 1.5. <a name='degToPix'></a>degToPix
-
-For a given field value in degrees of visual angle in the input `structure`,
-this computes its value in pixel using the pixel per degree value of the `cfg`
-structure and returns a structure with an additional field with Pix suffix
-holding that new value.
-
-### 1.6. <a name='computeFOV'></a>computeFOV
-
-Gives you the width of the field on view in degress of visual angle based on the
-screen width and distance to the screen in cm (taken from the `cfg`)
-
-### 1.7. <a name='eyeTracker'></a>eyeTracker
-
-This will handle the Eye Tracker (EyeLink set up) and can be called to
-initialize the connection and start the calibration, start/stop eye(s) movement
-recordings and save the `*.edf` file (named with BIDS specification from
-cpp-lln-lab/CPP_BIDS).
-
-There are several actions to perform:
-
--   Calibration: to initialize EyeLink and run calibration
-    -   'default calibration' (default) will run a calibration with 6 points
-    -   'custom calibration' (cfg.eyeTracker.defaultCalibration = 'false') will
-        run a calibration with 6 points but the experimenter can choose their
-        position on the screen
--   StartRecording: to start eye movements recording
--   Message: will add a tag (e.g. 'Block_n1') in the ET output file, the tag is
-    a string and it is input from `varargin`
--   StopRecordings: to stop eye movements recornding
--   Shutdown: to save the `.edf` file with BIDS compliant name, from
-    cpp-lln-lab/CPP_BIDS, in the output folder and shut the connection between
-    the stimulation computer and the EyeLink computer
-
-### 1.8. <a name='standByScreen'></a>standByScreen
-
-It shows a basic one-page instruction stored in `cfg.task.instruction` and wait
-for `space` stroke.
-
-### 1.9. <a name='waitForTrigger'></a>waitForTrigger
-
-Counts a certain number of triggers coming from the mri/scanner before
-returning. Requires number of triggers to wait for.
-
-This can also be used if you want to let the scanner pace the experiment and you
-want to synch stimulus presentation to the scanner trigger.
-
-### 1.10. <a name='waitFor'></a>waitFor
-
-A generic function that you can use to for a certain amount of time or a number
-of triggers
-
-### 1.11. <a name='readAndFilterLogfile'></a>readAndFilterLogfile
-
-Displays in the command window part of the `*events.tsv` file filtered by an
-element (e.g. 'trigger'). It can take the last output produced (through `cfg`)
-or any output BIDS compatible (through file path).
-
-## 2. <a name='Keyboardfunctions:responsecollectionandabortingexperiment'></a>Keyboard functions: response collection and aborting experiment
-
-### 2.1. <a name='testKeyboards'></a>testKeyboards
-
-Checks that the keyboards asked for are properly connected.
-
-If no key is pressed on the correct keyboard after the timeOut time this exits
-with an error.
-
-### 2.2. <a name='getResponse'></a>getResponse
-
-It is wrapper function to use `KbQueue` which is definitely what you should use
-to collect responses.
-
-You can easily collect responses while running some other code at the same time.
-
-It will only take responses from one device which can simply be the "main
-keyboard" (the default device that PTB will find) or another keyboard connected
-to the computer or the response box that the participant is using.
-
-You can use it in a way so that it only takes responses from certain keys and
-ignore others (like the triggers from an MRI scanner).
-
-If you want to know more on how to use it check its help section and the
-`CPP_getResponseDemo.m`.
-
-In brief, there are several actions you can execute with this function.
-
--   init: initialize the buffer for key presses on a given device (you can also
-    specify the keys of interest that should be listened to).
--   start: start listening to the key presses (carefully insert into your
-    script - where do you want to start buffering the responses).
--   check: till that point, it will check the buffer for all key presses. - It
-    only reports presses on the keys of interest mentioned at initialization. -
-    It **can** also check for presses on the escape key and abort if the escape
-    key is part of the keys of interest.
--   flush: empties the buffer of key presses in case you want to discard any
-    previous key presses.
--   stop: stops buffering key presses. You can still restart by calling "start"
-    again.
--   release: closes the buffer for good.
-
-### 2.3. <a name='pressSpaceForme'></a>pressSpaceForme
-
-Use that to stop your script and only restart when the space bar is pressed.
-
-This can be useful if as an experimenter you want to have one final check on
-some set up before giving the green light.
-
-### checkAbort
-
-A simple function that will quit your experiment if you press the key you have
-defined in `cfg.keyboard.escapeKey`.
-
-## 3. <a name='Fixations'></a>Fixations
-
-### 3.1. <a name='drawFixationCross'></a>drawFixationCross
-
-Define the parameters of the fixation cross in `cfg` and `expParameters` and
-this does the rest.
-
-## 4. <a name='Drawingdots'></a>Drawing dots
-
-## 5. <a name='Drawingapertures'></a>Drawing apertures
-
-## 6. <a name='Randomization'></a>Randomization
-
-Functions that can be used to create random stimuli sequences.
-
-### 6.1. <a name='shuffle'></a>shuffle
-
-Is just there to replace the Shuffle function from PTB in case it is not in the
-path. Can be useful for testing or for continuous integration.
-
-### 6.2. <a name='setTargetPositionInSequence'></a>setTargetPositionInSequence
-
-For a sequence of length `seqLength` where we want to insert `nbTarget` targets,
-this will return `nbTarget` random position in that sequence and make sure that
-they are not in consecutive positions.
-
-### 6.3. <a name='repeatShuffleConditions'></a>repeatShuffleConditions
-
-Given `baseConditionVector`, a vector of conditions (coded as numbers), this
-will create a longer vector made of `nbRepeats` of this base vector and make
-sure that a given condition is not repeated one after the other.

From 5a6dc1e6d9c156df27d2780e278a82bfe2e77481 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 30 Sep 2020 17:57:41 +0200
Subject: [PATCH 14/15] mh fix

---
 manualTests/test_radialMotion.m | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/manualTests/test_radialMotion.m b/manualTests/test_radialMotion.m
index 86e4db3..6cb305a 100644
--- a/manualTests/test_radialMotion.m
+++ b/manualTests/test_radialMotion.m
@@ -18,6 +18,4 @@
 
 cfg.timing.eventDuration = 1.8; % in seconds
 
-relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, nbEvents, doPlot)
-
-
+relativeDensityContrast = dotMotionSimulation(cfg, thisEvent, nbEvents, doPlot);

From 9e6f7a2934bd7e05b5ba1b8edf876edcf1f0fb62 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 30 Sep 2020 18:00:02 +0200
Subject: [PATCH 15/15] fix dead link

---
 README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README.md b/README.md
index ec3fcf5..3a249e2 100644
--- a/README.md
+++ b/README.md
@@ -183,7 +183,6 @@ In practice, we use the following regular expression for function names:
 >
 > -   A quick [intro to regular expression](https://www.rexegg.com/)
 > -   And many websites allow you to "design and test" your regular expression:
->     -   [regexr](https://regexr.com/)
 >     -   [regexper](https://regexper.com/#%5Ba-z%5D%2B%28%28%5BA-Z%5D%7C%5B0-9%5D%29%7B1%7D%5Ba-z%5D%2B%29)
 >     -   ...