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Merge pull request #56 from cpp-lln-lab/remi-localizer_update
Updates from localizer: move sub-functions into CPP_PTB and update readme
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‎README.md‎

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## How to install
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### Use the matlab package manager
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### Download with git
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``` bash
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cd fullpath_to_directory_where_to_install
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# use git to download the code
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git clone https://github.com/cpp-lln-lab/CPP_PTB.git
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# move into the folder you have just created
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cd CPP_PTB
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# add the src folder to the matlab path and save the path
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matlab -nojvm -nosplash -r "addpath(fullfile(pwd)); savepath ();"
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```
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This repository can be added as a dependencies by listing it in a [mpm-requirements.txt file](.mpm-requirements.txt)
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as follows:
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Then get the latest commit:
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```bash
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# from the directory where you downloaded the code
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git pull origin master
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```
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CPP_PTB -u https://github.com/cpp-lln-lab/CPP_PTB.git
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To work with a specific version, create a branch at a specific version tag number
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```bash
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# creating and checking out a branch that will be calle version1 at the version tag v0.0.1
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git checkout -b version1 v0.0.1
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```
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You can then use the [matlab package manager](https://github.com/mobeets/mpm), to simply download the appropriate version of those dependencies and add them to your path by running a `getDependencies` function like the one below where you just need to replace `YOUR_EXPERIMENT_NAME` by the name of your experiment.
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### Add as a submodule
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```matlab
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function getDependencies(action)
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% Will install on your computer the matlab dependencies specified in the mpm-requirements.txt
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% and add them to the matlab path. The path is never saved so you need to run getDependencies() when
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% you start matlab.
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%
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% getDependencies('update') will force the update and overwrite previous version of the dependencies.
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%
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% getDependencies() If you only already have the appropriate version but just want to add them to the matlab path.
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experimentName = YOUR_EXPERIMENT_NAME;
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if nargin<1
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action = '';
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end
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switch action
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case 'update'
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% install dependencies
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mpm install -i mpm-requirements.txt -f -c YOUR_EXPERIMENT_NAME
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end
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% adds them to the path
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mpm_folder = fileparts(which('mpm'));
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addpath(genpath(fullfile(mpm_folder, 'mpm-packages', 'mpm-collections', experimentName)));
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end
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Add it as a submodule in the repo you are working on.
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``` bash
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cd fullpath_to_directory_where_to_install
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# use git to download the code
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git submodule add https://github.com/cpp-lln-lab/CPP_PTB.git
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# move into the folder you have just created
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cd CPP_PTB
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# add the src folder to the matlab path and save the path
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matlab -nojvm -nosplash -r "addpath(fullfile(pwd))"
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```
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To get the latest commit you then need to update the submodule with the information
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on its remote repository and then merge those locally.
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```bash
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git submodule update --remote --merge
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```
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Remember that updates to submodules need to be commited as well.
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**TO DO**
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<!-- Submodules
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pros: in principle, downloading the experiment you have the whole package plus the benefit to stay updated and use version control of this dependency. Can probably handle a use case in which one uses different version on different projects (e.g. older and newer projects).
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cons: for pro users and not super clear how to use it at the moment. -->
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### Direct download
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Download the code. Unzip. And add to the matlab path.
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Pick a specific version:
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https://github.com/cpp-lln-lab/CPP_PTB/releases
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Or take the latest commit (NOT RECOMMENDED):
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https://github.com/cpp-lln-lab/CPP_PTB/archive/master.zip
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**TO DO**
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<!-- Download a specific version and c/p it in a subfun folder
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pros: the easiest solution to share the code and 'installing' it on the stimulation computer (usually not the one used to develop the code).
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cons: extreme solution useful only at the very latest stage (i.e. one minute before acquiring your data); prone to be customized/modified (is it what we want?) -->
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## Setting up keyboards
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To select a specific keyboard to be used by the experimenter or the participant, you need to know

‎apertureTexture.m‎

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function cfg = apertureTexture(action, cfg, thisEvent)
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transparent = [0 0 0 0];
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switch action
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case 'init'
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% we take the screen height as maximum aperture width if not
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% specified.
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if ~isfield(cfg.aperture, 'width') || isempty(cfg.aperture.width)
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cfg.aperture.width = cfg.screen.winRect(4) / cfg.screen.ppd;
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end
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cfg.aperture = degToPix('width', cfg.aperture, cfg);
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cfg.aperture.texture = Screen('MakeTexture', cfg.screen.win, ...
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cfg.color.background(1) * ones(cfg.screen.winRect([4 3])));
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case 'make'
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switch cfg.aperture.type
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case 'none'
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Screen('Fillrect', cfg.aperture.texture, transparent);
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case 'circle'
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diameter = cfg.aperture.widthPix;
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xPos = cfg.screen.center(1);
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yPos = cfg.screen.center(2);
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if isfield(cfg.aperture, 'xPosPix')
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xPos = cfg.screen.center(1) + cfg.aperture.xPosPix;
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end
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if isfield(cfg.aperture, 'yPosPix')
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yPos = cfg.screen.center(2) + cfg.aperture.yPosPix;
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end
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Screen('FillOval', cfg.aperture.texture, transparent, ...
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CenterRectOnPoint([0 0 repmat(diameter, 1, 2)], ...
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xPos, yPos));
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end
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case 'draw'
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Screen('DrawTexture', cfg.screen.win, cfg.aperture.texture);
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% Screen('DrawTexture', cfg.screen.win, apertureTexture, ...
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% cfg.screen.winRect, cfg.screen.winRect, current.apertureAngle - 90);
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end
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end

‎computeFOV.m‎

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%
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% computes the number of degrees of visual angle in the whole field of view
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%
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% δ = 2 arctan ( d / 2D )
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%
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% δ is the angular diameter, and d is the actual diameter of the object,
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% and D is the distance to the object.
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% The result obtained is in radians.
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%
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FOV = 2 * ...
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(180 * (atan(cfg.screen.monitorWidth / (2 * cfg.screen.monitorDistance)) / pi));
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FOV = ...
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180 / pi * ...
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2 * atan(cfg.screen.monitorWidth / (2 * cfg.screen.monitorDistance));
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end

‎decompMotion.m‎

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function [horVector, vertVector] = decompMotion(angleMotion)
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% decompose angle of start motion into horizontal and vertical vector
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horVector = cos(pi * angleMotion / 180);
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vertVector = -sin(pi * angleMotion / 180);
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end

‎degToPix.m‎

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deg = getfield(structure, fieldName); %#ok<GFLD>
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structure = setfield(structure, [fieldName 'Pix'], ...
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floor(cfg.screen.ppd * deg)) ; %#ok<SFLD>
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floor(deg * cfg.screen.ppd)) ; %#ok<SFLD>
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end

‎dotTexture.m‎

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function cfg = dotTexture(action, cfg, thisEvent)
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switch action
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case 'init'
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cfg.dot.texture = Screen('MakeTexture', cfg.screen.win, ...
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cfg.color.background(1) * ones(cfg.screen.winRect([4 3])));
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case 'make'
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dotType = 2;
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Screen('FillRect', cfg.dot.texture, cfg.color.background);
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Screen('DrawDots', cfg.dot.texture, ...
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thisEvent.dot.positions, ...
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cfg.dot.sizePix, ...
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cfg.dot.color, ...
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cfg.screen.center, ...
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dotType);
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case 'draw'
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Screen('DrawTexture', cfg.screen.win, cfg.dot.texture);
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end
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end

‎drawFixation.m‎

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function drawFixation(cfg)
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% Define the parameters of the fixation cross in `cfg` and `expParameters`
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if strcmp(cfg.fixation.type, 'cross')
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smooth = 1;
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Screen('DrawLines', ...
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cfg.screen.win, ...
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cfg.fixation.allCoords, ...
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cfg.fixation.lineWidthPix, ...
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cfg.fixation.color, ...
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[cfg.screen.center(1) cfg.screen.center(2)], smooth);
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end
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end

‎drawFixationCross.m‎

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This file was deleted.

‎farewellScreen.m‎

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function farewellScreen(cfg)
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Screen('FillRect', cfg.screen.win, cfg.color.background, cfg.screen.winRect);
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DrawFormattedText(cfg.screen.win, 'Thank you!', 'center', 'center', cfg.text.color);
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Screen('Flip', cfg.screen.win);
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WaitSecs(cfg.mri.repetitionTime * 2);
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end

‎getExperimentEnd.m‎

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function cfg = getExperimentEnd(cfg)
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drawFixation(cfg);
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endExpmt = Screen('Flip', cfg.screen.win);
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disp(' ');
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ExpmtDur = endExpmt - cfg.experimentStart;
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ExpmtDurMin = floor(ExpmtDur / 60);
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ExpmtDurSec = mod(ExpmtDur, 60);
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disp(['Experiment lasted ', ...
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num2str(ExpmtDurMin), ' minutes ', ...
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num2str(ExpmtDurSec), ' seconds']);
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disp(' ');
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end

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