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‎README.md‎

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[![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/CPP_PTB/actions)
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![](https://github.com/cpp-lln-lab/CPP_PTB/workflows/CI/badge.svg)
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[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_BIDS.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_PTB)
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[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_PTB.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_PTB)
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[![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_PTB/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/CPP_PTB)
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<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
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[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)

‎docs/functions_description.md‎

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* 1.6. [eyeTracker](#eyeTracker)
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* 1.7. [standByScreen](#standByScreen)
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* 1.8. [waitForTrigger](#waitForTrigger)
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* 1.9. [readAndFilterLogfile](#readAndFilterLogfile)
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* 2. [Keyboard functions: response collection and aborting experiment](#Keyboardfunctions:responsecollectionandabortingexperiment)
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* 2.1. [testKeyboards](#testKeyboards)
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* 2.2. [getResponse](#getResponse)
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* 3.1. [drawFixationCross](#drawFixationCross)
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* 4. [Drawing dots](#Drawingdots)
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* 5. [Drawing apertures](#Drawingapertures)
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* 6. [Randomization](#Randomization)
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* 6.1. [shuffle](#shuffle)
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* 6.2. [setTargetPositionInSequence](#setTargetPositionInSequence)
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* 6.3. [repeatShuffleConditions](#repeatShuffleConditions)
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<!-- vscode-markdown-toc-config
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numbering=true
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Counts a certain number of triggers coming from the mri/scanner before returning.
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Requires number of triggers to wait for.
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### 1.9. <a name='readAndFilterLogfile'></a>readAndFilterLogfile
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Displays in the command window part of the `*events.tsv` file filterd by an element (e.g. 'trigger'). It can take the last output produced (through `cfg`) or any output BIDS compatible (through file path).
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## 2. <a name='Keyboardfunctions:responsecollectionandabortingexperiment'></a>Keyboard functions: response collection and aborting experiment
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## 4. <a name='Drawingdots'></a>Drawing dots
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## 5. <a name='Drawingapertures'></a>Drawing apertures
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## 6. <a name='Randomization'></a>Randomization
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Functions that can be used to create random stimuli sequences.
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### 6.1. <a name='shuffle'></a>shuffle
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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.
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### 6.2. <a name='setTargetPositionInSequence'></a>setTargetPositionInSequence
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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.
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### 6.3. <a name='repeatShuffleConditions'></a>repeatShuffleConditions
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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.

‎manualTests/miss_hit.cfg‎

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

‎tests/manualTests/test_getResponse.m‎ renamed to ‎manualTests/test_getResponse.m‎

File renamed without changes.

‎miss_hit.cfg‎

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# styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
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# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
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line_length: 100
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regex_function_name: "[a-z]+(([A-Z]){1}[A-Za-z]+)*"
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suppress_rule: "copyright_notice"

‎src/isOctave.m‎

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function retval = isOctave
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% Return: true if the environment is Octave.
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persistent cacheval % speeds up repeated calls
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if isempty (cacheval)
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cacheval = (exist ('OCTAVE_VERSION', 'builtin') > 0);
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end
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retval = cacheval;
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end

‎src/randomization/repeatShuffleConditions.m‎

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function shuffledRepeats = repeatShuffleConditions(baseConditionVector, nbRepeats)
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% shuffledRepeats = repeatShuffleConditions(baseConditionVector, nbRepeats)
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%
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% given baseConditionVector, a vector of conditions (coded as numbers), this will
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% create a longer vector made of nbRepeats of this base vector and make sure
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% that a given condition is not repeated one after the other
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% TODO
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% - needs some input checks to make sure that there is actually a solution
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% for this randomization (e.g having [1 1 1 1 1 2] as input will lead to an
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% infinite loop)
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if numel(unique(baseConditionVector)) == 1
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error('There should be more than one condition to shuffle');
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end
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baseConditionVector = baseConditionVector(:)';
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while 1
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tmp = [];
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for iRepeat = 1:nbRepeats
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tmp = [tmp, shuffle(baseConditionVector)];
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end
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if ~any(diff(tmp, [], 2) == 0)
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break
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end
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end
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shuffledRepeats = tmp;
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end

‎src/randomization/setTargetPositionInSequence.m‎

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function chosenPositions = setTargetPositionInSequence(seqLength, nbTarget, forbiddenPos)
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% chosenPositions = setTargetPositionInSequence(seqLength, nbTarget, forbiddenPos)
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%
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% For a sequence of length seqLength where we want to insert nbTarget targets, this
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% will return nbTarget random position in that sequence and make sure that,
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% they are not consecutive positions.
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REPLACE = false;
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allowedPositions = setxor(forbiddenPos, 1:seqLength);
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chosenPositions = [];
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if nbTarget < 1
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return
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elseif nbTarget == 1
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chosenPositions = randsample(allowedPositions, nbTarget, REPLACE);
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else
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targetDifference = 0;
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while any(abs(targetDifference) < 2)
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chosenPositions = randsample(allowedPositions, nbTarget, REPLACE);
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chosenPositions = sort(chosenPositions);
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targetDifference = diff(chosenPositions, [], 2);
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end
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end
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end

‎src/randomization/shuffle.m‎

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function shuffled = shuffle(unshuffled)
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% in case PTB is not in the path
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% mostly for unit test
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%
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try
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shuffled = Shuffle(unshuffled);
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catch
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shuffled = unshuffled(randperm(length(unshuffled)));
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end
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end

‎src/readAndFilterLogfile.m‎

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function outputFiltered = readAndFilterLogfile(columnName, filterBy, varargin)
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% outputFiltered = readOutputFilter(filterHeader, filterContent, varargin)
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%
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% It will display in the command window the content of the `output.tsv' filtered by one element
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% of a target column.
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%
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% DEPENDENCIES:
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% - bids_matlab (from CPP_BIDS)
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%
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% INPUT:
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%
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% - columnName: string, the header of the column where the content of insterest is stored
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% (e.g., for 'trigger' will be 'trial type')
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% - filterBy: string, the content of the column you want to filter out. It can take just
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% part of the content name (e.g., you want to display the triggers and you have
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% 'trigger_motion' and 'trigger_static', 'trigger' as input will do)
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% - varargin: either cfg (to display the last run output) or the file path as string
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%
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% OUTPUT:
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%
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% - outputFiltered: dataset with only the specified content, to see it in the command window
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% use display(outputFiltered)
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% Checke if input is cfg or the file path
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if ischar(varargin{1})
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tsvFile = varargin{1};
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elseif isstruct(varargin{1})
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tsvFile = fullfile(varargin{1}.dir.outputSubject, ...
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varargin{1}.fileName.modality, ...
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varargin{1}.fileName.events);
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end
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% Check if the file exists
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if ~exist(tsvFile, 'file')
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error([newline 'Input file does not exist']);
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end
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% Read the the tsv file and store each column in a field of `output` structure
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output = bids.util.tsvread(tsvFile);
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% Get the index of the target contentent to filter and display
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filterIdx = find(strncmp(output.(columnName), filterBy, length(filterBy)));
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% Convert the structure to dataset
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outputDataset = struct2dataset(output);
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% Get the dataset with the content of intereset
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outputFiltered = outputDataset(filterIdx, :);
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end

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