Difference between revisions of "Gitlab Repository Biofysica"

Latest revision as of 12:24, 23 September 2024

Description

The biofysica repository is the main repository written by and used in the Biophysics Department. The code consists mainly of for matlab code for performing experiments and analysing experimental data.

Experiments:

Sound Localization experiments with TDT System 3 or RZ6
EEG experiments
NIRS experiments
Audiogram (arcMAA) with RZ6

Data analysis:

Audition
Bayesian data analysis
Pupillometry
Reaction time
Saccade analysis
Spike analysis

Other:

utilities

N.B. The Matlab files beginning with 'pa_' are developed by Marc van Wanrooij and are originally part of the Perception and Action Toolbox (PandA).

How to install the toolbox

Download the biofysica toolbox from Gitlab and save it in C:\Users\MyName\Documents\MATLAB\biofysica
Add to your startup.m file:

addpath('C:\Users\MyName\Documents\MATLAB\biofysica'); 
init_biofysica;

When you are not certain how to use Gitlab you can find more info here: Gitlab.

Repository content

The repository has several directories:

TDT

Contains all relevant TDT manuals for ActiveX programming, RZ6, system3 and RPvdsEx programming.

MF1: contains info about the MF1 speaker kit of tucker davis
PM2rRBOXRZ6: contains info about connecting the RBOXRZ6 to the PM2r control port (DB25 digital I/O).
Users/Marc van Wanrooij: contains some *.rcx files used by Marc van Wanrooij

audiogram

Contains matlab and rcx code for the arcMAA experiment. MAA stands for Minimum Audible Angle. The experiments is done in the NIRS-EEG lab with the speaker arc.

audition

Contains basic and advanced functions for manipulating audiological units and spectra.

HRTF: contains matlab functions for calculating and manipulating head-related transfer functions.
localization: contains matlab functions for localization of stimuli.
oldpa: contains older matlab functions from the Panda toolbox.

backwards

Contains only the script loadtdt.m that reads a *.tdt file. It is no longer used.

bayesdataanalysis

Contains matlab scripts for bayesian data analysis based on programs for use with the book:

Kruschke, J. K. (2015). Doing Bayesian Data Analysis

The codebase also includes code from JAGS (Just another Gibbs sampler ), which is a program for simulation from Bayesian hierarchical models using Markov chain Monte Carlo (MCMC), developed by Martyn Plummer

NHST: contains matlab script bayesfactor.m
anova: contains matlab scripts for ANalysis Of VAriance (ANOVA)
binomial: contains matlab scripts for binomial analysis
correlation: contains a matlab script for Pearson Correlation
diagnose: contains matlab scripts for Markov Chain Monte Carlo (MCMC) diagnostics
functions: contains matlab script for several useful functions
psychophysics: contains matlab scripts for analysing psychometric functions (curves)
regression: contains matlab scripts for regression analysis
reparametrization: contains matlab scripts for %todo
statistics: contains matlab scripts for calculating summary statistics.
HDI: contains matlab scripts for calculating Highest Density Intervals (HDI)
utilities: contains matlab scripts for several utility functions used in the bayesian data analysis code.

eeg

Contains two EEG demos (AM tones and Oddball) with matlab code and RZ6 circuits (RPvdsEx files).

experiment

Contains Matlab and other files for experiments and for controlling devices. See Gitlab Repository Biofysica/experiment.

Experiments: SpherePrime, SphereTTL, SphereMinor, NewSpherePrime, SLIMS, arcMAA, ripple_prt_experiment, Experiment generator (Exp), psychoILD, HRTF, EEG
Devices: Panasonic PLC Led controller, DCN-LED Led controller, Panasonic Servomotors, Pupillabs
Other: BIOX toolbox, HDF5 toolbox, Ini-file toolbox, FileIO utilities, IP utilities, Modbus utilities, Mewtocol utilities, LSL utilities

basics: contains Matlab files for fnirs hemodynamics
layout: contains EEG *.lay files and *.xml optode template files.

Colors: get color codes from names in English, German, Dutch and Spanisch. See Colors in Matlab.
Coordinates: coordinate functions, coordinate classes and coordinate transformations. See alsoCoordinate systems.
DSP: Signal processing: filters, power, smooth
FileIO: file utilities
Graphics: graphics utilities
Python: utilities for python installation and use in Matlab.
RL_utilities: a diverse set of utilities programmed by Ruurd Lof
Statistics: utilities for statistics
Text: function for finding strings in a textcellarray
Tutorials: How2 examples of all kinds of data analysis

@@ Line 1: / Line 1: @@
+back to [[Programming]]
 ==Description==
 The biofysica repository is the main repository written by and used in the Biophysics Department. The code consists mainly of for matlab code for performing experiments and analysing experimental data.
-experiments:
+Experiments:
-*Sound Localization experiments with TDT System 3 or RZ6
+*Sound Localization [[#experiments|experiments]] with TDT System 3 or RZ6
-*EEG experiments
+*[[#EEG|EEG experiments]]
-*NIRS experiments
+*[[#NIRS|NIRS experiments]]
-*Audiogram (arcMAA) with RZ6
+*[[#Audiogram|Audiogram]] (arcMAA) with RZ6
 Data analysis:
-*Bayesian data analysis
+*[[#Audition|Audition]]
-*Saccade analysis
+*[[#Bayesian|Bayesian data analysis]]
-*Spike analysis
+*[[#Pupillometry|Pupillometry]]
-*Pupillometry
+*[[#Reactiontime|Reaction time]]
-*Reaction time
+*[[#Saccade|Saccade  analysis]]
-*Audition
+*[[#Spike|Spike analysis]]
 Other:
-*Plot utilities
+*[[#utilities|utilities]]
+N.B. The Matlab files beginning with 'pa_' are developed by '''[https://www.ru.nl/personen/wanrooij-m-van Marc van Wanrooij]''' and are originally part of the Perception and Action Toolbox (PandA).
+==How to install the toolbox==
+*Download the biofysica toolbox from [https://gitlab.science.ru.nl/marcw/biofysica Gitlab] and save it in C:\Users\MyName\Documents\MATLAB\biofysica
+*Add to your startup.m file:
+<pre>
+addpath('C:\Users\MyName\Documents\MATLAB\biofysica');
+init_biofysica;
+</pre>
+When you are not certain how to use Gitlab you can find more info here: [[Gitlab]].
 ==Repository content==
@@ Line 23: / Line 36: @@
 ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/TDT?ref_type=heads TDT]===
 Contains all relevant TDT manuals for ActiveX programming, RZ6, system3 and RPvdsEx programming.
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/TDT/MF1?ref_type=heads MF1]====
-Contains info about the MF1 speaker kit of tucker davis
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/TDT/PM2rRBOXRZ6?ref_type=heads PM2rRBOXRZ6]====
+*MF1: contains info about the MF1 speaker kit of tucker davis
-Contains info about connecting the RBOXRZ6 to the PM2r control port (DB25 digital I/O).
+*PM2rRBOXRZ6: contains info about connecting the RBOXRZ6 to the PM2r control port (DB25 digital I/O).
+*Users/Marc van Wanrooij: contains some *.rcx files used by Marc van Wanrooij
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/TDT/Users/Marc%20van%20Wanrooij?ref_type=heads Users/Marc van Wanrooij]====
-Contains some *.rcx files used by Marc van Wanrooij
 ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/audiogram?ref_type=heads audiogram]===
-Contains matlab and rcx code for making an audiogram.
+<span id="Audiogram"></span>
+Contains matlab and rcx code for the arcMAA experiment. MAA stands for Minimum Audible Angle. The experiments is done in the NIRS-EEG lab with the speaker arc.
 ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/audition?ref_type=heads audition]===
+<span id="Audition"></span>
 Contains basic and advanced functions for manipulating audiological units and spectra.
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/audition/HRTF?ref_type=heads HRTF]====
+*HRTF: contains matlab functions for calculating and manipulating head-related transfer functions.
-Contains matlab functions for calculating and manipulating head-related transfer functions.
+*localization: contains matlab functions for localization of stimuli.
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/audition/Localization?ref_type=heads localization]====
+*oldpa: contains older matlab functions from the Panda toolbox.
-Contains matlab functions for localization of stimuli.
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/audition/oldpa?ref_type=heads oldpa]====
-Contains older matlab functions from the Panda toolbox.
 ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/backwards?ref_type=heads backwards]===
@@ Line 48: / Line 56: @@
 ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis?ref_type=heads bayesdataanalysis]===
+<span id="Bayesian"></span>
 Contains matlab scripts for bayesian data analysis based on programs for use with the book:
@@ Line 54: / Line 63: @@
 The codebase also includes code from JAGS (Just another Gibbs sampler ), which is a program for simulation from Bayesian hierarchical models using Markov chain Monte Carlo (MCMC), developed by Martyn Plummer
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/NHST?ref_type=heads NHST]====
+*NHST: contains matlab script bayesfactor.m
-Contains matlab script bayesfactor.m
+*anova: contains matlab scripts for ANalysis Of VAriance (ANOVA)
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/anova?ref_type=heads anova]====
+*binomial: contains matlab scripts for binomial analysis
-Contains matlab scripts for analysis of variance (anova)
+*correlation: contains a matlab script for Pearson Correlation
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/binomial?ref_type=heads binomial]====
+*diagnose: contains matlab scripts for Markov Chain Monte Carlo (MCMC) diagnostics
-Contains matlab scripts for binomial analysis
+*functions: contains matlab script for several useful functions
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/correlation?ref_type=heads correlation]====
+*psychophysics: contains matlab scripts for analysing psychometric functions (curves)
-Contains a matlab script for Pearson Correlation
+*regression: contains matlab scripts for regression analysis
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/diagnose?ref_type=heads diagnose]====
+*reparametrization: contains matlab scripts for %todo
-Contains matlab scripts for Markov Chain Monte Carlo (MCMC) diagnostics
+*statistics: contains matlab scripts for calculating summary statistics.
+*HDI: contains matlab scripts for calculating Highest Density Intervals (HDI)
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/functions?ref_type=heads functions]====
+*utilities: contains matlab scripts for several utility functions used in the bayesian data analysis code.
-Contains matlab script for several useful functions
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/psychophysics?ref_type=heads psychophysics]====
-Contains matlab scripts for analysing psychometric functions (curves)
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/regression?ref_type=heads regression]====
-Contains matlab scripts for regression analysis
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/reparametrization?ref_type=heads reparametrization]====
-Contains matlab scripts for %todo
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/statistics?ref_type=heads statistics]====
-Contains matlab scripts for calculating summary statistics.
-=====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/statistics/HDI?ref_type=heads HDI]=====
-Contains matlab scripts for calculating Highest Density Intervals (HDI)
-====[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis/utilities?ref_type=heads utilities]====
-Contains matlab scripts for several utility functions used in the bayesian data analysis code.
 ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/eeg?ref_type=heads eeg]===
+<span id="EEG"></span>
 Contains two EEG demos (AM tones and Oddball) with matlab code and RZ6 circuits (RPvdsEx files).
 ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/experiment?ref_type=heads experiment]===
-Contains Matlab and other files for experiments and for controlling devices.
+<span id="experiments"></span>
+Contains Matlab and other files for experiments and for controlling devices. See [[Gitlab Repository Biofysica/experiment]].
-See [[Gitlab Repository Biofysica/experiment]].
+*Experiments: SpherePrime, SphereTTL, SphereMinor, NewSpherePrime, SLIMS, arcMAA, ripple_prt_experiment, Experiment generator (Exp), psychoILD, HRTF, EEG
+*Devices: Panasonic PLC Led controller, DCN-LED Led controller, Panasonic Servomotors, Pupillabs
+*Other: BIOX toolbox, HDF5 toolbox, Ini-file toolbox, FileIO utilities, IP utilities, Modbus utilities, Mewtocol utilities, LSL utilities
 ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/init.d?ref_type=heads init.d]===
 Contains Matlab initialization code. Maintained by Günter Windau.
-===liblsl===
+===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/liblsl?ref_type=heads liblsl]===
 Contains LSL (LabStreamLayer) code. Maintained by Günter Windau.
-===nirs===
+===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/nirs?ref_type=heads nirs]===
+<span id="NIRS"></span>
 Contains NIRS related Matlab files and a NIRS analyse document.
-====basics====
+*basics: contains Matlab files for fnirs hemodynamics
-Contains Matlab files for fnirs hemodynamics
+*layout: contains EEG *.lay files and *.xml optode template files.
-====layout====
-Contains EEG *.lay files and *.xml optode template files.
-===plot===
+===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/plot?ref_type=heads plot]===
 Contains Matlab code for advanced plotting of figures and graphs
-===pupillometry===
+===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/pupillometry?ref_type=heads pupillometry]===
+<span id="Pupillometry"></span>
 Contains Matlab code for pupillometry measurements.
-===reactiontime===
+===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/reactiontime?ref_type=heads reactiontime]===
+<span id="Reactiontime"></span>
 Contains Matlab files for calculating reciprobit plots of saccadic latencies.
-===saccade===
+===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/saccade?ref_type=heads saccade]===
-Contains Matlab code for Saccade analysis. Part of PANDA toolbox.
+<span id="Saccade"></span>
+Contains Matlab code for Saccade analysis. Part of PANDA toolbox by Marc van Wanrooij.
-===spike===
+===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/spike?ref_type=heads spike]===
-Contains Matlab code for spike analysis for neuro-physiological experiments. Part of PANDA toolbox.
+<span id="Spike"></span>
+Contains Matlab code for spike analysis for neuro-physiological experiments. Part of PANDA toolbox by Marc van Wanrooij.
-===utilities===
+===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/utilities?ref_type=heads utilities]===
-Contains Matlab utilities:
+<span id="utilities"></span>
-*Signal processing: filters, power, smooth
+Contains general functions:
-*Tutorials: How2 examples of all kinds of data analysis
+*Colors: get color codes from names in English, German, Dutch and Spanisch. See [[Colors in Matlab]].
-*Coördinates: several conversion functions for Azimuth, Elevation, Cartesian, Radial, Degrees, Quaternions etc...
+*Coordinates: coordinate functions, coordinate classes and coordinate transformations. See also[[Coordinate systems]].
+*DSP: Signal processing: filters, power, smooth
 *FileIO: file utilities
 *Graphics: graphics utilities
 *Python: utilities for python installation and use in Matlab.
+*RL_utilities: a diverse set of utilities programmed by Ruurd Lof
 *Statistics: utilities for statistics
 *Text: function for finding strings in a textcellarray
+*Tutorials: How2 examples of all kinds of data analysis

Difference between revisions of "Gitlab Repository Biofysica"

Latest revision as of 12:24, 23 September 2024

Contents

Description

How to install the toolbox

Repository content

TDT

audiogram

audition

backwards

bayesdataanalysis

eeg

experiment

init.d

liblsl

nirs

plot

pupillometry

reactiontime

saccade

spike

utilities

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