Difference between revisions of "Gitlab Repository Biofysica"
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| + | back to [[Programming]] | ||
==Description== | ==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. | 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|experiments]] with TDT System 3 or RZ6 | *Sound Localization [[#experiments|experiments]] with TDT System 3 or RZ6 | ||
*[[#EEG|EEG experiments]] | *[[#EEG|EEG experiments]] | ||
| Line 9: | Line 10: | ||
Data analysis: | Data analysis: | ||
| − | *Bayesian data analysis | + | *[[#Audition|Audition]] |
| − | * | + | *[[#Bayesian|Bayesian data analysis]] |
| − | + | *[[#Pupillometry|Pupillometry]] | |
| − | + | *[[#Reactiontime|Reaction time]] | |
| − | *Reaction time | + | *[[#Saccade|Saccade analysis]] |
| − | * | + | *[[#Spike|Spike analysis]] |
Other: | Other: | ||
*[[#utilities|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== | ==Repository content== | ||
| Line 29: | Line 42: | ||
===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/audiogram?ref_type=heads audiogram]=== | ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/audiogram?ref_type=heads audiogram]=== | ||
| − | Contains matlab and rcx code for | + | <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]=== | ===[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. | Contains basic and advanced functions for manipulating audiological units and spectra. | ||
*HRTF: contains matlab functions for calculating and manipulating head-related transfer functions. | *HRTF: contains matlab functions for calculating and manipulating head-related transfer functions. | ||
| Line 41: | Line 56: | ||
===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/bayesdataanalysis?ref_type=heads bayesdataanalysis]=== | ===[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: | Contains matlab scripts for bayesian data analysis based on programs for use with the book: | ||
| Line 48: | Line 64: | ||
*NHST: contains matlab script bayesfactor.m | *NHST: contains matlab script bayesfactor.m | ||
| − | *anova: contains matlab scripts for | + | *anova: contains matlab scripts for ANalysis Of VAriance (ANOVA) |
*binomial: contains matlab scripts for binomial analysis | *binomial: contains matlab scripts for binomial analysis | ||
*correlation: contains a matlab script for Pearson Correlation | *correlation: contains a matlab script for Pearson Correlation | ||
| Line 61: | Line 77: | ||
===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/eeg?ref_type=heads eeg]=== | ===[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). | 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]=== | ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/experiment?ref_type=heads experiment]=== | ||
<span id="experiments"></span> | <span id="experiments"></span> | ||
| − | Contains Matlab and other files for experiments and for controlling devices. | + | 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 | ||
===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/init.d?ref_type=heads init.d]=== | ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/init.d?ref_type=heads init.d]=== | ||
| Line 76: | Line 95: | ||
===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/nirs?ref_type=heads 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. | Contains NIRS related Matlab files and a NIRS analyse document. | ||
*basics: contains Matlab files for fnirs hemodynamics | *basics: contains Matlab files for fnirs hemodynamics | ||
| Line 84: | Line 104: | ||
===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/pupillometry?ref_type=heads 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. | Contains Matlab code for pupillometry measurements. | ||
===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/reactiontime?ref_type=heads 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. | Contains Matlab files for calculating reciprobit plots of saccadic latencies. | ||
===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/saccade?ref_type=heads 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. | ||
===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/spike?ref_type=heads 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. | ||
===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/utilities?ref_type=heads utilities]=== | ===[https://gitlab.science.ru.nl/marcw/biofysica/-/tree/master/utilities?ref_type=heads utilities]=== | ||
<span id="utilities"></span> | <span id="utilities"></span> | ||
| − | Contains | + | Contains general functions: |
| − | * | + | *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 also[[Coordinate systems]]. |
| − | * | + | *DSP: Signal processing: filters, power, smooth |
*FileIO: file utilities | *FileIO: file utilities | ||
*Graphics: graphics utilities | *Graphics: graphics utilities | ||
*Python: utilities for python installation and use in Matlab. | *Python: utilities for python installation and use in Matlab. | ||
| + | *RL_utilities: a diverse set of utilities programmed by Ruurd Lof | ||
*Statistics: utilities for statistics | *Statistics: utilities for statistics | ||
*Text: function for finding strings in a textcellarray | *Text: function for finding strings in a textcellarray | ||
| + | *Tutorials: How2 examples of all kinds of data analysis | ||
Latest revision as of 12:24, 23 September 2024
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:
- Sound Localization experiments with TDT System 3 or RZ6
- EEG experiments
- NIRS experiments
- Audiogram (arcMAA) with RZ6
Data analysis:
Other:
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
init.d
Contains Matlab initialization code. Maintained by Günter Windau.
liblsl
Contains LSL (LabStreamLayer) code. Maintained by Günter Windau.
nirs
Contains NIRS related Matlab files and a NIRS analyse document.
- basics: contains Matlab files for fnirs hemodynamics
- layout: contains EEG *.lay files and *.xml optode template files.
plot
Contains Matlab code for advanced plotting of figures and graphs
pupillometry
Contains Matlab code for pupillometry measurements.
reactiontime
Contains Matlab files for calculating reciprobit plots of saccadic latencies.
saccade
Contains Matlab code for Saccade analysis. Part of PANDA toolbox by Marc van Wanrooij.
spike
Contains Matlab code for spike analysis for neuro-physiological experiments. Part of PANDA toolbox by Marc van Wanrooij.
utilities
Contains general functions:
- 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