diff --git a/docs/scripts/index.m b/docs/scripts/index.m index 596a3a09..2b01a611 100644 --- a/docs/scripts/index.m +++ b/docs/scripts/index.m @@ -5,7 +5,7 @@ % experiments and processing the resulting data. % % For instructions on how to run the examples from the -% , see +% , see % <./paper_examples.html this guide>. %% Installing Rigbox @@ -17,7 +17,7 @@ % # <./install.html Detailed install instructions> % # -% # <./updating_code.html Updating the code> +% # <./install_Timeline.html Install instructions for using Timeline only> % %% Setting up experiments @@ -108,11 +108,9 @@ % * <./glossary.html Glossary of Rigbox terminology> % * <./using_visual_stimuli.html Details of the Signals viewing model> % * <./contributing.html How to edit the documentation> -% * <./release_notes_v260.html v2.6.0 release notes> -% * <./release_notes_v270.html v2.7.0 release notes> % %% Etc. % Author: Miles Wells % -% v0.1.4 +% v0.1.3 diff --git a/docs/scripts/install_Timeline.m b/docs/scripts/install_Timeline.m new file mode 100644 index 00000000..7cbbab3c --- /dev/null +++ b/docs/scripts/install_Timeline.m @@ -0,0 +1,120 @@ +%% Installing Rigbox for Timeline only +% Below are some easy step-by-step instructions for installing Rigbox +% exclusively to run Timeline. + +%% Requirements +% Timeline runs on MATLAB 2018b or later for Windows. Currently only +% are supported for acquiring data from hardware +% devices. +% +%%% Software +% Rigbox requires the following software to work properly: +% +% * Windows Operating System (7 or later, 64-bit) +% * MATLAB (2018b, also known as version 9.5, or later) +% * The MATLAB Data Acquisition Toolbox +% * The NI-DAQmx support package (_free_) +% * Psychophysics Toolbox (v3 or later, _free_) +% +%%% Hardware +% +% Below are a few minimum PC hardware requirements. +% +% * *Processor*: Intel Core i5-6500 @ 3.0 GHz (or similar) +% * *Memory*: DDR4 16 GB @ 2133 MHz (e.g. Corsair Vengeance 16 GB) +% +% +%% Install steps +% Below are detailed steps on installing all required software. If you +% already have software installed for a particular step, feel free to skip +% that step. +% +% # Install Windows 7 or later (Windows 10 is recommended). Windows must +% be must be 64-bit (sometimes called x64, x86_64, AMD64 or Intel 64). +% # Download and install by +% following their +% (See note 1). At +% , make sure to check the box for the Data Acquisition Toolbox, +% along with any other MATLAB Mathworks toolboxes you want, though for +% testing Rigbox, no other toolboxes are required (See note 2). NB: This +% step may take a while. +% # Once downloaded, open MATLAB by double-clicking on the MATLAB icon in +% the start menu. +% # Within MATLAB, install the NI-DAQmx Support Package (See note 2). NB: +% This step may take a while. +% # Download and install (See note +% 3). +% # Download the +% and save it into your |Documents/MATLAB| folder. +% # In the MATLAB Command Window (See note 4), type +% |DownloadPsychtoolbox(userpath)| (no quotes) and press enter. This will +% download and install PsychToolbox to MATLAB folder. At certain points in +% the installation it will print stuff to the Command Window and ask you to +% press any key to continue. Do this until the two angled brackes ('|>>|') +% reappear. +% # Close MATLAB by pressing the '|X|' in the top right corner of the window. +% # Download and install (See note 5). Use all defaults. +% # Launch Git Bash (See note 6). A black command line window should appear. +% # Type the following line into Git Bash (or copy/paste): |cd +% ~/Documents/Github| +% # Copy this line and paste it into Git Bash (use right click for +% pasting): |git clone --recurse-submodules +% https://github.com/cortex-lab/Rigbox| +% # Launch MATLAB and navigate to the following folder (See note 7): +% |Documents\Github\Rigbox| +% # Type the following into the MATLAB Command Window and press enter (See +% note 8): |addRigboxPaths('strict', false)| +% # You should be done now. To test that the NI DAQ support package is +% correctly installed, run |daq.getDevices|. You should see a list of +% available NI devices connected to your computer. +% # See <./paths_config.html Setting up the paths> for how to configure the +% paths for loading harware config settings and saving data. +% # See the Timeline section of <./hardware_config.html#25 Configureing rig hardware> +% for details on setting up Timeline, and the <./Timeline.html Timeline> +% guide for instructions on using Timeline. + +%% Notes +% # MATLAB is not free and requires a MATLAB account in order to +% download. If you are part of an academic institution you may be able to +% get MATLAB for free. If in doubt ask your lab supervisor or institute IT +% department. For more information see +% . +% # Once MATLAB is installed, toolboxes can be downloaded and installed +% directly within MATLAB via the "Add-Ons" button in the "Home" top +% toolstrip. This opens the MATLAB 'AddOn Explorer' where you can search +% and install toolboxes. +% # To download and install , +% follow the link and click the blue button that says 'SVN 1.12.0, 64 bit' +% on the left-hand side. The numbers might be slightly different but the +% important thing is that you choose the one that says '64 bit'. Click +% 'OK' in the pop-up window to save the installer zip file. Once +% downloaded double-click the zip file and open the exe file contained. +% Follow all the steps in the installer. +% # The MATLAB Command Window is usually at the bottom of the MATLAB +% window and has a '|>>|' in it. For more information, please read the +% . +% # To download and install , follow the link and click 'Save file' when the download window +% pops up. Open the installer file and click 'Next' repeatedly until the +% end, then click 'Finish'. +% # There might be more than one program installed that has 'Git' in the +% name. Make sure the one you open is called 'Git Bash'. +% # To navigate to a folder in MATLAB, either use the +% or type the following into the MATLAB Command Window, +% replacing |USER| with the name of the Windows user that's currently +% logged in: |cd('C:\Users\USER\Documents\Github\rigbox\')| +% # If you've followed the above steps you can safely ignore any warnings +% you may see for trying out Timeline. + +%% Etc. +% Authors: Jai Bhagat, Matteo Caranini, Miles Wells +% +% v0.1.0 +% diff --git a/index.html b/index.html index 7a92923d..ecbfec64 100644 --- a/index.html +++ b/index.html @@ -6,7 +6,7 @@ Rigging Toolbox Documentation

Rigging Toolbox Documentation

Welcome to the main Rigging Toolbox (Rigbox) documentation. Here you can find detailed documentation and guides on how to set up Rigbox, including writing new experiments, setting up recording devices, running experiments and processing the resulting data.

For instructions on how to run the examples from the Rigbox paper, see this guide.

Contents

Installing Rigbox

Below are some instructions for installing Rigbox. There are two guides, the first is a thorough guide for users unfarmilliar with MATLAB and Git. The second is for 'power users' who have a basic understanding of these things.

Setting up experiments

Below is a set of steps for setting up a full experiment in Rigbox. A full experiment being one where you record quality, reliable data that gets saved into the main experiment repository.

Briefly, before you can run a full experiment you must 1) set up your paths so that Rigbox knows from where to load rig settings and parameters, 2) save a hardware configuration file so that Rigbox can properly initialize its hardware, and 3) locate or create an experiment definition function to define your experiment.

Running full experiments

Before you can run a complete experiment, you must set up Rigbox (see above section). Once this is done there you can follow on of the below sections to run a full experiment.

Creating experiments

The principle way to create a new is experiment (i.e. passive stimulation or behaviour task) is write an expDef. Below will be a set of guides for how to write an expDef, and how to test it.

Working with Rigbox Experiment data

Below are some guides on how to work with the experimental data saved by Rigbox. These guides instruduce some functions for loading and processing these data, and explain the forms in which data are saved.

Troubleshooting

Rigbox is a mountain of code and there are many things that can go wrong when using it. Below are a few guides for how to fix problems that arise in Rigbox.

  • Basic MATLAB troubleshooting - this guide is for users that are unfamiliar with MATLAB.
  • General troubleshooting - this guide gives a list of steps to follow when an error is encountered.
  • ID index - A list of Rigbox error/warning IDs along with the a detailed description of what they mean and an exhastive list of causes and solutions.
  • FAQ - A list of frequently asked questions regarding problems and pointers to the solutions.
  • Paths conflicts - Some tips on avoiding errors from conflicting paths.

User guides

Below is a list of in-depth guides for users who want to learn the ins-and-outs of various packages and classes in Rigbox.

  • The Data Package - How to query data locations and log experiments using the +dat package.
  • Parameters - How to create and edit experiment parameters.
  • Alyx - How to interact with an Alyx database
  • Timeline - Using Timeline for time alignment
  • The Window class - Using the stimWindow object
  • Clocks - Using the Clock class

Miscellaneous

Below is a list of useful topics:

Etc.

Author: Miles Wells

v0.1.4


Published with MATLAB® R2019b

Welcome to the main Rigging Toolbox (Rigbox) documentation. Here you can find detailed documentation and guides on how to set up Rigbox, including writing new experiments, setting up recording devices, running experiments and processing the resulting data.

For instructions on how to run the examples from the Rigbox paper, see this guide.

Contents

Installing Rigbox

Below are some instructions for installing Rigbox. There are two guides, the first is a thorough guide for users unfarmilliar with MATLAB and Git. The second is for 'power users' who have a basic understanding of these things.

Setting up experiments

Below is a set of steps for setting up a full experiment in Rigbox. A full experiment being one where you record quality, reliable data that gets saved into the main experiment repository.

Briefly, before you can run a full experiment you must 1) set up your paths so that Rigbox knows from where to load rig settings and parameters, 2) save a hardware configuration file so that Rigbox can properly initialize its hardware, and 3) locate or create an experiment definition function to define your experiment.

Running full experiments

Before you can run a complete experiment, you must set up Rigbox (see above section). Once this is done there you can follow on of the below sections to run a full experiment.

Creating experiments

The principle way to create a new is experiment (i.e. passive stimulation or behaviour task) is write an expDef. Below will be a set of guides for how to write an expDef, and how to test it.

Working with Rigbox Experiment data

Below are some guides on how to work with the experimental data saved by Rigbox. These guides instruduce some functions for loading and processing these data, and explain the forms in which data are saved.

Troubleshooting

Rigbox is a mountain of code and there are many things that can go wrong when using it. Below are a few guides for how to fix problems that arise in Rigbox.

  • Basic MATLAB troubleshooting - this guide is for users that are unfamiliar with MATLAB.
  • General troubleshooting - this guide gives a list of steps to follow when an error is encountered.
  • ID index - A list of Rigbox error/warning IDs along with the a detailed description of what they mean and an exhastive list of causes and solutions.
  • FAQ - A list of frequently asked questions regarding problems and pointers to the solutions.
  • Paths conflicts - Some tips on avoiding errors from conflicting paths.

User guides

Below is a list of in-depth guides for users who want to learn the ins-and-outs of various packages and classes in Rigbox.

  • The Data Package - How to query data locations and log experiments using the +dat package.
  • Parameters - How to create and edit experiment parameters.
  • Alyx - How to interact with an Alyx database
  • Timeline - Using Timeline for time alignment
  • The Window class - Using the stimWindow object
  • Clocks - Using the Clock class

Miscellaneous

Below is a list of useful topics:

Etc.

Author: Miles Wells

v0.1.3


Published with MATLAB® R2019a

\ No newline at end of file diff --git a/install_Timeline.html b/install_Timeline.html new file mode 100644 index 00000000..b1e4b3ea --- /dev/null +++ b/install_Timeline.html @@ -0,0 +1,269 @@ + + + + + Installing Rigbox for Timeline only

Installing Rigbox for Timeline only

Below are some easy step-by-step instructions for installing Rigbox exclusively to run Timeline.

Contents

Requirements

Timeline runs on MATLAB 2018b or later for Windows. Currently only National Instruments DAQs are supported for acquiring data from hardware devices.

Software

Rigbox requires the following software to work properly:

  • Windows Operating System (7 or later, 64-bit)
  • MATLAB (2018b, also known as version 9.5, or later)
  • The MATLAB Data Acquisition Toolbox
  • The NI-DAQmx support package (free)
  • Psychophysics Toolbox (v3 or later, free)

Hardware

Below are a few minimum PC hardware requirements.

  • Processor: Intel Core i5-6500 @ 3.0 GHz (or similar)
  • Memory: DDR4 16 GB @ 2133 MHz (e.g. Corsair Vengeance 16 GB)

Install steps

Below are detailed steps on installing all required software. If you already have software installed for a particular step, feel free to skip that step.

  1. Install Windows 7 or later (Windows 10 is recommended). Windows must be must be 64-bit (sometimes called x64, x86_64, AMD64 or Intel 64).
  2. Download and install MATLAB by following their installation guide (See note 1MATLAB is not free and requires a MATLAB account in order to download. If you are part of an academic institution you may be able to get MATLAB for free. If in doubt ask your lab supervisor or institute IT department. For more information see MATLAB's install guide.). At step 9, make sure to check the box for the Data Acquisition Toolbox, along with any other MATLAB Mathworks toolboxes you want, though for testing Rigbox, no other toolboxes are required (See note 2Once MATLAB is installed, toolboxes can be downloaded and installed directly within MATLAB via the "Add-Ons" button in the "Home" top toolstrip. This opens the MATLAB 'AddOn Explorer' where you can search and install toolboxes.). NB: This step may take a while.
  3. Once downloaded, open MATLAB by double-clicking on the MATLAB icon in the start menu.
  4. Within MATLAB, install the NI-DAQmx Support Package (See note 2Once MATLAB is installed, toolboxes can be downloaded and installed directly within MATLAB via the "Add-Ons" button in the "Home" top toolstrip. This opens the MATLAB 'AddOn Explorer' where you can search and install toolboxes.). NB: This step may take a while.
  5. Download and install SilkSVN (See note 3To download and install SilkSVN, follow the link and click the blue button that says 'SVN 1.12.0, 64 bit' on the left-hand side. The numbers might be slightly different but the important thing is that you choose the one that says '64 bit'. Click 'OK' in the pop-up window to save the installer zip file. Once downloaded double-click the zip file and open the exe file contained. Follow all the steps in the installer.).
  6. Download the PsychToolbox installer function and save it into your Documents/MATLAB folder.
  7. In the MATLAB Command Window (See note 4The MATLAB Command Window is usually at the bottom of the MATLAB window and has a '>>' in it. For more information, please read the MATLAB documentation about the Command Window.), type DownloadPsychtoolbox(userpath) (no quotes) and press enter. This will download and install PsychToolbox to MATLAB folder. At certain points in the installation it will print stuff to the Command Window and ask you to press any key to continue. Do this until the two angled brackes ('>>') reappear.
  8. Close MATLAB by pressing the 'X' in the top right corner of the window.
  9. Download and install Git Bash for Windows (See note 5To download and install Git Bash for Windows, follow the link and click 'Save file' when the download window pops up. Open the installer file and click 'Next' repeatedly until the end, then click 'Finish'.). Use all defaults.
  10. Launch Git Bash (See note 6There might be more than one program installed that has 'Git' in the name. Make sure the one you open is called 'Git Bash'.). A black command line window should appear.
  11. Type the following line into Git Bash (or copy/paste): cd ~/Documents/Github
  12. Copy this line and paste it into Git Bash (use right click for pasting): git clone --recurse-submodules https://github.com/cortex-lab/Rigbox
  13. Launch MATLAB and navigate to the following folder (See note 7To navigate to a folder in MATLAB, either use the Address Field or type the following into the MATLAB Command Window, replacing USER with the name of the Windows user that's currently logged in: cd('C:\Users\USER\Documents\Github\rigbox\')): Documents\Github\Rigbox
  14. Type the following into the MATLAB Command Window and press enter (See note 8If you've followed the above steps you can safely ignore any warnings you may see for trying out Timeline.): addRigboxPaths('strict', false)
  15. You should be done now. To test that the NI DAQ support package is correctly installed, run daq.getDevices. You should see a list of available NI devices connected to your computer.
  16. See Setting up the paths for how to configure the paths for loading harware config settings and saving data.
  17. See the Timeline section of Configureing rig hardware for details on setting up Timeline, and the Timeline guide for instructions on using Timeline.

Notes

  1. MATLAB is not free and requires a MATLAB account in order to download. If you are part of an academic institution you may be able to get MATLAB for free. If in doubt ask your lab supervisor or institute IT department. For more information see MATLAB's install guide.
  2. Once MATLAB is installed, toolboxes can be downloaded and installed directly within MATLAB via the "Add-Ons" button in the "Home" top toolstrip. This opens the MATLAB 'AddOn Explorer' where you can search and install toolboxes.
  3. To download and install SilkSVN, follow the link and click the blue button that says 'SVN 1.12.0, 64 bit' on the left-hand side. The numbers might be slightly different but the important thing is that you choose the one that says '64 bit'. Click 'OK' in the pop-up window to save the installer zip file. Once downloaded double-click the zip file and open the exe file contained. Follow all the steps in the installer.
  4. The MATLAB Command Window is usually at the bottom of the MATLAB window and has a '>>' in it. For more information, please read the MATLAB documentation about the Command Window.
  5. To download and install Git Bash for Windows, follow the link and click 'Save file' when the download window pops up. Open the installer file and click 'Next' repeatedly until the end, then click 'Finish'.
  6. There might be more than one program installed that has 'Git' in the name. Make sure the one you open is called 'Git Bash'.
  7. To navigate to a folder in MATLAB, either use the Address Field or type the following into the MATLAB Command Window, replacing USER with the name of the Windows user that's currently logged in: cd('C:\Users\USER\Documents\Github\rigbox\')
  8. If you've followed the above steps you can safely ignore any warnings you may see for trying out Timeline.

Etc.

Authors: Jai Bhagat, Matteo Caranini, Miles Wells

v0.1.0


Published with MATLAB® R2019a

\ No newline at end of file