Skip to content

Commit

Permalink
Fix index regression
Browse files Browse the repository at this point in the history
  • Loading branch information
@k1o0
k1o0 committed Dec 19, 2023
1 parent 3c2dfad commit 9a8cb4f
Show file tree
Hide file tree
Showing 3 changed files with 15 additions and 8 deletions.
7 changes: 4 additions & 3 deletions docs/html/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<!--
This HTML was auto-generated from MATLAB code.
To make changes, update the MATLAB code and republish this document.
--><title>Rigging Toolbox Documentation</title><meta name="generator" content="MATLAB 9.7"><link rel="schema.DC" href="http://purl.org/dc/elements/1.1/"><meta name="DC.date" content="2021-01-04"><meta name="DC.source" content="index.m"><style type="text/css">
--><title>Rigging Toolbox Documentation</title><meta name="generator" content="MATLAB 9.6"><link rel="schema.DC" href="http://purl.org/dc/elements/1.1/"><meta name="DC.date" content="2023-12-19"><meta name="DC.source" content="index.m"><style type="text/css">
html,body,div,span,applet,object,iframe,h1,h2,h3,h4,h5,h6,p,blockquote,pre,a,abbr,acronym,address,big,cite,code,del,dfn,em,font,img,ins,kbd,q,s,samp,small,strike,strong,sub,sup,tt,var,b,u,i,center,dl,dt,dd,ol,ul,li,fieldset,form,label,legend,table,caption,tbody,tfoot,thead,tr,th,td{margin:0;padding:0;border:0;outline:0;font-size:100%;vertical-align:baseline;background:transparent}body{line-height:1}ol,ul{list-style:none}blockquote,q{quotes:none}blockquote:before,blockquote:after,q:before,q:after{content:'';content:none}:focus{outine:0}ins{text-decoration:none}del{text-decoration:line-through}table{border-collapse:collapse;border-spacing:0}

html { min-height:100%; margin-bottom:1px; }
Expand Down Expand Up @@ -66,7 +66,7 @@



</style></head><body><div class="content"><h1>Rigging Toolbox Documentation</h1><!--introduction--><p>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.</p><p>For instructions on how to run the examples from the <a href="http://dx.doi.org/10.1523/ENEURO.0406-19.2020">Rigbox paper</a>, see <a href="./paper_examples.html">this guide</a>.</p><!--/introduction--><h2>Contents</h2><div><ul><li><a href="#1">Installing Rigbox</a></li><li><a href="#2">Setting up experiments</a></li><li><a href="#3">Running full experiments</a></li><li><a href="#4">Creating experiments</a></li><li><a href="#5">Working with Rigbox Experiment data</a></li><li><a href="#6">Troubleshooting</a></li><li><a href="#7">User guides</a></li><li><a href="#8">Miscellaneous</a></li><li><a href="#9">Etc.</a></li></ul></div><h2 id="1">Installing Rigbox</h2><p>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.</p><div><ol><li><a href="./install.html">Detailed install instructions</a></li><li><a href="https://github.com/cortex-lab/Rigbox/blob/master/README.md">Installing for power users</a></li><li><a href="./updating_code.html">Updating the code</a></li></ol></div><h2 id="2">Setting up experiments</h2><p>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 <a href="./glossary.html">main experiment repository</a>.</p><p>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.</p><div><ol><li><a href="./paths_config.html">Setting up dat.paths</a></li><li><a href="./hardware_config.html">How to configure hardware on the stimulus computer</a></li><li><a href="./websocket_config.html">Setting up communication between the stimulus computer and MC</a></li><li><a href="./using_single_rig.html">Setting up <tt>mc</tt> and <tt>srv.expServer</tt> on the same computer</a></li><li><a href="./Burgess_hardware_setup.html">Setting up hardware for the Burgess steering wheel task</a></li><li><a href="./Burgess_setup.html">Configuring harware for the Burgess steering wheel task</a></li></ol></div><h2 id="3">Running full experiments</h2><p>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.</p><h2 id="4">Creating experiments</h2><p>The principle way to create a new is experiment (i.e. passive stimulation or behaviour task) is write an <a href="./glossary.html">expDef</a>. Below will be a set of guides for how to write an expDef, and how to test it.</p><div><ul><li><a href="./using_test_gui.html">Playing around with Signals Experiment Definitions</a></li><li><a href="./using_signals.html">A guide to signals methods</a></li><li><a href="./expDef_inputs.html">A guide to writing expDefs</a></li><li><a href="./visual_stimuli.html">A guide to creating visual stimuli</a></li><li><a href="./signals_cookbook.html">Solutions and tips using Signals</a></li><li><a href="./using_ExpPanel.html">How to create a custom Experiment Panel</a></li><li><a href="./advanced_signals.html">Using Signals outside the Experiment Framework</a></li></ul></div><h2 id="5">Working with Rigbox Experiment data</h2><p>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.</p><div><ul><li><a href="./block_files.html">Working with block files</a></li><li>Working with ALF files</li><li><a href="./using_wheel.html">Working with wheel data</a></li><li><a href="./stim_window_analysis.html">Stimulus Window analysis</a></li></ul></div><h2 id="6">Troubleshooting</h2><p>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.</p><div><ul><li>Basic MATLAB troubleshooting - this guide is for users that are unfamiliar with MATLAB.</li><li><a href="troubleshooting.html">General troubleshooting</a> - this guide gives a list of steps to follow when an error is encountered.</li><li><a href="./id_index.html">ID index</a> - 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.</li><li>FAQ - A list of frequently asked questions regarding problems and pointers to the solutions.</li><li><a href="./paths_conflicts.html">Paths conflicts</a> - Some tips on avoiding errors from conflicting paths.</li></ul></div><h2 id="7">User guides</h2><p>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.</p><div><ul><li><a href="./using_dat_package.html">The Data Package</a> - How to query data locations and log experiments using the <tt>+dat</tt> package.</li><li><a href="./Parameters.html">Parameters</a> - How to create and edit experiment parameters.</li><li><a href="./AlyxMatlabPrimer.html">Alyx</a> - How to interact with an Alyx database</li><li><a href="./Timeline.html">Timeline</a> - Using Timeline for time alignment</li><li><a href="./using_stimWindow.html">The Window class</a> - Using the stimWindow object</li><li><a href="./clocks.html">Clocks</a> - Using the Clock class</li></ul></div><h2 id="8">Miscellaneous</h2><p>Below is a list of useful topics:</p><div><ul><li><a href="./using_services.html">Setting up auxiliary services</a></li><li><a href="./Experiment_framework.html">An overview of the Experiment Framework</a></li><li><a href="./glossary.html">Glossary of Rigbox terminology</a></li><li><a href="./using_visual_stimuli.html">Details of the Signals viewing model</a></li><li><a href="./contributing.html">How to edit the documentation</a></li><li><a href="./release_notes_v260.html">v2.6.0 release notes</a></li><li><a href="./release_notes_v270.html">v2.7.0 release notes</a></li></ul></div><h2 id="9">Etc.</h2><p>Author: Miles Wells</p><p>v0.1.4</p><p class="footer"><br><a href="https://www.mathworks.com/products/matlab/">Published with MATLAB&reg; R2019b</a><br></p></div><!--
</style></head><body><div class="content"><h1>Rigging Toolbox Documentation</h1><!--introduction--><p>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.</p><p>For instructions on how to run the examples from the <a href="http://dx.doi.org/10.1523/ENEURO.0406-19.2020">Rigbox paper</a>, see <a href="./paper_examples.html">this guide</a>.</p><!--/introduction--><h2>Contents</h2><div><ul><li><a href="#1">Installing Rigbox</a></li><li><a href="#2">Setting up experiments</a></li><li><a href="#3">Running full experiments</a></li><li><a href="#4">Creating experiments</a></li><li><a href="#5">Working with Rigbox Experiment data</a></li><li><a href="#6">Troubleshooting</a></li><li><a href="#7">User guides</a></li><li><a href="#8">Miscellaneous</a></li><li><a href="#9">Etc.</a></li></ul></div><h2 id="1">Installing Rigbox</h2><p>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.</p><div><ol><li><a href="./install.html">Detailed install instructions</a></li><li><a href="https://github.com/cortex-lab/Rigbox/blob/master/README.md">Installing for power users</a></li><li><a href="./updating_code.html">Updating the code</a></li><li><a href="./install_Timeline.html">Install instructions for using Timeline only</a></li></ol></div><h2 id="2">Setting up experiments</h2><p>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 <a href="./glossary.html">main experiment repository</a>.</p><p>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.</p><div><ol><li><a href="./paths_config.html">Setting up dat.paths</a></li><li><a href="./hardware_config.html">How to configure hardware on the stimulus computer</a></li><li><a href="./websocket_config.html">Setting up communication between the stimulus computer and MC</a></li><li><a href="./using_single_rig.html">Setting up <tt>mc</tt> and <tt>srv.expServer</tt> on the same computer</a></li><li><a href="./Burgess_hardware_setup.html">Setting up hardware for the Burgess steering wheel task</a></li><li><a href="./Burgess_setup.html">Configuring harware for the Burgess steering wheel task</a></li></ol></div><h2 id="3">Running full experiments</h2><p>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.</p><h2 id="4">Creating experiments</h2><p>The principle way to create a new is experiment (i.e. passive stimulation or behaviour task) is write an <a href="./glossary.html">expDef</a>. Below will be a set of guides for how to write an expDef, and how to test it.</p><div><ul><li><a href="./using_test_gui.html">Playing around with Signals Experiment Definitions</a></li><li><a href="./using_signals.html">A guide to signals methods</a></li><li><a href="./expDef_inputs.html">A guide to writing expDefs</a></li><li><a href="./visual_stimuli.html">A guide to creating visual stimuli</a></li><li><a href="./signals_cookbook.html">Solutions and tips using Signals</a></li><li><a href="./using_ExpPanel.html">How to create a custom Experiment Panel</a></li><li><a href="./advanced_signals.html">Using Signals outside the Experiment Framework</a></li></ul></div><h2 id="5">Working with Rigbox Experiment data</h2><p>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.</p><div><ul><li><a href="./block_files.html">Working with block files</a></li><li>Working with ALF files</li><li><a href="./using_wheel.html">Working with wheel data</a></li><li><a href="./stim_window_analysis.html">Stimulus Window analysis</a></li></ul></div><h2 id="6">Troubleshooting</h2><p>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.</p><div><ul><li>Basic MATLAB troubleshooting - this guide is for users that are unfamiliar with MATLAB.</li><li><a href="troubleshooting.html">General troubleshooting</a> - this guide gives a list of steps to follow when an error is encountered.</li><li><a href="./id_index.html">ID index</a> - 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.</li><li>FAQ - A list of frequently asked questions regarding problems and pointers to the solutions.</li><li><a href="./paths_conflicts.html">Paths conflicts</a> - Some tips on avoiding errors from conflicting paths.</li></ul></div><h2 id="7">User guides</h2><p>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.</p><div><ul><li><a href="./using_dat_package.html">The Data Package</a> - How to query data locations and log experiments using the <tt>+dat</tt> package.</li><li><a href="./Parameters.html">Parameters</a> - How to create and edit experiment parameters.</li><li><a href="./AlyxMatlabPrimer.html">Alyx</a> - How to interact with an Alyx database</li><li><a href="./Timeline.html">Timeline</a> - Using Timeline for time alignment</li><li><a href="./using_stimWindow.html">The Window class</a> - Using the stimWindow object</li><li><a href="./clocks.html">Clocks</a> - Using the Clock class</li></ul></div><h2 id="8">Miscellaneous</h2><p>Below is a list of useful topics:</p><div><ul><li><a href="./using_services.html">Setting up auxiliary services</a></li><li><a href="./Experiment_framework.html">An overview of the Experiment Framework</a></li><li><a href="./glossary.html">Glossary of Rigbox terminology</a></li><li><a href="./using_visual_stimuli.html">Details of the Signals viewing model</a></li><li><a href="./contributing.html">How to edit the documentation</a></li><li><a href="./release_notes_v260.html">v2.6.0 release notes</a></li><li><a href="./release_notes_v270.html">v2.7.0 release notes</a></li></ul></div><h2 id="9">Etc.</h2><p>Author: Miles Wells</p><p>v0.1.5</p><p class="footer"><br><a href="https://www.mathworks.com/products/matlab/">Published with MATLAB&reg; R2019a</a><br></p></div><!--
##### SOURCE BEGIN #####
%% Rigging Toolbox Documentation
% Welcome to the main Rigging Toolbox (Rigbox) documentation. Here you can
Expand All @@ -88,6 +88,7 @@
% # <https://github.com/cortex-lab/Rigbox/blob/master/README.md Installing
% for power users>
% # <./updating_code.html Updating the code>
% # <./install_Timeline.html Install instructions for using Timeline only>
%
%% Setting up experiments
Expand Down Expand Up @@ -185,7 +186,7 @@
%% Etc.
% Author: Miles Wells
%
% v0.1.4
% v0.1.5
##### SOURCE END #####
--></body></html>
7 changes: 5 additions & 2 deletions docs/scripts/index.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
% experiments and processing the resulting data.
%
% For instructions on how to run the examples from the
% <https://www.biorxiv.org/content/10.1101/672204v3 Rigbox paper>, see
% <http://dx.doi.org/10.1523/ENEURO.0406-19.2020 Rigbox paper>, see
% <./paper_examples.html this guide>.

%% Installing Rigbox
Expand All @@ -17,6 +17,7 @@
% # <./install.html Detailed install instructions>
% # <https://github.com/cortex-lab/Rigbox/blob/master/README.md Installing
% for power users>
% # <./updating_code.html Updating the code>
% # <./install_Timeline.html Install instructions for using Timeline only>
%

Expand Down Expand Up @@ -108,9 +109,11 @@
% * <./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
%
% v0.1.3
% v0.1.5
Loading

0 comments on commit 9a8cb4f

Please sign in to comment.