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Fix broken links and formatting
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jonnew committed Oct 4, 2024
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11 changes: 5 additions & 6 deletions source/Software Guide/OpenEphys.Onix1/index.rst
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Bonsai ONIX Package
=================================

`OpenEphys.Onix1
<https://open-ephys.github.io/onix1-bonsai-docs/index.html>`__ is the `Bonsai <https://bonsai-rx.org/>`__
package for ONIX hardware. This package contains `Bonsai Operators
``OpenEphys.Onix1`` is a `Bonsai <https://bonsai-rx.org/>`__ package for ONIX
hardware. This package contains `Bonsai Operators
<https://bonsai-rx.org/docs/articles/operators.html>`__ for acquiring and
sending data to ONIX hardware.

:Code: https://github.com/open-ephys/bonsai-onix1
:Code: https://github.com/open-ephys/bonsai-onix1
:Compatibility: All ONIX hardware, Neuropixels, UCLA miniscopes & variants
:Documentation: https://open-ephys.github.io/bonsai-onix1-docs/index.html

Expand All @@ -18,7 +17,7 @@ sending data to ONIX hardware.
<a href="https://open-ephys.github.io/bonsai-onix1-docs/index.html"><span class="std std-ref custom-card">
<div class="card text-center page-card">

<header>
<header>
<h1>Go to the OpenEphys.Onix1 Docs <i class="fas fa-external-link"></i></h1>
</header>
<img src="../../_static/images/bonsai-lettering.svg"
Expand All @@ -44,4 +43,4 @@ combining it with third-party data sources (e.g. machine vision cameras,
behavioral hardware, etc.), and for real-time processing and manipulation of
data streams. The documentation linked above contains detailed instructions on
how to use Bonsai with ONIX hardware along with fully useable example workflows,
data loading scripts, etc.
data loading scripts, etc.
10 changes: 5 additions & 5 deletions source/Software Guide/index.rst
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for real-time experiments. Bonsai is very good at processing the
heterogeneous data streams produced by ONIX hardware.

:ref:`Open Ephys GUI ONIX Plugin<open_ephys_gui>`
The `Open Ephys GUI <https://open-ephys.github.io/gui-docs/> excels at
:ref:`Open Ephys GUI ONIX Plugin <open_ephys_gui>`
The `Open Ephys GUI <https://open-ephys.github.io/gui-docs/>` excels at
electrophysiology data visualization and recording.

:ref:`oni-repl <oni_repl>`
A simple command-line application that can be used for debugging and basic
streaming IO with ONIX hardware.
:ref:`Command line application <oni_repl>`
`oni-repl` is a simple command-line application that can be used for
debugging and basic streaming IO with ONIX hardware.

.. tip:: ONIX uses an `ONI-compliant API
<https://open-ephys.github.io/ONI/api/index.html>`__ that is software
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13 changes: 7 additions & 6 deletions source/Software Guide/oni-repl/index.rst
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.. _oni_repl:

oni-repl
Command Line Application
===================================

.. toctree::
:hidden:
:maxdepth: 1

usage
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- Bulk initialize device register state

.. note:: ``oni-repl`` was created for hardware debugging and as a test program
for `liboni <https://open-ephys.github.io/ONI/api/liboni/index.html>`__.
However, its simplicity and lack of abstraction compared to
:ref:`bonsai_onixref` make it useful as an example of how to use
`liboni <https://open-ephys.github.io/ONI/api/liboni/index.html>`__ and
for quickly examining hardware state and hub firmware versions.
for `liboni <https://open-ephys.github.io/ONI/api/liboni/index.html>`__.
However, its simplicity and lack of abstraction compared to
:ref:`bonsai_onixref` make it useful as an example of how to use `liboni
<https://open-ephys.github.io/ONI/api/liboni/index.html>`__ and for quickly
examining hardware state and hub firmware versions.

.. code-block:: none
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64 changes: 32 additions & 32 deletions source/Software Guide/oni-repl/usage.rst
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.. _oni_repl_usage:

Usage
``oni-repl`` Usage
====================================

.. code-block:: console
oni-repl <driver> [slot] [-d] [-D <value>] [-n <value>] [-i <device index>]
[--rbytes=<bytes>] [--wbytes=<bytes>] [--dumppath=<path>] [-h,--help] [-v,--version]
oni-repl <driver> [slot] [-d] [-D <value>] [-n <value>] [-i <device index>]
[--rbytes=<bytes>] [--wbytes=<bytes>] [--dumppath=<path>] [-h,--help] [-v,--version]
Required Arguments
-----------------------------------
<driver>
<driver>
Hardware driver to dynamically link (e.g. **riffa**,
**ft600**, **test_driver**, etc.)
[slot]
[slot]
Index specifying the physical slot occupied by hardware being controlled.
If none is provided, the driver-defined default will be used.

Expand Down Expand Up @@ -58,33 +58,33 @@ index 0) and a single headstage (starting at device index 256).

.. code-block:: console
$ ./liboni-test riffa 0
$ ./liboni-test riffa 0
Jon Newman @ MIT **
Jie Zhang @ MIT ////
Aarón Cuevas López @ UPV ///.
Josh Seigle @ Allen ///,.
Jakob Voigts @ MIT *///,
*. ///,,
,####/ ///,,,
,,,,/####// *///,,.
,,,,, //##//// ///,,,
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,,,, //// ,/////./// ,,,
.,,,, .//// ,///##// ,,,
.,,,, //// */###/ .,,,
,///***,,..........,,,... ,//// /##(///,,,
.,,,,,,**,,..................,((((,..../(((((((((.
.,......, .*(((/...,(((,,,(###
......... //// ///. ///,
........, ,///* */// ////
Open Ephys Org. .,......, //// ///.///
........, *///(/////
Supporting open science .,......,//((((//
since 2010. ....,/(##(/
.,###.
Jon Newman @ MIT **
Jie Zhang @ MIT ////
Aarón Cuevas López @ UPV ///.
Josh Seigle @ Allen ///,.
Jakob Voigts @ MIT *///,
*. ///,,
,####/ ///,,,
,,,,/####// *///,,.
,,,,, //##//// ///,,,
,,,,, ,///#///// ///.,,,
,,,,, //// ////// *///,,,,
,,,,, ,//// /////, /// ,,,,
,,,, //// ,/////./// ,,,
.,,,, .//// ,///##// ,,,
.,,,, //// */###/ .,,,
,///***,,..........,,,... ,//// /##(///,,,
.,,,,,,**,,..................,((((,..../(((((((((.
.,......, .*(((/...,(((,,,(###
......... //// ///. ///,
........, ,///* */// ////
Open Ephys Org. .,......, //// ///.///
........, *///(/////
Supporting open science .,......,//((((//
since 2010. ....,/(##(/
.,###.
   +--------------------+-------+-------+-------+-------+---------------------
   |                    |       |Firm.  |Read   |Wrt.   |
Expand Down Expand Up @@ -150,4 +150,4 @@ index 0) and a single headstage (starting at device index 256).
        a - reset the acquisition clock counter
        x - issue a hardware reset
        q - quit
>>>
>>>

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