From 308cbf61fc7eede0b6f2d8e8b6f7c052126562d9 Mon Sep 17 00:00:00 2001 From: cjsha Date: Fri, 9 Aug 2024 14:05:10 -0400 Subject: [PATCH] Fix typos and syntax - Also: "library" -> "package" - Restructure the Bonsai page to create references to a OpenEphys.Onix1 section of the Bonsai page to address concerns about OpenEphys.Onix1 not being enough of a first-class citizen like Bonsai.Onix was --- source/Getting Started/warnings.rst | 4 +-- source/Hardware Guide/Commutators/index.rst | 2 +- .../Headstages/tether-voltage.rst | 14 +++++----- source/Hardware Guide/Miniscopes/index.rst | 4 +-- source/Hardware Guide/PCIe Host/overview.rst | 2 +- .../PCIe Host/setup-windows.rst | 2 +- .../Bonsai.ONIX/GettingStarted.rst | 2 +- .../Bonsai.ONIX/Installation.rst | 4 +-- .../Bonsai.ONIX/Nodes/NeuropixelsV1Device.rst | 2 +- .../Nodes/NeuropixelsV1eDevice.rst | 2 +- .../Bonsai.ONIX/Nodes/ONIContext.rst | 4 +-- .../Bonsai.ONIX/Nodes/RHS2116Device.rst | 2 +- source/Software Guide/Bonsai.ONIX/index.rst | 10 ++++---- .../Software Guide/Open Ephys GUI/index.rst | 4 +-- .../Software Guide/OpenEphys.Onix1/index.rst | 24 +++++++++++------- source/Software Guide/index.rst | 6 ++--- ...re.jpg => bonsai-package-architecture.jpg} | Bin ...re.pdf => bonsai-package-architecture.pdf} | Bin 18 files changed, 47 insertions(+), 41 deletions(-) rename source/_static/bonsai/{bonsai-library-architecture.jpg => bonsai-package-architecture.jpg} (100%) rename source/_static/bonsai/{bonsai-library-architecture.pdf => bonsai-package-architecture.pdf} (100%) diff --git a/source/Getting Started/warnings.rst b/source/Getting Started/warnings.rst index 0dcf1d93..61a34154 100644 --- a/source/Getting Started/warnings.rst +++ b/source/Getting Started/warnings.rst @@ -28,8 +28,8 @@ Headstage Voltages .. warning:: **Ensure each headstage is configured with the correct voltage.** Although headstages are quite tolerate of over-voltage and under-voltage conditions, - they are only gaurenteed to function wihtin a specified range. When using + they are only guaranteed to function within a specified range. When using long and/or thin tethers, the voltage drop across the cable can become - signficant. For more details, see :ref:`tether_voltage`. + significant. For more details, see :ref:`tether_voltage`. diff --git a/source/Hardware Guide/Commutators/index.rst b/source/Hardware Guide/Commutators/index.rst index c83532ac..f3006916 100644 --- a/source/Hardware Guide/Commutators/index.rst +++ b/source/Hardware Guide/Commutators/index.rst @@ -2,7 +2,7 @@ Coaxial Commutators =================================== -Active, near-zero torque commutators to prevent tether twisting during freely +Active, near-zero torque commutators prevent tether twisting during freely moving recordings with headstages and/or miniscopes. This page provides a very brief overview of the commutators; for a more extensive walkthrough, please follow the documentation link for `Commutators diff --git a/source/Hardware Guide/Headstages/tether-voltage.rst b/source/Hardware Guide/Headstages/tether-voltage.rst index 49f93f06..bd34293f 100644 --- a/source/Hardware Guide/Headstages/tether-voltage.rst +++ b/source/Hardware Guide/Headstages/tether-voltage.rst @@ -4,10 +4,10 @@ Headstage Voltages ============================== Each ONIX headstage has a required operating voltage that is specified on its documentation page. Because ONIX hardware supports headstages that have -different voltage requirements, it must be changed to to match the requirements +different voltage requirements, it must be changed to match the requirements of the headstage that is plugged into a port. If the headstage voltage is too -low, it will not function reliably. If the voltage is too high, it -there will be excess heat dissipation and the headstage may be damaged. +low, it will not function reliably. If the voltage is too high, the headstage +will dissipate excess heat and it may be damaged. Setting Headstage Voltage @@ -16,20 +16,20 @@ The headstage voltage is set using :ref:`onidatasheet_fmc_link_control` devices on the :ref:`pcie_host`. Each headstage has a minimum and maximum voltage requirement (e.g. 5.3 to 5.7 Volts for :ref:`headstage_64`) in order for circuits on the board to function properly. If the voltage is far too low, the -host computer will not be able to detect detect the headstage. A borderline +host computer will not be able to detect the headstage. A borderline voltage can still cause connectivity issues as the headstage occasionally dips below the level it needs to function properly. -.. attention:: The :ref:`openephys_onix1ref` library automatically sets the +.. attention:: The :ref:`openephys_onix1ref` Bonsai package automatically sets the headstage port voltage by default, but allows the user to override the voltage setting as well. The documentation linked shows how to use this functionality and what valid voltage ranges are for each headstage. This functionality has been been tuned for the tethers that are shipped with each - headstage. The override voltage is available when custom tethers are used + headstage. The voltage override is available when custom tethers are used (see :ref:`measure_voltage`). The voltage set in software is not identical to the voltage supplied to the -headstage, as some voltage drop will occur over the tether connects them. The +headstage, as some voltage drop will occur over the tether that connects them. The amount of voltage drop is proportional to the current draw of the headstage and inversely proportional to the thickness of the tether. The thin tethers used with ONIX headstages can result in significant voltage drops that need to be diff --git a/source/Hardware Guide/Miniscopes/index.rst b/source/Hardware Guide/Miniscopes/index.rst index 92d479ba..a17a374c 100644 --- a/source/Hardware Guide/Miniscopes/index.rst +++ b/source/Hardware Guide/Miniscopes/index.rst @@ -10,7 +10,7 @@ UCLA Miniscope V3 :Design Repository: https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB :Documentation: http://miniscope.org/index.php/Guides_and_Tutorials :Compatibility: :ref:`pcie_host`, :ref:`breakout` -:Software: :ref:`openephys_onix1ref` +:Software: :ref:`openephys_onix1ref` Bonsai package .. figure:: /_static/images/miniscopes/ucla-miniscope-v3-render.jpg :align: center @@ -21,7 +21,7 @@ UCLA Miniscope V4 :Design Repository: https://github.com/Aharoni-Lab/Miniscope-v4 :Documentation: https://github.com/Aharoni-Lab/Miniscope-v4/wiki :Compatibility: :ref:`pcie_host`, :ref:`breakout` -:Software: :ref:`openephys_onix1ref` +:Software: :ref:`openephys_onix1ref` Bonsai package .. figure:: /_static/images/miniscopes/ucla-miniscope-v4-render.png :align: center diff --git a/source/Hardware Guide/PCIe Host/overview.rst b/source/Hardware Guide/PCIe Host/overview.rst index b57af4e7..6fda6f17 100644 --- a/source/Hardware Guide/PCIe Host/overview.rst +++ b/source/Hardware Guide/PCIe Host/overview.rst @@ -33,7 +33,7 @@ The `ONIX FMC Host `__ module provides a host interface for serialized headstages and miniscopes, as well as general purpose analog and digital IO. It is a VITA-57.1 compliant mezzanine board that uses high pin-count FMC connector. In combination with a base FPGA -board , it provides host PC communication. +board, it provides host PC communication. - Two deserializers for any multifunction headstage conforming to the ONIX serialization protocol diff --git a/source/Hardware Guide/PCIe Host/setup-windows.rst b/source/Hardware Guide/PCIe Host/setup-windows.rst index 22e8b34c..3f2ebbce 100644 --- a/source/Hardware Guide/PCIe Host/setup-windows.rst +++ b/source/Hardware Guide/PCIe Host/setup-windows.rst @@ -118,6 +118,6 @@ Install Device Driver Install Software --------------------------------------- Have a look at the :ref:`software_guide` page for open-source software options. We -recommend using :ref:`openephys_onix1ref` because it provides first class +recommend using :ref:`bonsairef` and the :ref:`openephys_onix1ref` Bonsai package because it provides first class support for all ONIX hardware features. diff --git a/source/Software Guide/Bonsai.ONIX/GettingStarted.rst b/source/Software Guide/Bonsai.ONIX/GettingStarted.rst index a958dd26..a4210ef4 100644 --- a/source/Software Guide/Bonsai.ONIX/GettingStarted.rst +++ b/source/Software Guide/Bonsai.ONIX/GettingStarted.rst @@ -34,7 +34,7 @@ Bonsai Learning Resources * - `ReactiveX operator definitions `__ - Detailed information on many of the reactive operators you will find in - Bonsai's Reactive library, especially in the "Combinators" grouping + Bonsai's Reactive package, especially in the "Combinators" grouping Accessing Bonsai.ONIX Documentation ---------------------------------------- diff --git a/source/Software Guide/Bonsai.ONIX/Installation.rst b/source/Software Guide/Bonsai.ONIX/Installation.rst index 1645dcbf..f7ac5d6d 100644 --- a/source/Software Guide/Bonsai.ONIX/Installation.rst +++ b/source/Software Guide/Bonsai.ONIX/Installation.rst @@ -4,7 +4,7 @@ Installation =============================== -**Bonsai.ONIX** is a `Bonsai `__ library for ONIX +**Bonsai.ONIX** is a `Bonsai `__ package for ONIX hardware and can be installed using its package manager. #. First you will need to `install Bonsai `__ @@ -24,7 +24,7 @@ hardware and can be installed using its package manager. :align: center #. Search for "ONIX" and install. Installing **Bonsai.ONIX.Design** will - install both the base **Bonsai.ONIX** library and its visualization tools. + install both the base **Bonsai.ONIX** package and its visualization tools. .. tip:: It is recommended to also install **Bonsai.ONIX.Design** because it provides a substantial set of data visualization and graphical hardware diff --git a/source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1Device.rst b/source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1Device.rst index 5a298233..db0c1168 100644 --- a/source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1Device.rst +++ b/source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1Device.rst @@ -71,7 +71,7 @@ Parameters available through the property pane are as follows: Configuration GUI _________________________ The **Neuropixels 1.0 Configuration GUI**, which is a part of the -``Bonsai.ONIX.Design`` library, is opened by double clicking on the +``Bonsai.ONIX.Design`` package, is opened by double clicking on the NeuropixelsV1Device node when editing the workflow or clicking the ellipsis next to the ``NeuropixelsV1Configuration`` parameter option in the property pane. diff --git a/source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1eDevice.rst b/source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1eDevice.rst index 42ffa9a6..e1b12dae 100644 --- a/source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1eDevice.rst +++ b/source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1eDevice.rst @@ -77,7 +77,7 @@ Parameters available through the property pane are as follows: Configuration GUI _________________________ The **Neuropixels 1.0e Configuration GUI**, which is a part of the -``Bonsai.ONIX.Design`` library, is opened by double clicking on the +``Bonsai.ONIX.Design`` package, is opened by double clicking on the NeuropixelsV1eDevice node when editing the workflow or clicking the ellipsis next to the ``NeuropixelsV1Configuration`` parameter option in the property pane. diff --git a/source/Software Guide/Bonsai.ONIX/Nodes/ONIContext.rst b/source/Software Guide/Bonsai.ONIX/Nodes/ONIContext.rst index ef01db15..9cb9d0ed 100644 --- a/source/Software Guide/Bonsai.ONIX/Nodes/ONIContext.rst +++ b/source/Software Guide/Bonsai.ONIX/Nodes/ONIContext.rst @@ -34,7 +34,7 @@ it manages (e.g. :ref:`bonsai_heartbeatdev`, :ref:`bonsai_analogiodev`, etc.). S facts about the :ref:`bonsai_onicontext` node are useful for understanding how to use it. -.. figure:: /_static/bonsai/bonsai-library-architecture.jpg +.. figure:: /_static/bonsai/bonsai-package-architecture.jpg :align: center :width: 500px @@ -71,7 +71,7 @@ to use it. Configuration GUI -------------------------- :ref:`bonsai_onicontext` configuration is performed using a GUI provided in the -Bonsai.ONIX.Design library. It can be opened by double clicking on the +Bonsai.ONIX.Design package. It can be opened by double clicking on the :ref:`bonsai_onicontext` node if Bonsai.ONIX.Design has been installed. .. image:: /_static/bonsai/onicontext/ONIContext_configuration.png diff --git a/source/Software Guide/Bonsai.ONIX/Nodes/RHS2116Device.rst b/source/Software Guide/Bonsai.ONIX/Nodes/RHS2116Device.rst index 7edd3126..a7035c99 100644 --- a/source/Software Guide/Bonsai.ONIX/Nodes/RHS2116Device.rst +++ b/source/Software Guide/Bonsai.ONIX/Nodes/RHS2116Device.rst @@ -102,7 +102,7 @@ Parameters available through the property pane are as follows: Configuration GUI _________________________ The **RHS2116 Configuration GUI**, which is a part of the -``Bonsai.ONIX.Design`` library, is opened by double clicking on the +``Bonsai.ONIX.Design`` package, is opened by double clicking on the RHS2116Device node when editing the workflow or clicking the ellipsis next to the ``StimulusSequence`` parameter option in the property pane. It is used to define multichannel stimulus sequences. diff --git a/source/Software Guide/Bonsai.ONIX/index.rst b/source/Software Guide/Bonsai.ONIX/index.rst index 55867cbf..5f6ed69e 100644 --- a/source/Software Guide/Bonsai.ONIX/index.rst +++ b/source/Software Guide/Bonsai.ONIX/index.rst @@ -23,12 +23,12 @@ Bonsai.ONIX Bonsai Examples/index `Bonsai.ONIX `__ is a `Bonsai -`__ library for ONIX hardware. This library contains +`__ package for ONIX hardware. This package contains `Bonsai Operators `__ for -acquiring and sending data to ONIX hardware. An additional library, -``Bonsai.ONIX.Design``, contains GUI elements for the core library. Although it -is possible to use ``Bonsai.ONIX`` without the GUI library, it is not -recommended. There are three major classes of operators in the library: +acquiring and sending data to ONIX hardware. An additional package, +``Bonsai.ONIX.Design``, contains GUI elements for the core package. Although it +is possible to use ``Bonsai.ONIX`` without the GUI package, it is not +recommended. There are three major classes of operators in the package: #. :ref:`bonsai_onicontext` - This operator wraps the underlying **Acquisition Context** and provides access to the device table for a hardware slot. At least one of these diff --git a/source/Software Guide/Open Ephys GUI/index.rst b/source/Software Guide/Open Ephys GUI/index.rst index a1738eba..e2931055 100644 --- a/source/Software Guide/Open Ephys GUI/index.rst +++ b/source/Software Guide/Open Ephys GUI/index.rst @@ -10,8 +10,8 @@ experiments more flexible and enjoyable. It works equally well on macOS, Linux, and Windows. .. note:: An ONIX plugin for the Open Ephys is in development. To access all of - ONIX's capabilities right now, have a look at the :ref:`Bonsai library - `. **You can still take advantage of the GUI's excellent + ONIX's capabilities right now, have a look at the :ref:`openephys_onix1ref` Bonsai package. + **You can still take advantage of the GUI's excellent ephys visualizaiton tools by streaming data from Bonsai to the GUI using the** `Ephys Socket Plugin `__. diff --git a/source/Software Guide/OpenEphys.Onix1/index.rst b/source/Software Guide/OpenEphys.Onix1/index.rst index c8808647..36b16162 100644 --- a/source/Software Guide/OpenEphys.Onix1/index.rst +++ b/source/Software Guide/OpenEphys.Onix1/index.rst @@ -1,12 +1,11 @@ -.. _openephys_onix1ref: +.. _bonsairef: Bonsai ======================== `Bonsai `__ is a visual programming language (think LabView) for `reactive programming -`__. Its simple looks are -deceiving. Bonsai is a very advanced piece of software with features such as +`__ with features such as: - Real-time compilation of workflows to machine code as they are edited (zero-overhead). @@ -15,11 +14,18 @@ deceiving. Bonsai is a very advanced piece of software with features such as - Lots of support for all sorts of hardware outside of ONIX. Bonsai is ideal for accessing the full power of ONIX hardware and combining it -with third-party data sources (e.g. machine visiion cameras, +with third-party data sources (e.g. machine vision cameras, behavioral hardware, etc.), and for real-time processing and manipulation of -data streams. `OpenEphys.Onix1 -`__ is a Bonsai -library for ONIX hardware. This library contains `Bonsai Operators +data streams. + +.. _openephys_onix1ref: + +OpenEphys.Onix1 +---------------- + +`OpenEphys.Onix1 +`__ is the Bonsai +package for ONIX hardware. This package contains `Bonsai Operators `__ for acquiring and sending data to ONIX hardware. @@ -33,10 +39,10 @@ sending data to ONIX hardware.
-

Go to the ONIX library Docs

+

Go to the OpenEphys.Onix1 Docs

OpenEphys.Onix1 bonsai - library documentation + package documentation">
diff --git a/source/Software Guide/index.rst b/source/Software Guide/index.rst index 9219b9ca..e72ac82e 100644 --- a/source/Software Guide/index.rst +++ b/source/Software Guide/index.rst @@ -14,8 +14,8 @@ oni-repl/index Bonsai.ONIX (DEPRECATED) -:ref:`Bonsai ` - A `Bonsai `__ library for acquiring data from ONIX +:ref:`Bonsai ` + :ref:`openephys_onix1ref` is a :ref:`bonsairef` package for acquiring data from ONIX hardware for real-time experiments. Bonsai is very good at processing the heterogeneous data streams produced by ONIX hardware. @@ -35,5 +35,5 @@ Deprecated Software ___________________________________ - The :ref:`bonsai_onixref` pages provide information about the original Bonsai - library, which has been superseded by :ref:`openephys_onix1ref` + package, which has been superseded by :ref:`openephys_onix1ref` diff --git a/source/_static/bonsai/bonsai-library-architecture.jpg b/source/_static/bonsai/bonsai-package-architecture.jpg similarity index 100% rename from source/_static/bonsai/bonsai-library-architecture.jpg rename to source/_static/bonsai/bonsai-package-architecture.jpg diff --git a/source/_static/bonsai/bonsai-library-architecture.pdf b/source/_static/bonsai/bonsai-package-architecture.pdf similarity index 100% rename from source/_static/bonsai/bonsai-library-architecture.pdf rename to source/_static/bonsai/bonsai-package-architecture.pdf