Merge pull request #36 from open-ephys/ChucklesOnGitHub-patch-1

added hs NP1.0e example workflow and usage caveats

Author: jonnew

.gitignore

@@ -1,5 +1,6 @@
 # sphinx build folder
 docs/*
+source/_build/*
 
 # Compiled source #
 ###################

source/Hardware Guide/Breakout Board/setup.rst

@@ -3,6 +3,8 @@
 Breakout Board Guide
 #########################
 
+.. warning:: Always make sure the PC is powered off **before** connecting or disconnecting the Breakout Board. Neglecting to do this will damage the PCIe Host.
+
 Setup
 -------------------------
 The Breakout Board provides access to signals to and from the PCIe host. Each

source/Hardware Guide/Headstages/headstage-neuropix-1.rst

@@ -18,8 +18,8 @@ targeting `Neuropixels 1.0 probes <https://www.neuropixels.org/probe>`__.
 
 Coaxial Link
 ***********************************
-For details on data serialiation and headstage gateware, have a look at the
-:ref:`serialization` page, which describes how coax headstages operatate in
+For details on data serialization and headstage gateware, have a look at the
+:ref:`serialization` page, which describes how coax headstages operate in
 general terms. The Neuropixels-1.0 Headstage has the following coaxial link
 properties:
 
@@ -39,10 +39,5 @@ properties:
     | PCLK Frequency         | 42                 |          |          | MHz      |
     +------------------------+--------------------+----------+----------+----------+
 
-.. important:: \*The headstage includes an undervoltage and overvoltage lockout
-    circuit that will only allow it to turn on when the proper link voltage is
-    present headstage. If the headstage is not turning on, make sure that the
-    voltage at the headstage itself is within the valid range
-
-.. note:: Have a look at the :ref:`tethers` page for more details on mirco-coax
+.. note:: Have a look at the :ref:`tethers` page for more details on micro-coax
     headstage tethers

source/Hardware Guide/Headstages/headstage-neuropix-1e.rst

@@ -1,4 +1,4 @@
-.. _headstage_neuropix1:
+.. _headstage_neuropix1e:
 
 Neuropixels-1.0e Headstage
 ##############################
@@ -15,8 +15,8 @@ targeting `Neuropixels 1.0 probes <https://www.neuropixels.org/probe>`__.
 
 Coaxial Link
 ***********************************
-For details on data serialiation and headstage gateware, have a look at the
-:doc:`serialization` page, which describes how coax headstages operatate in
+For details on data serialization and headstage gateware, have a look at the
+:doc:`serialization` page, which describes how coax headstages operate in
 general terms. The Neuropixels-1.0e Headstage has the following coaxial link
 properties:
 
@@ -32,6 +32,6 @@ properties:
     | Coax Voltage           | 5.0*               | 3.0      | 5.5      | Volts    |
     +------------------------+--------------------+----------+----------+----------+
 
-.. note:: Have a look at the :doc:`tethers` page for more details on mirco-coax headstage tethers
+.. note:: Have a look at the :doc:`tethers` page for more details on micro-coax headstage tethers
 
 .. important:: \*If your headstage is misbehaving, have a look at the :doc:`tether-voltage` page to confirm headstage power voltages 

source/Hardware Guide/Miniscopes/index.rst

@@ -29,8 +29,8 @@ UCLA Miniscope V4
 
 NINScope
 ------------------------------------------
-.. todo:: Comming soon.
+.. todo:: Coming soon.
 
 FeatherScope & Kiloscope
 ------------------------------------------
-.. todo:: Comming soon.
+.. todo:: Coming soon.

source/Hardware Guide/PCIe Host/overview.rst

@@ -37,7 +37,7 @@ board , it provides host PC communication.
 
     The ONIX FMC Host module.
 
-- Two deserailizers for any multifunction headstage conforming to the ONIX
+- Two deserializers for any multifunction headstage conforming to the ONIX
   serialization protocol
 - 12x ±10V analog outputs or inputs. Direction selected via analog switch
   controllable over the FMC connector. 

source/Software Guide/Bonsai.ONIX/Bonsai Examples/Headstage64.rst

@@ -3,7 +3,7 @@
 Headstage-64 Workflow
 ===============================
 This example workflow shows how the data streams produced by
-:ref:`headstage_64` can be acquired and saved. Each group workflow at the top
+:ref:`headstage_64` can be acquired and saved, as well as used for commutation. Each group workflow at the top
 level contains acquisition code for a different sensor on the headstage. Example
 Python and MATLAB scripts are provided to load the data produced by the
 workflow. 
@@ -23,19 +23,19 @@ RHD2164 Ephys Chip
     64-channels of extracellular electrophysiology input
 
 TS4231 Lighthouse Receivers
-    3D position of the headstage in space when used with approriate lighthouse setup. 
+    3D position of the headstage in space when used with appropriate lighthouse setup. 
 
 Headstage Port Control
     Control over the headstage port and connectivity status logging 
 
 .. note:: 
-    This workflow does not demonstrate stimulation capabilites of the
+    This workflow does not demonstrate stimulation capabilities of the
     headstage. See :ref:`bonsai_estimdev` and :ref:`bonsai_ostimdev` for
     examples of how to control onboard stimulation.
 
 Loading Scripts
 --------------------------
-The following scripts can be used to load the data produce by this workflow in Python (using Numpy) or MATLAB:
+The following scripts can be used to load the data produced by this workflow in Python (using Numpy) or MATLAB:
 
 - Python: :download:`load_headstage64.py <../../../_static/bonsai/workflows/load_headstage64.py>` 
 - MATLAB: :download:`load_headstage64.m <../../../_static/bonsai/workflows/load_headstage64.m>` 

source/Software Guide/Bonsai.ONIX/Bonsai Examples/HeadstageNP1e.rst

@@ -0,0 +1,31 @@
+.. _bonsai_headstage_neuropix1e:
+
+Headstage Neuropixels 1.0e Workflow
+============================================
+This example workflow shows how the data streams produced by
+:ref:`headstage_neuropix1e` can be acquired and saved, as well as used for commutation. Each group workflow at the top
+level contains acquisition code for a different sensor on the headstage. A probe visualizer is included.
+
+.. important:: \Bonsai workflows that contain the :ref:`bonsai_NeuropixelsV1edev` node such as this one will not
+    open/load unless the headstage is on. Make sure to configure the headstage port voltage and mode correctly using the :ref:`bonsai_onicontext` node with the parameters for the :ref:`headstage_neuropix1e` before connecting the headstage.
+    
+.. raw:: html
+
+    {% with static_path = '../../../_static', name = 'HeadstageNeuropixelsV1e' %}
+        {% include 'workflow.html' %}
+    {% endwith %}
+
+
+BNO055 9-Axis IMU
+    Absolute orientation measurement of the headstage along with a lot of other information
+
+Neuropixels V1.0e Device
+    384 channels of extracellular electrophysiology input from 960 selectable neuropixels 1.0 probe electrodes
+
+.. note:: \Remember to configure the probe as described in :ref:`bonsai_NeuropixelsV1edev`. To save data, remember to configure and enable the appropriate workflow nodes.
+    
+Loading Scripts
+--------------------------
+The following script can be used to load the data produced by this workflow in Python (using Numpy):
+
+- Python: :download:`load_headstage64.py <../../../_static/bonsai/workflows/load_neuropixelsv1e.py>` 

source/Software Guide/Bonsai.ONIX/Bonsai Examples/index.rst

@@ -10,6 +10,7 @@ third-party tools at the software level.
     :maxdepth: 1
 
     Headstage64
+    HeadstageNP1e
     LatencyTest
     CameraSync
     Commutator

source/Software Guide/Bonsai.ONIX/GettingStarted.rst

@@ -21,10 +21,10 @@ Bonsai Learning Resources
 
     * - `Bonsai's learn page <https://bonsai-rx.org/learn/>`__
       - Videos and links for understanding how Bonsai can be used to process
-        data streams ranging from beginer to advanced use.
+        data streams ranging from beginner to advanced use.
 
     * - `Bonsai's docs page <https://bonsai-rx.org/docs>`__
-      - Installation, package managment, use guide. These pages also contain an
+      - Installation, package management, use guide. These pages also contain an
         overview of the reactive architecture at the core of Bonsai, and why
         it's useful and powerful. It concludes with a guide on how to use the
         editor to create Bonsai workflows.

source/Software Guide/Bonsai.ONIX/Installation.rst

@@ -25,7 +25,7 @@ hardware and can be installed using its package manager.
    install both the base **Bonsai.ONIX** library and its visualization tools.
 
    .. tip:: It is recommended to also install **Bonsai.ONIX.Design** because
-       it provides a substantial set of data visualation and graphical hardare
+       it provides a substantial set of data visualization and graphical hardware
        configuration elements.
 
    .. image:: /_static/bonsai/package-manager-search-onix.png

source/Software Guide/Bonsai.ONIX/Nodes/ClockOutputDevice.rst

@@ -44,11 +44,11 @@ options.
 
     * - Delay
       - double
-      - If SyncToRun is true, this determins the delay from the start of the
+      - If SyncToRun is true, this determines the delay from the start of the
         hardware running state to the start of the clock output in seconds. 
 
     * - SyncToRun
       - bool
       - If true, then the clock output will remain low until hardware
-        aquisition starts. Otherwise it will free run independent of acqusition
+        acquisition starts. Otherwise it will free run independent of acquisition
         state. 

source/Software Guide/Bonsai.ONIX/Nodes/ElectricalStimulationDevice.rst

@@ -49,7 +49,7 @@ Parameters available through the property pane are as follows:
 
     * - PowerOn
       - boolean
-      - If true, the stimulator power circutiry is turned on. When not in
+      - If true, the stimulator power circuitry is turned on. When not in
         use, its a good idea to keep this false to reduce headstage power
         consumption and possible increased noise.
 
@@ -67,7 +67,7 @@ Parameters available through the property pane are as follows:
 
     * - PhaseOneDuration
       - double
-      - Phase 1 pulse duration (msec). This value can be 0 for monophasic stimuluation.
+      - Phase 1 pulse duration (msec). This value can be 0 for monophasic stimulation.
 
     * - InterPhaseDuration
       - double
@@ -76,7 +76,7 @@ Parameters available through the property pane are as follows:
 
     * - PhaseTwoDuration
       - double
-      - Phase 2 pulse duration (msec). This value can be 0 for monophasic stimuluation.
+      - Phase 2 pulse duration (msec). This value can be 0 for monophasic stimulation.
 
     * - PulsePeriod
       - double

source/Software Guide/Bonsai.ONIX/Nodes/HeadstagePortControlDevice.rst

@@ -2,6 +2,8 @@
 
 HeadstagePortControlDevice
 ===============================
+.. warning:: This node configures hardware parameters when it is placed in a workflow, even if the workflow is not running. Always check voltage configurations before connecting headstages to the system.
+
 A `Bonsai source <https://bonsai-rx.org/docs/editor/#toolbox>`__ that wraps a
 :ref:`onidatasheet_fmc_link_control` device.
 

source/Software Guide/Bonsai.ONIX/Nodes/HeartbeatDevice.rst

@@ -6,7 +6,7 @@ A `Bonsai source <https://bonsai-rx.org/docs/editor/#toolbox>`__ that wraps a
 :ref:`onidatasheet_heartbeat` device.
 
 :Inputs:  None
-:Outputs: A single ``HearbeatDataFrame`` that is produced periodically by
+:Outputs: A single ``HeartbeatDataFrame`` that is produced periodically by
           hardware. This type is a wrapper around the :ref:`Device To Host Data
           Frame <onidatasheet_heartbeat_d2h>` specified on the
           :ref:`onidatasheet_heartbeat` device datasheet.

source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1Device.rst

@@ -55,12 +55,13 @@ Parameters available through the property pane are as follows:
 
     * - RequireSNMatch
       - boolean
-      - If true, then require configuration and probe serial numbers to match
-        to start acqusition. Keeping this parameter set to True is good
+      - If True, the configuration and probe serial numbers must match
+        to start acquisition. Keeping this parameter set to True is good
         practice because the correct calibration files must be loaded in order
         for the probe to function properly.
+        Error message if set to True and not properly configured: Probe and configuration serial numbers do not match.
 
-    * - NueuropixelsV1Configuration
+    * - NeuropixelsV1Configuration
       - N/A
       - Editing this parameter will open the Configuration GUI, just like
         double clicking on the node.
@@ -70,7 +71,7 @@ _________________________
 The **Neuropixels 1.0 Configuration GUI**, which is a part of the
 ``Bonsai.ONIX.Design`` library, is opened by double clicking on the
 NeuropixelsV1Device node when editing the workflow or clicking the ellipsis
-next to the ``NueuropixelsV1Configuration`` parameter option in the property
+next to the ``NeuropixelsV1Configuration`` parameter option in the property
 pane.
 
 .. figure:: /_static/bonsai/neuropixelsv1/neuropixelsv1_configuration-gui-callouts.png
@@ -192,14 +193,14 @@ bottom left of the GUI. A progress bar will indicate the upload progress.
 Saving Configurations
 **********************************
 Complete probe configurations can be saved in easy to parse JSON or XML
-formats. These fikes contain complete information about the state of a given
+formats. These files contain complete information about the state of a given
 probe. This includes all calibration file information, active electrodes, gains
 etc, and therefore can be useful metadata during analysis.
 
 #. Select **Export...** from the **File** menu;
 
     .. image:: /_static/bonsai/neuropixelsv1/neuropixelsv1_export_cropped.png
-       :alt: The configuraiton GUI with export selected
+       :alt: The configuration GUI with export selected
        :align: left
 
 #. Choose if JSON or XML should be used in the file selection dialog and save:
@@ -221,7 +222,7 @@ active electrodes.
 #. Select **Import** from the **File** menu:
 
     .. image:: /_static/bonsai/neuropixelsv1/neuropixelsv1_import_cropped.png
-        :alt: The configuraiton GUI with import selected
+        :alt: The configuration GUI with import selected
         :align: left
 
 #. Select a previously exported configuration file:

source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1eDevice.rst

@@ -4,7 +4,9 @@ NeuropixelsV1eDevice
 ===============================
 
 .. important:: To use this device with ONIX hardware, you must first use the :ref:`bonsai_onicontext` configuration GUI to set the headstage port to :ref:`"Passthrough Mode" <bonsai_onicontext_hubsettings>`
-
+.. important:: Bonsai workflows that contain this node will not
+    open/load unless the headstage is on - Error message: There was an error opening the workflow. Make sure to configure the headstage port voltage and mode correctly using the :ref:`bonsai_onicontext` node with the parameters for the :ref:`headstage_neuropix1e` before connecting the headstage.
+    
 A `Bonsai source <https://bonsai-rx.org/docs/editor/#toolbox>`__  that wraps a
 Neuropixels 1.0e device.
 
@@ -58,10 +60,12 @@ Parameters available through the property pane are as follows:
 
     * - RequireSNMatch
       - boolean
-      - If true, then require configuration and probe serial numbers to match
-        to start acqusition. Keeping this parameter set to True is good
+        If True, the configuration and probe serial numbers must match
+        to start acquisition. Keeping this parameter set to True is good
         practice because the correct calibration files must be loaded in order
         for the probe to function properly.
+        Error message if set to True and not properly configured: Probe and configuration serial numbers do not match.
+
 
     * - NeuropixelsV1Configuration
       - N/A
@@ -195,14 +199,14 @@ bottom left of the GUI. A progress bar will indicate the upload progress.
 Saving Configurations
 **********************************
 Complete probe configurations can be saved in easy to parse JSON or XML
-formats. These fikes contain complete information about the state of a given
+formats. These files contain complete information about the state of a given
 probe. This includes all calibration file information, active electrodes, gains
 etc, and therefore can be useful metadata during analysis.
 
 #. Select **Export...** from the **File** menu;
 
     .. image:: /_static/bonsai/neuropixelsv1/neuropixelsv1_export_cropped.png
-       :alt: The configuraiton GUI with export selected
+       :alt: The configuration GUI with export selected
        :align: left
 
 #. Choose if JSON or XML should be used in the file selection dialog and save:
@@ -224,7 +228,7 @@ active electrodes.
 #. Select **Import** from the **File** menu:
 
     .. image:: /_static/bonsai/neuropixelsv1/neuropixelsv1_import_cropped.png
-        :alt: The configuraiton GUI with import selected
+        :alt: The configuration GUI with import selected
         :align: left
 
 #. Select a previously exported configuration file:

source/Software Guide/Bonsai.ONIX/Nodes/ONIContext.rst

@@ -5,6 +5,9 @@
 
 ONIContext
 ===============================
+
+.. warning:: This node configures hardware parameters when it is placed in a workflow, even if the workflow is not running. Always check voltage configurations before connecting headstages to the system.
+
 A `Bonsai source <https://bonsai-rx.org/docs/editor/#toolbox>`__ that manages a
 :ref:`oni_h_acquisition_context` and allows basic acquisition parameterization.
 There must be at least one of these in every workflow that uses ONIX hardware.
@@ -128,7 +131,7 @@ with a synchronization cable.
     selected *Sync Channel*. Any number of listeners can be assigned to a
     single *Sync Channel*.
 
-.. important:: Only the aquisition start trigger is shared from Sources to
+.. important:: Only the acquisition start trigger is shared from Sources to
     Listeners. The acquisition clock may or may not be shared depending on the
     type of host hardware being used. For example, if all hardware consists of
     :ref:`PCIe Hosts <pcie_host>` on the same motherboard, then both start

source/Software Guide/Bonsai.ONIX/Nodes/RHD2164Device.rst

@@ -54,10 +54,10 @@ options.
       - Select a low-frequency cutoff from allowable options. This filtering is
         performed prior to analog to digital conversion.
 
-    * - DSPCuttoff
+    * - DSPCutoff
       - enum
-      - Select the low-frequency cutoff for the integrated digtial offset
-        removal filter. This fitering is performed following analog to digital
+      - Select the low-frequency cutoff for the integrated digital offset
+        removal filter. This filtering is performed following analog to digital
         conversion.
 
     * - EphysDataFormat

source/Software Guide/Bonsai.ONIX/Nodes/RHS2116Device.rst

@@ -56,10 +56,10 @@ Parameters available through the property pane are as follows:
         - TwosCompliment: raw 16-bit signed integer conversion results.
         - MicroVolts: 32-bit floating-point voltages (EphysData in uV; DCData in Volts)
 
-    * - DSPCuttoff
+    * - DSPCutoff
       - enum
-      - Select the low-frequency cutoff for the integrated digtial offset
-        removal filter. This fitering is performed following analog to digital
+      - Select the low-frequency cutoff for the integrated digital offset
+        removal filter. This filtering is performed following analog to digital
         conversion.
 
     * - AnalogHighCutoff
@@ -86,7 +86,7 @@ Parameters available through the property pane are as follows:
 
     * - StimulusSequence
       - RHS2116StimulusSequence
-      - The stimulus sequence defintion for this device. Editing this parameter
+      - The stimulus sequence definition for this device. Editing this parameter
         will open the configuration GUI, just like double clicking the node.
 
     * - Trigger