Fix broken reference after merging the tutorial in

- Also, add references to the GUI in the template - This is WIP, but I want to get something out so that users have tutorial content for np2 headstages
open-ephys · Aug 28, 2024 · 76c200f · 76c200f
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diff --git a/template/partials/tutorials/main.tmpl.partial b/template/partials/tutorials/main.tmpl.partial
@@ -25,7 +25,7 @@
 
 <h2> Configuring the {{{hub}}} </h2>
 
-<p>We start by configuring the hardware using a configuration chain. This chain creates a hardware context using <a class="xref" href="../api/OpenEphys.Onix1.CreateContext.html">CreateContext</a>, adds a {{{hub}}} configuration using <a class="xref" href="../api/OpenEphys.Onix1.Configure{{{configureOperator}}}.html">{{{configureOperator}}}</a>, and then starts acquisition using <a class="xref" href="../api/OpenEphys.Onix1.StartAcquisition.html">StartAcquisition</a>. Here we break down each of these operators. </p>
+<p>We start by configuring the hardware using a configuration chain. This chain creates a hardware context using <a class="xref" href="../api/OpenEphys.Onix1.CreateContext.html">CreateContext</a>, adds a {{{hub}}} configuration using <a class="xref" href="../api/OpenEphys.Onix1.Configure{{{configureOperator}}}.html">{{{configureOperator}}}</a>, and then starts acquisition using <a class="xref" href="../api/OpenEphys.Onix1.StartAcquisition.html">StartAcquisition</a>. Here we break down each of these operators.</p>
 
 <div class="workflow">
     <p><img src="../workflows/examples/{{{configureOperator}}}.bonsai" alt="{{{configureOperator}}} Workflow"></p>
@@ -37,7 +37,10 @@
 
 <h3> {{{configureOperator}}} </h3>
 
-<p>The <a class="xref" href="../api/OpenEphys.Onix1.Configure{{{configureOperator}}}.html">{{{configureOperator}}}</a> operator is used to configure the {{hub}}. Configuration settings for the {{hub}} can be examined and edited by clicking on the operator to open its property pane to the right of the editor. Expanding the members of the property pane allows you to configure each of the devices contained by the {{hub}}. {{^nonDefaultProperties}}In this demo, the {{hub}} properties are set to their default values.{{/nonDefaultProperties}}{{#nonDefaultProperties}}In this demo, the {{hub}} properties are set to their default values, except:{{/nonDefaultProperties}}</p>
+<p>The <a class="xref" href="../api/OpenEphys.Onix1.Configure{{{configureOperator}}}.html">{{{configureOperator}}}</a> operator is used to configure the {{hub}}. Configuration settings for the {{hub}} can be examined and edited by clicking on the operator to open its property pane to the right of the editor. Expanding the members of the property pane allows you to configure each of the devices contained by the {{hub}}. 
+{{#gui}}This {{hub}} has a configuration GUI that can be accessed by following the <a class="xref" href="./{{hubSnakeCase}}-gui-tut.html">{{hub}} GUI Tutorial</a>.{{/gui}}
+{{^nonDefaultProperties}}In this demo, the {{hub}} properties are set to their default values.{{/nonDefaultProperties}}
+{{#nonDefaultProperties}}In this demo, the {{hub}} properties are set to their default values, except:{{/nonDefaultProperties}}</p>
 
 <ul>
     {{#nonDefaultProperties}}<li>{{{.}}}</li>{{/nonDefaultProperties}}
@@ -51,7 +54,7 @@
 
 {{/configure}}
 
-<h2> Streaming Data </h2>
+<h2> Streaming data </h2>
 
 <p>The rest of the workflow concerns capturing data to and from the {{{hub}}}, using a set of discrete "processing graphs" that either produce data from hardware (inputs/sources) or accept data produced by software (outputs/sinks). We describe these graphs in the following sections.</p>
 
@@ -61,3 +64,21 @@
 </div>
 
 {{#dataIOOperators}}{{>partials/tutorials/device}}{{/dataIOOperators}}
+
+<!---
+<h2>Loading data</h2>
+<p>The following python script can be used to load and plot the data produced by the workflow described in this tutorial.</p>
+
+[!code-python[](../workflows/examples/load-breakoutboard.py)]
+
+<div class="NOTE alert alert-info">
+    <h5>NOTE</h5>
+    <p>This script will attempt to load entire files into arrays. For long recordings, data will need to be split into more manageable chunks by:</p>
+    <ul>
+        <li>Modifying this script to partially load files</li>
+        <li>Modifying the workflow to cyclically creating new files after a certain duration</li>
+    </ul>
+</div>
+--->
+
+
diff --git a/tutorials/neuropixelsv1e-tut.md b/tutorials/neuropixelsv1e-tut.md
@@ -10,7 +10,8 @@ overview:
         -   Streams Neuropixels 1.0 and BNO055 data.
         -   Commutates the tether automatically if there is a proper commutator connection.
 configure: 
-    nonDefaultProperties: 
+    gui: false
+    nonDefaultProperties:
 dataIOOperators: 
     -   operator: PortStatus
         data: Port Status
@@ -24,3 +25,11 @@ dataIOOperators:
         data: BNO055
         graphDescription: This processing graph generates data from the headstage's BNO055, writes it to a .csv file, and selects <code>Quaternion</code> data to send to a node that commutates the tether automatically if there is a proper commutator connection. Because <code>CsvWriter</code> is a <code>Sink</code> operator, it emits the same item downstream as it receives from upstream. Therefore, Bno55DataFrame members can by selected by hovering over <code>Output</code> in the context menu that appears by right-clicking the <code>CsvWriter</code> node. 
 ---
+<!---
+[!code-python[](../workflows/examples/load-np1.py)]
+
+> [!NOTE]
+> This script will attempt to load entire files into arrays. For long recordings, data will need to be split into more manageable chunks by:
+> - Modifying this script to partially load files
+> - Modifying the workflow to cyclically creating new files after a certain duration
+--->
diff --git a/tutorials/neuropixelsv2e-gui-tut.md b/tutorials/neuropixelsv2e-gui-tut.md
@@ -1,6 +1,6 @@
 # NeuropixelsV2e GUI
 
-In addition to the capabilities described in <xref:NeuropixelsV2eTutorial>, the `NeuropixelsV2e` headstage has a graphical user interface when the `OpenEphys.Onix1.Design` package is downloaded. For more information on how to install that library, check out the <xref:BonsaiInstallationAndConfiguration> page.
+In addition to the capabilities described in <xref:np2e-tut>, the `NeuropixelsV2e` headstage has a graphical user interface when the `OpenEphys.Onix1.Design` package is downloaded. For more information on how to install that library, check out the <xref:BonsaiInstallationAndConfiguration> page.
 
 ## Overview
 

diff --git a/tutorials/neuropixelsv2e-tut.md b/tutorials/neuropixelsv2e-tut.md
@@ -10,7 +10,8 @@ overview:
         -   Streams Neuropixels 2.0 and BNO055 data.
         -   Commutates the tether automatically if there is a proper commutator connection.
 configure: 
-    nonDefaultProperties: 
+    gui: true
+    nonDefaultProperties:
 dataIOOperators:
     -   operator: PortStatus
         data: Port Status
@@ -23,6 +24,12 @@ dataIOOperators:
     -   operator: NeuropixelsV2eBno055Data
         data: BNO055
         graphDescription: This processing graph generates data from the headstage's BNO055, writes it to a .csv file, and selects <code>Quaternion</code> data to send to a node that commutates the tether automatically if there is a proper commutator connection. Because <code>CsvWriter</code> is a <code>Sink</code> operator, it emits the same item downstream as it receives from upstream. Therefore, Bno55DataFrame members can by selected by hovering over <code>Output</code> in the context menu that appears by right-clicking the <code>CsvWriter</code> node. 
-
-
 ---
+<!---
+[!code-python[](../workflows/examples/load-np2.py)]
+
+> [!NOTE]
+> This script will attempt to load entire files into arrays. For long recordings, data will need to be split into more manageable chunks by:
+> - Modifying this script to partially load files
+> - Modifying the workflow to cyclically creating new files after a certain duration
+--->