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‎api/configure.md

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@@ -3,4 +3,7 @@ uid: configure
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title: Configuration Operators
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---
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Device configuration operators belong in a top-level chain of operators between [`CreateContext`](xref:OpenEphys.Onix1.CreateContext) and [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) to configure devices contained by ONIX hardware hubs.
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Aggregate configuration operators belong in a top-level chain of operators between
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[`CreateContext`](xref:OpenEphys.Onix1.CreateContext) and [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) to
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configure ONIX hardware hubs. These are known as aggregate configuration operators because they configure an aggregation
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of devices (also referred to as a hub) on a given headstage, miniscope, breakout board, etc..

‎api/constants.md

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---
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uid: constants
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title: Constants
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---
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These constants are used throughout the <xref:OpenEphys.Onix1> Bonsai package to assign names to numbered values.

‎api/data-elements.md

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---
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uid: data-elements
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title: Data Elements
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---
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Data elements are produced by <xref:OpenEphys.Onix1> Bonsai operators.

‎api/device-configure.md

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@@ -3,7 +3,7 @@ uid: device-configure
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title: Device Configuration Operators
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---
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> [!IMPORTANT]
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> [!TIP]
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> Device configuration operators are not recommended for using off-the-shelf Open Ephys hardware. Use aggregate [configuration operators](xref:configure) instead. Aggregate [configuration operators](xref:configure) confer the following benefits:
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> - The `address` and `name` properties of aggregate configuration operators undergo automatic configuration which reduces the risk of erroneous configuration.
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> - The workflow is less cluttered with configuration operators as one aggregate configuration operator corresponds to multiple device operators. This improves workflow legibility and expedites the workflow scripting process.

‎api/overview.md

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---
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uid: OpenEphys.Onix1
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title: OpenEphys.Onix1
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---
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`OpenEphys.Onix1` is a Bonsai package containing interfaces for data acquisition and control of ONIX hardware. This section
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of the docs is dedicated to facilitate construction of workflows using the OpenEphys.Onix1 package.
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In Bonsai, press <kbd>F1</kbd> while an OpenEphys.Onix1 node is selected in the workflow editor to quickly open this reference.

‎docfx.json

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@@ -3,9 +3,7 @@
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{
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"src": [
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{
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"files": [
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"src/**.csproj"
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]
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"files": ["src/**.csproj"]
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}
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],
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"dest": "api",
@@ -19,35 +17,20 @@
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"index.md": "landing"
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}
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},
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"content": [
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"articles/**.{md,yml}",
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"api/**.{md,yml}",
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"toc.yml",
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"index.md"
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],
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"resource": [
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"logo.svg",
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"favicon.png",
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"images/**",
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"workflows/**"
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"content": [
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{
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"files": ["articles/**.{md,yml}", "api/**.{md,yml}", "toc.yml", "index.md"],
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"exclude": ["api/overview.md"]
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}
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],
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"resource": ["logo.svg", "favicon.png", "images/**", "workflows/**"],
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"output": "_site",
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"overwrite": [
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{
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"files": [
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],
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"exclude": [
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"obj/**",
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"_site/**"
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]
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"files": ["api/overview.md"]
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}
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],
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"template": [
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"default",
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"modern",
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"template",
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"docfx-tools/template"
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],
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"template": ["default", "modern", "template", "docfx-tools/template"],
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"globalMetadata": {
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"_enableNewTab": true,
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"_enableSearch": true,
@@ -77,4 +60,4 @@
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"rules": {
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"InvalidBookmark": "suggestion"
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}
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}
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}

‎template/ManagedReference.html.primary.tmpl

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@@ -8,4 +8,14 @@
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{{#isEnum}}
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{{>partials/enum}}
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{{/isEnum}}
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{{/isEnum}}
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{{#isNamespace}}
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<div>
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<h1 data-uid="{{{uid}}}" class="text-break">
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{{{title}}}
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<a class="header-action link-secondary" title="View source" href="https://github.com/open-ephys/bonsai-onix1/tree/main/OpenEphys.Onix1"><i class="bi bi-code-slash"></i></a>
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</h1>
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</div>
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{{{conceptual}}}
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{{/isNamespace}}

‎template/partials/class.tmpl.partial

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{{#oe.operator.configureDevice}}
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<div class="CAUTION alert alert-danger">
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<h5>Caution</h5>
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<p>
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This is a device configuration operator. Device configuration operators are not recommended for interfacing with off-the-shelf ONIX hardware. Use <a class="xref" href="configure.html">aggregate configuration operators</a> to do that instead.
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</p>
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<p>
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To understand the benefits of <a class="xref" href="configure.html">aggregate configuration operators</a>, refer to the <a class="xref" href="device-configure.html">device configuration operators</a> page.
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</p>
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</div>
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<div class="Important alert alert-info">
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<h5>TIP</h5>
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<p>
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This is a device configuration operator. <a class="xref" href="configure.html">Aggregate configuration operators</a> are recommended in lieu of <a class="xref" href="device-configure.html">device configuration operators</a> for interfacing with Open Ephys Onix hardware.
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</p>
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</div>
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{{/oe.operator.configureDevice}}
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<div>

‎template/toc.extension.js

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@@ -8,84 +8,98 @@ exports.preTransform = function (model) {
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if (model.items[0].name === 'OpenEphys.Onix1'){
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if (model.items[0].items){
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itemsItemsLength = model.items[0].items.length;
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let items = [{
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'name': 'Core Operators',
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'href' : 'core.html',
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'topicHref': 'core.html',
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'topicUid': 'core',
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'items': []}, {
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'name': 'Configuration Operators',
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'href' : 'configure.html',
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'topicHref': 'configure.html',
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'topicUid': 'configure',
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'items': []}, {
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'name': 'Data I/O Operators',
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'href' : 'dataio.html',
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'topicHref': 'dataio.html',
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'topicUid': 'dataio',
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'items': []}, {
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'name': 'Other',
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'items': [
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let items = [
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{
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'name': 'Core Operators',
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'href' : 'core.html',
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'topicHref': 'core.html',
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'topicUid': 'core',
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'items': []
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},
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{
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'name': 'Configuration Operators',
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'href' : 'configure.html',
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'topicHref': 'configure.html',
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'topicUid': 'configure',
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'items': []
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},
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{
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'name': 'Data I/O Operators',
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'href' : 'dataio.html',
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'topicHref': 'dataio.html',
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'topicUid': 'dataio',
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'items': []
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},
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{
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'name': 'Data Elements',
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'href' : 'data-elements.html',
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'topicHref': 'data-elements.html',
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'topicUid': 'data-elements',
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'items': []
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},
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{
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'name': 'Other',
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'topicUid': 'other',
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'items':
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[
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{
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'name': 'Device Configuration Operators',
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'href' : 'device-configure.html',
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'topicHref': 'device-configure.html',
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'topicUid': 'device-configure',
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'items': []
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},
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{
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'name': 'Constants',
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'href' : 'constants.html',
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'topicHref': 'constants.html',
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'topicUid': 'constants',
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'items': []
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}
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]
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}
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];
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for (let i = 0; i < itemsItemsLength; i++)
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{
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globalYml = '~/api/' + model.items[0].items[i].topicUid + '.yml';
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globalModel = model.__global._shared[globalYml];
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if (globalModel?.type === 'class' || globalModel?.type === 'struct')
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{
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if (model.items[0].items[i].name.includes('CreateContext') || model.items[0].items[i].name.includes('StartAcquisition'))
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{
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'name': 'Device Configuration Operators',
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'href' : 'device-configure.html',
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'topicHref': 'device-configure.html',
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'topicUid': 'device-configure',
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'items': [],
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items[0].items.push(model.items[0].items[i]);
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}
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]
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}];
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for (let i = 0; i < itemsItemsLength; i++) {
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globalYml = '~/api/' + model.items[0].items[i].topicUid + '.yml';
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if (model.items[0].items[i].name.includes('Frame') ||
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model.items[0].items[i].name.includes('DeviceFactory') ||
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model.items[0].items[i].name.includes('ContextTask') ||
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model.items[0].items[i].name.includes('DeviceNameConverter') ||
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model.items[0].items[i].name.includes('ConfigureDS90UB9x') ||
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model.items[0].items[i].name.includes('ConfigureFmcLinkController') ||
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model.items[0].items[i].name.includes('DeviceContext') ||
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model.items[0].items[i].name.includes('NeuropixelsV2QuadShankElectrode') ||
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model.items[0].items[i].name.includes('NeuropixelsV2QuadShankProbeConfiguration') ||
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model.items[0].items[i].name.includes('NeuropixelsV1eAdc')){
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model.items[0].items[i].hide = true;
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}
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else if (model.__global._shared[globalYml] && model.__global._shared[globalYml].type === 'enum') {
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model.items[0].items[i].hide = true;
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}
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else {
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if (model.__global._shared[globalYml] && model.__global._shared[globalYml].type === 'class'){
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const inheritanceLength = model.__global._shared[globalYml].inheritance.length;
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device = false;
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hub = false;
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for (let j = 0; j < inheritanceLength; j++){
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if (model.__global._shared[globalYml].inheritance[j].uid === 'OpenEphys.Onix1.SingleDeviceFactory'){
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device = true;
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}
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else if (model.__global._shared[globalYml].inheritance[j].uid === 'OpenEphys.Onix1.MultiDeviceFactory'){
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hub = true;
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}
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}
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if (model.items[0].items[i].name.includes('CreateContext') || model.items[0].items[i].name.includes('StartAcquisition')){
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items[0].items.push(model.items[0].items[i]);
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}
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else if (device){
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items[3].items[0].items.push(model.items[0].items[i]);
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}
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else if (hub){
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items[1].items.push(model.items[0].items[i]);
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}
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else {
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items[2].items.push(model.items[0].items[i]);
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}
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else if (globalModel?.inheritance.some(inherited => inherited.uid === 'OpenEphys.Onix1.MultiDeviceFactory'))
73+
{
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items[1].items.push(model.items[0].items[i]);
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}
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else if (globalModel?.inheritance.some(inherited => inherited.uid === 'OpenEphys.Onix1.SingleDeviceFactory'))
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{
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items[4].items[0].items.push(model.items[0].items[i]);
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}
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else if ((globalModel.syntax?.content[0].value.includes('ElementCategory.Source') ||
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globalModel.syntax?.content[0].value.includes('ElementCategory.Sink') ||
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globalModel?.inheritance.some(inherited => inherited.uid.includes('Bonsai.Source')) ||
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globalModel?.inheritance.some(inherited => inherited.uid.includes('Bonsai.Sink'))) &&
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!globalModel.syntax?.content[0].value.includes('abstract'))
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{
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items[2].items.push(model.items[0].items[i]);
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}
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else if (model.items[0].items[i].name.includes('ContextTask') ||
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model.items[0].items[i].name.includes('OutputClockParameters') ||
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globalModel?.inheritance.some(inherited => inherited.uid === 'OpenEphys.Onix1.DataFrame' || inherited.uid === 'OpenEphys.Onix1.BufferedDataFrame'))
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{
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items[3].items.push(model.items[0].items[i]);
93+
}
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}
95+
else if (globalModel && globalModel.type === 'enum')
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{
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items[4].items[1].items.push(model.items[0].items[i]);
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}
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}
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model.items[0].items = items;
84101
}
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}
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// if (model.items[1].name === 'OpenEphys.Onix1.Design'){
87-
// model.items.splice(1, 1);
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// }
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return model;
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}
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