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Presentation.html
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<!DOCTYPE html>
<html lang="en"><head>
<script src="Presentation_files/libs/clipboard/clipboard.min.js"></script>
<script src="Presentation_files/libs/quarto-html/tabby.min.js"></script>
<script src="Presentation_files/libs/quarto-html/popper.min.js"></script>
<script src="Presentation_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="Presentation_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="Presentation_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="Presentation_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
<meta name="generator" content="quarto-1.2.242">
<meta name="author" content="Alejandro Morales Sierra">
<title>What is VPL?</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<link rel="stylesheet" href="Presentation_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="Presentation_files/libs/revealjs/dist/reveal.css">
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1.6em;
vertical-align: middle;
}
</style>
<link rel="stylesheet" href="Presentation_files/libs/revealjs/dist/theme/quarto.css" id="theme">
<link href="Presentation_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="Presentation_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="Presentation_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="Presentation_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
.callout.callout-style-simple {
padding: 0em 0.5em;
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
display: flex;
}
.callout.callout-style-default {
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
}
.callout .callout-body-container {
flex-grow: 1;
}
.callout.callout-style-simple .callout-body {
font-size: 1rem;
font-weight: 400;
}
.callout.callout-style-default .callout-body {
font-size: 0.9rem;
font-weight: 400;
}
.callout.callout-captioned.callout-style-simple .callout-body {
margin-top: 0.2em;
}
.callout:not(.callout-captioned) .callout-body {
display: flex;
}
.callout:not(.no-icon).callout-captioned.callout-style-simple .callout-content {
padding-left: 1.6em;
}
.callout.callout-captioned .callout-header {
padding-top: 0.2em;
margin-bottom: -0.2em;
}
.callout.callout-captioned .callout-caption p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
.callout.callout-captioned.callout-style-simple .callout-content p {
margin-top: 0;
}
.callout.callout-captioned.callout-style-default .callout-content p {
margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-caption {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
.callout.callout-style-default div.callout-caption {
border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-default div.callout-content {
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-simple .callout-icon::before {
height: 1rem;
width: 1rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 1rem 1rem;
}
.callout.callout-style-default .callout-icon::before {
height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-caption {
display: flex
}
.callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
.callout.no-icon::before {
display: none !important;
}
.callout.callout-captioned .callout-body > .callout-content > :last-child {
margin-bottom: 0.5rem;
}
.callout.callout-captioned .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-captioned) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-note.callout-style-default .callout-caption {
background-color: #dae6fb
}
div.callout-important {
border-left-color: #d9534f !important;
}
div.callout-important .callout-icon::before {
background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAYAAABzenr0AAAAAXNSR0IArs4c6QAAAERlWElmTU0AKgAAAAgAAYdpAAQAAAABAAAAGgAAAAAAA6ABAAMAAAABAAEAAKACAAQAAAABAAAAIKADAAQAAAABAAAAIAAAAACshmLzAAAEKklEQVRYCcVXTWhcVRS+575MJym48A+hSRFr00ySRQhURRfd2HYjk2SSTokuBCkU2o0LoSKKraKIBTcuFCoidGFD08nkBzdREbpQ1EDNIv8qSGMFUboImMSZd4/f9zJv8ibJMC8xJQfO3HPPPef7zrvvvnvviIkpC9nsw0UttFunbUhpFzFtarSd6WJkStVMw5xyVqYTvkwfzuf/5FgtkVoB0729j1rjXwThS7Vio+Mo6DNnvLfahoZ+i/o32lULuJ3NNiz7q6+pyAUkJaFF6JwaM2lUJlV0MlnQn5aTRbEu0SEqHUa0A4AdiGuB1kFXRfVyg5d87+Dg4DL6m2TLAub60ilj7A1Ec4odSAc8X95sHh7+ZRPCFo6Fnp7HfU/fBng/hi10CjCnWnJjsxvDNxWw0NfV6Rv5GgP3I3jGWXumdTD/3cbEOP2ZbOZp69yniG3FQ9z1jD7bnBu9Fc2tKGC2q+uAJOQHBDRiZX1x36o7fWBs7J9ownbtO+n0/qWkvW7UPIfc37WgT6ZGR++EOJyeQDSb9UB+DZ1G6DdLDzyS+b/kBCYGsYgJbSQHuThGKRcw5xdeQf8YdNHsc6ePXrlSYMBuSIAFTGAtQo+VuALo4BX83N190NWZWbynBjhOHsmNfFWLeL6v+ynsA58zDvvAC8j5PkbOcXCMg2PZFk3q8MjI7WAG/Dp9AwP7jdGBOOQkAvlFUB+irtm16I1Zw9YBcpGTGXYmk3kQIC/Cds55l+iMI3jqhjAuaoe+am2Jw5GT3Nbz3CkE12NavmzN5+erJW7046n/CH1RO/RVa8lBLozXk9uqykkGAyRXLWlLv5jyp4RFsG5vGVzpDLnIjTWgnRy2Rr+tDKvRc7Y8AyZq10jj8DqXdnIRNtFZb+t/ZRtXcDiVnzpqx8mPcDWxgARUqx0W1QB9MeUZiNrV4qP+Ehc+BpNgATsTX8ozYKL2NtFYAHc84fG7ndxUPr+AR/iQSns7uSUufAymwDOb2+NjK27lEFocm/EE2WpyIy/Hi66MWuMKJn8RvxIcj87IM5Vh9663ziW36kR0HNenXuxmfaD8JC7tfKbrhFr7LiZCrMjrzTeGx+PmkosrkNzW94ObzwocJ7A1HokLolY+AvkTiD/q1H0cN48c5EL8Crkttsa/AXQVDmutfyku0E7jShx49XqV3MFK8IryDhYVbj7Sj2P2eBxwcXoe8T8idsKKPRcnZw1b+slFTubwUwhktrfnAt7J++jwQtLZcm3sr9LQrjRzz6cfMv9aLvgmnAGvpoaGLxM4mAEaLV7iAzQ3oU0IvD5x9ix3yF2RAAuYAOO2f7PEFWCXZ4C9Pb2UsgDeVnFSpbFK7/IWu7TPTvBqzbGdCHOJQSxiEjt6IyZmxQyEJHv6xyQsYk//moVFsN2zP6fRImjfq7/n/wFDguUQFNEwugAAAABJRU5ErkJggg==');
}
div.callout-important.callout-style-default .callout-caption {
background-color: #f7dddc
}
div.callout-warning {
border-left-color: #f0ad4e !important;
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<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">What is VPL?</h1>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
Alejandro Morales Sierra
</div>
<p class="quarto-title-affiliation">
Centre for Crop Systems Analysis - Wageningen University
</p>
</div>
</div>
<p class="date">29/03/2023</p>
</section>
<section>
<section id="the-virtual-plant-laboratory-vpl" class="title-slide slide level1 center">
<h1>The Virtual Plant Laboratory (VPL)</h1>
</section>
<section id="what-is-vpl" class="slide level2">
<h2>What is VPL?</h2>
<ul>
<li>A <strong>package</strong> written in the Julia language<br>
</li>
<li>The <strong>API</strong> offers <strong>data structures</strong> and <strong>algorithms</strong> to help you build, simulate and visualize FSP models
<ul>
<li>Development is driven by the needs of our research<br>
</li>
<li>Plant-level models where functionality is defined at the organ and plant level<br>
</li>
<li>Emphasis on plant-plant and plant-environment interactions</li>
<li>Crop systems (vertical farming, greenhouse, mono- and intercropping, perennials)</li>
</ul></li>
</ul>
</section>
<section id="what-is-the-vplverse" class="slide level2">
<h2>What is the <em>VPLverse</em>?</h2>
<ul>
<li><p>VPL + website + other packages</p></li>
<li><p>Optional <strong>packages</strong> to help build FSP models:</p>
<ul>
<li><strong>Sky.jl</strong> to solar radiation and generate light sources for ray tracing<br>
</li>
<li><strong>Ecophys.jl</strong> that contains modules for ecophysiological processes<br>
</li>
<li><strong>VPLTutorials.jl</strong> with examples and tutorials on how to use VPL</li>
</ul></li>
<li><p>A website with all the documentation and tutorials on VPLverse</p></li>
</ul>
</section>
<section id="what-vpl-will-never-be" class="slide level2">
<h2>What VPL will never be</h2>
<ul>
<li>A Julia implementation of other FSPM software</li>
<li>A modelling language</li>
<li>A large model with lots of plugins</li>
<li>A standalone modelling studio/platform</li>
<li>An attempt to support every possible FSP model</li>
</ul>
</section>
<section id="why-not-a-standalone-studio" class="slide level2">
<h2>Why not a standalone studio?</h2>
<p>When building an studio/platform you are responsible for:</p>
<ul>
<li>Platform compatibility (Windows, Mac, Linux…)<br>
</li>
<li>Visualization (3D rendering, graphs)<br>
</li>
<li>Input (text editor)<br>
</li>
<li>Code organization (projects)<br>
</li>
<li>Graphical user interface to organize input/output (GUI)</li>
</ul>
<p>Since VPL is just a Julia package we get (most of) this for “free”</p>
<p>How do I do X in VPL = How do I do X in Julia (in most cases)</p>
</section>
<section id="why-not-a-modelling-language" class="slide level2">
<h2>Why not a modelling language?</h2>
<p>Domain specific languages have advantages:</p>
<ul>
<li>Succinct and powerful in describing elaborate computations</li>
<li>Can generate optimized code<br>
</li>
<li>The user can avoid learning technical details or even progranming</li>
</ul>
<p>And disadvantages:</p>
<ul>
<li>It can be more limiting than an API-based approach<br>
</li>
<li>The code being executed is not visible to the user (<em>magic</em> happening in the background, many assumptions being made)<br>
</li>
<li>A new language requires its own development support (syntax highlighting, code completion, Github copilot? GPT?, etc.)<br>
</li>
<li>The user needs to learn the domain specific language which is not useful for anything else</li>
</ul>
</section>
<section id="why-did-i-build-vpl" class="slide level2">
<h2>Why did I build VPL?</h2>
<ul>
<li><p>I wanted to have an FSPM platform where I could:</p>
<ul>
<li>Use it as part of a reproducible computing workflow for plotting, I/O, analysis…<br>
</li>
<li>Easily extend it without touching the source code<br>
</li>
<li>Read the source code and understand what is going on<br>
</li>
<li>Read the documentation and understand how it works<br>
</li>
<li>Use it to teach FSPM to students<br>
</li>
<li>Run it anywhere (Windows, Mac, Linux, HPC, Cloud, etc.)</li>
</ul></li>
</ul>
</section></section>
<section>
<section id="section" class="title-slide slide level1 center">
<h1></h1>
<img data-src="img/Julia.png" class="r-stretch quarto-figure-center"></section>
<section id="what-is-julia" class="slide level2">
<h2>What is Julia?</h2>
<ul>
<li>A dynamic JIT compiled programming language</li>
<li>Julia 0.0 beta released in 2012 by 4 people @ MIT</li>
<li>Julia 1.0 in 2018 (stable since then)</li>
<li>Reads like Matlab-Python, feels like R, runs like C</li>
<li>It is very easy to integrate with R and Python, native support for C/C++</li>
</ul>
</section>
<section id="why-julia" class="slide level2">
<h2>Why Julia?</h2>
<ul>
<li>Classic dynamic languages (R, Python, Matlab)
<ul>
<li>Rapid development</li>
<li>Easy to learn</li>
<li>Code runs slow</li>
</ul></li>
<li>Two language problem: Bottlenecks lowered to classic static languages (C/C++/Fortran)
<ul>
<li>Need to maintain code in two languages, plus the interface</li>
<li>To really benefit, most of the FSPM would have to be lowered</li>
</ul></li>
<li>Julia was designed to solve the two language problem
<ul>
<li>Write all the code in a single language</li>
<li>Achieve performance by incrementally improving the code</li>
</ul></li>
</ul>
</section></section>
<section>
<section id="vpl-design" class="title-slide slide level1 center">
<h1>VPL design</h1>
</section>
<section id="vpl-overview" class="slide level2">
<h2>VPL overview</h2>
<p>VPL addresses four main components in FSPM:</p>
<ul>
<li><strong>Graphs</strong> to represent the topology of the plants
<ul>
<li>Inspired by Relational Growth Grammars (GroIMP) but procedural<br>
</li>
</ul></li>
<li><strong>Geometry</strong> to represent the 3D structure of the plants plus other scene elements
<ul>
<li>Inspired by turtle graphics and based on triangular meshes compatible with other Julia packages<br>
</li>
</ul></li>
<li>Interactive <strong>3D visualization</strong> of the structure
<ul>
<li>Based on Makie.jl (support OpenGL and WebGL)</li>
</ul></li>
<li>Radiation transport within the scene
<ul>
<li>Multi-threaded, multi-wavelength <strong>Monte Carlo ray tracer</strong></li>
</ul></li>
</ul>
</section>
<section id="graphs" class="slide level2">
<h2>Graphs</h2>
<ul>
<li><p>A tree graph represents <strong>topology</strong> of a plant (nodes, internodes, leaves, etc.)</p></li>
<li><p>A node can store any <strong>user-defined data type</strong> (<code><: Node</code>) as well as the graph itself (<code>vars</code>)</p></li>
<li><p>Each data type has a method that defines its <strong>geometry, material and color</strong> (<code>feed!</code>)</p></li>
<li><p>Graph edges created by a simply <strong>node algebra</strong>:</p>
<ul>
<li>Phytomer: <code>Node() + (Bud(), Leaf()) + Internode() + Meristem()</code></li>
</ul></li>
<li><p>User defines functions to implement:</p>
<ul>
<li><p><strong>Relational growth rules</strong> can replace nodes by subgraphs (<code>Rule</code> & <code>rewrite!</code>)</p></li>
<li><p><strong>Relational queries</strong> can extract combinations of nodes (<code>Query</code> & <code>apply</code>)</p></li>
</ul></li>
<li><p>Different graphs can be queried/rewritten in <strong>parallel</strong> (multi-threading)</p></li>
</ul>
</section>
<section id="geometry" class="slide level2">
<h2>Geometry</h2>
<ul>
<li><p>A <code>Scene</code> contains</p>
<ul>
<li>3D <strong>triangular mesh</strong></li>
<li>Optional <strong>colors</strong> (for rendering)</li>
<li>Optional <strong>materials</strong> (for ray tracing)</li>
</ul></li>
<li><p>Scenes are created from graphs using <code>feed!</code></p></li>
<li><p>Individual elements can be added to the scene manually (<code>add!</code>)</p></li>
<li><p>Mesh constructors are provided for common shapes (cylinder, rectangle, etc.)</p></li>
<li><p>Meshes can be exported/imported to/from other formats (e.g. OBJ, STL, PLY)</p></li>
</ul>
</section>
<section id="visualization" class="slide level2">
<h2>Visualization</h2>
<ul>
<li><p>Graphs can be rendered as <strong>networks diagrams</strong> and labels can be customized</p></li>
<li><p>Scenes can be rendered with a simple <strong>3D interactive engine</strong></p></li>
<li><p>All visualization based on Makie.jl that supports OpenGL and WebGL</p></li>
<li><p>Snapshots can be exported</p></li>
</ul>
</section>
<section id="ray-tracing" class="slide level2">
<h2>Ray tracing</h2>
<ul>
<li><p>Multi-threaded, multi-wavelength forward <strong>Monte Carlo ray tracer</strong></p></li>
<li><p><strong>Acceleration</strong> with SAH-based Bounding Volume Hierarchy</p></li>
<li><p>Common <strong>radiation sources</strong> are available (point, directional, area, line)</p></li>
<li><p>Common <strong>materials</strong> are available (Black, Sensor, Lambertian, Modified Phong)</p></li>
<li><p>Users can add new materials and light sources and choose the number generator, including low-discrepancy sequences (not documented yet)</p></li>
<li><p><strong>Sky.jl</strong> creates light sources for diffuse and direct solar radiation from location and day of year</p></li>
<li><p>Use instancing to approximate large canopies (<strong>grid cloner</strong>)</p></li>
<li><p>Could have multiple ray tracers in the same model</p></li>
</ul>
</section></section>
<section>
<section id="future-roadmap" class="title-slide slide level1 center">
<h1>Future roadmap</h1>
</section>
<section id="short-term" class="slide level2">
<h2>Short term</h2>
<ul>
<li>Finish tutorials</li>
<li>Develop reference models and extend Ecophys.jl and Sky.jl<br>
</li>
<li>Technical documentation for developers</li>
<li>Move rendering and raytracing to separate packages in the VPLverse</li>
<li>Prepare package for collaboration and register it</li>
</ul>
</section>
<section id="long-term" class="slide level2">
<h2>Long term</h2>
<ul>
<li>Plant internal transport via ODEs<br>
</li>
<li>Interface with environment (soil and atmosphere)
<ul>
<li>Mapping 3D geometry to a 3D grid<br>
</li>
<li>Support PDE models for environment<br>
</li>
</ul></li>
<li>Hybrid models (e.g. FSPM + MAESPA-like models, Raycaster + radiative transfer)</li>
</ul>
<div class="footer footer-default">
</div>
</section></section>
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