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Documenter.jl committed Jun 13, 2024
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{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-27T07:17:56","documenter_version":"1.4.1"}}
{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-13T13:03:49","documenter_version":"1.4.1"}}
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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · PlantGeom.jl</title><meta name="title" content="Home · PlantGeom.jl"/><meta property="og:title" content="Home · PlantGeom.jl"/><meta property="twitter:title" content="Home · PlantGeom.jl"/><meta name="description" content="Documentation for PlantGeom.jl."/><meta property="og:description" content="Documentation for PlantGeom.jl."/><meta property="twitter:description" content="Documentation for PlantGeom.jl."/><meta property="og:url" content="https://VEZY.github.io/PlantGeom.jl/"/><meta property="twitter:url" content="https://VEZY.github.io/PlantGeom.jl/"/><link rel="canonical" href="https://VEZY.github.io/PlantGeom.jl/"/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>PlantGeom.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a></li><li><span class="tocitem">Plot recipes</span><ul><li><input class="collapse-toggle" id="menuitem-2-1" type="checkbox"/><label class="tocitem" for="menuitem-2-1"><span class="docs-label">MTG diagrams</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="plot_diagram/makie_diagram/">Makie.jl</a></li><li><a class="tocitem" href="plot_diagram/plots_diagram/">Plots.jl</a></li></ul></li><li><a class="tocitem" href="makie_3d/">3D Makie recipes</a></li></ul></li><li><a class="tocitem" href="API/">API</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/VEZY/PlantGeom.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/VEZY/PlantGeom.jl/blob/main/docs/src/index.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="PlantGeom"><a class="docs-heading-anchor" href="#PlantGeom">PlantGeom</a><a id="PlantGeom-1"></a><a class="docs-heading-anchor-permalink" href="#PlantGeom" title="Permalink"></a></h1><p>Documentation for <a href="https://github.com/VEZY/PlantGeom.jl">PlantGeom</a>, a package about everything 3D-related for plants.</p><p>The package is designed around <a href="https://github.com/VEZY/MultiScaleTreeGraph.jl">MultiScaleTreeGraph</a> for the basic structure of plants (or any 3D object) topology and attributes.</p><p>The package provides different functionalities, the main ones being:</p><ul><li>IO for the OPF file format (see <a href="API/#PlantGeom.read_opf-Tuple{Any}"><code>read_opf</code></a> and <a href="API/#PlantGeom.write_opf-Tuple{Any, Any}"><code>write_opf</code></a>);</li><li>plotting using <code>viz</code> and <code>viz!</code>, optionally using coloring by attribute;</li><li>mesh transformations using <a href="API/#PlantGeom.transform_mesh!-Tuple{MultiScaleTreeGraph.Node, Any}"><code>transform_mesh!</code></a></li></ul><p>Note that PlantGeom reserves the <code>:geometry</code> attribute in the nodes (<em>e.g.</em> organs). It uses it to store the 3D geometry as a special structure (<a href="API/#PlantGeom.geometry"><code>geometry</code></a>).</p><p><video src="plant_animation.mp4" controls="true" title><a href="plant_animation.mp4"></a></video></p><p>If you want to reproduce the animation, you can look at the code below. Otherwise, please head to the next section.</p><pre><code class="language-julia hljs">using PlantGeom, MultiScaleTreeGraph, CairoMakie
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · PlantGeom.jl</title><meta name="title" content="Home · PlantGeom.jl"/><meta property="og:title" content="Home · PlantGeom.jl"/><meta property="twitter:title" content="Home · PlantGeom.jl"/><meta name="description" content="Documentation for PlantGeom.jl."/><meta property="og:description" content="Documentation for PlantGeom.jl."/><meta property="twitter:description" content="Documentation for PlantGeom.jl."/><meta property="og:url" content="https://VEZY.github.io/PlantGeom.jl/"/><meta property="twitter:url" content="https://VEZY.github.io/PlantGeom.jl/"/><link rel="canonical" href="https://VEZY.github.io/PlantGeom.jl/"/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>PlantGeom.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a></li><li><span class="tocitem">Plot recipes</span><ul><li><input class="collapse-toggle" id="menuitem-2-1" type="checkbox"/><label class="tocitem" for="menuitem-2-1"><span class="docs-label">MTG diagrams</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="plot_diagram/makie_diagram/">Makie.jl</a></li><li><a class="tocitem" href="plot_diagram/plots_diagram/">Plots.jl</a></li></ul></li><li><a class="tocitem" href="makie_3d/">3D Makie recipes</a></li></ul></li><li><a class="tocitem" href="API/">API</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/VEZY/PlantGeom.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/VEZY/PlantGeom.jl/blob/main/docs/src/index.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="PlantGeom"><a class="docs-heading-anchor" href="#PlantGeom">PlantGeom</a><a id="PlantGeom-1"></a><a class="docs-heading-anchor-permalink" href="#PlantGeom" title="Permalink"></a></h1><p>Documentation for <a href="https://github.com/VEZY/PlantGeom.jl">PlantGeom</a>, a package about everything 3D-related for plants.</p><p>The package is designed around <a href="https://github.com/VEZY/MultiScaleTreeGraph.jl">MultiScaleTreeGraph</a> for the basic structure of plants (or any 3D object) topology and attributes.</p><p>The package provides different functionalities, the main ones being:</p><ul><li>IO for the OPF file format (see <a href="API/#PlantGeom.read_opf-Tuple{Any}"><code>read_opf</code></a> and <a href="API/#PlantGeom.write_opf-Tuple{Any, Any}"><code>write_opf</code></a>);</li><li>plotting using <code>viz</code> and <code>viz!</code>, optionally using coloring by attribute;</li><li>mesh transformations using <a href="API/#PlantGeom.transform_mesh!-Tuple{MultiScaleTreeGraph.Node, Any}"><code>transform_mesh!</code></a></li></ul><p>Note that PlantGeom reserves the <code>:geometry</code> attribute in the nodes (<em>e.g.</em> organs). It uses it to store the 3D geometry as a special structure (<a href="API/#PlantGeom.geometry"><code>geometry</code></a>).</p><p><video src="plant_animation.mp4" controls="true" title><a href="plant_animation.mp4"></a></video></p><p>If you want to reproduce the animation, you can look at the code below. Otherwise, please head to the next section.</p><pre><code class="language-julia hljs">using CairoMakie, Meshes, PlantGeom, MultiScaleTreeGraph
opf = read_opf(joinpath(dirname(dirname(pathof(PlantGeom))),&quot;test&quot;,&quot;files&quot;,&quot;simple_plant.opf&quot;))

# First, we compute the 3D coordinates for each node in the MTG:
transform!(opf, refmesh_to_mesh!)
# And compute the max z of each node based on their mesh:
transform!(opf, zmax =&gt; :z_node, ignore_nothing = true)
# Or the z coordinate of each vertez of each node mesh:
transform!(opf, :geometry =&gt; (x -&gt; [i.coords[3] for i in x.mesh.vertices]) =&gt; :z_vertex, ignore_nothing = true)
transform!(opf, :geometry =&gt; (x -&gt; [Meshes.coords(i)z for i in Meshes.vertices(x.mesh)]) =&gt; :z_vertex, ignore_nothing = true)


# Then we make a Makie figure:
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# And making a little animation out of it:
CairoMakie.record(f, &quot;plant_animation.mp4&quot;, 1:120) do frame
ax2.azimuth[] = 0.3π + 0.3 * sin(2π * frame / 120)
end</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="plot_diagram/makie_diagram/">Makie.jl »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Monday 27 May 2024 07:17">Monday 27 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
end</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="plot_diagram/makie_diagram/">Makie.jl »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Thursday 13 June 2024 13:03">Thursday 13 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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