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open-AIMS · Oct 29, 2024 · 919feb4 · 919feb4
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diff --git a/dev/assets/api.md.DG0CSgDl.js → dev/assets/api.md.DuPAeFTW.js b/dev/assets/api.md.DG0CSgDl.js → dev/assets/api.md.DuPAeFTW.js
diff --git a/dev/assets/api.md.DG0CSgDl.lean.js → dev/assets/api.md.DuPAeFTW.lean.js b/dev/assets/api.md.DG0CSgDl.lean.js → dev/assets/api.md.DuPAeFTW.lean.js
diff --git a/dev/docker.html b/dev/docker.html
diff --git a/dev/getting_started.html b/dev/getting_started.html
@@ -43,7 +43,7 @@
 <span class="line"><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">(</span><span style="--shiki-light:#6F42C1;--shiki-dark:#B392F0;">sandbox</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">) </span><span style="--shiki-light:#6F42C1;--shiki-dark:#B392F0;">julia</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">&gt; </span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;">]add</span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;"> Revise</span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;"> Infiltrator</span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;"> Chairmarks</span></span>
 <span class="line"><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">(</span><span style="--shiki-light:#6F42C1;--shiki-dark:#B392F0;">sandbox</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">) </span><span style="--shiki-light:#6F42C1;--shiki-dark:#B392F0;">julia</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">&gt; </span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;">]dev</span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;"> ..</span></span></code></pre></div><p>Copy the quickstart to a file (e.g., <code>dev_server.jl</code>).</p><p>Create the <code>.config.toml</code> file and save to the sandbox directory.</p><p>Assuming VS Code is configured to default to the sandbox environment and start the Julia REPL at project root:</p><div class="language-julia vp-adaptive-theme"><button title="Copy Code" class="copy"></button><span class="lang">julia</span><pre class="shiki shiki-themes github-light github-dark vp-code" tabindex="0"><code><span class="line"><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">;cd sandbox</span></span>
 <span class="line"><span style="--shiki-light:#005CC5;--shiki-dark:#79B8FF;">include</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">(</span><span style="--shiki-light:#032F62;--shiki-dark:#9ECBFF;">&quot;dev_server.jl&quot;</span><span style="--shiki-light:#24292E;--shiki-dark:#E1E4E8;">)</span></span></code></pre></div><p>Note that the server now caches the initially loaded spatial data in between server launches to reduce downtime. It will be necessary to restart the Julia session to reload spatial data.</p><h2 id="Performance-notes" tabindex="-1">Performance notes <a class="header-anchor" href="#Performance-notes" aria-label="Permalink to &quot;Performance notes {#Performance-notes}&quot;"></a></h2><p>The config setting <code>COG_THREADS</code> controls how many threads should be requested when writing out COGs. Ideally this will be set to at least 2 (preferably 4). Higher values do seem to reduce write times but with diminishing returns (tested up to 8). Locally, write times with four threads configured range from 10 to 15 seconds.</p><h2 id="Reef-edge-alignment-for-site-searching" tabindex="-1">Reef edge alignment for site searching <a class="header-anchor" href="#Reef-edge-alignment-for-site-searching" aria-label="Permalink to &quot;Reef edge alignment for site searching {#Reef-edge-alignment-for-site-searching}&quot;"></a></h2><p><code>identify_edge_aligned_sites()</code> can be used to identify potential sites that only align with the nearest reef edge (or specified rotations away from this angle). This method works by identifying the closest edge of reef polygon geometries that have been converted into lines.</p><p>The following processing is required before use:</p><ul><li><p>Reef polygons should be simplified (<code>GO.simplify()</code>) and buffered to avoid matching possibly inaccurate reef edges.</p></li><li><p>Simplified reef polygons should be provided as vertex-vertex lines with <code>polygon_to_lines()</code>.</p></li><li><p>Require raster of target pixels to search, and their indices (currently a vector of <code>CartesianIndices</code> for identifying search pixels). Use <code>findall(bool_search_raster)</code> to return pixel indices.</p></li><li><p>Raster of search pixels should be masked by reef polygons or simplified reef polygons.</p></li><li><p>The target region name should be specified in GBRMPA format.</p><ul><li>E.g. &quot;Townsville/Whitsunday Management Area&quot; rather than &quot;Townsville-Whitsunday&quot;.</li></ul></li></ul><h3 id="Parquet-assessment-additional-setup" tabindex="-1">Parquet assessment additional setup <a class="header-anchor" href="#Parquet-assessment-additional-setup" aria-label="Permalink to &quot;Parquet assessment additional setup {#Parquet-assessment-additional-setup}&quot;"></a></h3><ul><li><p>A parquet GeoDataFrame must be loaded and filtered for unsuitable pixels based on user criteria thresholds using a Dict and <code>within_thresholds()</code>.</p></li><li><p><code>lon</code> and <code>lat</code> columns (FLoat64) must be added to the GeoDataFrame.</p><ul><li>E.g. <code>valid_pixels.lon = first.(GI.coordinates.(valid_pixels.geometry))</code></li></ul><p>The column used for masking should be the same as the column specified as geometry_col in <code>identify_edge_aligned_sites</code>(default =<code>:geometry</code>).</p></li></ul></div></div></main><footer class="VPDocFooter" data-v-83890dd9 data-v-4f9813fa><!--[--><!--]--><div class="edit-info" data-v-4f9813fa><div class="edit-link" data-v-4f9813fa><a class="VPLink link vp-external-link-icon no-icon edit-link-button" href="https://github.com/open-AIMS/ReefGuideAPI.jl/edit/main/docs/src/getting_started.md" target="_blank" rel="noreferrer" data-v-4f9813fa><!--[--><span class="vpi-square-pen edit-link-icon" data-v-4f9813fa></span> Edit this page<!--]--></a></div><!----></div><!----></footer><!--[--><!--]--></div></div></div><!--[--><!--]--></div></div><footer class="VPFooter" data-v-a9a9e638 data-v-c970a860><div class="container" data-v-c970a860><p class="message" data-v-c970a860>Made with <a href="https://luxdl.github.io/DocumenterVitepress.jl/dev/" target="_blank"><strong>DocumenterVitepress.jl</strong></a><br></p><p class="copyright" data-v-c970a860>© Copyright 2024.</p></div></footer><!--[--><!--]--></div></div>
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