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<!DOCTYPE html>
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<li><a href="#vectors" id="toc-vectors" class="nav-link active" data-scroll-target="#vectors"> <span class="header-section-number">1</span> Vectors</a></li>
<li><a href="#data-cube" id="toc-data-cube" class="nav-link" data-scroll-target="#data-cube"> <span class="header-section-number">2</span> Data cube</a></li>
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<h1 class="title">v gdal</h1>
</div>
<div class="quarto-title-meta">
</div>
</header>
<div class="cell" data-hash="STAC_cache/html/unnamed-chunk-1_e51964575ee4128e2ea4a872052c6aa5">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(rstac)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(gdalcubes)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(osmdata)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(terra)</span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(dplyr)</span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(glue)</span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(gdalUtils)</span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(stars)</span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(colorspace)</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="co"># Install gdalUtils package if not already installed</span></span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">requireNamespace</span>(<span class="st">"gdalUtils"</span>, <span class="at">quietly =</span> <span class="cn">TRUE</span>)) {</span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"gdalUtils"</span>)</span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(glue)</span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a><span class="co"># Load the gdalUtils library</span></span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(gdalUtils)</span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(sf)</span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(osmdata)</span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a><span class="fu">gdalcubes_options</span>(<span class="at">parallel =</span> <span class="dv">8</span>)</span>
<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a>sf<span class="sc">::</span><span class="fu">sf_extSoftVersion</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> GEOS GDAL proj.4 GDAL_with_GEOS USE_PROJ_H
"3.10.2" "3.4.2" "8.2.1" "false" "true"
PROJ
"8.2.1" </code></pre>
</div>
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">gdalcubes_gdal_has_geos</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] FALSE</code></pre>
</div>
</div>
<section id="vectors" class="level2" data-number="1">
<h2 data-number="1" class="anchored" data-anchor-id="vectors"><span class="header-section-number">1</span> Vectors</h2>
<div class="cell" data-hash="STAC_cache/html/unnamed-chunk-2_d4e2220022b4ff30e0b6e6107fc58ac7">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>base <span class="ot"><-</span> <span class="st">"https://datadownload-production.s3.amazonaws.com"</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>y2017 <span class="ot"><-</span> <span class="st">"GMW_v3_2017.zip"</span></span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>y2020 <span class="ot"><-</span> <span class="st">"GMW_v3_2020.zip"</span></span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a>Mountains_and_forests <span class="ot"><-</span> <span class="st">"Generalised_Biogeographic_Realms_2004.zip"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell" data-hash="STAC_cache/html/unnamed-chunk-3_292828371687f9bbc6b6db6dac85d227">
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>india <span class="ot"><-</span> spData<span class="sc">::</span>world <span class="sc">|></span> dplyr<span class="sc">::</span><span class="fu">filter</span>(name_long <span class="sc">==</span> <span class="st">"India"</span>) <span class="sc">|></span> <span class="fu">vect</span>()</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>USA <span class="ot"><-</span> spData<span class="sc">::</span>world <span class="sc">|></span> dplyr<span class="sc">::</span><span class="fu">filter</span>(name_long <span class="sc">==</span> <span class="st">"United States"</span>) <span class="sc">|></span> <span class="fu">vect</span>()</span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a>gmw2017_india <span class="ot"><-</span> <span class="fu">glue</span>(<span class="st">"/vsizip/vsicurl/{base}/{y2017}"</span>) <span class="sc">|></span> <span class="fu">vect</span>(<span class="at">filter =</span> india) </span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a>gmw2020_india <span class="ot"><-</span><span class="fu">glue</span>(<span class="st">"/vsizip/vsicurl/{base}/{y2020}"</span>) <span class="sc">|></span> <span class="fu">vect</span>()</span>
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a>MaF <span class="ot"><-</span><span class="fu">glue</span>(<span class="st">"/vsizip/vsicurl/{base}/{Mountains_and_forests}"</span>) <span class="sc">|></span> <span class="fu">summary</span>()</span>
<span id="cb6-7"><a href="#cb6-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-8"><a href="#cb6-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-10"><a href="#cb6-10" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(india)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<p><img src="STAC_files/figure-html/unnamed-chunk-3-1.png" class="img-fluid" width="672"></p>
</div>
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(gmw2017_india)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<p><img src="STAC_files/figure-html/unnamed-chunk-3-2.png" class="img-fluid" width="672"></p>
</div>
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(gmw2020_india)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<p><img src="STAC_files/figure-html/unnamed-chunk-3-3.png" class="img-fluid" width="672"></p>
</div>
</div>
</section>
<section id="data-cube" class="level2" data-number="2">
<h2 data-number="2" class="anchored" data-anchor-id="data-cube"><span class="header-section-number">2</span> Data cube</h2>
<p>A “data cube” (x,y,time) is a common metaphor here. An abstract may have a particular spatial and temporal resolution that need not match the underlying data – for instance, satellite images may be taken every few days, but a cube may use monthly time step – all images in this interval will then be averaged. This can leverage clever things like first masking out clouds, such that the monthly average creates a ‘cloudless’ composite. Similarly, spatial resolution can be lower (allowing for rapid computation and visualization) or higher (using a range of interpolation methods) than the underlying data. Obviously analysts must be mindful of these effects.</p>
<div class="cell" data-hash="STAC_cache/html/unnamed-chunk-4_4316a95f652363314366661c59f171fb">
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>osm_bbox <span class="ot"><-</span> osmdata<span class="sc">::</span><span class="fu">getbb</span>(<span class="st">"Boulder,CO"</span>, <span class="at">format_out =</span> <span class="st">"sf_polygon"</span>)</span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(osm_bbox<span class="sc">$</span>multipolygon[<span class="dv">1</span>,])</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<p><img src="STAC_files/figure-html/unnamed-chunk-4-1.png" class="img-fluid" width="672"></p>
</div>
<div class="sourceCode cell-code" id="cb10"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>osm_bbox<span class="sc">$</span>multipolygon[<span class="dv">1</span>,] <span class="sc">|></span> <span class="fu">st_transform</span>(<span class="st">"EPSG:4326"</span>) <span class="sc">|></span></span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">st_bbox</span>() <span class="ot">-></span> bbox_4326</span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a>osm_bbox<span class="sc">$</span>multipolygon[<span class="dv">1</span>,] <span class="sc">|></span> <span class="fu">st_transform</span>(<span class="st">"EPSG:32618"</span>) <span class="sc">|></span></span>
<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">st_bbox</span>() <span class="ot">-></span> bbox_32618</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell" data-hash="STAC_cache/html/unnamed-chunk-5_4962fbf538a23a7e095b4247f166a56d">
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>s <span class="ot">=</span> <span class="fu">stac</span>(<span class="st">"https://earth-search.aws.element84.com/v0"</span>)</span>
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a> items <span class="ot">=</span> s <span class="sc">|></span></span>
<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">stac_search</span>(<span class="at">collections =</span> <span class="st">"sentinel-s2-l2a-cogs"</span>,</span>
<span id="cb11-4"><a href="#cb11-4" aria-hidden="true" tabindex="-1"></a> <span class="at">bbox =</span> <span class="fu">c</span>(bbox_4326[<span class="st">"xmin"</span>],bbox_4326[<span class="st">"ymin"</span>],</span>
<span id="cb11-5"><a href="#cb11-5" aria-hidden="true" tabindex="-1"></a> bbox_4326[<span class="st">"xmax"</span>],bbox_4326[<span class="st">"ymax"</span>]), </span>
<span id="cb11-6"><a href="#cb11-6" aria-hidden="true" tabindex="-1"></a> <span class="at">datetime =</span> <span class="st">"2021-06-01/2021-07-30"</span>) <span class="sc">|></span></span>
<span id="cb11-7"><a href="#cb11-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">post_request</span>() <span class="sc">|></span> <span class="fu">items_fetch</span>(<span class="at">progress =</span> <span class="cn">FALSE</span>)</span>
<span id="cb11-8"><a href="#cb11-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">length</span>(items<span class="sc">$</span>features)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<pre><code>[1] 23</code></pre>
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<div class="sourceCode cell-code" id="cb13"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(gdalcubes)</span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a>assets <span class="ot">=</span> <span class="fu">c</span>(<span class="st">"B01"</span>,<span class="st">"B02"</span>,<span class="st">"B03"</span>,<span class="st">"B04"</span>,<span class="st">"B05"</span>,<span class="st">"B06"</span>, <span class="st">"B07"</span>,<span class="st">"B08"</span>,<span class="st">"B8A"</span>,<span class="st">"B09"</span>,<span class="st">"B11"</span>,<span class="st">"SCL"</span>)</span>
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a>s2_collection <span class="ot">=</span> <span class="fu">stac_image_collection</span>(items<span class="sc">$</span>features, <span class="at">asset_names =</span> assets)</span>
<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a>s2_collection</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<pre><code>Image collection object, referencing 23 images with 12 bands
Images:
name left top bottom right
1 S2A_13TDE_20210730_0_L2A -106.1832 40.65079 39.65576 -104.8846
2 S2A_13TDE_20210727_0_L2A -105.3595 40.65083 39.66106 -104.8846
3 S2B_13TDE_20210725_0_L2A -106.1832 40.65079 39.65576 -104.8846
4 S2B_13TDE_20210722_0_L2A -105.3653 40.65083 39.66104 -104.8846
5 S2A_13TDE_20210720_0_L2A -106.1832 40.65079 39.65576 -104.8846
6 S2A_13TDE_20210717_0_L2A -105.3595 40.65083 39.66106 -104.8846
datetime srs
1 2021-07-30T18:02:58 EPSG:32613
2 2021-07-27T17:53:02 EPSG:32613
3 2021-07-25T18:02:57 EPSG:32613
4 2021-07-22T17:53:01 EPSG:32613
5 2021-07-20T18:02:58 EPSG:32613
6 2021-07-17T17:53:02 EPSG:32613
[ omitted 17 images ]
Bands:
name offset scale unit nodata image_count
1 B01 0 1 23
2 B02 0 1 23
3 B03 0 1 23
4 B04 0 1 23
5 B05 0 1 23
6 B06 0 1 23
7 B07 0 1 23
8 B08 0 1 23
9 B09 0 1 23
10 B11 0 1 23
11 B8A 0 1 23
12 SCL 0 1 23</code></pre>
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<div class="sourceCode cell-code" id="cb15"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a>v <span class="ot">=</span> <span class="fu">cube_view</span>(<span class="at">srs=</span><span class="st">"EPSG:32618"</span>, <span class="at">dx=</span><span class="dv">20</span>, <span class="at">dy=</span><span class="dv">20</span>, <span class="at">dt=</span><span class="st">"P1D"</span>, </span>
<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a> <span class="at">aggregation=</span><span class="st">"median"</span>, <span class="at">resampling =</span> <span class="st">"average"</span>,</span>
<span id="cb15-3"><a href="#cb15-3" aria-hidden="true" tabindex="-1"></a> <span class="at">extent=</span><span class="fu">list</span>(<span class="at">t0 =</span> <span class="st">"2021-06-01"</span>, <span class="at">t1 =</span> <span class="st">"2021-07-30"</span>,</span>
<span id="cb15-4"><a href="#cb15-4" aria-hidden="true" tabindex="-1"></a> <span class="at">left=</span>bbox_32618[<span class="st">"xmin"</span>], <span class="at">right=</span>bbox_32618[<span class="st">"xmax"</span>],</span>
<span id="cb15-5"><a href="#cb15-5" aria-hidden="true" tabindex="-1"></a> <span class="at">top=</span>bbox_32618[<span class="st">"ymax"</span>], <span class="at">bottom=</span>bbox_32618[<span class="st">"ymin"</span>]))</span>
<span id="cb15-6"><a href="#cb15-6" aria-hidden="true" tabindex="-1"></a>v</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<pre><code>A data cube view object
Dimensions:
low high count pixel_size
t 2021-06-01 2021-07-30 60 P1D
y 4888331.09301011 4902971.09301011 732 20
x -2102910.18631556 -2089230.18631556 684 19.9999999999997
SRS: "EPSG:32618"
Temporal aggregation method: "median"
Spatial resampling method: "average"</code></pre>
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<div class="sourceCode cell-code" id="cb17"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a><span class="fu">raster_cube</span>(s2_collection, v) <span class="sc">|></span></span>
<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">select_bands</span>(<span class="fu">c</span>(<span class="st">"B02"</span>,<span class="st">"B03"</span>,<span class="st">"B04"</span>)) <span class="sc">|></span></span>
<span id="cb17-3"><a href="#cb17-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">reduce_time</span>(<span class="fu">c</span>(<span class="st">"median(B02)"</span>, <span class="st">"median(B03)"</span>, <span class="st">"median(B04)"</span>)) <span class="sc">|></span> </span>
<span id="cb17-4"><a href="#cb17-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">plot</span>(<span class="at">rgb=</span><span class="dv">3</span><span class="sc">:</span><span class="dv">1</span>, <span class="at">na.color =</span> <span class="st">"white"</span>) <span class="sc">|></span> </span>
<span id="cb17-5"><a href="#cb17-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">system.time</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p><img src="STAC_files/figure-html/unnamed-chunk-7-1.png" class="img-fluid" width="672"></p>
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<pre><code> user system elapsed
35.484 2.569 106.788 </code></pre>
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<div class="sourceCode cell-code" id="cb19"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a>ndvi.col <span class="ot">=</span> <span class="cf">function</span>(n) {</span>
<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">rev</span>(<span class="fu">sequential_hcl</span>(n, <span class="st">"Green-Yellow"</span>))</span>
<span id="cb19-3"><a href="#cb19-3" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb19-4"><a href="#cb19-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb19-5"><a href="#cb19-5" aria-hidden="true" tabindex="-1"></a>S2.mask <span class="ot">=</span> <span class="fu">image_mask</span>(<span class="st">"SCL"</span>, <span class="at">values=</span><span class="fu">c</span>(<span class="dv">3</span>,<span class="dv">8</span>,<span class="dv">9</span>)) <span class="co"># clouds and cloud shadows</span></span>
<span id="cb19-6"><a href="#cb19-6" aria-hidden="true" tabindex="-1"></a><span class="fu">raster_cube</span>(s2_collection, v, <span class="at">mask =</span> S2.mask) <span class="sc">%>%</span></span>
<span id="cb19-7"><a href="#cb19-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">select_bands</span>(<span class="fu">c</span>(<span class="st">"B04"</span>, <span class="st">"B08"</span>)) <span class="sc">%>%</span></span>
<span id="cb19-8"><a href="#cb19-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">apply_pixel</span>(<span class="st">"(B08-B04)/(B08+B04)"</span>, <span class="st">"NDVI"</span>) <span class="sc">%>%</span></span>
<span id="cb19-9"><a href="#cb19-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">reduce_time</span>(<span class="fu">c</span>(<span class="st">"median(NDVI)"</span>)) <span class="sc">%>%</span> </span>
<span id="cb19-10"><a href="#cb19-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">plot</span>(<span class="at">col=</span>ndvi.col, <span class="at">zlim=</span><span class="fu">c</span>(<span class="sc">-</span><span class="fl">0.2</span>,<span class="dv">1</span>), <span class="at">na.color =</span> <span class="st">"white"</span>) <span class="sc">%>%</span> </span>
<span id="cb19-11"><a href="#cb19-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">system.time</span>() </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p><img src="STAC_files/figure-html/unnamed-chunk-8-1.png" class="img-fluid" width="672"></p>
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<pre><code> user system elapsed
28.797 1.718 81.597 </code></pre>
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<div class="sourceCode cell-code" id="cb21"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a>output <span class="ot"><-</span> <span class="fu">raster_cube</span>(s2_collection, v, <span class="at">mask =</span> S2.mask) <span class="sc">%>%</span></span>
<span id="cb21-2"><a href="#cb21-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">select_bands</span>(<span class="fu">c</span>(<span class="st">"B04"</span>, <span class="st">"B08"</span>)) <span class="sc">%>%</span></span>
<span id="cb21-3"><a href="#cb21-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">apply_pixel</span>(<span class="st">"(B08-B04)/(B08+B04)"</span>, <span class="st">"NDVI"</span>) <span class="sc">%>%</span></span>
<span id="cb21-4"><a href="#cb21-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">reduce_time</span>(<span class="fu">c</span>(<span class="st">"median(NDVI)"</span>)) <span class="sc">|></span></span>
<span id="cb21-5"><a href="#cb21-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">write_tif</span>()</span>
<span id="cb21-6"><a href="#cb21-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb21-7"><a href="#cb21-7" aria-hidden="true" tabindex="-1"></a>new_star <span class="ot"><-</span> stars<span class="sc">::</span><span class="fu">read_stars</span>(output, <span class="at">proxy =</span> T)</span>
<span id="cb21-8"><a href="#cb21-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb21-9"><a href="#cb21-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb21-10"><a href="#cb21-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>() <span class="sc">+</span> </span>
<span id="cb21-11"><a href="#cb21-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_stars</span>(<span class="at">data =</span> new_star) <span class="sc">+</span></span>
<span id="cb21-12"><a href="#cb21-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>() <span class="sc">+</span> </span>
<span id="cb21-13"><a href="#cb21-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_continuous_sequential</span>(<span class="at">palette =</span> <span class="st">"Green-Yellow"</span>, <span class="at">rev =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<p><img src="STAC_files/figure-html/unnamed-chunk-9-1.png" class="img-fluid" width="672"></p>
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<div class="sourceCode cell-code" id="cb22"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a>ndvi.col <span class="ot">=</span> <span class="cf">function</span>(n) {</span>
<span id="cb22-2"><a href="#cb22-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">rev</span>(<span class="fu">sequential_hcl</span>(n, <span class="st">"Green-Yellow"</span>))</span>
<span id="cb22-3"><a href="#cb22-3" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb22-4"><a href="#cb22-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb22-5"><a href="#cb22-5" aria-hidden="true" tabindex="-1"></a>S2.mask <span class="ot">=</span> <span class="fu">image_mask</span>(<span class="st">"SCL"</span>, <span class="at">values=</span><span class="fu">c</span>(<span class="dv">3</span>,<span class="dv">8</span>,<span class="dv">9</span>)) <span class="co"># clouds and cloud shadows</span></span>
<span id="cb22-6"><a href="#cb22-6" aria-hidden="true" tabindex="-1"></a><span class="fu">raster_cube</span>(s2_collection, v, <span class="at">mask =</span> S2.mask) <span class="sc">|></span></span>
<span id="cb22-7"><a href="#cb22-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">select_bands</span>(<span class="fu">c</span>(<span class="st">"B04"</span>, <span class="st">"B08"</span>)) <span class="sc">|></span></span>
<span id="cb22-8"><a href="#cb22-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">apply_pixel</span>(<span class="st">"(B08-B04)/(B08+B04)"</span>, <span class="st">"NDVI"</span>) <span class="sc">|></span></span>
<span id="cb22-9"><a href="#cb22-9" aria-hidden="true" tabindex="-1"></a> gdalcubes<span class="sc">::</span><span class="fu">animate</span>(<span class="at">col =</span> ndvi.col, <span class="at">zlim=</span><span class="fu">c</span>(<span class="sc">-</span><span class="fl">0.2</span>,<span class="dv">1</span>), <span class="at">key.pos =</span> <span class="dv">1</span>, <span class="at">save_as =</span> <span class="st">"anim.gif"</span>, <span class="at">fps =</span> <span class="dv">4</span>, <span class="at">na.color =</span> <span class="st">"white"</span>)<span class="sc">|></span> <span class="fu">system.time</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> user system elapsed
149.412 14.029 199.455 </code></pre>
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<div class="sourceCode cell-code" id="cb24"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a><span class="fu">raster_cube</span>(s2_collection, v) <span class="sc">|></span> <span class="co"># no mask</span></span>
<span id="cb24-2"><a href="#cb24-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">select_bands</span>(<span class="fu">c</span>(<span class="st">"B02"</span>,<span class="st">"B03"</span>,<span class="st">"B04"</span>,<span class="st">"B08"</span>)) <span class="sc">|></span></span>
<span id="cb24-3"><a href="#cb24-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">apply_pixel</span>(<span class="st">"(B08-B04)/(B08+B04)"</span>, <span class="st">"NDVI"</span>, <span class="at">keep_bands =</span> <span class="cn">TRUE</span>) <span class="ot">-></span> ms_cube</span>
<span id="cb24-4"><a href="#cb24-4" aria-hidden="true" tabindex="-1"></a>ms_cube</span>
<span id="cb24-5"><a href="#cb24-5" aria-hidden="true" tabindex="-1"></a>x <span class="ot">=</span> <span class="fu">extract_geom</span>(ms_cube, osm_bbox<span class="sc">$</span>multipolygon[<span class="dv">1</span>,], <span class="at">FUN =</span> median)</span>
<span id="cb24-6"><a href="#cb24-6" aria-hidden="true" tabindex="-1"></a>x</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<div class="cell" data-hash="STAC_cache/html/unnamed-chunk-12_990a23c35cb62eb941e61a3ae5cf54c3">
<div class="sourceCode cell-code" id="cb25"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a>items_2019 <span class="ot"><-</span> s <span class="sc">%>%</span></span>
<span id="cb25-2"><a href="#cb25-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">stac_search</span>(<span class="at">collections =</span> <span class="st">"sentinel-s2-l2a-cogs"</span>,</span>
<span id="cb25-3"><a href="#cb25-3" aria-hidden="true" tabindex="-1"></a> <span class="at">bbox =</span> <span class="fu">c</span>(<span class="sc">-</span><span class="fl">66.2</span>,<span class="sc">-</span><span class="fl">9.3</span>, <span class="sc">-</span><span class="fl">65.5</span>, <span class="sc">-</span><span class="fl">8.7</span>),</span>
<span id="cb25-4"><a href="#cb25-4" aria-hidden="true" tabindex="-1"></a> <span class="at">datetime =</span> <span class="st">"2019-05-01/2019-06-30"</span>,</span>
<span id="cb25-5"><a href="#cb25-5" aria-hidden="true" tabindex="-1"></a> <span class="at">limit =</span> <span class="dv">500</span>) <span class="sc">%>%</span> </span>
<span id="cb25-6"><a href="#cb25-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">post_request</span>() </span>
<span id="cb25-7"><a href="#cb25-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-8"><a href="#cb25-8" aria-hidden="true" tabindex="-1"></a>items_2020 <span class="ot"><-</span> s <span class="sc">%>%</span></span>
<span id="cb25-9"><a href="#cb25-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">stac_search</span>(<span class="at">collections =</span> <span class="st">"sentinel-s2-l2a-cogs"</span>,</span>
<span id="cb25-10"><a href="#cb25-10" aria-hidden="true" tabindex="-1"></a> <span class="at">bbox =</span> <span class="fu">c</span>(<span class="sc">-</span><span class="fl">66.2</span>,<span class="sc">-</span><span class="fl">9.3</span>, <span class="sc">-</span><span class="fl">65.5</span>, <span class="sc">-</span><span class="fl">8.7</span>),</span>
<span id="cb25-11"><a href="#cb25-11" aria-hidden="true" tabindex="-1"></a> <span class="at">datetime =</span> <span class="st">"2020-05-01/2020-06-30"</span>,</span>
<span id="cb25-12"><a href="#cb25-12" aria-hidden="true" tabindex="-1"></a> <span class="at">limit =</span> <span class="dv">500</span>) <span class="sc">%>%</span> </span>
<span id="cb25-13"><a href="#cb25-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">post_request</span>() </span>
<span id="cb25-14"><a href="#cb25-14" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-15"><a href="#cb25-15" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-16"><a href="#cb25-16" aria-hidden="true" tabindex="-1"></a>col_2019 <span class="ot">=</span> <span class="fu">stac_image_collection</span>(items_2019<span class="sc">$</span>features, <span class="at">asset_names =</span> assets, </span>
<span id="cb25-17"><a href="#cb25-17" aria-hidden="true" tabindex="-1"></a> <span class="at">property_filter =</span> <span class="cf">function</span>(x) {x[[<span class="st">"eo:cloud_cover"</span>]] <span class="sc"><</span> <span class="dv">10</span>})</span>
<span id="cb25-18"><a href="#cb25-18" aria-hidden="true" tabindex="-1"></a>col_2020 <span class="ot">=</span> <span class="fu">stac_image_collection</span>(items_2020<span class="sc">$</span>features, <span class="at">asset_names =</span> assets, </span>
<span id="cb25-19"><a href="#cb25-19" aria-hidden="true" tabindex="-1"></a> <span class="at">property_filter =</span> <span class="cf">function</span>(x) {x[[<span class="st">"eo:cloud_cover"</span>]] <span class="sc"><</span> <span class="dv">10</span>})</span>
<span id="cb25-20"><a href="#cb25-20" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-21"><a href="#cb25-21" aria-hidden="true" tabindex="-1"></a>v_2019 <span class="ot">=</span> <span class="fu">cube_view</span>(<span class="at">srs =</span> <span class="st">"EPSG:32720"</span>, <span class="at">extent =</span> <span class="fu">list</span>(<span class="at">t0 =</span> <span class="st">"2019-05-01"</span>, <span class="at">t1 =</span> <span class="st">"2019-06-30"</span>,</span>
<span id="cb25-22"><a href="#cb25-22" aria-hidden="true" tabindex="-1"></a> <span class="at">left =</span> <span class="dv">143510</span>, <span class="at">right =</span> <span class="dv">226241</span>, <span class="at">top =</span> <span class="dv">9037300</span>, <span class="at">bottom =</span> <span class="dv">8972318</span>),</span>
<span id="cb25-23"><a href="#cb25-23" aria-hidden="true" tabindex="-1"></a> <span class="at">dx =</span> <span class="dv">100</span>, <span class="at">dy =</span> <span class="dv">100</span>, <span class="at">dt =</span> <span class="st">"P1D"</span>, <span class="at">aggregation =</span> <span class="st">"median"</span>, <span class="at">resampling =</span> <span class="st">"bilinear"</span>)</span>
<span id="cb25-24"><a href="#cb25-24" aria-hidden="true" tabindex="-1"></a>v_2020 <span class="ot">=</span> <span class="fu">cube_view</span>(v_2019, <span class="at">extent =</span> <span class="fu">list</span>(<span class="at">t0 =</span> <span class="st">"2020-05-01"</span>, <span class="at">t1 =</span> <span class="st">"2020-06-30"</span>))</span>
<span id="cb25-25"><a href="#cb25-25" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-26"><a href="#cb25-26" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-27"><a href="#cb25-27" aria-hidden="true" tabindex="-1"></a>max_ndvi_mosaic <span class="ot"><-</span> <span class="cf">function</span>(col, v) {</span>
<span id="cb25-28"><a href="#cb25-28" aria-hidden="true" tabindex="-1"></a> <span class="fu">raster_cube</span>(col, v, <span class="at">mask =</span> S2.mask) <span class="sc">%>%</span></span>
<span id="cb25-29"><a href="#cb25-29" aria-hidden="true" tabindex="-1"></a> <span class="fu">select_bands</span>(<span class="fu">c</span>(<span class="st">"B04"</span>, <span class="st">"B08"</span>)) <span class="sc">%>%</span></span>
<span id="cb25-30"><a href="#cb25-30" aria-hidden="true" tabindex="-1"></a> <span class="fu">apply_pixel</span>(<span class="fu">c</span>(<span class="st">"(B08-B04)/(B08+B04)"</span>), <span class="at">names=</span><span class="st">"NDVI"</span>) <span class="sc">%>%</span></span>
<span id="cb25-31"><a href="#cb25-31" aria-hidden="true" tabindex="-1"></a> <span class="fu">reduce_time</span>(<span class="st">"max(NDVI)"</span>)</span>
<span id="cb25-32"><a href="#cb25-32" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb25-33"><a href="#cb25-33" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-34"><a href="#cb25-34" aria-hidden="true" tabindex="-1"></a><span class="fu">suppressPackageStartupMessages</span>(<span class="fu">library</span>(stars))</span>
<span id="cb25-35"><a href="#cb25-35" aria-hidden="true" tabindex="-1"></a><span class="fu">max_ndvi_mosaic</span>(col_2019, v_2019) <span class="sc">%>%</span></span>
<span id="cb25-36"><a href="#cb25-36" aria-hidden="true" tabindex="-1"></a> <span class="fu">st_as_stars</span>() <span class="ot">-></span> maxndvi_2019</span>
<span id="cb25-37"><a href="#cb25-37" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-38"><a href="#cb25-38" aria-hidden="true" tabindex="-1"></a><span class="fu">max_ndvi_mosaic</span>(col_2020, v_2020) <span class="sc">%>%</span></span>
<span id="cb25-39"><a href="#cb25-39" aria-hidden="true" tabindex="-1"></a> <span class="fu">st_as_stars</span>() <span class="ot">-></span> maxndvi_2020</span>
<span id="cb25-40"><a href="#cb25-40" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-41"><a href="#cb25-41" aria-hidden="true" tabindex="-1"></a>difference <span class="ot">=</span> maxndvi_2020 <span class="sc">-</span> maxndvi_2019</span>
<span id="cb25-42"><a href="#cb25-42" aria-hidden="true" tabindex="-1"></a>difference[difference <span class="sc">></span> <span class="sc">-</span><span class="fl">0.15</span>] <span class="ot">=</span> <span class="cn">NA</span></span>
<span id="cb25-43"><a href="#cb25-43" aria-hidden="true" tabindex="-1"></a><span class="fu">names</span>(difference) <span class="ot"><-</span> <span class="st">"Difference of max NDVI (2020 - 2019)"</span></span>
<span id="cb25-44"><a href="#cb25-44" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-45"><a href="#cb25-45" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tmap)</span>
<span id="cb25-46"><a href="#cb25-46" aria-hidden="true" tabindex="-1"></a><span class="fu">tmap_mode</span>(<span class="st">"view"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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