Skip to content

Commit

Permalink
Built site for gh-pages
Browse files Browse the repository at this point in the history
  • Loading branch information
Quarto GHA Workflow Runner committed Nov 28, 2023
1 parent 16b9dec commit 0d9cce5
Show file tree
Hide file tree
Showing 5 changed files with 45 additions and 60 deletions.
2 changes: 1 addition & 1 deletion .nojekyll
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
94a82968
57919ab7
89 changes: 37 additions & 52 deletions contents/python-ex.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -230,7 +230,7 @@
<p>This Jupyter (ipynb) notebook provides a brief introduction to a cloud-native workflow. A more complete version of this example can be found in the intro.qmd Quarto notebook. Here, we merely include an <code>ipynb</code> version to demonstrate how Jupyter notebooks may be included in quarto.</p>
<p><em>Note: in Codespaces editor, choose “Select Kernel” -&gt; “Jupyter Kernels” to get started.</em></p>
<p>Developer note: At this time, Gitpod VSCode editor will not detect the default python environment (VIRTUAL_ENV variable, pointing to <code>/opt/venv/bin/python</code>), or any other kernelspec added with ipykernel.</p>
<div class="cell" data-tags="[]">
<div class="cell" data-tags="[]" data-execution_count="1">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> pystac_client <span class="im">import</span> Client</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> odc.stac</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pystac_client</span>
Expand All @@ -239,7 +239,7 @@
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> warnings</span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>warnings.filterwarnings(<span class="st">'ignore'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell" data-tags="[]">
<div class="cell" data-tags="[]" data-execution_count="2">
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>box <span class="op">=</span> [<span class="op">-</span><span class="fl">122.51006</span>, <span class="fl">37.70801</span>, <span class="op">-</span><span class="fl">122.36268</span>, <span class="fl">37.80668</span>]</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>client <span class="op">=</span> Client.<span class="bu">open</span>(<span class="st">"https://earth-search.aws.element84.com/v1"</span>)</span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>search <span class="op">=</span> client.search(</span>
Expand All @@ -249,63 +249,48 @@
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> query<span class="op">=</span>{<span class="st">"eo:cloud_cover"</span>: {<span class="st">"lt"</span>: <span class="dv">20</span>}}</span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell" data-tags="[]">
<div class="cell" data-tags="[]" data-execution_count="3">
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>items <span class="op">=</span> search.get_all_items()</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="co"># items[0] # peak at an item</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>data <span class="op">=</span> odc.stac.load(</span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> items,</span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a> crs<span class="op">=</span><span class="st">"EPSG:32610"</span>,</span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a> bands<span class="op">=</span>[<span class="st">"nir08"</span>, <span class="st">"red"</span>],</span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a> resolution<span class="op">=</span><span class="dv">30</span>,</span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a> bbox<span class="op">=</span>box</span>
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell" data-execution_count="4">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>data <span class="op">=</span> odc.stac.load(</span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> items,</span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> crs<span class="op">=</span><span class="st">"EPSG:32610"</span>,</span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a> bands<span class="op">=</span>[<span class="st">"nir08"</span>, <span class="st">"red"</span>],</span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a> resolution<span class="op">=</span><span class="dv">30</span>,</span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a> bbox<span class="op">=</span>box</span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>red <span class="op">=</span> data.red</span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>nir <span class="op">=</span> data.nir08</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 class="co"># summarize over time. </span></span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a><span class="co"># quite probably better to use resampling strategy in odc.stac.load though.</span></span>
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> dask.diagnostics</span>
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a><span class="cf">with</span> dask.diagnostics.ProgressBar():</span>
<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a> ndvi <span class="op">=</span> ( ((nir <span class="op">-</span> red) <span class="op">/</span> (red <span class="op">+</span> nir)).</span>
<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a> resample(time<span class="op">=</span><span class="st">"MS"</span>).</span>
<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a> median(<span class="st">"time"</span>, keep_attrs<span class="op">=</span><span class="va">True</span>).</span>
<span id="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a> compute()</span>
<span id="cb5-13"><a href="#cb5-13" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb5-14"><a href="#cb5-14" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-15"><a href="#cb5-15" aria-hidden="true" tabindex="-1"></a><span class="co"># mask out bad pixels</span></span>
<span id="cb5-16"><a href="#cb5-16" aria-hidden="true" tabindex="-1"></a>ndvi <span class="op">=</span> ndvi.where(ndvi <span class="op">&lt;=</span> <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" data-execution_count="5">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>red <span class="op">=</span> data.red</span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>nir <span class="op">=</span> data.nir08</span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a><span class="co"># summarize over time. </span></span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a><span class="co"># quite probably better to use resampling strategy in odc.stac.load though.</span></span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> dask.diagnostics</span>
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a><span class="cf">with</span> dask.diagnostics.ProgressBar():</span>
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a> ndvi <span class="op">=</span> ( ((nir <span class="op">-</span> red) <span class="op">/</span> (red <span class="op">+</span> nir)).</span>
<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a> resample(time<span class="op">=</span><span class="st">"MS"</span>).</span>
<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a> median(<span class="st">"time"</span>, keep_attrs<span class="op">=</span><span class="va">True</span>).</span>
<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a> compute()</span>
<span id="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb5-13"><a href="#cb5-13" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-14"><a href="#cb5-14" aria-hidden="true" tabindex="-1"></a><span class="co"># mask out bad pixels</span></span>
<span id="cb5-15"><a href="#cb5-15" aria-hidden="true" tabindex="-1"></a>ndvi <span class="op">=</span> ndvi.where(ndvi <span class="op">&lt;=</span> <span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> matplotlib <span class="im">as</span> plt</span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>cmap <span class="op">=</span> plt.colormaps.get_cmap(<span class="st">'viridis'</span>) <span class="co"># viridis is the default colormap for imshow</span></span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a>cmap.set_bad(color<span class="op">=</span><span class="st">'black'</span>)</span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a>ndvi.plot.imshow(row<span class="op">=</span><span class="st">"time"</span>, cmap<span class="op">=</span>cmap, add_colorbar<span class="op">=</span><span class="va">False</span>, size<span class="op">=</span><span class="dv">4</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell" data-execution_count="6">
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> matplotlib <span class="im">as</span> plt</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>cmap <span class="op">=</span> plt.colormaps.get_cmap(<span class="st">'viridis'</span>) <span class="co"># viridis is the default colormap for imshow</span></span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>cmap.set_bad(color<span class="op">=</span><span class="st">'black'</span>)</span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a>ndvi.plot.imshow(row<span class="op">=</span><span class="st">"time"</span>, cmap<span class="op">=</span>cmap, add_colorbar<span class="op">=</span><span class="va">False</span>, size<span class="op">=</span><span class="dv">4</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-display" data-execution_count="6">
<pre><code>&lt;xarray.plot.facetgrid.FacetGrid at 0x7fec26fd96c0&gt;</code></pre>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> geopandas <span class="im">as</span> gpd</span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>sf <span class="op">=</span> <span class="st">"/vsicurl/https://dsl.richmond.edu/panorama/redlining/static/downloads/geojson/CASanFrancisco1937.geojson"</span></span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a>poly <span class="op">=</span> gpd.read_file(sf)</span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a>poly <span class="op">=</span> poly.to_crs(epsg<span class="op">=</span><span class="st">"32610"</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-display">
<p><img src="python-ex_files/figure-html/cell-7-output-2.png" class="img-fluid"></p>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> rasterstats</span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>result <span class="op">=</span> rasterstats.zonal_stats(</span>
<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a> vectors <span class="op">=</span> sf, </span>
<span id="cb8-5"><a href="#cb8-5" aria-hidden="true" tabindex="-1"></a> raster <span class="op">=</span> ndvi.values,</span>
<span id="cb8-6"><a href="#cb8-6" aria-hidden="true" tabindex="-1"></a> nodata <span class="op">=</span> src_srtm.nodata, </span>
<span id="cb8-7"><a href="#cb8-7" aria-hidden="true" tabindex="-1"></a> affine <span class="op">=</span> src_srtm.transform,</span>
<span id="cb8-8"><a href="#cb8-8" aria-hidden="true" tabindex="-1"></a> stats <span class="op">=</span> [<span class="st">'mean'</span>, <span class="st">'min'</span>, <span class="st">'max'</span>]</span>
<span id="cb8-9"><a href="#cb8-9" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb8-10"><a href="#cb8-10" aria-hidden="true" tabindex="-1"></a>result</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>


Expand Down
Binary file added contents/python-ex_files/figure-html/cell-7-output-2.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading

0 comments on commit 0d9cce5

Please sign in to comment.