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<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../setup/setup.html">Setting up the correct environnment and parameters</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="input_preparation.html">Preparing the inputs for Modspa-Pixel</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="ndvi_cube.html">Preparing the NDVI data cube</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Preparing the weather data cube</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#modspa_pixel.preprocessing.download_ERA5_weather.request_ER5_weather"><code class="docutils literal notranslate"><span class="pre">request_ER5_weather()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#precipitation">Precipitation</a></li>
<li class="toctree-l3"><a class="reference internal" href="#reference-evapotranspiration">Reference evapotranspiration</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#modspa_pixel.preprocessing.lib_era5_land_pixel.call_era5land_daily_for_MODSPA"><code class="docutils literal notranslate"><span class="pre">call_era5land_daily_for_MODSPA()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="#formatting-and-preprocessing-the-raw-data">Formatting and preprocessing the raw data</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#modspa_pixel.preprocessing.lib_era5_land_pixel.calculate_ET0_pixel"><code class="docutils literal notranslate"><span class="pre">calculate_ET0_pixel()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="#modspa_pixel.preprocessing.lib_era5_land_pixel.combine_weather2netcdf"><code class="docutils literal notranslate"><span class="pre">combine_weather2netcdf()</span></code></a></li>
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<section id="preparing-the-weather-data-cube">
<span id="weather"></span><h1>Preparing the weather data cube<a class="headerlink" href="#preparing-the-weather-data-cube" title="Link to this heading"></a></h1>
<p>The modspa models (<em>SAMIR</em> and <em>SAFY</em>) require preprocessed weather data to run. The <em>SAMIR</em> model needs spatialized <strong>precipitation</strong> and <strong>reference evapotranspiration</strong> as inputs. This requires various raw weather variables to be downloaded and processed to create a data cube with the same structure and georeferencing as the <a class="reference internal" href="ndvi_cube.html#ndvi"><span class="std std-ref">NDVI data cube</span></a>. The raw weather data is downloaded and processed to produce the necessary variables.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>As of now, only the <strong>ERA 5</strong> data download is implemented. It allows to download weather data all over the world with a simple python api.</p>
</div>
<p>The weather dataset can be automatically created with the following function:</p>
<dl class="py function">
<dt class="sig sig-object py" id="modspa_pixel.preprocessing.download_ERA5_weather.request_ER5_weather">
<span class="sig-prename descclassname"><span class="pre">modspa_pixel.preprocessing.download_ERA5_weather.</span></span><span class="sig-name descname"><span class="pre">request_ER5_weather</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">config_file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ndvi_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">raw_S2_image_ref</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shapefile</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'pixel'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">str</span></span></span><a class="reference internal" href="../_modules/modspa_pixel/preprocessing/download_ERA5_weather.html#request_ER5_weather"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#modspa_pixel.preprocessing.download_ERA5_weather.request_ER5_weather" title="Link to this definition"></a></dt>
<dd><p>Download ERA5 reanalysis daily weather files, concatenate and calculate ET0
to obtain a netCDF4 dataset for precipitation and ET0 values. Weather data
reprojection and conversion can take some time for large spatial windows.</p>
<section id="arguments">
<h2>Arguments<a class="headerlink" href="#arguments" title="Link to this heading"></a></h2>
<ol class="arabic simple">
<li><dl class="simple">
<dt>config_file: <code class="docutils literal notranslate"><span class="pre">str</span></code></dt><dd><p>json configuration file</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>ndvi_path: <code class="docutils literal notranslate"><span class="pre">str</span></code></dt><dd><p>path to ndvi cube, used for weather data reprojection</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>raw_S2_image_ref: <code class="docutils literal notranslate"><span class="pre">str</span></code> <code class="docutils literal notranslate"><span class="pre">default</span> <span class="pre">=</span> <span class="pre">None</span></code></dt><dd><p>unmodified sentinel-2 image at correct resolution for
weather data reprojection in pixel mode</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>shapefile: <code class="docutils literal notranslate"><span class="pre">str</span></code> <code class="docutils literal notranslate"><span class="pre">default</span> <span class="pre">=</span> <span class="pre">None</span></code></dt><dd><p>path to shapefile for extraction in parcel mode</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>mode: <code class="docutils literal notranslate"><span class="pre">str</span></code> <code class="docutils literal notranslate"><span class="pre">default</span> <span class="pre">=</span> <span class="pre">'pixel'</span></code></dt><dd><p>choose between <code class="docutils literal notranslate"><span class="pre">'pixel'</span></code> and <code class="docutils literal notranslate"><span class="pre">'parcel'</span></code> mode</p>
</dd>
</dl>
</li>
</ol>
</section>
<section id="returns">
<h2>Returns<a class="headerlink" href="#returns" title="Link to this heading"></a></h2>
<ol class="arabic simple">
<li><dl class="simple">
<dt>weather_file: <code class="docutils literal notranslate"><span class="pre">str</span></code></dt><dd><p>path to netCDF4 file containing weather data</p>
</dd>
</dl>
</li>
</ol>
</section>
</dd></dl>
<section id="precipitation">
<h2>Precipitation<a class="headerlink" href="#precipitation" title="Link to this heading"></a></h2>
<p>No special calculation is necessary for this variable. Only the reprojection to the NDVI data cube is necessary. This variable is also used to calculate the reference evapotranspiration.</p>
</section>
<section id="reference-evapotranspiration">
<h2>Reference evapotranspiration<a class="headerlink" href="#reference-evapotranspiration" title="Link to this heading"></a></h2>
<p>Reference crop evapotranspiration or reference evapotranspiration is the estimation of the evapotranspiration from the “reference surface.” The reference surface is a hypothetical grass reference crop with an assumed crop height of 0.12 m, a fixed surface resistance of 70 s/m and an albedo of 0.23. The reference surface closely resembles an extensive surface of green, well-watered grass of uniform height, actively growing and completely shading the ground.</p>
<p>The calculation of the reference evapotranspiration is done using the <a class="reference external" href="https://github.com/Evapotranspiration/ETo">ETo</a> module. The following variables are downloaded for this calculation:</p>
<ul class="simple">
<li><p><strong>2m_temperature</strong>: air temperature 2 meters above the surface.</p></li>
<li><p><strong>2m_dewpoint_temperature</strong>: air dewpoint temperature 2 meters above the surface.</p></li>
<li><p><strong>surface_solar_radiation_downward</strong>: total downward solar radiation.</p></li>
<li><p><strong>total_precipitation</strong>: total precipitation.</p></li>
<li><p><strong>10m_u_component_of_wind</strong>: north/south wind speed 10 meters above the surface.</p></li>
<li><p><strong>10m_v_component_of_wind</strong>: east/west wind speed 10 meters above the surface.</p></li>
</ul>
<p>The following function is called by the main <code class="docutils literal notranslate"><span class="pre">request_ER5_weather</span></code> function to download the data. It calls other necessary sub-functions for the request. It produces netCDF4 datasets for each month of the requested time window, with daily values in each of those datasets.</p>
<dl class="py function">
<dt class="sig sig-object py" id="modspa_pixel.preprocessing.lib_era5_land_pixel.call_era5land_daily_for_MODSPA">
<span class="sig-prename descclassname"><span class="pre">modspa_pixel.preprocessing.lib_era5_land_pixel.</span></span><span class="sig-name descname"><span class="pre">call_era5land_daily_for_MODSPA</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">start_date</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end_date</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">area</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">processes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference internal" href="../_modules/modspa_pixel/preprocessing/lib_era5_land_pixel.html#call_era5land_daily_for_MODSPA"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#modspa_pixel.preprocessing.lib_era5_land_pixel.call_era5land_daily_for_MODSPA" title="Link to this definition"></a></dt>
<dd><p>request ERA5-land daily variables needed for ET0 calculus and MODSPA forcing
<a class="reference external" href="https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-land?tab=overview">reanalysis_era5</a></p>
<section id="information-on-requested-variables">
<h3>Information on requested variables<a class="headerlink" href="#information-on-requested-variables" title="Link to this heading"></a></h3>
<dl class="simple">
<dt>called land surface variables :</dt><dd><ul class="simple">
<li><p><strong>2m_temperature</strong></p></li>
<li><p><strong>2m_dewpoint_temperature</strong></p></li>
<li><p><strong>surface_solar_radiation_downward</strong></p></li>
<li><p><strong>surface_net_solar_radiation</strong></p></li>
<li><p><strong>surface_pressure</strong></p></li>
<li><p><strong>mean_sea_level_pressure</strong></p></li>
<li><p><strong>potential_evaporation</strong></p></li>
<li><p><strong>evaporation</strong></p></li>
<li><p><strong>total_evaporation</strong></p></li>
<li><p><strong>total_precipitation</strong></p></li>
<li><p><strong>snowfall</strong></p></li>
<li><p><strong>10m_u_component_of_wind</strong></p></li>
<li><p><strong>10m_v_component_of_wind</strong></p></li>
</ul>
</dd>
</dl>
<section id="id1">
<h4>Arguments<a class="headerlink" href="#id1" title="Link to this heading"></a></h4>
<ol class="arabic simple">
<li><dl class="simple">
<dt>start_date: <code class="docutils literal notranslate"><span class="pre">str</span></code></dt><dd><p>start date in YYYY-MM-DD format</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>end_date: <code class="docutils literal notranslate"><span class="pre">str</span></code></dt><dd><p>end date in YYYY-MM-DD format</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>area: <code class="docutils literal notranslate"><span class="pre">List[float]</span></code></dt><dd><p>bounding box of the demanded area
area = [lat_max, lon_min, lat_min, lon_max]</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>output_path: <code class="docutils literal notranslate"><span class="pre">str</span></code></dt><dd><p>output file name, <code class="docutils literal notranslate"><span class="pre">.nc</span></code> extension</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>processes: <code class="docutils literal notranslate"><span class="pre">int</span></code> <code class="docutils literal notranslate"><span class="pre">default</span> <span class="pre">=</span> <span class="pre">9</span></code></dt><dd><p>number of logical processors on which to run the download command.
can be higher than your actual number of processor cores,
download operations have a low CPU demand.</p>
</dd>
</dl>
</li>
</ol>
</section>
<section id="id2">
<h4>Returns<a class="headerlink" href="#id2" title="Link to this heading"></a></h4>
<p><code class="docutils literal notranslate"><span class="pre">None</span></code></p>
</section>
</section>
</dd></dl>
<p>This then produces a spatialized <span class="math notranslate nohighlight">\(ET_0\)</span> dataset.</p>
</section>
<section id="formatting-and-preprocessing-the-raw-data">
<h2>Formatting and preprocessing the raw data<a class="headerlink" href="#formatting-and-preprocessing-the-raw-data" title="Link to this heading"></a></h2>
<p>The raw dataset now has a precipitation variable and a <span class="math notranslate nohighlight">\(ET_0\)</span> variable.</p>
<p>Downloaded data from the ERA-5 Land server is projected on a WGS 84 lattitude/longitude projection, at 0.1° resolution. This data then needs to be reprojected on the same grid as the NDVI data, which is usually at a much higher resolution (of the order of 10 meters). The reprojection and clipping is done by the <code class="docutils literal notranslate"><span class="pre">OTB</span></code> <a class="reference external" href="https://www.orfeo-toolbox.org/CookBook/Applications/app_Superimpose.html">**Superimpose**</a> application, which has the advantage of being very efficient for large datasets. However, it only handles <strong>Geotiff</strong> images and not <strong>netCDF4</strong> files. The low resolution dataset first has to be saved as Geotiff files (one per variable), reprojected and clipped with <code class="docutils literal notranslate"><span class="pre">otbcli_Superimpose</span></code> and then opened and converted to a netCDF4 file. This can take some time for large datasets.</p>
<p>The output dataset is the one used by the processing chain to run the models. This dataset can be create using this function:</p>
<p><span class="math notranslate nohighlight">\(ET_0\)</span> calculation is done with this function:</p>
<dl class="py function">
<dt class="sig sig-object py" id="modspa_pixel.preprocessing.lib_era5_land_pixel.calculate_ET0_pixel">
<span class="sig-prename descclassname"><span class="pre">modspa_pixel.preprocessing.lib_era5_land_pixel.</span></span><span class="sig-name descname"><span class="pre">calculate_ET0_pixel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pixel_dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lat</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lon</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">h</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/modspa_pixel/preprocessing/lib_era5_land_pixel.html#calculate_ET0_pixel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#modspa_pixel.preprocessing.lib_era5_land_pixel.calculate_ET0_pixel" title="Link to this definition"></a></dt>
<dd><p>Calculate ET0 over the year for a single pixel of the ERA5 weather dataset.</p>
<section id="id3">
<h3>Arguments<a class="headerlink" href="#id3" title="Link to this heading"></a></h3>
<ol class="arabic simple">
<li><dl class="simple">
<dt>pixel_dataset: <code class="docutils literal notranslate"><span class="pre">xr.Dataset</span></code></dt><dd><p>extracted dataset that contains all information for a single pixel</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>lat: <code class="docutils literal notranslate"><span class="pre">float</span></code></dt><dd><p>latitudinal coordinate of that pixel</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>lon: <code class="docutils literal notranslate"><span class="pre">float</span></code></dt><dd><p>longitudinal coordinate of that pixel</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>h: <code class="docutils literal notranslate"><span class="pre">float</span></code> <code class="docutils literal notranslate"><span class="pre">default</span> <span class="pre">=</span> <span class="pre">10</span></code></dt><dd><p>height of ERA5 wind measurement in meters</p>
</dd>
</dl>
</li>
</ol>
</section>
<section id="id4">
<h3>Returns<a class="headerlink" href="#id4" title="Link to this heading"></a></h3>
<ol class="arabic simple">
<li><dl class="simple">
<dt>ET0_values: <code class="docutils literal notranslate"><span class="pre">np.ndarray</span></code></dt><dd><p>numpy array containing the ET0 values for each day</p>
</dd>
</dl>
</li>
</ol>
</section>
</dd></dl>
<p>And the Geotiff conversion to netCDF4 files is done with this function:</p>
<dl class="py function">
<dt class="sig sig-object py" id="modspa_pixel.preprocessing.lib_era5_land_pixel.combine_weather2netcdf">
<span class="sig-prename descclassname"><span class="pre">modspa_pixel.preprocessing.lib_era5_land_pixel.</span></span><span class="sig-name descname"><span class="pre">combine_weather2netcdf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rain_file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ET0_tile</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ndvi_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">available_ram</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference internal" href="../_modules/modspa_pixel/preprocessing/lib_era5_land_pixel.html#combine_weather2netcdf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#modspa_pixel.preprocessing.lib_era5_land_pixel.combine_weather2netcdf" title="Link to this definition"></a></dt>
<dd><p>Convert the Rain and ET0 geotiffs into a single weather netcdf dataset.</p>
<section id="id5">
<h3>Arguments<a class="headerlink" href="#id5" title="Link to this heading"></a></h3>
<ol class="arabic simple">
<li><dl class="simple">
<dt>rain_file: <code class="docutils literal notranslate"><span class="pre">str</span></code></dt><dd><p>path to Rain tif</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>ET0_tile: <code class="docutils literal notranslate"><span class="pre">str</span></code></dt><dd><p>path to ET0 tif</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>ndvi_path: <code class="docutils literal notranslate"><span class="pre">str</span></code></dt><dd><p>path to ndvi cube</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>save_path: <code class="docutils literal notranslate"><span class="pre">str</span></code></dt><dd><p>save path of weather netcdf dataset</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>available_ram: <code class="docutils literal notranslate"><span class="pre">int</span></code></dt><dd><p>available ram in GiB for conversion</p>
</dd>
</dl>
</li>
</ol>
</section>
<section id="id6">
<h3>Returns<a class="headerlink" href="#id6" title="Link to this heading"></a></h3>
<p><code class="docutils literal notranslate"><span class="pre">None</span></code></p>
</section>
</dd></dl>
</section>
</section>
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