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<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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"><a class="reference internal" href="../mode/mode.html">Choosing the run mode</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"><a class="reference internal" href="weather_cube.html">Preparing the weather data cube</a></li>
<li class="toctree-l2"><a class="reference internal" href="land_cover.html">Preparing the land cover raster</a></li>
<li class="toctree-l2"><a class="reference internal" href="soil_data.html">Preparing the soil data raster</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Preparing the SAMIR parameter csv file</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#the-parameter-name">The parameter name</a></li>
<li class="toctree-l3"><a class="reference internal" href="#the-scale-factor">The scale factor</a></li>
<li class="toctree-l3"><a class="reference internal" href="#the-default-column">The Default column</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#modspa_pixel.parameters.params_samir_class.samir_parameters"><code class="docutils literal notranslate"><span class="pre">samir_parameters</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="../samir/run_samir.html">Run the SAMIR model</a></li>
<li class="toctree-l1"><a class="reference internal" href="../file_structure.html">Project file structure</a></li>
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<section id="preparing-the-samir-parameter-csv-file">
<span id="samir-params"></span><h1>Preparing the SAMIR parameter csv file<a class="headerlink" href="#preparing-the-samir-parameter-csv-file" title="Link to this heading"></a></h1>
<p>All the <em>SAMIR</em> model parameters are written in a csv file. Here is an example of such a file:</p>
<table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p>ClassName</p></td>
<td><p>scale_factor</p></td>
<td><p>Default</p></td>
<td><p>no_sim</p></td>
<td><p>straw_cereal</p></td>
<td><p>oilseed</p></td>
<td><p>soy</p></td>
<td><p>sunflower</p></td>
<td><p>corn</p></td>
<td><p>grassland</p></td>
<td><p>orchard</p></td>
<td><p>vineyards</p></td>
<td><p>broadleaf_forest</p></td>
<td><p>conifer_forest</p></td>
<td><p>heathland</p></td>
</tr>
<tr class="row-even"><td><p>ClassNumber</p></td>
<td><p>1</p></td>
<td><p>0</p></td>
<td><p>1</p></td>
<td><p>2</p></td>
<td><p>3</p></td>
<td><p>4</p></td>
<td><p>5</p></td>
<td><p>6</p></td>
<td><p>7</p></td>
<td><p>8</p></td>
<td><p>9</p></td>
<td><p>10</p></td>
<td><p>11</p></td>
<td><p>12</p></td>
</tr>
<tr class="row-odd"><td><p>NDVIsol</p></td>
<td><p>1</p></td>
<td><p>0.15</p></td>
<td></td>
<td><p>0.15</p></td>
<td><p>0.15</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-even"><td><p>NDVImax</p></td>
<td><p>1</p></td>
<td><p>0.85</p></td>
<td></td>
<td><p>0.85</p></td>
<td><p>0.85</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-odd"><td><p>FCmax</p></td>
<td><p>1000</p></td>
<td><p>1</p></td>
<td><p>0</p></td>
<td><p>1</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-even"><td><p>Fslope</p></td>
<td><p>1000</p></td>
<td><p>1.4</p></td>
<td><p>0</p></td>
<td><p>1.18</p></td>
<td><p>1.22</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-odd"><td><p>Foffset</p></td>
<td><p>1000</p></td>
<td><p>-0.075</p></td>
<td><p>0</p></td>
<td><p>-0.165</p></td>
<td><p>-0.17</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-even"><td><p>Kcmax</p></td>
<td><p>0</p></td>
<td><p>1.15</p></td>
<td><p>0</p></td>
<td><p>1.15</p></td>
<td><p>0.7</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-odd"><td><p>Kslope</p></td>
<td><p>1000</p></td>
<td><p>1.2</p></td>
<td><p>0</p></td>
<td><p>1.47</p></td>
<td><p>1.35</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-even"><td><p>Koffset</p></td>
<td><p>1000</p></td>
<td><p>-0.24</p></td>
<td><p>0</p></td>
<td><p>-0.17</p></td>
<td><p>-0.16</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-odd"><td><p>Zsoil</p></td>
<td><p>1</p></td>
<td><p>2000</p></td>
<td></td>
<td><p>2000</p></td>
<td><p>2000</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-even"><td><p>Ze</p></td>
<td><p>1</p></td>
<td><p>300</p></td>
<td></td>
<td><p>125</p></td>
<td><p>125</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-odd"><td><p>Init_RU</p></td>
<td><p>1000</p></td>
<td><p>0.87</p></td>
<td></td>
<td><p>0.5</p></td>
<td><p>0.5</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-even"><td><p>DiffE</p></td>
<td><p>1</p></td>
<td><p>1</p></td>
<td><p>0</p></td>
<td><p>0</p></td>
<td><p>0</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-odd"><td><p>DiffR</p></td>
<td><p>1</p></td>
<td><p>5</p></td>
<td><p>0</p></td>
<td><p>0</p></td>
<td><p>0</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-even"><td><p>REW</p></td>
<td><p>1</p></td>
<td><p>0</p></td>
<td></td>
<td><p>9</p></td>
<td><p>9</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-odd"><td><p>minZr</p></td>
<td><p>1</p></td>
<td><p>150</p></td>
<td><p>0</p></td>
<td><p>125</p></td>
<td><p>125</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-even"><td><p>maxZr</p></td>
<td><p>1</p></td>
<td><p>600</p></td>
<td><p>0</p></td>
<td><p>1250</p></td>
<td><p>1450</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-odd"><td><p>p</p></td>
<td><p>1000</p></td>
<td><p>0.55</p></td>
<td><p>0</p></td>
<td><p>0.55</p></td>
<td><p>0.65</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-even"><td><p>FW</p></td>
<td><p>1000</p></td>
<td><p>1</p></td>
<td><p>0</p></td>
<td><p>1</p></td>
<td><p>1</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-odd"><td><p>Irrig_auto</p></td>
<td><p>1</p></td>
<td><p>1</p></td>
<td><p>0</p></td>
<td><p>1</p></td>
<td><p>1</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-even"><td><p>Irrig_man</p></td>
<td><p>1</p></td>
<td><p>0</p></td>
<td><p>0</p></td>
<td><p>0</p></td>
<td><p>0</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr class="row-odd"><td><p>Kcb_stop_irrig</p></td>
<td><p>1</p></td>
<td><p>0.5</p></td>
<td><p>0</p></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
</tbody>
</table>
<p>Here is how the file is organised:</p>
<ul class="simple">
<li><p><strong>model parameters</strong> are located in the <strong>first column</strong> (row header), a row contains the values of a parameter for <strong>different classes</strong>.</p></li>
<li><p>the file contains <strong>three header columns</strong>: the <strong>parameter name</strong> (<code class="docutils literal notranslate"><span class="pre">ClassName</span></code> leftmost), the <strong>scale factors</strong> (<code class="docutils literal notranslate"><span class="pre">scale_factor</span></code> used to manage data types in the <em>SAMIR</em> calculations) and the <strong>default</strong> (<code class="docutils literal notranslate"><span class="pre">Default</span></code>) parameter values column.</p></li>
<li><p>the other columns have the <code class="docutils literal notranslate"><span class="pre">ClassName</span></code> as a header and contain the different parameter values. If a cell is <strong>empty</strong>, it will take the <code class="docutils literal notranslate"><span class="pre">Default</span></code> column value.</p></li>
<li><p>the <code class="docutils literal notranslate"><span class="pre">ClassNumber</span></code> row should not be changed for the <code class="docutils literal notranslate"><span class="pre">scale_factor</span></code> and <code class="docutils literal notranslate"><span class="pre">Default</span></code> columns. For the classes, it should correspond to the integer values contained in the <a class="reference internal" href="land_cover.html#land-cover"><span class="std std-ref">land cover raster</span></a>.</p></li>
</ul>
<section id="the-parameter-name">
<h2>The parameter name<a class="headerlink" href="#the-parameter-name" title="Link to this heading"></a></h2>
<p>This column should not be changed. It contains the names of all the necessary <em>SAMIR</em> parameters. It is used in the <code class="docutils literal notranslate"><span class="pre">modspa_samir.py</span></code> script to generate a dictionnary containing the rasterized parameters and the scale factors. In the parameter dictionnary, the <strong>rasterized parameters</strong> have the suffix <code class="docutils literal notranslate"><span class="pre">_</span></code> after the parameter name, the <strong>scale factors</strong> have the prefix <code class="docutils literal notranslate"><span class="pre">s_</span></code> before the parameter name.</p>
</section>
<section id="the-scale-factor">
<h2>The scale factor<a class="headerlink" href="#the-scale-factor" title="Link to this heading"></a></h2>
<p>This column is used to scale the parameters to store the rasterized parameters as <strong>integer</strong> arrays (<code class="docutils literal notranslate"><span class="pre">int16</span></code>), this reduces the memory usage of the model (a parameter of value <code class="docutils literal notranslate"><span class="pre">1.24</span></code> with scale factor <code class="docutils literal notranslate"><span class="pre">1000</span></code> will be stored as <code class="docutils literal notranslate"><span class="pre">1240</span></code>). Adapt the scale factor to the <strong>value of the parameter</strong> and the <strong>desired precision</strong>.</p>
<p>If the scale factor is <strong>equal to 0</strong>, the parameter <strong>will not be spatialized</strong>, it will stay as a <strong>scalar</strong> and the associated scale factor will be set at <strong>1</strong> (some parameters do not need to be spatialized).</p>
</section>
<section id="the-default-column">
<h2>The Default column<a class="headerlink" href="#the-default-column" title="Link to this heading"></a></h2>
<p>This column contains the default values for the parameters for which you do not have any data. All empy cells for a given parameter will be filled with the default value.</p>
<p>You can have different parameter files, the file to use for a simulation is set in the <a class="reference internal" href="../setup/json_config_file.html#json-config"><span class="std std-ref">json configuration file</span></a>. This csv table is then loaded in an object as a <code class="docutils literal notranslate"><span class="pre">pandas</span> <span class="pre">DataFrame</span></code> attribute with the following function:</p>
<dl class="py class">
<dt class="sig sig-object py" id="modspa_pixel.parameters.params_samir_class.samir_parameters">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">modspa_pixel.parameters.params_samir_class.</span></span><span class="sig-name descname"><span class="pre">samir_parameters</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">paramFile</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/modspa_pixel/parameters/params_samir_class.html#samir_parameters"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#modspa_pixel.parameters.params_samir_class.samir_parameters" title="Link to this definition"></a></dt>
<dd><p>Load all parameters for multiples classes in one object.</p>
<section id="attributes">
<h3>Attributes<a class="headerlink" href="#attributes" title="Link to this heading"></a></h3>
<ol class="arabic">
<li><dl>
<dt>.table: <code class="docutils literal notranslate"><span class="pre">pd.DataFrame</span></code></dt><dd><p><code class="docutils literal notranslate"><span class="pre">pandas</span> <span class="pre">DataFrame</span></code> with all paramters (rows) for all classes (columns)</p>
<p>It also contains :</p>
<ul class="simple">
<li><p>a <code class="docutils literal notranslate"><span class="pre">scale_factor</span></code> column (first column) that allows to convert all parameters to integer values for reduced memory usage</p></li>
<li><p>a <code class="docutils literal notranslate"><span class="pre">Default</span></code> column (second column) that contains default values to fill in missing values</p></li>
</ul>
<p>Example of the parameter table:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span> <span class="n">scale_factor</span> <span class="n">Default</span> <span class="n">class1</span> <span class="n">class2</span> <span class="n">class3</span>
<span class="n">ClassName</span>
<span class="n">ClassNumber</span> <span class="mi">1</span> <span class="mf">0.00</span> <span class="mf">1.00</span> <span class="mf">2.000</span> <span class="mf">3.000</span>
<span class="n">FminNDVI</span> <span class="mi">1000</span> <span class="mf">0.20</span> <span class="mf">0.20</span> <span class="mf">0.100</span> <span class="mf">0.100</span>
<span class="n">FmaxNDVI</span> <span class="mi">1000</span> <span class="mf">0.90</span> <span class="mf">0.90</span> <span class="mf">0.900</span> <span class="mf">0.900</span>
<span class="n">FminFC</span> <span class="mi">1000</span> <span class="mf">0.90</span> <span class="mf">0.90</span> <span class="mf">0.900</span> <span class="mf">0.900</span>
<span class="n">FmaxFC</span> <span class="mi">1000</span> <span class="mf">1.00</span> <span class="mf">0.90</span> <span class="mf">1.000</span> <span class="mf">1.000</span>
<span class="n">Fslope</span> <span class="mi">1000</span> <span class="mf">1.40</span> <span class="mf">1.50</span> <span class="mf">1.500</span> <span class="mf">1.500</span>
<span class="n">Foffset</span> <span class="mi">1000</span> <span class="o">-</span><span class="mf">0.10</span> <span class="o">-</span><span class="mf">0.10</span> <span class="o">-</span><span class="mf">0.100</span> <span class="o">-</span><span class="mf">0.100</span>
<span class="n">Plateau</span> <span class="mi">1</span> <span class="mf">70.00</span> <span class="mf">70.00</span> <span class="mf">70.000</span> <span class="mf">70.000</span>
<span class="n">KminNDVI</span> <span class="mi">1000</span> <span class="mf">0.10</span> <span class="mf">0.10</span> <span class="mf">0.100</span> <span class="mf">0.100</span>
<span class="n">KmaxNDVI</span> <span class="mi">1000</span> <span class="mf">0.90</span> <span class="mf">0.90</span> <span class="mf">0.900</span> <span class="mf">0.900</span>
<span class="n">KminKcb</span> <span class="mi">1000</span> <span class="mf">0.00</span> <span class="mf">0.20</span> <span class="mf">0.000</span> <span class="mf">0.000</span>
<span class="n">KmaxKcb</span> <span class="mi">1000</span> <span class="mf">0.98</span> <span class="mf">1.00</span> <span class="mf">1.100</span> <span class="mf">1.100</span>
<span class="n">Kslope</span> <span class="mi">1000</span> <span class="mf">1.60</span> <span class="mf">1.60</span> <span class="mf">1.600</span> <span class="mf">1.600</span>
<span class="n">Koffset</span> <span class="mi">1000</span> <span class="o">-</span><span class="mf">0.10</span> <span class="o">-</span><span class="mf">0.10</span> <span class="o">-</span><span class="mf">0.100</span> <span class="o">-</span><span class="mf">0.100</span>
<span class="n">Zsoil</span> <span class="mi">1</span> <span class="mf">2000.00</span> <span class="mf">1600.00</span> <span class="mf">1550.000</span> <span class="mf">1550.000</span>
<span class="o">...</span> <span class="o">...</span> <span class="o">...</span> <span class="o">...</span> <span class="o">...</span> <span class="o">...</span>
<span class="n">Kcmax</span> <span class="mi">1000</span> <span class="mf">1.15</span> <span class="mf">1.15</span> <span class="mf">1.15</span> <span class="mf">1.15</span>
<span class="n">Fc_stop</span> <span class="mi">1000</span> <span class="mf">0.15</span> <span class="mf">0.15</span> <span class="mf">0.15</span> <span class="mf">0.15</span>
<span class="n">Start_date_Irr</span> <span class="mi">1</span> <span class="mf">0.00</span> <span class="mf">0.00</span> <span class="mf">0.00</span> <span class="mf">0.00</span>
<span class="n">p_trigger</span> <span class="mi">1</span> <span class="mf">0.00</span> <span class="mf">0.00</span> <span class="mf">0.00</span> <span class="mf">0.00</span>
</pre></div>
</div>
</dd>
</dl>
</li>
</ol>
</section>
<section id="methods">
<h3>Methods<a class="headerlink" href="#methods" title="Link to this heading"></a></h3>
<dl class="py method">
<dt class="sig sig-object py" id="modspa_pixel.parameters.params_samir_class.samir_parameters.__init__">
<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">paramFile</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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/parameters/params_samir_class.html#samir_parameters.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#modspa_pixel.parameters.params_samir_class.samir_parameters.__init__" title="Link to this definition"></a></dt>
<dd><p>Create pandas table from the csv parameter file.</p>
<section id="arguments">
<h4>Arguments<a class="headerlink" href="#arguments" title="Link to this heading"></a></h4>
<ol class="arabic simple">
<li><dl class="simple">
<dt>paramFile: <code class="docutils literal notranslate"><span class="pre">str</span></code></dt><dd><p>path to csv parameter file</p>
</dd>
</dl>
</li>
</ol>
</section>
</dd></dl>
</section>
</dd></dl>
<p>This object is used to build a dictionnary containing a raster for each parameter (spatialized parameters) in the <em>SAMIR</em> functions.</p>
</section>
</section>
</div>
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