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<li class="toctree-l1 current"><a class="reference internal" href="setup.html">Setting up the correct environnment and parameters</a><ul class="current">
<li class="toctree-l2 current"><a class="current reference internal" href="#">Installing the conda environment</a></li>
<li class="toctree-l2"><a class="reference internal" href="json_config_file.html">Understanding the json config file</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../mode/mode.html">Choosing the run mode</a></li>
<li class="toctree-l1"><a class="reference internal" href="../preprocessing/input_preparation.html">Preparing the inputs for Modspa-Pixel</a></li>
<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="installing-the-conda-environment">
<h1>Installing the conda environment<a class="headerlink" href="#installing-the-conda-environment" title="Link to this heading"></a></h1>
<p>If you have not yet installed <strong>conda</strong> on your machine, you should start with this step : <a class="reference external" href="https://conda.io/projects/conda/en/latest/user-guide/install/index.html">conda installation</a>.</p>
<p>A <code class="docutils literal notranslate"><span class="pre">yml</span></code> file is included to automatically create a conda virtual environnment with the correct libraries and dependencies installed. To install it run this command in the root directory of the modspa_pixel project:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="o">(</span>base<span class="o">)</span><span class="w"> </span>/modspa_pixel$<span class="w"> </span>conda<span class="w"> </span>env<span class="w"> </span>create<span class="w"> </span>-f<span class="w"> </span>modspa_pixel_env.yml
</pre></div>
</div>
<p>To activate the environment:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="o">(</span>base<span class="o">)</span><span class="w"> </span>/modspa_pixel$<span class="w"> </span>conda<span class="w"> </span>activate<span class="w"> </span>modspa_pixel
<span class="o">(</span>modspa_pixel<span class="o">)</span><span class="w"> </span>/modspa_pixel$
</pre></div>
</div>
<p>That’s all for this step!</p>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>The OTB package might not be properly installed with conda, to check its installation run the following command:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="o">(</span>modspa_pixel<span class="o">)</span><span class="w"> </span>/modspa_pixel$<span class="w"> </span>otbcli_ReadImageInfo<span class="w"> </span><span class="c1"># some random otb application</span>
ERROR:<span class="w"> </span>Waiting<span class="w"> </span><span class="k">for</span><span class="w"> </span>at<span class="w"> </span>least<span class="w"> </span>one<span class="w"> </span>parameter.
This<span class="w"> </span>is<span class="w"> </span>the<span class="w"> </span>ReadImageInfo<span class="w"> </span>application,<span class="w"> </span>version<span class="w"> </span><span class="m">8</span>.0.0
Get<span class="w"> </span>information<span class="w"> </span>about<span class="w"> </span>the<span class="w"> </span>image
Complete<span class="w"> </span>documentation:<span class="w"> </span>https://www.orfeo-toolbox.org/CookBook/Applications/app_ReadImageInfo.html<span class="w"> </span>or<span class="w"> </span>-help
Parameters:
MISSING<span class="w"> </span>-in<span class="w"> </span><string><span class="w"> </span>Input<span class="w"> </span>Image<span class="w"> </span><span class="o">(</span>mandatory<span class="o">)</span>
<span class="w"> </span>-imagemetadata<span class="w"> </span><boolean><span class="w"> </span>Display<span class="w"> </span>the<span class="w"> </span>image<span class="w"> </span>metadata<span class="w"> </span><span class="o">(</span>mandatory,<span class="w"> </span>default<span class="w"> </span>value<span class="w"> </span>is<span class="w"> </span><span class="nb">false</span><span class="o">)</span>
<span class="w"> </span>-outgeom<span class="w"> </span><string><span class="w"> </span>Write<span class="w"> </span>the<span class="w"> </span>image<span class="w"> </span>metadata<span class="w"> </span>to<span class="w"> </span>a<span class="w"> </span>geom<span class="w"> </span>file<span class="w"> </span><span class="o">(</span>optional,<span class="w"> </span>off<span class="w"> </span>by<span class="w"> </span>default<span class="o">)</span>
<span class="w"> </span>-rgb<span class="w"> </span><group><span class="w"> </span>Default<span class="w"> </span>RGB<span class="w"> </span>Display
<span class="w"> </span>-progress<span class="w"> </span><boolean><span class="w"> </span>Report<span class="w"> </span>progress
<span class="w"> </span>-help<span class="w"> </span><string<span class="w"> </span>list><span class="w"> </span>Display<span class="w"> </span>long<span class="w"> </span><span class="nb">help</span><span class="w"> </span><span class="o">(</span>empty<span class="w"> </span>list<span class="o">)</span>,<span class="w"> </span>or<span class="w"> </span><span class="nb">help</span><span class="w"> </span><span class="k">for</span><span class="w"> </span>given<span class="w"> </span>parameters<span class="w"> </span>keys
Use<span class="w"> </span>-help<span class="w"> </span>param1<span class="w"> </span><span class="o">[</span>...<span class="w"> </span>paramN<span class="o">]</span><span class="w"> </span>to<span class="w"> </span>see<span class="w"> </span>detailed<span class="w"> </span>documentation<span class="w"> </span>of<span class="w"> </span>those<span class="w"> </span>parameters.
Examples:
otbcli_ReadImageInfo<span class="w"> </span>-in<span class="w"> </span>QB_Toulouse_Ortho_XS.tif
free<span class="o">()</span>:<span class="w"> </span>invalid<span class="w"> </span>pointer
Aborted
</pre></div>
</div>
<p>If you receive a <code class="docutils literal notranslate"><span class="pre">Command</span> <span class="pre">'otbcli_ReadImageInfo'</span> <span class="pre">not</span> <span class="pre">found</span></code> error, you should refer to this link to get a correct <code class="docutils literal notranslate"><span class="pre">OTB</span></code> installation: <a class="reference external" href="https://www.orfeo-toolbox.org/CookBook/Installation.html">OTB installation</a>.</p>
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