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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"><a class="reference internal" href="mode/mode.html">Choosing the run mode</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>
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  <section id="project-file-structure">
<h1>Project file structure<a class="headerlink" href="#project-file-structure" title="Link to this heading"></a></h1>
<p>Here is an outlay of the current file strucutre:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>├── __init__.py
├── main_prepare_inputs.py
├── parameters
│   ├── __init__.py
│   ├── csv_files
│   │   ├── params_samir_test.csv
│   │   ├── params_samir_Aurade_test.csv
│   │   ├── params_samir_min_max.csv
│   │   └── params_samir.csv
│   ├── parameter_estimation.ipynb
│   └── params_samir_class.py
├── main_run_samir.py
├── modspa_pixel_env.yml
├── source
│   ├── code_toolbox.py
│   └── modspa_samir.py
├── SAMIR_xls
│   ├── SAMIRxls_Reference_ReadAndPlot.py
│   ├── SAMIRv5_juin2015.xlsx
│   ├── SAMIRxls_Reference.FR-Lam2019.xls
│   └── SAMIRpixel_Reference_Simonneaux2012.xls
├── config
│   ├── config.py
│   ├── select_config_modspa.py
├── preprocessing
│   ├── download_S2.py
│   ├── csv_files
│   │   ├── class_conversion.csv
│   │   └── class_conversion_parcel.csv
│   ├── extract_ndvi.py
│   ├── parcel_to_pixel.py
│   ├── lib_era5_land_pixel.py
│   ├── calculate_ndvi.py
│   ├── input_toolbox.py
│   ├── custom_inputs_pixel.ipynb
│   ├── download_ERA5_weather.py
│   └── custom_inputs_parcel.ipynb
├── README.md
├── postprocessing
│   ├── plot_parcel_GIFs.py
│   ├── explore_parcel_outputs.ipynb
│   ├── output_toolbox.py
│   ├── pixel_to_parcel.py
│   ├── plot_pixel_GIFs.py
│   └── explore_pixel_outputs.ipynb
└── docs
    ├── source
    │   ├── conf.py
    │   ├── file_structure.rst
    │   ├── .templates
    │   ├── filetree.rst
    │   ├── samir
    │   │   ├── data_and_ram_management.rst
    │   │   ├── samir_functions.rst
    │   │   └── run_samir.rst
    │   ├── preprocessing
    │   │   ├── samir_params.rst
    │   │   ├── weather_cube.rst
    │   │   ├── land_cover.rst
    │   │   ├── ndvi_cube.rst
    │   │   ├── input_preparation.rst
    │   │   └── soil_data.rst
    │   ├── index.rst
    │   ├── .static
    │   │   └── custom.css
    │   ├── mode
    │   │   ├── pixel.rst
    │   │   ├── mode.rst
    │   │   └── parcel.rst
    │   └── setup
    │       ├── json_config_file.rst
    │       ├── eodag_config.rst
    │       ├── conda_env.rst
    │       └── setup.rst
    ├── build
    └── Makefile
</pre></div>
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<p>…</p>
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