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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"><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 current"><a class="current reference internal" href="#">Project file structure</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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