I/O bug correction for SAMIR. Renaming of directories. Improvements of doc.

config/config.py

@@ -6,27 +6,27 @@
 """
 # Create class that contains configuration file date
 
-import json  # to open config file
+from json import load  # to open config file
 
 
 class config:
     """
     The `Config` class contains input parameters necessary for the Vegetation and Weather parts to run.
     
-    It loads all these parameters from the `.json` input file and loads it automatically.
+    It loads all these parameters from the ``.json`` input file and loads it automatically.
 
     ### Attributes
-    - start_date: `str`
-    - end_date: `str`
-    - path_to_config_file: `str`
-    - shapefile_path: `str`
-    - download_path: `str`
-    - era5_path: `str`
-    - run_name: `str`
-    - preferred_provider: `str`
+    - start_date: ``str``
+    - end_date: ``str``
+    - path_to_config_file: ``str``
+    - shapefile_path: ``str``
+    - download_path: ``str``
+    - era5_path: ``str``
+    - run_name: ``str``
+    - preferred_provider: ``str``
     - ndvi_overwrite: `bool`
-    - cloud_cover_limit: `int`
-    - max_cpu: `int`
+    - cloud_cover_limit: ``int``
+    - max_cpu: ``int``
     """
 
     # Constructor 
@@ -34,7 +34,7 @@ class config:
 
         # Load json file
         with open(config_file, "r") as read_file:
-            input_data = json.load(read_file)
+            input_data = load(read_file)
 
         # Add attributes in new object
         for key, value in input_data.items():

docs/build/html/_modules/index.html

@@ -72,12 +72,12 @@
            <div itemprop="articleBody">
              
   <h1>All modules for which code is available</h1>
-<ul><li><a href="modspa_pixel/code/modspa_samir.html">modspa_pixel.code.modspa_samir</a></li>
-<li><a href="modspa_pixel/input/calculate_ndvi.html">modspa_pixel.input.calculate_ndvi</a></li>
-<li><a href="modspa_pixel/input/download_ERA5_weather.html">modspa_pixel.input.download_ERA5_weather</a></li>
-<li><a href="modspa_pixel/input/download_S2.html">modspa_pixel.input.download_S2</a></li>
-<li><a href="modspa_pixel/input/lib_era5_land_pixel.html">modspa_pixel.input.lib_era5_land_pixel</a></li>
-<li><a href="modspa_pixel/parameters/params_samir_class.html">modspa_pixel.parameters.params_samir_class</a></li>
+<ul><li><a href="modspa_pixel/parameters/params_samir_class.html">modspa_pixel.parameters.params_samir_class</a></li>
+<li><a href="modspa_pixel/preprocessing/calculate_ndvi.html">modspa_pixel.preprocessing.calculate_ndvi</a></li>
+<li><a href="modspa_pixel/preprocessing/download_ERA5_weather.html">modspa_pixel.preprocessing.download_ERA5_weather</a></li>
+<li><a href="modspa_pixel/preprocessing/download_S2.html">modspa_pixel.preprocessing.download_S2</a></li>
+<li><a href="modspa_pixel/preprocessing/lib_era5_land_pixel.html">modspa_pixel.preprocessing.lib_era5_land_pixel</a></li>
+<li><a href="modspa_pixel/source/modspa_samir.html">modspa_pixel.source.modspa_samir</a></li>
 </ul>
 
            </div>

docs/build/html/_sources/filetree.rst.txt

@@ -7,7 +7,6 @@
     │   ├── csv_files
     │   │   └── params_samir_test.csv
     │   └── params_samir_class.py
-    ├── output
     ├── DEV_inputs_test
     │   ├── soil_100.nc
     │   ├── ndvi_100.nc
@@ -30,49 +29,51 @@
     ├── test_samir_dask.py
     ├── tests.py
     ├── modspa_pixel_env.yml
+    ├── source
+    │   ├── code_toolbox.py
+    │   └── modspa_samir.py
     ├── SAMIR_xls
     │   ├── SAMIRv5_juin2015.xlsx
     │   └── SAMIRpixel_Reference_Simonneaux2012.xls
-    ├── input
-    │   ├── download_S2.py
-    │   ├── lib_era5_land_pixel.py
-    │   ├── calculate_ndvi.py
-    │   ├── input_toolbox.py
-    │   └── download_ERA5_weather.py
     ├── test_S2_one_tile.csv
     ├── config
     │   ├── config.py
     │   └── config_modspa.json
     ├── dev_samir_xarray.ipynb
+    ├── preprocessing
+    │   ├── download_S2.py
+    │   ├── parcel_to_pixel.py
+    │   ├── lib_era5_land_pixel.py
+    │   ├── calculate_ndvi.py
+    │   ├── input_toolbox.py
+    │   └── download_ERA5_weather.py
     ├── test_samir.py
     ├── README.md
-    ├── docs
-    │   ├── source
-    │   │   ├── inputs
-    │   │   │   ├── samir_params.rst
-    │   │   │   ├── weather_cube.rst
-    │   │   │   ├── land_cover.rst
-    │   │   │   ├── ndvi_cube.rst
-    │   │   │   ├── input_preparation.rst
-    │   │   │   └── soil_data.rst
-    │   │   ├── conf.py
-    │   │   ├── file_structure.rst
-    │   │   ├── .templates
-    │   │   ├── filetree.rst
-    │   │   ├── samir
-    │   │   │   ├── data_and_ram_management.rst
-    │   │   │   ├── samir_functions.rst
-    │   │   │   └── run_samir.rst
-    │   │   ├── index.rst
-    │   │   ├── .static
-    │   │   └── setup
-    │   │       ├── json_config_file.rst
-    │   │       ├── conda_env.rst
-    │   │       └── setup.rst
-    │   ├── build
-    │   └── Makefile
-    └── code
-        ├── code_toolbox.py
-        └── modspa_samir.py
+    ├── postprocessing
+    └── docs
+        ├── source
+        │   ├── inputs
+        │   │   ├── samir_params.rst
+        │   │   ├── weather_cube.rst
+        │   │   ├── land_cover.rst
+        │   │   ├── ndvi_cube.rst
+        │   │   ├── input_preparation.rst
+        │   │   └── soil_data.rst
+        │   ├── conf.py
+        │   ├── file_structure.rst
+        │   ├── .templates
+        │   ├── filetree.rst
+        │   ├── samir
+        │   │   ├── data_and_ram_management.rst
+        │   │   ├── samir_functions.rst
+        │   │   └── run_samir.rst
+        │   ├── index.rst
+        │   ├── .static
+        │   └── setup
+        │       ├── json_config_file.rst
+        │       ├── conda_env.rst
+        │       └── setup.rst
+        ├── build
+        └── Makefile
 
 ...
\ No newline at end of file

docs/build/html/_sources/inputs/ndvi_cube.rst.txt

@@ -28,11 +28,11 @@ Download satellite imagery
 
 The Sentinel-2 images can be automatically downloaded with the ``eodag`` module by using the following function:
 
-.. autofunction:: modspa_pixel.input.download_S2.download_S2_data
+.. autofunction:: modspa_pixel.preprocessing.download_S2.download_S2_data
 
 This will download all the Sentinel-2 images found during the specified window and over the specified area (in the config file) into the download directory as ``zip`` or ``tar`` archives. Specific bands can then be extracted from the archive using this function:
 
-.. autofunction:: modspa_pixel.input.download_S2.extract_zip_archives
+.. autofunction:: modspa_pixel.preprocessing.download_S2.extract_zip_archives
 
 The archives can then be deleted, freeing up some disk space.
 
@@ -48,14 +48,14 @@ To limit the size of the input datasets, the NDVI data is converted to the ``uin
 
 The NDVI pre_cube can be created with the following function:
 
-.. autofunction:: modspa_pixel.input.calculate_ndvi.calculate_ndvi
+.. autofunction:: modspa_pixel.preprocessing.calculate_ndvi.calculate_ndvi
 
 Once this data cube is written, it needs to be interpolated along the time dimension. The processing chain requires NDVI data at a daily frequency, and high resolution satellite imagery rarely has a revisit time smaller than 5 days. The daily interpolation is also done with the ``xarray`` module. The resulting dataset is also saved with the ``uint8`` data type.
 
 The final NDVI cube can be created with the following function:
 
 
-.. autofunction:: modspa_pixel.input.calculate_ndvi.interpolate_ndvi
+.. autofunction:: modspa_pixel.preprocessing.calculate_ndvi.interpolate_ndvi
 
 
 .. warning:: Both of the previous functions are ressource hungry (**CPU** and **RAM**), it can take up to an hour or more depending on the size of the dataset and the specifications of your machine.
\ No newline at end of file

docs/build/html/_sources/inputs/weather_cube.rst.txt

@@ -9,7 +9,7 @@ The modspa models (*SAMIR* and *SAFY*) require preprocessed weather data to run.
 
 The weather dataset can be automatically created with the following function:
 
-.. autofunction:: modspa_pixel.input.download_ERA5_weather.request_ER5_weather
+.. autofunction:: modspa_pixel.preprocessing.download_ERA5_weather.request_ER5_weather
 
 
 Precipitation
@@ -34,7 +34,7 @@ The calculation of the reference evapotranspiration is done using the `ETo <http
 
 The following function is called by the main ``request_ER5_weather`` 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.
 
-.. autofunction:: modspa_pixel.input.lib_era5_land_pixel.call_era5land_daily_for_MODSPA
+.. autofunction:: modspa_pixel.preprocessing.lib_era5_land_pixel.call_era5land_daily_for_MODSPA
 
 This then produces a spatialized :math:`ET_0` dataset.
 
@@ -48,12 +48,12 @@ Downloaded data from the ERA-5 Land server is projected on a WGS 84 lattitude/lo
 The output dataset is the one used by the processing chain to run the models. This dataset can be create using this function:
 
 
-.. autofunction:: modspa_pixel.input.lib_era5_land_pixel.era5Land_daily_to_yearly_nc
+.. autofunction:: modspa_pixel.preprocessing.lib_era5_land_pixel.era5Land_daily_to_yearly_nc
 
 :math:`ET_0` calculation is done with this function:
 
-.. autofunction:: modspa_pixel.input.lib_era5_land_pixel.calculate_ET0_pixel
+.. autofunction:: modspa_pixel.preprocessing.lib_era5_land_pixel.calculate_ET0_pixel
 
 And the Geotiff conversion to netCDF4 files is done with this function:
 
-.. autofunction:: modspa_pixel.input.lib_era5_land_pixel.combine_weather2netcdf
\ No newline at end of file
+.. autofunction:: modspa_pixel.preprocessing.lib_era5_land_pixel.combine_weather2netcdf
\ No newline at end of file

docs/build/html/_sources/samir/samir_functions.rst.txt

@@ -2,5 +2,5 @@ How the SAMIR functions works
 =============================
 
 
-.. autofunction:: modspa_pixel.code.modspa_samir.run_samir
-.. autofunction:: modspa_pixel.code.modspa_samir.samir_daily
\ No newline at end of file
+.. autofunction:: modspa_pixel.source.modspa_samir.run_samir
+.. autofunction:: modspa_pixel.source.modspa_samir.samir_daily
\ No newline at end of file

docs/build/html/file_structure.html

@@ -84,7 +84,6 @@
 │   ├── csv_files
 │   │   └── params_samir_test.csv
 │   └── params_samir_class.py
-├── output
 ├── DEV_inputs_test
 │   ├── soil_100.nc
 │   ├── ndvi_100.nc
@@ -107,50 +106,52 @@
 ├── test_samir_dask.py
 ├── tests.py
 ├── modspa_pixel_env.yml
+├── source
+│   ├── code_toolbox.py
+│   └── modspa_samir.py
 ├── SAMIR_xls
 │   ├── SAMIRv5_juin2015.xlsx
 │   └── SAMIRpixel_Reference_Simonneaux2012.xls
-├── input
-│   ├── download_S2.py
-│   ├── lib_era5_land_pixel.py
-│   ├── calculate_ndvi.py
-│   ├── input_toolbox.py
-│   └── download_ERA5_weather.py
 ├── test_S2_one_tile.csv
 ├── config
 │   ├── config.py
 │   └── config_modspa.json
 ├── dev_samir_xarray.ipynb
+├── preprocessing
+│   ├── download_S2.py
+│   ├── parcel_to_pixel.py
+│   ├── lib_era5_land_pixel.py
+│   ├── calculate_ndvi.py
+│   ├── input_toolbox.py
+│   └── download_ERA5_weather.py
 ├── test_samir.py
 ├── README.md
-├── docs
-│   ├── source
-│   │   ├── inputs
-│   │   │   ├── samir_params.rst
-│   │   │   ├── weather_cube.rst
-│   │   │   ├── land_cover.rst
-│   │   │   ├── ndvi_cube.rst
-│   │   │   ├── input_preparation.rst
-│   │   │   └── soil_data.rst
-│   │   ├── conf.py
-│   │   ├── file_structure.rst
-│   │   ├── .templates
-│   │   ├── filetree.rst
-│   │   ├── samir
-│   │   │   ├── data_and_ram_management.rst
-│   │   │   ├── samir_functions.rst
-│   │   │   └── run_samir.rst
-│   │   ├── index.rst
-│   │   ├── .static
-│   │   └── setup
-│   │       ├── json_config_file.rst
-│   │       ├── conda_env.rst
-│   │       └── setup.rst
-│   ├── build
-│   └── Makefile
-└── code
-    ├── code_toolbox.py
-    └── modspa_samir.py
+├── postprocessing
+└── docs
+    ├── source
+    │   ├── inputs
+    │   │   ├── samir_params.rst
+    │   │   ├── weather_cube.rst
+    │   │   ├── land_cover.rst
+    │   │   ├── ndvi_cube.rst
+    │   │   ├── input_preparation.rst
+    │   │   └── soil_data.rst
+    │   ├── conf.py
+    │   ├── file_structure.rst
+    │   ├── .templates
+    │   ├── filetree.rst
+    │   ├── samir
+    │   │   ├── data_and_ram_management.rst
+    │   │   ├── samir_functions.rst
+    │   │   └── run_samir.rst
+    │   ├── index.rst
+    │   ├── .static
+    │   └── setup
+    │       ├── json_config_file.rst
+    │       ├── conda_env.rst
+    │       └── setup.rst
+    ├── build
+    └── Makefile
 </pre></div>
 </div>
 <p>…</p>

docs/build/html/filetree.html

@@ -80,7 +80,6 @@
 │   ├── csv_files
 │   │   └── params_samir_test.csv
 │   └── params_samir_class.py
-├── output
 ├── DEV_inputs_test
 │   ├── soil_100.nc
 │   ├── ndvi_100.nc
@@ -103,50 +102,52 @@
 ├── test_samir_dask.py
 ├── tests.py
 ├── modspa_pixel_env.yml
+├── source
+│   ├── code_toolbox.py
+│   └── modspa_samir.py
 ├── SAMIR_xls
 │   ├── SAMIRv5_juin2015.xlsx
 │   └── SAMIRpixel_Reference_Simonneaux2012.xls
-├── input
-│   ├── download_S2.py
-│   ├── lib_era5_land_pixel.py
-│   ├── calculate_ndvi.py
-│   ├── input_toolbox.py
-│   └── download_ERA5_weather.py
 ├── test_S2_one_tile.csv
 ├── config
 │   ├── config.py
 │   └── config_modspa.json
 ├── dev_samir_xarray.ipynb
+├── preprocessing
+│   ├── download_S2.py
+│   ├── parcel_to_pixel.py
+│   ├── lib_era5_land_pixel.py
+│   ├── calculate_ndvi.py
+│   ├── input_toolbox.py
+│   └── download_ERA5_weather.py
 ├── test_samir.py
 ├── README.md
-├── docs
-│   ├── source
-│   │   ├── inputs
-│   │   │   ├── samir_params.rst
-│   │   │   ├── weather_cube.rst
-│   │   │   ├── land_cover.rst
-│   │   │   ├── ndvi_cube.rst
-│   │   │   ├── input_preparation.rst
-│   │   │   └── soil_data.rst
-│   │   ├── conf.py
-│   │   ├── file_structure.rst
-│   │   ├── .templates
-│   │   ├── filetree.rst
-│   │   ├── samir
-│   │   │   ├── data_and_ram_management.rst
-│   │   │   ├── samir_functions.rst
-│   │   │   └── run_samir.rst
-│   │   ├── index.rst
-│   │   ├── .static
-│   │   └── setup
-│   │       ├── json_config_file.rst
-│   │       ├── conda_env.rst
-│   │       └── setup.rst
-│   ├── build
-│   └── Makefile
-└── code
-    ├── code_toolbox.py
-    └── modspa_samir.py
+├── postprocessing
+└── docs
+    ├── source
+    │   ├── inputs
+    │   │   ├── samir_params.rst
+    │   │   ├── weather_cube.rst
+    │   │   ├── land_cover.rst
+    │   │   ├── ndvi_cube.rst
+    │   │   ├── input_preparation.rst
+    │   │   └── soil_data.rst
+    │   ├── conf.py
+    │   ├── file_structure.rst
+    │   ├── .templates
+    │   ├── filetree.rst
+    │   ├── samir
+    │   │   ├── data_and_ram_management.rst
+    │   │   ├── samir_functions.rst
+    │   │   └── run_samir.rst
+    │   ├── index.rst
+    │   ├── .static
+    │   └── setup
+    │       ├── json_config_file.rst
+    │       ├── conda_env.rst
+    │       └── setup.rst
+    ├── build
+    └── Makefile
 </pre></div>
 </div>
 <p>…</p>