Doc update and param management update

.gitignore

@@ -6,8 +6,7 @@ dev_samir_xarray.ipynb
 config/config_modspa.json
 DEV_inputs_test*
 config/config_modspa.*
-parameters/csv_files/params_samir_test_dev.csv
-parameters/csv_files/params_samir_Sigpac_test.csv
+parameters/csv_files/params_samir.**.csv
 
 # figures
 *.png
@@ -22,3 +21,4 @@ __pycache__/
 
 
 # Directory & Files not ignored: !
+! parameters/csv_files/params_samir.csv
\ No newline at end of file

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

@@ -7,7 +7,8 @@
     │   ├── csv_files
     │   │   ├── params_samir_test.csv
     │   │   ├── params_samir_Aurade_test.csv
-    │   │   └── params_samir_min_max.csv
+    │   │   ├── params_samir_min_max.csv
+    │   │   └── params_samir.csv
     │   ├── parameter_estimation.ipynb
     │   └── params_samir_class.py
     ├── main_run_samir.py

docs/build/html/_sources/preprocessing/input_preparation.rst.txt

@@ -14,6 +14,7 @@ To download the necessary data and prepare the input datasets, run the :code:`ma
 
    (modspa_pixel) /modspa_pixel$ python main_prepare_inputs.py
 
+
 In the next sections you will find more detail on the input preparation.
 
 .. toctree::

docs/build/html/_sources/preprocessing/samir_params.rst.txt

@@ -6,7 +6,7 @@ Preparing the SAMIR parameter csv file
 All the *SAMIR* model parameters are written in a csv file. Here is an example of such a file:
 
 .. csv-table::
-    :file: ../../../parameters/csv_files/params_samir_test.csv
+    :file: ../../../parameters/csv_files/params_samir.csv
 
 
 Here is how the file is organised:

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

@@ -8,12 +8,11 @@ After you have run the :ref:`input preparation <prepare_inputs>` script, created
    (modspa_pixel) /modspa_pixel$ python main_run_samir.py
 
 .. note::
-   Depending on the size of your datasets and your machine's specifications, this script can take some time to run. A progress bar will keep you informed on the script's progress and operations.
+   Depending on the size of your datasets and your machine's specifications, this script can take some time to run. A **progress bar** will keep you informed on the script's progress and operations.
 
 Once the script is finished, the output dataset (or daframe and shapefile for the **parcel** mode) will be found in the **output** directory, in a subdirectory carrying the **run_name**. Plotting scripts and notebooks are located in the :code:`modspa_pixel/postprocessing/` directory.
 
 
-
 .. toctree::
    :maxdepth: 1
    :caption: Contents:

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

@@ -3,4 +3,5 @@ How the SAMIR functions works
 
 
 .. 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

@@ -86,7 +86,8 @@
 │   ├── csv_files
 │   │   ├── params_samir_test.csv
 │   │   ├── params_samir_Aurade_test.csv
-│   │   └── params_samir_min_max.csv
+│   │   ├── params_samir_min_max.csv
+│   │   └── params_samir.csv
 │   ├── parameter_estimation.ipynb
 │   └── params_samir_class.py
 ├── main_run_samir.py

docs/build/html/filetree.html

@@ -82,7 +82,8 @@
 │   ├── csv_files
 │   │   ├── params_samir_test.csv
 │   │   ├── params_samir_Aurade_test.csv
-│   │   └── params_samir_min_max.csv
+│   │   ├── params_samir_min_max.csv
+│   │   └── params_samir.csv
 │   ├── parameter_estimation.ipynb
 │   └── params_samir_class.py
 ├── main_run_samir.py

docs/build/html/preprocessing/samir_params.html

@@ -101,13 +101,18 @@
 <tr class="row-odd"><td><p>ClassName</p></td>
 <td><p>scale_factor</p></td>
 <td><p>Default</p></td>
-<td><p>class1</p></td>
-<td><p>class2</p></td>
-<td><p>class3</p></td>
-<td><p>class4</p></td>
-<td><p>class5</p></td>
-<td><p>class6</p></td>
-<td><p>class7</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>
@@ -119,10 +124,20 @@
 <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>FCmax</p></td>
-<td><p>1000</p></td>
+<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>
@@ -131,9 +146,14 @@
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p>Fslope</p></td>
-<td><p>10000</p></td>
-<td><p>1.4286</p></td>
+<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>
@@ -142,9 +162,14 @@
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p>Foffset</p></td>
+<tr class="row-odd"><td><p>FCmax</p></td>
 <td><p>1000</p></td>
-<td><p>-0.214</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>
@@ -153,9 +178,14 @@
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p>Kcmax</p></td>
+<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>1.8</p></td>
+<td><p>1.18</p></td>
+<td><p>1.22</p></td>
+<td></td>
+<td></td>
 <td></td>
 <td></td>
 <td></td>
@@ -164,9 +194,14 @@
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p>Kslope</p></td>
-<td><p>10000</p></td>
-<td><p>2.5714</p></td>
+<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>
@@ -175,9 +210,14 @@
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p>Koffset</p></td>
-<td><p>1000</p></td>
-<td><p>-0.386</p></td>
+<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>
@@ -186,9 +226,14 @@
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p>NDVIsol</p></td>
-<td><p>1</p></td>
-<td><p>0.15</p></td>
+<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>
@@ -197,9 +242,14 @@
 <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>
+<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>
@@ -210,7 +260,12 @@
 </tr>
 <tr class="row-odd"><td><p>Zsoil</p></td>
 <td><p>1</p></td>
-<td><p>3000</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>
@@ -221,7 +276,12 @@
 </tr>
 <tr class="row-even"><td><p>Ze</p></td>
 <td><p>1</p></td>
-<td><p>50</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>
@@ -232,7 +292,12 @@
 </tr>
 <tr class="row-odd"><td><p>Init_RU</p></td>
 <td><p>1000</p></td>
-<td><p>0.64</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>
@@ -244,6 +309,11 @@
 <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>
@@ -255,6 +325,11 @@
 <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>
@@ -267,6 +342,11 @@
 <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>
@@ -276,7 +356,12 @@
 </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>
@@ -287,7 +372,12 @@
 </tr>
 <tr class="row-even"><td><p>maxZr</p></td>
 <td><p>1</p></td>
-<td><p>1000</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>
@@ -299,6 +389,11 @@
 <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>
@@ -310,6 +405,11 @@
 <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>
@@ -321,6 +421,11 @@
 <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>
@@ -332,6 +437,11 @@
 <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>
@@ -343,6 +453,11 @@
 <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>

docs/build/html/samir/run_samir.html

@@ -89,7 +89,7 @@
 </div>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>Depending on the size of your datasets and your machine’s specifications, this script can take some time to run. A progress bar will keep you informed on the script’s progress and operations.</p>
+<p>Depending on the size of your datasets and your machine’s specifications, this script can take some time to run. A <strong>progress bar</strong> will keep you informed on the script’s progress and operations.</p>
 </div>
 <p>Once the script is finished, the output dataset (or daframe and shapefile for the <strong>parcel</strong> mode) will be found in the <strong>output</strong> directory, in a subdirectory carrying the <strong>run_name</strong>. Plotting scripts and notebooks are located in the <code class="code docutils literal notranslate"><span class="pre">modspa_pixel/postprocessing/</span></code> directory.</p>
 <div class="toctree-wrapper compound">

docs/source/filetree.rst

@@ -7,7 +7,8 @@
     │   ├── csv_files
     │   │   ├── params_samir_test.csv
     │   │   ├── params_samir_Aurade_test.csv
-    │   │   └── params_samir_min_max.csv
+    │   │   ├── params_samir_min_max.csv
+    │   │   └── params_samir.csv
     │   ├── parameter_estimation.ipynb
     │   └── params_samir_class.py
     ├── main_run_samir.py

docs/source/preprocessing/samir_params.rst

@@ -6,7 +6,7 @@ Preparing the SAMIR parameter csv file
 All the *SAMIR* model parameters are written in a csv file. Here is an example of such a file:
 
 .. csv-table::
-    :file: ../../../parameters/csv_files/params_samir_test.csv
+    :file: ../../../parameters/csv_files/params_samir.csv
 
 
 Here is how the file is organised: