Getting-started.md

@@ -14,6 +14,7 @@ Summary:
     - [Running](#running-1)
     - [Plotting](#plotting-1)
     - [Better figures](#better-figures)
+    - [HDF5-formatted output](#hdf5-formatted-output)
 
 # Prerequisites
 If you downloaded the archive in the [_dist_](https://gitlab.obspm.fr/dblain/exorem/-/tree/master/dist) directory, you should have everything you need, except a stellar spectrum (see point 4 below), and more importantly the k-coefficients tables (see point 3 below). Otherwise, check the following:
@@ -29,6 +30,7 @@ To plot the figures using the provided plot functions, you will need Python3, an
 - numpy
 - scipy
 - matplotlib
+- h5py
 
 # First run
 ## Setup
@@ -243,4 +245,31 @@ Not happy with the figures you get ? What if for example you wanted to see the c
 
 There is much other things you can do. Do not hesitate to check the _src/python/plot_figures.py_ file to look at the docstrings of the functions.
 
+## HDF5-formatted output
+To read the HDF5-formatted outputs, you can use [HDFView](https://www.hdfgroup.org/downloads/hdfview/).
+You can also read them using Python and h5py.
+1. To do the latter, open a python console:
+    ```bash
+    python
+    ```
+2. Import the h5py module:
+    ```python
+    from src.python.plot_figures import *
+    ```
+    Note: you can also simply `import h5py`.
+3. Open the result file, here we assume that the result file is _./outputs/exorem/example.h5_: 
+    ```python
+    data = load_result('./outputs/exorem/example.h5')
+    ```
+4. You can explore the file using: 
+    ```python
+    list(data)  # print >['model_parameters', 'outputs']
+    list(data['outputs'])  # print all sub-groups and datasets in group 'outputs'
+    pressure_level = np.asarray(data['outputs']['levels']['pressure'])  # get the pressure array
+    cloud_fraction = data['model_parameters']['clouds']['fraction'][()]  # get the cloud fraction scalar
+    eddy_mode = str(data['model_parameters']['atmosphere']['eddy_mode'][()], 'utf-8')  # get the eddy mode string
+    ```
+
+More on the HDF5-output file [here](Documentation).
+
 Enjoy Exo-REM !
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