.. _fit_msa_spectrum_tutorial:


Tutorial: Fit and quantify individual spectra exported by commercial EDS software
=================================================================================

This tutorial shows how to fit--and optionall quantify-- a single EDS spectrum,
using the ``Fit_Quant_Single_MSA_Spectrum.py`` script.

This allows to load an individual spectrum from an exported file (typically
``.msa``, ``.emsa``, ``.txt``), fit and quantify it and visualize the fitted spectrum
 for inspection of model fitting performance.

This script also prints the full fitting and quantification process steps, prints
the employed fit parameters and their final values. 

It also enables further customization options for fitting and quantification 
for evaluating the performance of different EDS models, allowing to define a set
of parameters to use in your standard EDS quantification operations.

**Note**: This script has so far been tested with spectra output with `Thermofisher 
Phenom` SEM-EDS and by `Oxford Aztec` software.


Step 1 - Open script to edit
-------------------------------

Open ``autoemxsp/scripts/Fit_Quant_Single_MSA_Spectrum.py``.


Step 2 - Define Spectrum to Fit
-------------------------------

Set the spectrum to analyse by defining:

- ``spectrum_path``: Path to spectrum file.
- ``els_sample``: list of elements present in the sample.
- ``els_substrate``: list of elements present in the sample substrate (e.g. carbon tape).
- ``is_particle``: set to ``True`` if measurement is from particles or from a rough surface.
  Set to ``False`` if measurement is from a flat, polished surface.
        
        
Step 3 - Modify Parameters
-------------------------------

Modify the rest of the parameters to match to the sample you're fitting.

For details on the parameters, see the  :ref:`API <runners_fit_single_spectrum>` for the ``fit_and_quantify_spectrum``
function.


Step 4 - Launch script
-------------------------------

Visualise the fitted spectrum and evaluate goodness of fit.

.. figure:: /_static/Example_fit.png
   :alt: Example fitted spectrum
   :width: 70%
   :align: center

The background fitting is especially important when it comes to peak-to-background EDS quantification.

.. figure:: /_static/Example_fit_zoom.png
   :alt: Zoom on example fitted spectrum
   :width: 70%
   :align: center