.. _fit_autoemxsp_spectrum_tutorial:


Tutorial: Fit and quantify individual spectra acquired with `AutoEMXSp`
=======================================================================

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

This allows to select an individual spectrum from the acquired data 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.


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

Open ``autoemxsp/scripts/Fit_Quant_Single_AutoEMXSp_Spectrum.py``.


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

Set the spectrum to analyse by defining:

- ``sample_ID``: name of the sample folder. Include any counter if present (e.g. 'Wulfenite_2').
- ``spectrum_ID``: ID of the spectrum to fit. You'll find this int number in the first column of `Data.csv`
  inside the folder named ``sample_ID``.
- ``results_path``: absolute or relative path to the project folder, containing the ``sample_ID`` data.
  `AutoEMXSp` will search for a folder named ``sample_ID`` in any of the subfolders within ``results_path``.
        
        
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