===========================================
X-ray Fluorescence Analysis
===========================================

X-ray Fluorescence (XRF) Data can be manipulated, viewed, and analyzed with
Larch.  In this chapter, we'll discuss how to transform data into Larch
Groups of XRF data and how to use the Graphical visualization tool `XRF
Display` to visualize and work with XRF spectr.  We'll also discuss how to
analyze XRF spectra to quantify elemental compositions of samples.  As part
of that discussion of fitting XRF spectra, we'll review some of the
fundamental concepts of XRF Analysis and discuss how these features can
affect the results of XRF analysis.

Since XRF spectra can be collected in as little as a few milliseconds with
modern X-ray sources and solid-state detectors, it is common to build 2- or
even 3-dimensional maps of XRF data, with each pixel in the map holding an
XRF spectrum that can be analyzed.  Larch's `GSE MapViewer` is designed to
work with and display such XRF maps, and to support the quantitative XRF
analysis shown here.

A basic XRF spectrum from a solid-state detector -- a silicon drift
detector -- as displayed in the `XRF Display` program is shown below.  The
spectrum consists of two arrays of a few thousand points: an `energy` array
that holds energy at each point (or "channel") in the array and a `counts`
array that holds the counts in each channel.


.. _xrf_fig1:

.. figure::  _images/xrf_display1.png
    :target: _images/xrf_display1.png
    :width: 65%
    :align: center

    Typical X-ray fluorescence spectrum.

The peaks in this specra correpsond to characteristic X-ray emission lines
from the elements.  The presence of a particular peak in the spectrum
indicates that the corresponding element was in the illuminated X-ray beam
-- the spectrum above indicates that Cu and Mn (and also Ca, V, and Co) are
present in the sample.  Furthermore, the intensity of each peak can be used
to determine (or at least "infer") the concentration of that particular
element in the illuminated sample.

From a spectroscopic point-of-view XRF spectra are relatively easy to
interpret: the characteristic emission energies for each atom are well
known to high precision and the absorption and emission probabilities are
known to pretty good precision (though perhaps only 10%).  In this sense, a
crude approach to XRF analysis is to use the area under the appropriate
peaks as a quantifiable value for the elements abundance.  This should
definitely be taken as a rough approximation.  The complications preventing
such a simle interpretion of XRF spectra are due mostly to:

    1. Strong X-ray attenuation effects.  The attenuation of X-rays goes
    approximately as :math:`\mu \sim Z^4E^{-3}`, which is to say it has
    extremely high and non-linear dependence on the atomic number Z of the
    elements in the X-ray beam, and extremely high and non-linear
    dependence on the X-ray energy.

    2. Overlaps of elemental peaks.  That is, the emission energies for
    each element are known, but not unique.  Each element will have
    multiple series of lines (K, L, M, etc), and these can be close enough
    in energy to cause some uncertainty in which elements are present.

    3. Detector artefacts. Even the best energy-discriminating detectors
    used for most XRF analysis are limited in the resolution with which
    they can determine an X-ray energy. They also need some finite time
    (:math:`100ns` to  :math:`10{\mu}s`) to count each X-ray and so have a
    "dead time" and can suffer from "pileup" that can distort the spectra.

These effects are understood pretty well and can mostly be compensated for
in a thorough analysis, as will be discussed in more detail below.
Importantly, together they means that simply taking the area under a
portion of the curve in the XRF spectrum is generally not a good measure of
the absolute abundance of an atom in the illuminated sample.  In limited
cases, where the bulk of the sample composition does change much, where
peak overlaps are small, and where the detector is not saturated, the
integrated intensities of selected peaks can be a good relative measure of
elemental abundance.

.. module:: _xrf
   :synopsis: X-ray Fluorescence Analysis

.. toctree::
   :maxdepth: 2

   xrf_mca
   xrf_viewer
   xrf_modelling
