.. include:: _config.rst

==============================================
XAFS: Post-edge Background Subtraction
==============================================

.. :noindex: module:: larch.xafs

Background subtraction is one of the most important data processing steps
in EXAFS analysis, converting the measured :math:`\mu(E)` into the
:math:`\chi(k)` ready for quantitative analysis.  In Larch, this step is
performed by the :func:`autobk` function, which has many options and
subtleties.  This section is devoted to background subtraction with the
:func:`autobk` function and the underlying algorithm it uses.

The :func:`autobk` function
=============================



..  function:: autobk(energy, mu=None, group=None, rbkg=1.0, ...)

    Determine the post-edge background function, :math:`\mu_0(E)`, and
    corresponding :math:`\chi(k)`.

    :param energy:    1-d array of x-ray energies, in eV
    :param mu:        1-d array of :math:`\mu(E)`
    :param group:     output group (and input group for ``e0`` and ``edge_step``).
    :param rbkg:      distance (in :math:`\rm\AA`) for :math:`\chi(R)` above
		      which the signal is ignored. Default = 1.
    :param e0:        edge energy, in eV.  If `None`, it will be determined.
    :param edge_step: edge step.  If `None`, it will be determined.
    :param pre_edge_kws:  dictionary containing keyword arguments to pass to :func:`pre_edge`.
    :param nknots:    number of knots in spline.  If `None`, it will be determined.
    :param kmin:      minimum :math:`k` value   [0]
    :param kmax:      maximum :math:`k` value   [``None``, full data range].
    :param kweight:   :math:`k` weight for FFT.  [1]
    :param dk:        FFT window window parameter.  [0.1]
    :param win:       FFT window function name.     ['hanning']
    :param nfft:      array size to use for FFT [2048]
    :param kstep:     :math:`k` step size to use for FFT [0.05]
    :param k_std:     optional :math:`k` array for standard :math:`\chi(k)` [``None``]
    :param chi_std:   optional :math:`\chi` array for standard :math:`\chi(k)` [``None``]
    :param nclamp:    number of energy end-points for clamp [2]
    :param clamp_lo:  weight of low-energy clamp [1]
    :param clamp_hi:  weight of high-energy clamp [1]
    :param calc_uncertaintites:  Flag to calculate uncertainties in  :math:`\mu_0(E)` and :math:`\chi(k)` [``True``]
    :param err_sigma: sigma level for uncertainties in mu_0(E) and chi(k) [1]
    :returns: ``None``.

    Follows the First Argument Group convention, using group members named ``energy`` and ``mu``.
    The following data is put into the output group:

       ================= ===============================================================
	attribute         meaning
       ================= ===============================================================
	bkg               array of :math:`\mu_0(E)` (not normalized)
	chie              array of :math:`\chi(E)` values.
	k                 array of :math:`k` values, on uniform grid.
	chi               array of :math:`\chi(k)` values, the EXAFS.
	*delta_chi*       array of uncertainty in :math:`\chi(k)`.
	*delta_bkg*       array of uncertainty in :math:`\mu_0(E)`.
	autobk_details    Group of arrays with autobk details.
       ================= ===============================================================

    Here, the arrays ``group.k``, ``group.chi`` will be the same length,
    giving :math:`\chi(k)` from 0 to a maximum k value set by ``kmax`` or
    the range of available data.  The arrays ``group.bkg`` and
    ``group.chie`` will correspond to the input ``energy`` array.

    The parameters ``e0`` and ``edge_step`` are needed to determine
    :math:`\chi(k)`, and can be specified here.  If they are not, but the
    input ``group`` has attributes ``e0`` and ``edge_step`` -- say, from
    running :func:`pre_edge` -- those values will be used.  If values
    cannot be found in either place, they will be determined by calling
    :func:`pre_edge` from within :func:`autobk`, and the output parameters
    from :func:`pre_edge` will be added to the output ``group`` here.
    The ``pre_edge_kws`` argument can be used here to hold a dictionary of
    parameters to pass to :func:`pre_edge`.


    If ``calc_uncertainties`` is set to ``True``, the outputs
    ``group.delta_chi`` and ``group.delta_bkg``, holding the uncertainties
    in :math:`\chi(k)` and :math:`\mu_0(E)`, respectively.  These
    calculations are relatively costly, and can take 20 times longer to
    determine :math:`\chi(k)` and :math:`\mu_0(E)` themselves.

    The ``group.autobk_details`` group will contain the following attributes:

       ================= ===========================================================
	attribute         meaning
       ================= ===========================================================
	spline_pars       Parameters used for determining :math:`\mu_0(E)` spline.
	init_bkg          Initial value for :math:`\mu_0(E)`
	init_chi          Initial value for :math:`\chi(k)`
	knots_e           Spline knot energies
	knots_y           Spline knot values
	init_knots_y      Initial Spline knot values
       ================= ===========================================================


The AUTOBK Algorithm
======================

The background subtraction method used is the **AUTOBK** algorithm
(see :cite:`autobk`), in which a spline function is matched to the
low-*R* components of the resulting :math:`\chi(k)`.

For reference, :math:`k = \sqrt{2m_e (E-E_0)/\hbar^2}` is the wavenumber of
the ejected photo-electron, where :math:`E_0` is the absorption threshold
energy (the 0 of photo-electron energy).  For :math:`k` in units of
:math:`\rm \AA^{-1}` and :math:`E` in units of eV, :math:`k \approx
\sqrt{(E-E_0)/3.81}`.  With this conversion of energy to wavenumber,
:math:`\chi(k)` is defined from

    :math:`\chi(E) = \frac{\mu(E)-\mu_0(E)}{\Delta\mu}`

where :math:`\mu_0(E)` represents the idealized x-ray absorption of a
bare atom, embedded in the molecular or solid environment, but without
scattering of the outgoing photo-electron that gives rise to the EXAFS, and
:math:`\Delta\mu` is the edge step in :math:`\mu(E)`.

The quantity :math:`\mu_0(E)` cannot be independently measured.  Instead,
we empirically determine it here given the dxta for :math:`\mu(E)` by
fitting a spline (a piece-polynomial function that is easily adjusted even
while its smoothness is controlled) to :math:`\mu(E)`.  An advantage to
what could easily be described as an *ad hoc* approach is that the data for
:math:`\mu(E)` can include many systematic drifts and dependencies that are
slowly varying with energy.

The definition above normalizes to the edge step :math:`\Delta\mu`
(``edge_step``) instead of the energy-dependent :math:`\mu_0(E)`, as is
often described in introductory texts on EXAFS.  The reason for this is
essentially the same -- so that we do not need to carefully take care of
slow energy drifts in the measured :math:`\mu(E)` or worry about having an
absolute measure of :math:`\mu(E)`.

:math:`R_{\rm bkg}` and spline for :math:`\mu_0(E)`
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

A spline is a general mathematical function, and so using one to match
:math:`\mu(E)` that we will subtract from the same :math:`\mu(E)` could
easily match *too* well, and erase much of the data we're interested in.
Therefore, we have to carefully consider two aspects:

  1. what portions of the spectrum we want it to match, and
  2. how flexible the spline can be.

What we want is a :math:`\mu_0(E)` that removes the low frequency (low-*R*)
portions of the :math:`\chi` spectra, and recognizing this can tell us how
to determine both of these.

First, since we know the EXAFS oscillations do not extend far below the
near-neighbor distance and since atoms are essentially never closer than 1
:math:`\rm\AA`, and generally more like 2 :math:`\rm\AA`, we can say that
we want to remove the frequencies of :math:`\chi` below some distance,
:math:`R_{\rm bkg}` (``rbkg``).  That is, we want the spline function to
be adjusted so that the components of :math:`\chi(R)` below :math:`R_{\rm
bkg}` are minimized.  We can use a default of 1 :math:`\rm\AA`, and
recommend that the value be roughly half the expected near-neighbor
distance.

To do this, we create a spline function consisting of :math:`N_{\rm knots}`
adjustable points (*knots* in the spline, where the second derivatives are
allowed to change), evenly spaced in :math:`k` (that is, quadratic in
energy).  We do a fit that adjusts the values of the function at each knot,
computes :math:`\mu_0(E)` by simple spline interpolation, calculates
:math:`\chi(k)`, does a Fourier transform to :math:`\chi(R)`, and then
seeks to minimize the components of :math:`\chi(R)` below :math:`R_{\rm
bkg}`.

This leads to the second question of how flexible to make the spline is
answered from basic signal processing through the `Nyquist-Shannon sampling
theorem <https://en.wikipedia.org/wiki/Nyquist-Shannon_sampling_theorem>`_,
which tells us how many adjustable parameters to use for our spline:

.. math::

  N_{\rm knots}  =  1 + \frac{2R_{\rm bkg} \Delta k}{\pi}

where :math:`\Delta k` is the :math:`k` range of the data.  This value can
be over-ridden by specifing ``nknots``, but this is strongly recommended
against.

In this way we satisfy both considerations above: limiting the number of
knots prevents the spline from being able to follow the frequencies of
:math:`\chi(k)` we care about most, and limiting the portion of the
spectrum to be minimized to the very low-:math:`R` components, we do not
even try to match those frequencies.  Thus, we are ensured of a
:math:`\mu_0(E)` that only removes the low-:math:`R` components of
:math:`\chi`.

Selecting Fourier transform parameters
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In order to determine :math:`\mu_0(E)`, we must do a Fourier transform.
These are discussed in more detail in the next section, but here we give
the parameters affecting the Fourier transform used, and their default
values.

    ========== ====================== ============================================
     argument   meaning                default, recommended values
    ========== ====================== ============================================
     kmin       :math:`k_{\rm min}`    0. should be below 1.0
     kmax       :math:`k_{\rm max}`    highest :math:`k` value. Useful data range.
     kweight    :math:`kw`             1. should be 0 or 1 (but not > 2)
     win        window function name   Hanning, Parzen works well too.
     dk         window sill size       0. should be 0 or 1
     nfft       FFT array size           2048.  No reason to change this.
     kstep      :math:`k` step size     0.05.  No reason to change this.
    ========== ====================== ============================================

The most important point is that the Fourier transform used to fit
and visualize :math:`\chi(k)` is not necessarily the one to use here.  In
particular, the ``kweight`` parameter should be 0 or 1 here, as we want to
emphasize the low-:math:`k` portion of :math:`\chi(k)`.  The default
parameter values for :func:`autobk` are generally sufficient, and need only
minor adjustments except in unusual cases.


Using a standard :math:`\chi(k)`
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

We said above that we want to minimize the low-:math:`R` components of
:math:`\chi`.  In principle, there should be some leakage of the first
shell to fairly low-:math:`R`.  This is especially noticeable for a short
ligand (say, below 1.75 :math:`\rm\AA` or so) of a low-Z atom (notably, C,
N, and O).  Normally, this is not a serious problem, but it does point out
that :math:`\mu_0(E)` might want to leave some first-shell leakage at
low-:math:`R`.

To accout for this, you can proved a spectrum of :math:`\chi(k)` for a
standard that is meant to be close to the spectrum being analyzed.  This is
done by providing 2 arrays: ``k_std`` and ``chi_std``, which need to be the
same lenth.  By providing these, the best values for :math:`\mu_0(E)` will
be those that minimize the Fourier transorm of the difference of
:math:`\chi(k)` for the data and standard.  This can be especially helpful
to give more consistent background for a set of related spectra.

End-point clamps for the spline
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Because the spline is chosen to match the low-:math:`R` components of
:math:`\chi`, the process does not even look at how the resulting
:math:`\mu_0(E)` looks.  This can lead to some unstable behavior at the
end-points of the spline, causing :math:`\chi(k)` to diverge at the ends.

This can be remedied by adding *clamps* to the end-points of :math:`chi(k)`
to the fit.  That is, a few points at the low- and high-ends of the
:math:`\chi(k)` array are appended to the array to be minimized in the fit,
which has the tendency to push the end-points of :math:`\chi(k)` to zero.

There are three parameters influencing these end-points clamps.  ``nclamp``
sets the number of data points of :math:`\chi(k)` at the beginning and end
of the :math:`k` range to add to the fit.  ``clamp_lo`` sets the weighting
factor applied to the first ``nclamp`` points for the low-:math:`k` end fo
the data range, and ``clamp_hi`` sets the weighting factor applied to the
last ``nclamp`` points at the high-:math:`k` end.

There is not an easy way to determine ahead of time what the clamp
parameters will be.  Typically, ``nclamp`` need only be 1 to 5 data points
(with 2 being the default).  Setting ``nclamp`` to 0 will remove the clamps
completely.  Values for ``clamp_lo`` and ``clamp_hi`` are floating point
numbers, and should range from about 1 (the default) to 10 or 20 for a very
strong clamp that will almost certainly force :math:`\chi(k)` to be 0 at
the end-points.



Recommendations
~~~~~~~~~~~~~~~~~

Here, we give a few recommendations on what parameters most affect the
background subtraction.  These parameters are (in roughly increasing
order):

 0. ``rbkg``:  This is the main parameter that sets how flaexible the
 spline function can be.

 1.  ``e0``: It can be hard to know what :math:`E_0` should be for any XAFS
 spectra.  As this sets the value of :math:`k=0`, it will affect the
 location of the knots, and can have a profound affect on the results.  If
 you're unhappy with the :math:`\mu_0(E)` and :math:`\chi(k)`, playing with
 the ``e0`` parameter.

 2. ``kweight``: Increasing this emphasizes the fit at high *k*.  Trying
 both values of 0 and 1 is always a good idea.

 3. ``clamp_lo`` and ``clamp_hi``: If :math:`\mu_0(E)` swoops up or down at
 the endpoints too much, increasing these values can help greatly.


Examples
============

Here, we give a few examples using :func:`autobk`, and outline some of its
features.


Basic example
~~~~~~~~~~~~~~~~~~

The simplest example of reading data and doing background subtraction would
using all the default inputs would be:

.. literalinclude:: ../examples/xafs/doc_autobk1.lar

with the resulting outputs looking like this:

.. subfigstart::

.. _fig_xafs2a:

.. figure::  _images/xafs_autobk1a.png
    :target: _images/xafs_autobk1a.png
    :width: 100%
    :align: center

    :math:`\mu(E)` and background :math:`\mu_0(E)`

.. _fig_xafs2b:

.. figure::  _images/xafs_autobk1b.png
    :target: _images/xafs_autobk1b.png
    :width: 100%
    :align: center

    resulting :math:`k\chi(k)`

.. subfigend::
    :width: 0.45
    :label: fig-xafs2

    Example of simple usage of :func:`autobk` for Cu metal.


Thus demonstrating that we can process data on Cu metal.

For a slightly more challenging example, we try the As K-edge of scorodite
(:math:`\rm FeAsO4 \cdot (nH_2O)`).  Here, we start by reading in data and
constructing :math:`\mu(E)`, then run :func:`autobk`.  We take most of the
default values for pararmeters, but pass explicit parameters such as
``nnorm`` to :func:`pre_edge` using ``pre_edge_kws``.  Setting these
parameters is not critically important for this data set, and is mostly
here to demonstrate the method for passing arguments to :func:`pre_edge`.

.. literalinclude:: ../examples/xafs/doc_autobk2.lar

The resulting outputs looks OK:

.. subfigstart::

.. _fig-xafs3a:

.. figure::  _images/xafs_autobk2a.png
    :target: _images/xafs_autobk2a.png
    :width: 100%

.. _fig-xafs3b:

.. figure::  _images/xafs_autobk2b.png
    :target: _images/xafs_autobk2b.png
    :width: 100%

.. subfigend::
    :width: 0.45
    :label: fig-xafs3

    Example usage of :func:`autobk` for :math:`\rm FeAsO4 \cdot (nH_2O)`.


A close examimation of :math:`k^2\chi(k)` suggests we might be able to do
better, which brings us to the next section.

Adjusting spline clamps
~~~~~~~~~~~~~~~~~~~~~~~~~

For the scorodite example above, the XAFS diverges from 0 at the
high-:math:`k` end of the spectra.  Playing with the spline clamps
discussed above, we try a few options to study the effect of adding a
clamp:

.. literalinclude:: ../examples/xafs/doc_autobk3.lar

results in the following comparison:

.. _xafs_fig4:

.. figure::  _images/xafs_autobk3.png
    :target: _images/xafs_autobk3.png
    :width: 65%

    Influence of spline clamps of :math:`\chi(k)`


Using a Standard :math:`\chi(k)`
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Since the EXAFS contribution from the first shell is not perfectly isolated
in :math:`R`, it can leak into portion of :math:`\chi(R)` below
:math:`R_{\rm bkg}`.  It may be desirable to not simply reduce the portion
of :math:`\chi(R)` below :math:`R_{\rm bkg}`, but to account for the
expected leakage from the first shell.  To do this, you can provide a
*standard* :math:`\chi(k)` spectrum that will simulate the first shell by
specify arrays for `k_std` and `chi_std` arrays to the :func:`autobk`
function.

As an example:


.. literalinclude:: ../examples/xafs/doc_autobk4.lar
