.. pr_help.rst

.. This is a port of the original SasView html help file to ReSTructured text
.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.

P(r) Calculation
================

Description
-----------

This tool calculates a real-space distance distribution function, *P(r)*, using
the inversion approach (Moore, 1980).

*P(r)* is set to be equal to an expansion of base functions of the type

.. math::
  \Phi_{n(r)} = 2 r sin(\frac{\pi n r}{D_{max}})

The coefficient of each base function in the expansion is found by performing
a least square fit with the following fit function

.. math::

  \chi^2=\frac{\sum_i (I_{meas}(Q_i)-I_{th}(Q_i))^2}{error^2}+Reg\_term


where $I_{meas}(Q_i)$ is the measured scattering intensity and $I_{th}(Q_i)$ is
the prediction from the Fourier transform of the *P(r)* expansion.

The $Reg\_term$ term is a regularization term set to the second derivative
$d^2P(r)/d^2r$ integrated over $r$. It is used to produce a smooth *P(r)* output.

.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ

Using P(r) inversion
--------------------

The user must enter

*  *Number of terms*: the number of base functions in the P(r) expansion.

*  *Regularization constant*: a multiplicative constant to set the size of
   the regularization term.

*  *Maximum distance*: the maximum distance between any two points in the
   system.

P(r) inversion requires that the background be perfectly subtracted.  This is
often difficult to do well and thus many data sets will include a background.
For those cases, the user should check the "Estimate background level" option
and the module will do its best to estimate it. If you know the background value
for your data, select the "Input manual background level" option. Note that
this value will be treated as having 0 error.

The P(r) module is constantly computing in the background what the optimum
*number of terms* should be as well as the optimum *regularization constant*.
These are constantly updated in the buttons next to the entry boxes on the GUI.
These are almost always close and unless the user has a good reason to choose
differently they should just click on the buttons to accept both.  {D_max} must
still be set by the user.  However, besides looking at the output, the user can
click the explore button which will bring up a graph of chi^2 vs Dmax over a
range around the current Dmax.  The user can change the range and the number of
points to explore in that range.  They can also choose to plot several other
parameters as a function of Dmax including: I0, Rg, Oscillation parameter,
background, positive fraction, and 1-sigma positive fraction.

.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ

.. _Batch_Pr_Mode:

Batch P(r) inversion
--------------------

The p(r) calculator accepts any number of data sets, and supports batch fitting
for all data sets in the p(r) data set combo box. Switching between data sets in
the combo box allows for individual fits and review of fit parameters. The
displayed plots will also update to include the latest fit results for the
selected data set.

The 'Calculate All' button will run the p(r) calculation for each file,
sequentially. The calculator will estimate the number of terms, background, and
regularization constant for each file prior to running the p(r) calculation.
The final results for all data sets are then presented in a savable data table.

.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ

Reference
---------

P.B. Moore
*J. Appl. Cryst.*, 13 (1980) 168-175

.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ

.. note::  This help document was last modified by Jeff Krzywon, 18 April 2018
