Index: src/sas/sasgui/perspectives/pr/media/pr_help.rst
===================================================================
--- src/sas/sasgui/perspectives/pr/media/pr_help.rst (revision b64b87c874ab0edc565e9c415decc839e3214c8c)
+++ src/sas/sasgui/perspectives/pr/media/pr_help.rst (revision 0391dae728cc7e22bcc7ec329200722cd14f829f)
@@ -15,18 +15,20 @@
*P(r)* is set to be equal to an expansion of base functions of the type
- |bigphi|\_n(r) = 2.r.sin(|pi|\ .n.r/D_max)
+.. 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
+The coefficient of each base function in the expansion is found by performing
a least square fit with the following fit function
- |chi|\ :sup:`2` = |bigsigma|\ :sub:`i` [ I\ :sub:`meas`\ (Q\ :sub:`i`\ ) - I\ :sub:`th`\ (Q\ :sub:`i`\ ) ] :sup:`2` / (Error) :sup:`2` + Reg_term
+.. math::
-where I\ :sub:`meas`\ (Q) is the measured scattering intensity and
-I\ :sub:`th`\ (Q) is the prediction from the Fourier transform of the *P(r)*
-expansion.
+ \chi^2=\frac{\sum_i (I_{meas}(Q_i)-I_{th}(Q_i))^2}{error^2}+Reg\_term
+
-The *Reg_term* term is a regularization term set to the second derivative
-d\ :sup:`2`\ *P(r)* / dr\ :sup:`2` integrated over *r*. It is used to produce a
-smooth *P(r)* output.
+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.
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@@ -45,4 +47,21 @@
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" box and the
+module will do its best to estimate it.
+
+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
@@ -55,3 +74,3 @@
.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-.. note:: This help document was last changed by Steve King, 01May2015
+.. note:: This help document was last modified by Paul Butler, 05 September, 2016