Index: src/sas/sasgui/perspectives/calculator/media/data_operator_help.rst
===================================================================
--- src/sas/sasgui/perspectives/calculator/media/data_operator_help.rst	(revision d85c194ea2f78cb2b9b3de9c969e1b8ebea6b6d2)
+++ 	(revision )
@@ -1,55 +1,0 @@
-.. data_operator_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.
-
-Data Operations Tool
-====================
-
-Description
------------
-
-This tool permits arithmetic operations between two data sets. Alternatively, 
-the last data set can be a number.
-
-*NOTE! When* Data1 *and* Data2 *are both data, their Q (or Qx and Qy for 2D) 
-value(s) must match with each other UNLESS using the 'append' operator.*
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Using the tool
---------------
-
-1) Ensure you have loaded data into the *Data Explorer* (see :ref:`Loading_data`).
-
-2) Select *Data Operation* from the *Tool* menu on the SasView toolbar.
-
-3) Select a dataset/theory in the drop-down menu *Data1*. A mini-plot of the
-   data will appear underneath.
-
-4) Select a dataset/theory in the drop-down menu *Data2* or select *Number* 
-   and enter a number in the box that appears alongside.
-
-5) Select an arithmetic operator symbol from the *Operator* drop-down. The 
-   available operators are:
-   
-*   \+ (for addition)
-*   \- (for subtraction) 
-*   \* (for multiplication)
-*   \/ (for division)
-*   \| (for combination of two data sets)
-
-   If two data sets do not match, the operation will fail and the background 
-   color of the combo box items will turn to red (WIN only).
-
-6) If the operation is successful, hit the Apply button to make the new dataset.
-   The new dataset will appear in the *Data Explorer*.
-
-*NOTE! Any errors and warnings will be displayed at the bottom of the SasView
-window.*
-
-.. image:: data_oper_pic.png
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Steve King, 01May2015
Index: src/sas/sasgui/perspectives/calculator/media/density_calculator_help.rst
===================================================================
--- src/sas/sasgui/perspectives/calculator/media/density_calculator_help.rst	(revision 6aad2e8b144e92be94b299c8ae7f4f418c094f1d)
+++ 	(revision )
@@ -1,35 +1,0 @@
-.. density_calculator_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.
-
-Density/Volume Calculator Tool
-==============================
-
-Description
------------
-
-This tool calculates the mass density from the molar volume or vice 
-versa. To calculate the mass density, the chemical formula and molar volume 
-should be provided.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Using the tool
---------------
-
-1) Select *Density/Volume Calculator* from the *Tool* menu on the SasView toolbar.
-
-2) Enter the empirical formula of a molecule. For mixtures, the ratio of each 
-   of the molecules should be used, for example, (H2O)0.5(D2O)0.5.
-
-3) Use the input combo box to choose between molar volume or mass density and 
-   then type in an input value.
-
-4) Click the 'Calculate' button to perform the calculation.
-
-.. image:: density_tutor.png
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Steve King, 01May2015
Index: src/sas/sasgui/perspectives/calculator/media/gen_sas_help.html
===================================================================
--- src/sas/sasgui/perspectives/calculator/media/gen_sas_help.html	(revision 6aad2e8b144e92be94b299c8ae7f4f418c094f1d)
+++ 	(revision )
@@ -1,147 +1,0 @@
-<body>
-<h4>Generic Scattering Calculator:</h4>
-Polarization and Magnetic Scattering
-<br>
-<br>
-<ul>
-<li><a href="#theory">Theory:</a></li>
-<li><a href="#gui">GUI</a></li>
-<li><a href="#pdb">PDB Data</a></li>
-</ul>
-<br>
-<br>
-<b>1. <a name="theory">Theory</a> </b>
-<br>
-In general, a particle with a volume V can be described by an ensemble containing N 
-3-dimensional rectangular pixels where each pixels are much smaller than V. 
-Assuming that
-all the pixel sizes are same, the elastic scattering intensity 
-by the particle 
-<p>
-<img src="gen_i.png"/>
-</p>
-<br>
-where &#946;<sub>j</sub> and r<sub>j</sub> are the scattering 
-length density and the position 
-of the j'th pixel respectively. And the total volume
-<p>
-<img src="v_j.png"/>
-</p>
-<br>
-for &#946;<sub>j</sub> &#8800; 0 where v<sub>j</sub> is the volume of the j'th pixel 
-(or the j'th natural atomic volume (= atomic mass/natural molar density/Avogadro number) 
- for the atomic structures). The total volume V can be corrected by users. 
-This correction is useful especially for an atomic structure (taken from a pdb file) to get the right 
-normalization. Note that the  &#946;<sub>j</sub> displayed in GUI may be incorrect but will not 
-affect the scattering computation if the correction of the total volume is made.
-<br>
-The scattering length density (SLD) of each pixel where the SLD is uniform, is a combination of the nuclear and magnetic SLDs 
-and depends on the spin states of the neutrons as follows:
-<br>
-<br>
-For magnetic scattering, only the magnetization component, <b>M</b><sub>perp</sub>, 
-perpendicular to the scattering vector <b>Q</b> contributes to the the magnetic 
-scattering length. (Figure below).
-<p>
-<img src="mag_vector.png"/>
-</p>
-<br>
-The magnetic scattering length density is then
-<p>
-<img src="dm_eq.png"/>
-</p>
-<br>
-where &#947; = -1.913 the gyromagnetic ratio,  	&#956;<sub>B</sub> is the Bohr magneton, 
-r<sub>0</sub> is the classical radius of electron, 
-and <b>&#963;</b> is the Pauli spin.
-<br>
-For polarized neutron, the magnetic scattering is depending on the spin states.
-Let's consider that the incident neutrons are polarized parallel (+)/anti-parallel 
-(&#8211;) to the x' axis (See both Figures above).
-The possible out-coming states then are + and - states for both incident states.
-<br>
- - Non-spin-flips:  	(+ +) and  	(- -)
-<br>
- - Spin-flips:  	(+ -) and  	(- +)
-<br>
-<p>
-<img src="gen_mag_pic.png"/>
-</p>
-<br>
-<br>
-Now, let's assume that the angles of the <b>Q</b> vector and the spin-axis (x') from x-axis 
-are &#966; and  &#952;<sub>up</sub>, respectively (See Figure above).
-Then, depending upon the polarization (spin) state of neutrons, the scattering length
-densities , including the nuclear scattering length density (&#946; <sub>N</sub>) are given as, for non-spin-flips,
-<p>
-<img src="sld1.png"/>
-</p>
-<br>
-<br>
-for spin-flips,
-<p>
-<img src="sld2.png"/>
-</p>
-<br>
-<br>
-where
-<p>
-<img src="mxp.png"/>
-</p>
-<p>
-<img src="myp.png"/>
-</p>
-<p>
-<img src="mzp.png"/>
-</p>
-<p>
-<img src="mqx.png"/>
-</p>
-<p>
-<img src="mqy.png"/>
-</p>
-<br>
-<br>
-Here, the M<sub>0x</sub>, M<sub>0y</sub> and M<sub>0z</sub> are the x, y and z 
-components of the magnetization vector given in the xyz lab frame.
-<br>
-<br>
-<b>2. <a name="gui">GUI</a> </b>
-<br>
-<p>
-<img src="gen_gui_help.png"/>
-</p>
-<br>
-<p>
-After the computation, the result will be listed in the 'Theory' box 
-in the data explorer panel on the main window.
-<br>
-The 'Up_frac_in' and 'Up_frac_out' are the ratio, (spin up) /(spin up + spin down) neutrons 
-before the sample and at the analyzer, respectively.
-</p>
-<br>
-*Note I: The values of 'Up_frac_in' and 'Up_frac_out' must be in the range between 0 and 1.
-For example, both values are 0.5 for unpolarized neutrons.
-<br>
-*Note II: This computation is totally based on the pixel (or atomic) data fixed
-in the xyz coordinates. Thus no angular orientational averaging is considered.
-<br>
-*Note III: For the nuclear scattering length density, only the real component is taken account.
-<br>
-<br>
-<b>3. <a name="pdb">PDB Data</a> </b>
-<br>
-This Generic scattering calculator also supports some pdb files without considering polarized/magnetic scattering
- so that the related parameters such as Up_*** will be ignored (see the Picture below). The calculation for fixed orientation uses (the first) Equation above resulting 
-in a 2D output, whileas the scattering calculation averaged over all the orientations uses the Debye equation providing a 1D output:
- <p>
-<img src="gen_debye_eq.png"/>
-</p>
-<br>
-where v<sub>j</sub>&#946;<sub>j</sub> &#8801; b<sub>j</sub> is the scattering length of the j'th atom.
-The resultant outputs will be displayed in the DataExporer for further uses. 
-<br>
- <p>
-<img src="pdb_combo.jpg"/>
-</p>
-</body>
Index: src/sas/sasgui/perspectives/calculator/media/image_viewer_help.rst
===================================================================
--- src/sas/sasgui/perspectives/calculator/media/image_viewer_help.rst	(revision 412e9e8b8f844bae61656ffb2a2d0c1c53e6e8de)
+++ 	(revision )
@@ -1,57 +1,0 @@
-.. image_viewer_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.
-
-.. _Image_Viewer_Tool:
-
-Image Viewer Tool
-=================
-
-Description
------------
-
-This tool loads image files and displays them as 2D (x-y coordinate against 
-counts per pixel). The plot can then can be saved, printed, and copied. The 
-plot can also be resized by dragging the corner of the panel.
-
-The supported input image formats are:
-
-*  BMP (bitmap format)
-*  GIF (graphical interchange format)
-*  JPG (joint photographic experts group format)
-*  PNG (portable network graphics format)
-*  TIF (tagged image format)
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Using the tool
---------------
-
-1) Select *Image Viewer* from the *Tool* menu on the SasView toolbar.
-
-2) Select a file and then click *Open*. If the loading is successful the image 
-   will be displayed.
-
-.. image:: load_image.png
-
-3) To save, print, or copy the image, or to apply a grid overlay, right-click 
-   anywhere in the plot.
-
-.. image:: pic_plot.png
-
-4. If the image is taken from a 2D detector, SasView can attempt to convert 
-   the colour/grey scale into pseudo-intensity 2D data using 
-
-   z = (0.299 x R) + (0.587 x G) + (0.114 x B)
-
-   unless the image is formatted as 8-bit grey-scale TIF.
-
-5. In the *Convert to Data* dialog, set the parameters relevant to the data and 
-   then click the OK.
-
-.. image:: pic_convert.png
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Steve King, 01May2015
Index: src/sas/sasgui/perspectives/calculator/media/kiessig_calculator_help.rst
===================================================================
--- src/sas/sasgui/perspectives/calculator/media/kiessig_calculator_help.rst	(revision 5ed76f8390eac56ff5d3779fd9c454d0c8fe1dc0)
+++ 	(revision )
@@ -1,33 +1,0 @@
-.. kiessig_calculator_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.
-
-Kiessig Thickness Calculator Tool
-=================================
-
-Description
------------
-
-This tool estimates real space dimensions from the position or spacing of
-features in recipricol space.  In particular a particle of size $d$ will
-give rise to Bragg peaks with spacing $\Delta q$ according to the relation
-
-.. math::
-
-    d = 2\pi / \Delta q
-
-Similarly, the spacing between the peaks in Kiessig fringes in reflectometry
-data arise from layers of thickness $d$.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Using the tool
---------------
-
-To get a rough thickness or particle size, simply type the fringe or peak
-position (in units of 1/|Ang|\) and click on the *Compute* button.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Paul Kienzle, 05Apr2017
Index: src/sas/sasgui/perspectives/calculator/media/python_shell_help.rst
===================================================================
--- src/sas/sasgui/perspectives/calculator/media/python_shell_help.rst	(revision afb93df217e14e8e535194c24504152151ad5adb)
+++ 	(revision )
@@ -1,37 +1,0 @@
-.. python_shell_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.
-.. Text revised during Code Camp V in Oct 2016.
-
-.. _Python_shell:
-
-Python Shell-Editor Tool
-========================
-
-Description 
------------
-
-This is a Python shell/editor provided with WxPython.
-
-For the help about Python, visit the website http://docs.python.org/tutorial/
-
-.. note:: This shell/editor has its own help, but the Help() and Credits() calls do not work on Macs.
-
-The NumPy, SciPy, and Matplotlib, etc, libraries are shipped with SasView and so functions from these can be imported into the shell/editor, however, some functionality may not work.
-
-.. image:: new_pycrust_example.png
-   :align: center
-
-When a Python file, for example a fitting model, is created or loaded with the *New* or *Open* options from the menu, a new tab opens with an editing notebook.
-
-.. image:: new_pycrust_example_2.png
-   :align: center
-
-If a Python (.py) model has a linked C (.c) subroutine *in the same folder* then the shell/editor will open both! However input focus is usually transferred to the tab with the .c file.
-
-To compile a model, select *Run* > *Check Model* from the shell/editor menu. If the model contains a unit test (which it should!!!) then this will also run and a popup window will report the success/failure of the test.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Steve King, 10Oct2015
Index: src/sas/sasgui/perspectives/calculator/media/resolution_calculator_help.rst
===================================================================
--- src/sas/sasgui/perspectives/calculator/media/resolution_calculator_help.rst	(revision 5ed76f8390eac56ff5d3779fd9c454d0c8fe1dc0)
+++ 	(revision )
@@ -1,103 +1,0 @@
-.. resolution_calculator_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.
-
-Q Resolution Estimator Tool
-===========================
-
-Description
------------
-
-This tool is approximately estimates the resolution of $Q$ from SAS instrumental
-parameter values assuming that the detector is flat and normal to the
-incident beam.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Using the tool
---------------
-
-1) Select *SAS Resolution Estimator* from the *Tool* menu on the SasView toolbar.
-
-2) Select the source (Neutron or Photon) and source type (Monochromatic or TOF).
-
-   *NOTE! The computational difference between the sources is only the
-   gravitational contribution due to the mass of the particles.*
-
-3) Change the default values of the instrumental parameters as required. Be
-   careful to note that distances are specified in cm!
-
-4) Enter values for the source wavelength(s), $\lambda$, and its spread (= $\text{FWHM}/\lambda$).
-
-   For monochromatic sources, the inputs are just one value. For TOF sources,
-   the minimum and maximum values should be separated by a '-' to specify a
-   range.
-
-   Optionally, the wavelength (BUT NOT of the wavelength spread) can be extended
-   by adding '; nn' where the 'nn' specifies the number of the bins for the
-   numerical integration. The default value is nn = 10. The same number of bins
-   will be used for the corresponding wavelength spread.
-
-5) For TOF, the default wavelength spectrum is flat. A custom spectral
-   distribution file (2-column text: wavelength (|Ang|\) vs Intensity) can also
-   be loaded by selecting *Add new* in the combo box.
-
-6) When ready, click the *Compute* button. Depending on the computation the
-   calculation time will vary.
-
-7) 1D and 2D $dQ$ values will be displayed at the bottom of the panel, and a 2D
-   resolution weight distribution (a 2D elliptical Gaussian function) will also
-   be displayed in the plot panel even if the $Q$ inputs are outside of the
-   detector limit (the red lines indicate the limits of the detector).
-
-   TOF only: green lines indicate the limits of the maximum $Q$ range accessible
-   for the longest wavelength due to the size of the detector.
-
-   Note that the effect from the beam block/stop is ignored, so in the small $Q$
-   region near the beam block/stop
-
-   [i.e., $Q < (2 \pi \cdot \text{beam block diameter}) / (\text{sample-to-detector distance} \cdot \lambda_\text{min})$]
-
-   the variance is slightly under estimated.
-
-8) A summary of the calculation is written to the SasView *Console* at the
-   bottom of the main SasView window.
-
-.. image:: resolution_tutor.png
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Theory
-------
-
-The scattering wave transfer vector is by definition
-
-.. image:: q.png
-
-In the small-angle limit, the variance of $Q$ is to a first-order
-approximation
-
-.. image:: sigma_q.png
-
-The geometric and gravitational contributions can then be summarised as
-
-.. image:: sigma_table.png
-
-Finally, a Gaussian function is used to describe the 2D weighting distribution
-of the uncertainty in $Q$.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-References
-----------
-
-D.F.R. Mildner and J.M. Carpenter
-*J. Appl. Cryst.* 17 (1984) 249-256
-
-D.F.R. Mildner, J.M. Carpenter and D.L. Worcester
-*J. Appl. Cryst.* 19 (1986) 311-319
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Steve King, 01May2015
Index: src/sas/sasgui/perspectives/calculator/media/sas_calculator_help.rst
===================================================================
--- src/sas/sasgui/perspectives/calculator/media/sas_calculator_help.rst	(revision 5ed76f8390eac56ff5d3779fd9c454d0c8fe1dc0)
+++ 	(revision )
@@ -1,160 +1,0 @@
-.. sas_calculator_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.
-
-.. _SANS_Calculator_Tool:
-
-Generic SANS Calculator Tool
-============================
-
-Description
------------
-
-This tool attempts to simulate the SANS expected from a specified
-shape/structure or scattering length density profile. The tool can
-handle both nuclear and magnetic contributions to the scattering.
-
-Theory
-------
-
-In general, a particle with a volume $V$ can be described by an ensemble
-containing $N$ 3-dimensional rectangular pixels where each pixel is much
-smaller than $V$.
-
-Assuming that all the pixel sizes are the same, the elastic scattering
-intensity from the particle is
-
-.. image:: gen_i.png
-
-Equation 1.
-
-where $\beta_j$ and $r_j$ are the scattering length density and
-the position of the $j^\text{th}$ pixel respectively.
-
-The total volume $V$
-
-.. math::
-
-    V = \sum_j^N v_j
-
-for $\beta_j \ne 0$ where $v_j$ is the volume of the $j^\text{th}$
-pixel (or the $j^\text{th}$ natural atomic volume (= atomic mass / (natural molar
-density * Avogadro number) for the atomic structures).
-
-$V$ can be corrected by users. This correction is useful especially for an
-atomic structure (such as taken from a PDB file) to get the right normalization.
-
-*NOTE! $\beta_j$ displayed in the GUI may be incorrect but this will not
-affect the scattering computation if the correction of the total volume V is made.*
-
-The scattering length density (SLD) of each pixel, where the SLD is uniform, is
-a combination of the nuclear and magnetic SLDs and depends on the spin states
-of the neutrons as follows.
-
-Magnetic Scattering
-^^^^^^^^^^^^^^^^^^^
-
-For magnetic scattering, only the magnetization component, $M_\perp$,
-perpendicular to the scattering vector $Q$ contributes to the magnetic
-scattering length.
-
-.. image:: mag_vector.png
-
-The magnetic scattering length density is then
-
-.. image:: dm_eq.png
-
-where the gyromagnetic ratio is $\gamma = -1.913$, $\mu_B$ is the Bohr
-magneton, $r_0$ is the classical radius of electron, and $\sigma$ is the
-Pauli spin.
-
-For a polarized neutron, the magnetic scattering is depending on the spin states.
-
-Let us consider that the incident neutrons are polarised both parallel (+) and
-anti-parallel (-) to the x' axis (see below). The possible states after
-scattering from the sample are then
-
-*  Non-spin flips: (+ +) and (- -)
-*  Spin flips:     (+ -) and (- +)
-
-.. image:: gen_mag_pic.png
-
-Now let us assume that the angles of the *Q* vector and the spin-axis (x')
-to the x-axis are $\phi$ and $\theta_\text{up}$ respectively (see above). Then,
-depending upon the polarization (spin) state of neutrons, the scattering
-length densities, including the nuclear scattering length density ($\beta_N$)
-are given as
-
-*  for non-spin-flips
-
-   .. image:: sld1.png
-
-*  for spin-flips
-
-   .. image:: sld2.png
-
-where
-
-.. image:: mxp.png
-
-.. image:: myp.png
-
-.. image:: mzp.png
-
-.. image:: mqx.png
-
-.. image:: mqy.png
-
-Here the $M0_x$, $M0_y$ and $M0_z$ are the $x$, $y$ and $z$
-components of the magnetisation vector in the laboratory $xyz$ frame.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Using the tool
---------------
-
-.. image:: gen_gui_help.png
-
-After computation the result will appear in the *Theory* box in the SasView
-*Data Explorer* panel.
-
-*Up_frac_in* and *Up_frac_out* are the ratio
-
-   (spin up) / (spin up + spin down)
-
-of neutrons before the sample and at the analyzer, respectively.
-
-*NOTE 1. The values of* Up_frac_in *and* Up_frac_out *must be in the range
-0.0 to 1.0. Both values are 0.5 for unpolarized neutrons.*
-
-*NOTE 2. This computation is totally based on the pixel (or atomic) data fixed
-in xyz coordinates. No angular orientational averaging is considered.*
-
-*NOTE 3. For the nuclear scattering length density, only the real component
-is taken account.*
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Using PDB/OMF or SLD files
---------------------------
-
-The SANS Calculator tool can read some PDB, OMF or SLD files but ignores
-polarized/magnetic scattering when doing so, thus related parameters such as
-*Up_frac_in*, etc, will be ignored.
-
-The calculation for fixed orientation uses Equation 1 above resulting in a 2D
-output, whereas the scattering calculation averaged over all the orientations
-uses the Debye equation below providing a 1D output
-
-.. image:: gen_debye_eq.png
-
-where $v_j \beta_j \equiv b_j$ is the scattering
-length of the $j^\text{th}$ atom. The calculation output is passed to the *Data Explorer*
-for further use.
-
-.. image:: pdb_combo.jpg
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Steve King, 01May2015
Index: src/sas/sasgui/perspectives/calculator/media/sld_calculator_help.rst
===================================================================
--- src/sas/sasgui/perspectives/calculator/media/sld_calculator_help.rst	(revision 5ed76f8390eac56ff5d3779fd9c454d0c8fe1dc0)
+++ 	(revision )
@@ -1,58 +1,0 @@
-.. sld_calculator_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.
-
-SLD Calculator Tool
-===================
-
-Description
------------
-
-The neutron scattering length density (SLD, $\beta_N$) is defined as
-
-.. math::
-
-  \beta_N = (b_{c1} + b_{c2} + ... + b_{cn}) / V_m
-
-where $b_{ci}$ is the bound coherent scattering length of ith of n atoms in a molecule
-with the molecular volume $V_m$.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Specifying the Compound Name
-----------------------------
-
-To calculate scattering length densities enter the empirical formula of a
-compound and its mass density and click "Calculate".
-
-Entering a wavelength value is optional (a default value of 6.0 |Ang| will
-be used).
-
-TIPS!
-
-*  Formula strings consist of atoms and the number of them, such as "CaCO3+6H2O".
-
-*  Groups can be separated by *'+'* or *space*, so "CaCO3 6H2O" works as well.
-
-*  Groups can be defined using parentheses, such as "CaCO3(H2O)6".
-
-*  Parentheses can be nested, such as "(CaCO3(H2O)6)1".
-
-*  Isotopes are represented by their atomic number in *square brackets*, such
-   as "CaCO[18]3+6H2O", H[1], or H[2].
-
-*  Numbers of atoms can be integer or decimal, such as "CaCO3+(3HO0.5)2".
-
-*  The SLD of mixtures can be calculated as well. For example, for a 70-30
-   mixture of H2O/D2O write "H14O7+D6O3" or more simply "H7D3O5" (i.e. this says
-   7 hydrogens, 3 deuteriums, and 5 oxygens) and enter a mass density calculated
-   on the percentages of H2O and D2O.
-
-*  Type "C[13]6 H[2]12 O[18]6" for C(13)6H(2)12O(18)6 (6 Carbon-13 atoms, 12
-   deuterium atoms, and 6 Oxygen-18 atoms).
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Paul Kienzle, 05Apr2017
-
Index: src/sas/sasgui/perspectives/calculator/media/slit_calculator_help.rst
===================================================================
--- src/sas/sasgui/perspectives/calculator/media/slit_calculator_help.rst	(revision 5ed76f8390eac56ff5d3779fd9c454d0c8fe1dc0)
+++ 	(revision )
@@ -1,40 +1,0 @@
-.. slit_calculator_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.
-
-
-Slit Size Calculator Tool
-=========================
-
-Description
------------
-
-This tool enables X-ray users to calculate the slit size (FWHM/2) for smearing
-based on their half beam profile data.
-
-*NOTE! Whilst it may have some more generic applicability, the calculator has
-only been tested with beam profile data from Anton-Paar SAXSess:sup:`TM` software.*
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Using the tool
---------------
-
-1) Select *Slit Size Calculator* from the *Tool* menu on the SasView toolbar.
-
-2) Load a beam profile file in the *Data* field using the *Browse* button.
-
-   *NOTE! To see an example of the beam profile file format, visit the file
-   beam profile.DAT in your {installation_directory}/SasView/test folder.*
-
-3) Once a data is loaded, the slit size is automatically computed and displayed
-   in the tool window.
-
-*NOTE! The beam profile file does not carry any information about the units of
-the Q data. This calculator assumes the data has units of 1/\ |Ang|\ . If the
-data is not in these units it must be manually converted beforehand.*
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Steve King, 01May2015
Index: src/sas/sasgui/perspectives/corfunc/media/corfunc_help.rst
===================================================================
--- src/sas/sasgui/perspectives/corfunc/media/corfunc_help.rst	(revision ad476d193c0864f278ac1d0d3573c4836631790c)
+++ 	(revision )
@@ -1,298 +1,0 @@
-.. corfunc_help.rst
-
-.. _Correlation_Function_Analysis:
-
-Correlation Function Analysis
-=============================
-
-Description
------------
-
-This currently performs correlation function analysis on SAXS/SANS data, 
-but in the the future is also planned to generate model-independent volume 
-fraction profiles from the SANS from adsorbed polymer/surfactant layers. 
-The two types of analyses differ in the mathematical transform that is 
-applied to the data (Fourier vs Hilbert). However, both functions are 
-returned in *real space*.
-
-A correlation function may be interpreted in terms of an imaginary rod moving
-through the structure of the material. Î(x) is the probability that a rod of 
-length x has equal electron/neutron scattering length density at either end. 
-Hence a frequently occurring spacing within a structure will manifest itself 
-as a peak in Î(x). *SasView* will return both the one-dimensional ( Î\ :sub:`1`\ (x) ) 
-and three-dimensional ( Î\ :sub:`3`\ (x) ) correlation functions, the difference 
-being that the former is only averaged in the plane of the scattering vector.
-
-A volume fraction profile :math:`\Phi`\ (z) describes how the density of polymer 
-segments/surfactant molecules varies with distance, z, normal to an (assumed 
-locally flat) interface. The form of :math:`\Phi`\ (z) can provide information 
-about the arrangement of polymer/surfactant molecules at the interface. The width 
-of the profile provides measures of the layer thickness, and the area under 
-the profile is related to the amount of material that is adsorbed.
-
-Both analyses are performed in 3 stages:
-
-*  Extrapolation of the scattering curve to :math:`Q = 0` and toward 
-   :math:`Q = \infty`
-*  Smoothed merging of the two extrapolations into the original data
-*  Fourier / Hilbert Transform of the smoothed data to give the correlation
-   function or volume fraction profile, respectively
-*  (Optional) Interpretation of Î\ :sub:`1`\ (x) assuming the sample conforms 
-   to an ideal lamellar morphology
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-
-Extrapolation
--------------
-
-To :math:`Q = 0`
-................
-
-The data are extrapolated to q = 0 by fitting a Guinier function to the data
-points in the low-q range.
-
-The equation used is:
-
-.. math::
-    I(q) = A e^{Bq^2}
-
-Where the parameter :math:`B` is related to the effective radius-of-gyration of 
-a spherical object having the same small-angle scattering in this region.
-	
-Note that as q tends to zero this function tends to a limiting value and is 
-therefore less appropriate for use in systems where the form factor does not 
-do likewise. However, because of the transform, the correlation functions are 
-most affected by the Guinier back-extrapolation at *large* values of x where 
-the impact on any extrapolated parameters will be least significant.
-
-To :math:`Q = \infty`
-.....................
-
-The data are extrapolated towards q = :math:`\infty` by fitting a Porod model to
-the data points in the high-q range and then computing the extrapolation to 100 
-times the maximum q value in the experimental dataset. This should be more than 
-sufficient to ensure that on transformation any truncation artefacts introduced 
-are at such small values of x that they can be safely ignored.
-
-The equation used is:
-
-.. math::
-    I(q) = K q^{-4}e^{-q^2\sigma^2} + Bg
-
-Where :math:`Bg` is the background, :math:`K` is the Porod constant, and :math:`\sigma` (which 
-must be > 0) describes the width of the electron/neutron scattering length density 
-profile at the interface between the crystalline and amorphous regions as shown below.
-
-.. figure:: fig1.png
-   :align: center
-
-
-Smoothing
----------
-
-The extrapolated data set consists of the Guinier back-extrapolation from q ~ 0
-up to the lowest q value in the original data, then the original scattering data, 
-and then the Porod tail-fit beyond this. The joins between the original data and 
-the Guinier/Porod extrapolations are smoothed using the algorithm below to try 
-and avoid the formation of truncation ripples in the transformed data:
-
-Functions :math:`f(x_i)` and :math:`g(x_i)` where :math:`x_i \in \left\{
-{x_1, x_2, ..., x_n} \right\}`, are smoothed over the range :math:`[a, b]`
-to produce :math:`y(x_i)`, by the following equations:
-
-.. math::
-    y(x_i) = h_ig(x_i) + (1-h_i)f(x_i)
-
-where:
-
-.. math::
-    h_i = \frac{1}{1 + \frac{(x_i-b)^2}{(x_i-a)^2}}
-
-
-Transformation
---------------
-
-Fourier
-.......
-
-If "Fourier" is selected for the transform type, *SasView* will perform a
-discrete cosine transform on the extrapolated data in order to calculate the
-1D correlation function as:
-
-.. math::
-    \Gamma _{1}(x) = \frac{1}{Q^{*}} \int_{0}^{\infty }I(q) q^{2} cos(qx) dq
-
-where Q\ :sup:`*` is the Scattering (also called Porod) Invariant.
-
-The following algorithm is applied:
-
-.. math::
-    \Gamma(x_k) = 2 \sum_{n=0}^{N-1} x_n \cos{\left[ \frac{\pi}{N}
-    \left(n + \frac{1}{2} \right) k \right] } \text{ for } k = 0, 1, \ldots,
-    N-1, N
-
-The 3D correlation function is calculated as:
-
-.. math::
-    \Gamma _{3}(x) = \frac{1}{Q^{*}} \int_{0}^{\infty}I(q) q^{2}
-    \frac{sin(qx)}{qx} dq
-
-.. note:: It is always advisable to inspect Î\ :sub:`1`\ (x) and Î\ :sub:`3`\ (x) 
-    for artefacts arising from the extrapolation and transformation processes:
-	
-	- do they tend to zero as x tends to :math:`\infty`?
-	- do they smoothly curve onto the ordinate at x = 0? (if not check the value 
-	  of :math:`\sigma` is sensible)
-	- are there ripples at x values corresponding to (2 :math:`pi` over) the two 
-	  q values at which the extrapolated and experimental data are merged?
-	- are there any artefacts at x values corresponding to 2 :math:`pi` / q\ :sub:`max` in 
-	  the experimental data? 
-	- and lastly, do the significant features/peaks in the correlation functions 
-	  actually correspond to anticpated spacings in the sample?!!!
-
-Finally, the program calculates the interface distribution function (IDF) g\ :sub:`1`\ (x) as 
-the discrete cosine transform of:
-
-.. math::
-    -q^{4} I(q)
-
-The IDF is proportional to the second derivative of Î\ :sub:`1`\ (x).
-
-Hilbert
-.......
-	
-If "Hilbert" is selected for the transform type, the analysis will perform a
-Hilbert transform on the extrapolated data in order to calculate the Volume
-Fraction Profile.
-
-.. note:: The Hilbert transform functionality is not yet implemented in SasView.
-
-
-Interpretation
---------------
-
-Correlation Function
-....................
-
-Once the correlation functions have been calculated *SasView* can be asked to 
-try and interpret Î\ :sub:`1`\ (x) in terms of an ideal lamellar morphology 
-as shown below.
-
-.. figure:: fig2.png
-   :align: center
-
-The structural parameters extracted are:
-
-*   Long Period :math:`= L_p`
-*   Average Hard Block Thickness :math:`= L_c`
-*   Average Core Thickness :math:`= D_0`
-*   Average Interface Thickness :math:`\text{} = D_{tr}`
-*   Polydispersity :math:`= \Gamma_{\text{min}}/\Gamma_{\text{max}}`
-*   Local Crystallinity :math:`= L_c/L_p`
-
-Volume Fraction Profile
-.......................
-
-SasView does not provide any automatic interpretation of volume fraction profiles 
-in the same way that it does for correlation functions. However, a number of 
-structural parameters are obtainable by other means:
-
-*   Surface Coverage :math:`=\theta`
-*   Anchor Separation :math:`= D`
-*   Bound Fraction :math:`= <p>`
-*   Second Moment :math:`= \sigma`
-*   Maximum Extent :math:`= \delta_{\text{h}}`
-*   Adsorbed Amount :math:`= \Gamma`
-
-.. figure:: profile1.png
-   :align: center
-
-.. figure:: profile2.png
-   :align: center
-
-The reader is directed to the references for information on these parameters.
-
-References
-----------
-
-Correlation Function
-....................
-
-Strobl, G. R.; Schneider, M. *J. Polym. Sci.* (1980), 18, 1343-1359
-
-Koberstein, J.; Stein R. *J. Polym. Sci. Phys. Ed.* (1983), 21, 2181-2200
-
-BaltÃ¡ Calleja, F. J.; Vonk, C. G. *X-ray Scattering of Synthetic Poylmers*, Elsevier. Amsterdam (1989), 247-251
-
-BaltÃ¡ Calleja, F. J.; Vonk, C. G. *X-ray Scattering of Synthetic Poylmers*, Elsevier. Amsterdam (1989), 257-261
-
-BaltÃ¡ Calleja, F. J.; Vonk, C. G. *X-ray Scattering of Synthetic Poylmers*, Elsevier. Amsterdam (1989), 260-270
-
-GÃ¶schel, U.; Urban, G. *Polymer* (1995), 36, 3633-3639
-
-Stribeck, N. *X-Ray Scattering of Soft Matter*, Springer. Berlin (2007), 138-161
-
-:ref:`FDR` (PDF format)
-
-Volume Fraction Profile
-.......................
-
-Washington, C.; King, S. M. *J. Phys. Chem.*, (1996), 100, 7603-7609
-
-Cosgrove, T.; King, S. M.; Griffiths, P. C. *Colloid-Polymer Interactions: From Fundamentals to Practice*, Wiley. New York (1999), 193-204
-
-King, S. M.; Griffiths, P. C.; Cosgrove, T. *Applications of Neutron Scattering to Soft Condensed Matter*, Gordon & Breach. Amsterdam (2000), 77-105
-
-King, S.; Griffiths, P.; Hone, J.; Cosgrove, T. *Macromol. Symp.* (2002), 190, 33-42
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-
-Usage
------
-Upon sending data for correlation function analysis, it will be plotted (minus
-the background value), along with a *red* bar indicating the *upper end of the
-low-Q range* (used for Guinier back-extrapolation), and 2 *purple* bars indicating 
-the range to be used for Porod forward-extrapolation. These bars may be moved by 
-grabbing and dragging, or by entering appropriate values in the Q range input boxes.
-
-.. figure:: tutorial1.png
-   :align: center
-
-Once the Q ranges have been set, click the "Calculate Bg" button to determine the 
-background level. Alternatively, enter your own value into the box. If the box turns 
-yellow this indicates that background subtraction has created some negative intensities.
-
-Now click the "Extrapolate" button to extrapolate the data. The graph window will update 
-to show the extrapolated data, and the values of the parameters used for the Guinier and 
-Porod extrapolations will appear in the "Extrapolation Parameters" section of the SasView 
-GUI.
-
-.. figure:: tutorial2.png
-   :align: center
-
-Now select which type of transform you would like to perform, using the radio
-buttons:
-
-*   **Fourier**: to perform a Fourier Transform to calculate the correlation
-    functions
-*   **Hilbert**: to perform a Hilbert Transform to calculate the volume fraction
-    profile
-
-and click the "Transform" button to perform the selected transform and plot
-the results.
-
- .. figure:: tutorial3.png
-    :align: center
-
-If a Fourier Transform was performed, the "Compute Parameters" button can now be 
-clicked to interpret the correlation function as described earlier. The parameters 
-will appear in the "Output Parameters" section of the SasView GUI.
-
- .. figure:: tutorial4.png
-    :align: center
-
-
-.. note::
-    This help document was last changed by Steve King, 26Sep2017
Index: src/sas/sasgui/perspectives/corfunc/media/fdr-pdfs.rst
===================================================================
--- src/sas/sasgui/perspectives/corfunc/media/fdr-pdfs.rst	(revision 959eb0181ad06828a748f04512f953aad5b31659)
+++ 	(revision )
@@ -1,10 +1,0 @@
-.. fdr-pdfs.rst
-
-.. _FDR:
-
-Fibre Diffraction Review References
-===================================
-
-:download:`Fibre_Diffraction_Review_1994_3_25-29.pdf <Fibre_Diffraction_Review_1994_3_25-29.pdf>`
-:download:`Fibre_Diffraction_Review_2004_12_24.pdf <Fibre_Diffraction_Review_2004_12_24.pdf>`
-:download:`Fibre_Diffraction_Review_2005_13_19-22.pdf <Fibre_Diffraction_Review_2005_13_19-22.pdf>`
Index: src/sas/sasgui/perspectives/fitting/media/fitting.rst
===================================================================
--- src/sas/sasgui/perspectives/fitting/media/fitting.rst	(revision 3bd677bda9477bbd07235d9fba448f09ae1b3932)
+++ 	(revision )
@@ -1,33 +1,0 @@
-.. _Fitting_Documentation:
-
-Fitting Documentation
-=====================
-
-.. note:: In Windows use [Alt]-[Cursor left] to return to the previous page
-
-.. toctree::
-   :maxdepth: 1
-
-   Fitting Data <fitting_help>
-
-   Assessing Fit Quality <residuals_help>
-
-   Polydispersity Distributions <pd/polydispersity>
-
-   Smearing Functions <resolution>
-
-   Polarisation/Magnetic Scattering <magnetism/magnetism>
-
-   Information on the SasView Optimisers <optimizer>
-
-   Converting SANS to SESANS for Fitting <sesans/sans_to_sesans>
-
-   Fitting SESANS Data <sesans/sesans_fitting>
-
-   Writing a Plugin Model <plugin>
-
-   Computations with a GPU <gpu_setup>
-
-   Scripting interface to sasmodels <scripting>
-
-   References <refs>
Index: src/sas/sasgui/perspectives/fitting/media/fitting_help.rst
===================================================================
--- src/sas/sasgui/perspectives/fitting/media/fitting_help.rst	(revision 5005ae0a7e3ed07742271fca99651ba5c55aa8b0)
+++ 	(revision )
@@ -1,769 +1,0 @@
-.. fitting_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.
-
-Fitting
-=======
-
-.. note:: If some code blocks are not readable, expand the documentation window
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Preparing to fit data
----------------------
-
-To fit some data you must first load some data, activate one or more data sets,
-send those data sets to fitting, and select a model to fit to each data set.
-
-Instructions on how to load and activate data are in the section :ref:`Loading_data`.
-
-SasView can fit data in one of three ways:
-
-*  in *Single* fit mode - individual data sets are fitted independently one-by-one
-
-*  in *Simultaneous* fit mode - multiple data sets are fitted simultaneously to
-   the *same* model with/without constrained parameters (this might be useful,
-   for example, if you have measured the same sample at different contrasts)
-
-*  in *Batch* fit mode - multiple data sets are fitted sequentially to the
-   *same* model (this might be useful, for example, if you have performed
-   a kinetic or time-resolved experiment and have *lots* of data sets!)
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Selecting a model
------------------
-
-The models in SasView are grouped into categories. By default these consist of:
-
-*  *Cylinder* - cylindrical shapes (disc, right cylinder, cylinder with endcaps
-   etc)
-*  *Ellipsoid* - ellipsoidal shapes (oblate,prolate, core shell, etc)
-*  *Parellelepiped* - as the name implies
-*  *Sphere* - sheroidal shapes (sphere, core multishell, vesicle, etc)
-*  *Lamellae* - lamellar shapes (lamellar, core shell lamellar, stacked
-   lamellar, etc)
-*  *Shape-Independent* - models describing structure in terms of density
-   correlation functions, fractals, peaks, power laws, etc
-*  *Paracrystal* - semi ordered structures (bcc, fcc, etc)
-*  *Structure Factor* - S(Q) models
-*  *Plugin Models* - User-created (custom/non-library) Python models
-
-Use the *Category* drop-down menu to chose a category of model, then select
-a model from the drop-down menu beneath. A graph of the chosen model, calculated
-using default parameter values, will appear. The graph will update dynamically
-as the parameter values are changed.
-
-You can decide your own model categorizations using the :ref:`Category_Manager`.
-
-Once you have selected a model you can read its help documentation by clicking
-on the *Description* button to the right.
-
-Show 1D/2D
-^^^^^^^^^^
-
-Models are normally fitted to 1D (ie, I(Q) vs Q) data sets, but some models in
-SasView can also be fitted to 2D (ie, I(Qx,Qy) vs Qx vs Qy) data sets.
-
-*NB: Magnetic scattering can only be fitted in SasView in 2D.*
-
-To activate 2D fitting mode, click the *Show 2D* button on the *Fit Page*. To
-return to 1D fitting model, click the same button (which will now say *Show 1D*).
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. _Category_Manager:
-
-Category Manager
-----------------
-
-To change the model categorizations, either choose *Category Manager* from the
-*View* option on the menubar, or click on the *Modify* button on the *Fit Page*.
-
-.. image:: cat_fig0.png
-
-The categorization of all models except the user supplied Plugin Models can be
-reassigned, added to, and removed using *Category Manager*. Models can also be
-hidden from view in the drop-down menus.
-
-.. image:: cat_fig1.png
-
-Changing category
-^^^^^^^^^^^^^^^^^
-
-To change category, highlight a model in the list by left-clicking on its entry
-and then click the *Modify* button. Use the *Change Category* panel that appears
-to make the required changes.
-
-.. image:: cat_fig2.png
-
-To create a category for the selected model, click the *Add* button. In order
-to delete a category, select the category name and click the *Remove Selected*
-button. Then click *Done*.
-
-Showing/hiding models
-^^^^^^^^^^^^^^^^^^^^^
-
-Use the *Enable All / Disable All* buttons and the check boxes beside each model
-to select the models to show/hide. To apply the selection, click *Ok*. Otherwise
-click *Cancel*.
-
-*NB: It may be necessary to change to a different category and then back again*
-*before any changes take effect.*
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Model Functions
----------------
-
-For a complete list of all the library models available in SasView, see
-the `Model Documentation <../../../index.html>`_ .
-
-It is also possible to add your own models.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. _Adding_your_own_models:
-
-Adding your own Models
-----------------------
-
-There are essentially three ways to generate new fitting models for SasView:
-
-*  Using the SasView :ref:`New_Plugin_Model` helper dialog (best for beginners
-   and/or relatively simple models)
-*  By copying/editing an existing model (this can include models generated by
-   the New Plugin Model* dialog) in the :ref:`Python_shell` or
-   :ref:`Advanced_Plugin_Editor` (suitable for all use cases)
-*  By writing a model from scratch outside of SasView (only recommended for code
-   monkeys!)
-
-Please read the guidance on :ref:`Writing_a_Plugin` before proceeding.
-
-**To be found by SasView your model must reside in the *~\\.sasview\\plugin_models* folder.**
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. _Plugin_Model_Operations:
-
-Plugin Model Operations
------------------------
-
-From the *Fitting* option in the menu bar, select *Plugin Model Operations*
-
-.. image:: edit_model_menu.png
-
-and then one of the sub-options
-
-*  *New Plugin Model* - to create a plugin model template with a helper dialog
-*  *Sum|Multi(p1,p2)* - to create a plugin model by summing/multiplying *existing models* in the model library
-*  *Advanced Plugin Editor* - to create/edit a plugin model in a Python shell
-*  *Delete Plugin Models* - to delete a plugin model
-*  *Load Plugin Models* - to (re-)load plugin models
-
-.. _New_Plugin_Model:
-
-New Plugin Model
-^^^^^^^^^^^^^^^^
-
-Relatively straightforward models can be programmed directly from the SasView
-GUI using the *New Plugin Model Function*.
-
-.. image:: new_model.png
-
-When using this feature, be aware that even if your code has errors, including
-syntax errors, a model file is still generated. When you then correct the errors
-and click 'Apply' again to re-compile you will get an error informing you that
-the model already exists if the 'Overwrite' box is not checked. In this case you
-will need to supply a new model function name. By default the 'Overwrite' box is
-*checked*\ .
-
-Also note that the 'Fit Parameters' have been split into two sections: those
-which can be polydisperse (shape and orientation parameters) and those which are
-not (eg, scattering length densities).
-
-A model file generated by this option can be viewed and further modified using
-the :ref:`Advanced_Plugin_Editor` .
-
-**SasView version 4.2** made it possible to specify whether a plugin created with
-the *New Plugin Model* dialog is actually a form factor P(Q) or a structure factor
-S(Q). To do this, simply add one or other of the following lines under the *import*
-statements.
-
-For a form factor::
-
-     form_factor = True
-
-or for a structure factor::
-
-     structure_factor = True
-
-If the plugin is a structure factor it is *also* necessary to add two variables to
-the parameter list::
-
-     parameters = [
-                     ['radius_effective', '', 1, [0.0, numpy.inf], 'volume', ''],
-                     ['volfraction', '', 1, [0.0, 1.0], '', ''],
-                     [...],
-
-and to the declarations of the functions Iq and Iqxy:::
-
-     def Iq(x , radius_effective, volfraction, ...):
-
-     def Iqxy(x, y, radius_effective, volfraction, ...):
-
-Such a plugin should then be available in the S(Q) drop-down box on a FitPage (once
-a P(Q) model has been selected).
-
-Sum|Multi(p1,p2)
-^^^^^^^^^^^^^^^^
-
-.. image:: sum_model.png
-
-This option creates a custom Plugin Model of the form::
-
-     Plugin Model = scale_factor * {(scale_1 * model_1) +/- (scale_2 * model_2)} + background
-
-or::
-
-     Plugin Model = scale_factor * (model1 * model2) + background
-
-In the *Easy Sum/Multi Editor* give the new model a function name and brief
-description (to appear under the *Details* button on the *FitPage*). Then select
-two existing models, as p1 and p2, and the required operator, '+' or '*' between
-them. Finally, click the *Apply* button to generate and test the model and then click *Close*.
-
-Any changes to a plugin model generated in this way only become effective *after* it is re-selected
-from the plugin models drop-down menu on the FitPage. If the model is not listed you can force a
-recompilation of the plugins by selecting *Fitting* > *Plugin Model Operations* > *Load Plugin Models*.
-
-**SasView version 4.2** introduced a much simplified and more extensible structure for plugin models
-generated through the Easy Sum/Multi Editor. For example, the code for a combination of a sphere model
-with a power law model now looks like this::
-
-     from sasmodels.core import load_model_info
-     from sasmodels.sasview_model import make_model_from_info
-
-     model_info = load_model_info('sphere+power_law')
-     model_info.name = 'MyPluginModel'
-     model_info.description = 'sphere + power_law'
-     Model = make_model_from_info(model_info)
-
-To change the models or operators contributing to this plugin it is only necessary to edit the string
-in the brackets after *load_model_info*, though it would also be a good idea to update the model name
-and description too!!!
-
-The model specification string can handle multiple models and combinations of operators (+ or *) which
-are processed according to normal conventions. Thus 'model1+model2*model3' would be valid and would
-multiply model2 by model3 before adding model1. In this example, parameters in the *FitPage* would be
-prefixed A (for model2), B (for model3) and C (for model1). Whilst this might appear a little
-confusing, unless you were creating a plugin model from multiple instances of the same model the parameter
-assignments ought to be obvious when you load the plugin.
-
-If you need to include another plugin model in the model specification string, just prefix the name of
-that model with *custom*. For instance::
-
-     sphere+custom.MyPluginModel
-
-To create a P(Q)*\S(Q) model use the @ symbol instead of * like this::
-
-     sphere@hardsphere
-
-This streamlined approach to building complex plugin models from existing library models, or models
-available on the *Model Marketplace*, also permits the creation of P(Q)*\S(Q) plugin models, something
-that was not possible in earlier versions of SasView.
-
-.. _Advanced_Plugin_Editor:
-
-Advanced Plugin Editor
-^^^^^^^^^^^^^^^^^^^^^^
-
-Selecting this option shows all the plugin models in the plugin model folder, on Windows this is
-
-  *C:\\Users\\{username}\\.sasview\\plugin_models*
-
-You can edit, modify, and save the Python code in any of these models using the
-*Advanced Plugin Model Editor*. Note that this is actually the same tool as the :ref:`Python_shell` .
-
-For details of the SasView plugin model format see :ref:`Writing_a_Plugin` .
-
-.. note:: Model files generated with the Sum/Multi option are still using the SasView 3.x model format. Unless you are confident about what you are doing, it is recommended that you only modify lines denoted with the ## <----- comments!
-
-When editing is complete, select *Run* > *Check Model* from the *Advanced Plugin Model Editor* menu bar. An *Info* box will appear with the results of the compilation and model unit tests. The model will only be usable if the tests 'pass'.
-
-.. image:: ../calculator/new_pycrust_example_2.png
-
-To use the model, go to the relevant *Fit Page*, select the *Plugin Models*
-category and then select the model from the drop-down menu.
-
-Any changes to a plugin model generated in this way only become effective *after* it is re-selected from the model drop-down menu on the FitPage.
-
-Delete Plugin Models
-^^^^^^^^^^^^^^^^^^^^
-
-Simply highlight the plugin model to be removed. The operation is final!!!
-
-*NB: Models shipped with SasView cannot be removed in this way.*
-
-Load Plugin Models
-^^^^^^^^^^^^^^^^^^
-
-This option loads (or re-loads) all models present in the
-*~\\.sasview\\plugin_models* folder.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. _Fitting_Options:
-
-Fitting Options
----------------
-
-It is possible to specify which optimiser SasView should use to fit the data, and
-to modify some of the configurational parameters for each optimiser.
-
-From *Fitting* in the menu bar select *Fit Options*, then select one of the following
-optimisers:
-
-*  DREAM
-*  Levenberg-Marquardt
-*  Quasi-Newton BFGS
-*  Differential Evolution
-*  Nelder-Mead Simplex
-
-The DREAM optimiser is the most sophisticated, but may not necessarily be the best
-option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser
-initially.
-
-These optimisers form the *Bumps* package written by P Kienzle. For more information
-on each optimiser, see the :ref:`Fitting_Documentation`.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Fitting Limits
---------------
-
-By default, *SasView* will attempt to model fit the full range of the data; ie,
-across all *Q* values. If necessary, however, it is possible to specify only a
-sub-region of the data for fitting.
-
-In a *FitPage* or *BatchPage* change the *Q* values in the *Min* and/or *Max*
-text boxes. Vertical coloured bars will appear on the graph with the data and
-'theory' indicating the current *Q* limits (red = *Qmin*, purple = *Qmax*).
-
-To return to including all data in the fit, click the *Reset* button.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-
-Shortcuts
----------
-
-Copy/Paste Parameters
-^^^^^^^^^^^^^^^^^^^^^
-
-It is possible to copy the parameters from one *Fit Page* and to paste them into
-another *Fit Page* using the same model.
-
-To *copy* parameters, either:
-
-*  Select *Edit -> Copy Params* from the menu bar, or
-*  Use Ctrl(Cmd on Mac) + Left Mouse Click on the *Fit Page*.
-
-To *paste* parameters, either:
-
-*  Select *Edit -> Paste Params* from the menu bar, or
-*  Use Ctrl(Cmd on Mac) + Shift + Left-click on the *Fit Page*.
-
-If either operation is successful a message will appear in the info line at the
-bottom of the SasView window.
-
-Bookmark
-^^^^^^^^
-
-To *Bookmark* a *Fit Page* either:
-
-*  Select a *Fit Page* and then click on *Bookmark* in the tool bar, or
-*  Right-click and select the *Bookmark* in the popup menu.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. _Status_bar:
-
-Status Bar & Console
---------------------
-
-The status bar is located at the bottom of the SasView window and displays
-messages, hints, warnings and errors.
-
-At the right-hand side of the status bar is a button marked *Console*. The *Console*
-displays available message history and some run-time traceback information.
-
-During a long task the *Console* can also be used to monitor the progress.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. _Single_Fit_Mode:
-
-Single Fit Mode
----------------
-
-*NB: Before proceeding, ensure that the Single Mode radio button at the bottom of*
-*the Data Explorer is checked (see the section* :ref:`Loading_data` *).*
-
-This mode fits one data set.
-
-When data is sent to the fitting it is plotted in a graph window as markers.
-
-If a graph does not appear, or a graph window appears but is empty, then the data
-has not loaded correctly. Check to see if there is a message in the :ref:`Status_Bar`
-or in the *Console* window.
-
-Assuming the data has loaded correctly, when a model is selected a green model
-calculation (or what SasView calls a 'Theory') line will appear in the earlier graph
-window, and a second graph window will appear displaying the residuals (the
-difference between the experimental data and the theory) at the same X-data values.
-See :ref:`Assessing_Fit_Quality`.
-
-The objective of model-fitting is to find a *physically-plausible* model, and set
-of model parameters, that generate a theory that reproduces the experimental data
-and gives residual values as close to zero as possible.
-
-Change the default values of the model parameters by hand until the theory line
-starts to represent the experimental data. Then uncheck the tick boxes alongside
-all parameters *except* the 'background' and the 'scale'. Click the *Fit* button.
-SasView will optimise the values of the 'background' and 'scale' and also display
-the corresponding uncertainties on the optimised values.
-
-*NB: If no uncertainty is shown it generally means that the model is not very*
-*dependent on the corresponding parameter (or that one or more parameters are*
-*'correlated').*
-
-In the bottom left corner of the *Fit Page* is a box displaying the normalised value
-of the statistical $\chi^2$ parameter returned by the optimiser.
-
-Now check the box for another model parameter and click *Fit* again. Repeat this
-process until most or all parameters are checked and have been optimised. As the
-fit of the theory to the experimental data improves the value of 'chi2/Npts' will
-decrease. A good model fit should easily produce values of 'chi2/Npts' that are
-close to one, and certainly <100. See :ref:`Assessing_Fit_Quality`.
-
-SasView has a number of different optimisers (see the section :ref:`Fitting_Options`).
-The DREAM optimiser is the most sophisticated, but may not necessarily be the best
-option for fitting simple models. If uncertain, try the Levenberg-Marquardt optimiser
-initially.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Simultaneous Fit Mode
----------------------
-
-*NB: Before proceeding, ensure that the Single Mode radio button at the bottom of*
-*the Data Explorer is checked (see the section* :ref:`Loading_data` *).*
-
-This mode is an extension of the :ref:`Single_Fit_Mode` that fits two or more data
-sets *to the same model* simultaneously. If necessary it is possible to constrain
-fit parameters between data sets (eg, to fix a background level, or radius, etc).
-
-If the data to be fit are in multiple files, load each file, then select each file
-in the *Data Explorer*, and *Send To Fitting*. If multiple data sets are in one file,
-load that file, *Unselect All Data*, select just those data sets to be fitted, and
-*Send To Fitting*. Either way, the result should be that for *n* data sets you have
-2\ *n* graphs (*n* of the data and model fit, and *n* of the resulting residuals). But
-it may be helpful to minimise the residuals plots for clarity. Also see
-:ref:`Assessing_Fit_Quality`.
-
-*NB: If you need to use a custom Plugin Model, you must ensure that model is
-available first (see* :ref:`Adding_your_own_models` *).*
-
-Method
-^^^^^^
-
-Now go to each *FitPage* in turn and:
-
-  Select the required category and model;
-
-  Unselect all the model parameters;
-
-  Enter some starting guesses for the parameters;
-
-  Enter any parameter limits (recommended);
-
-  Select which parameters will refine (selecting all is generally a bad idea...);
-
-When done, select *Constrained or Simultaneous Fit* under *Fitting* in the menu bar.
-
-In the *Const & Simul Fit* page that appears, select which data sets are to be
-simultaneously fitted (this will probably be all of them or you would not have loaded
-them in the first place!).
-
-To tie parameters between the data sets with constraints, check the 'yes' radio button
-next to *Add Constraint?* in the *Fit Constraints* box.
-
-*NB: You can only constrain parameters that are set to refine.*
-
-When ready, click the *Fit* button on the *Const & Simul Fit* page, NOT the *Fit*
-button on the individual *FitPage*'s.
-
-Simultaneous Fits without Constraints
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The results of the model-fitting will be returned to each of the individual
-*FitPage*'s.
-
-Note that the chi2/Npts value returned is the SUM of the chi2/Npts of each fit. To
-see the chi2/Npts value for a specific *FitPage*, click the *Compute* button at the
-bottom of that *FitPage* to recalculate. Also see :ref:`Assessing_Fit_Quality`.
-
-Simultaneous Fits with Constraints
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Use the *Easy Setup* drop-down buttons in the *Const & Simul Fit* page to set
-up constraints between *FitPage*'s.
-
-Constraints will generally be of the form
-
-  Mi Parameter1 = Mj.Parameter1
-
-however the text box after the '=' sign can be used to adjust this
-relationship; for example
-
-  Mi Parameter1 = scalar \* Mj.Parameter1
-
-A 'free-form' constraint box is also provided.
-
-Many constraints can be entered for a single fit.
-
-The results of the model-fitting will be returned to each of the individual
-*FitPage*'s.
-
-Note that the chi2/Npts value returned is the SUM of the chi2/Npts of each fit. To
-see the chi2/Npts value for a specific *FitPage*, click the *Compute* button at the
-bottom of that *FitPage* to recalculate. Also see :ref:`Assessing_Fit_Quality`.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. _Batch_Fit_Mode:
-
-Batch Fit Mode
---------------
-
-*NB: Before proceeding, ensure that the Single Mode radio button at the bottom of*
-*the Data Explorer is checked (see the section* :ref:`Loading_data` *). The Batch*
-*Mode button will be used later on!*
-
-This mode *sequentially* fits two or more data sets *to the same model*. Unlike in
-simultaneous fitting, in batch fitting it is not possible to constrain fit parameters
-between data sets.
-
-If the data to be fit are in multiple files, load each file in the *Data Explorer*.
-If multiple data sets are in one file, load just that file. *Unselect All Data*, then
-select a single initial data set to be fitted. Fit that selected data set as described
-above under :ref:`Single_Fit_Mode`.
-
-*NB: If you need to use a custom Plugin Model, you must ensure that model is
-available first (see* :ref:`Adding_your_own_models` *).*
-
-Method
-^^^^^^
-
-Now *Select All Data* in the *Data Explorer*, check the *Batch Mode* radio button
-at the bottom of that panel and *Send To Fitting*. A *BatchPage* will be created.
-
-.. image:: batch_button_area.png
-
-*NB: The Batch Page can also be created by checking the Batch Mode radio button*
-*and selecting New Fit Page under Fitting in the menu bar.*
-
-Using the drop-down menus in the *BatchPage*, now set up the *same* data set
-with the *same* model that you just fitted in single fit mode. A quick way to
-set the model parameter values is to just copy them from the earlier Single
-Fit. To do this, go back to the Single Fit *FitPage*, select *Copy Params*
-under *Edit* in the menu bar, then go back to the *BatchPage* and *Paste Params*.
-
-When ready, use the *Fit* button on the *BatchPage* to perform the fitting, NOT
-the *Fit* button on the individual *FitPage*'s.
-
-Unlike in single fit mode, the results of batch fits are not returned to
-the *BatchPage*. Instead, a spreadsheet-like :ref:`Grid_Window` will appear.
-
-If you want to visually check a graph of a particular fit, click on the name of
-a *Data set* in the *Grid Window* and then click the *View Fits* button. The
-data and the model fit will be displayed. If you select mutliple data sets they
-will all appear on one graph.
-
-.. image:: view_button.png
-
-*NB: In theory, returning to the BatchPage and changing the name of the I(Q)*
-*data source should also work, but at the moment whilst this does change the*
-*data set displayed it always superimposes the 'theory' corresponding to the*
-*starting parameters.*
-
-If you select a 'Chi2' value and click the *View Fits* button a graph of the
-residuals for that data set is displayed. Again, if you select multiple 'Chi2'
-values then all the residuals data will appear on one graph. Also see
-:ref:`Assessing_Fit_Quality`.
-
-Chain Fitting
-^^^^^^^^^^^^^
-
-By default, the *same* parameter values copied from the initial single fit into
-the *BatchPage* will be used as the starting parameters for all batch fits. It
-is, however, possible to get *SasView* to use the results of a fit to a preceding
-data set as the starting parameters for the next fit in the sequence. This
-variation of batch fitting is called *Chain Fitting*, and will considerably speed
-up model-fitting if you have lots of very similar data sets where a few parameters
-are gradually changing. Do not use chain fitting on disparate data sets.
-
-To use chain fitting, select *Chain Fitting* under *Fitting* in the menu bar. It
-toggles on/off, so selecting it again will switch back to normal batch fitting.
-
-.. _Grid_Window:
-
-Grid Window
-^^^^^^^^^^^
-
-The *Grid Window* provides an easy way to view the results from batch fitting.
-It will be displayed automatically when a batch fit completes, but may be
-opened at any time by selecting *Show Grid Window* under *View* in the menu
-bar.
-
-.. image:: restore_batch_window.png
-
-Once a batch fit is completed, all model parameters are displayed but *not*
-their uncertainties. To view the uncertainties, click on a given column then
-go to *Edit* in the menu bar, select *Insert Column Before* and choose the
-required data from the list. An empty column can be inserted in the same way.
-
-To remove a column from the grid, click on the column header and choose
-*Remove Column* under *Edit* in the menu bar. The same functionality also
-allows you to re-order columns.
-
-*NB: You cannot insert/remove/re-order the rows in the Grid Window.*
-
-All of the above functions are also available by right-clicking on a column
-label.
-
-.. image:: edit_menu.png
-
-*NB: If there is an existing Grid Window and another batch fit is performed,*
-*an additional 'Table' tab will be added to the Grid Window.*
-
-The parameter values in the *currently selected* table of the *Grid Window*
-can be output to a CSV file by choosing *Save As* under *File* in the (*Grid*
-*Window*) menu bar. The default filename includes the date and time that the
-batch fit was performed.
-
-Saved CSV files can be reloaded by choosing *Open* under *File* in the *Grid*
-*Window* menu bar. The loaded parameters will appear in a new table tab.
-
-.. image:: file_menu.png
-
-*NB: Saving the Grid Window does not save any experimental data, residuals*
-*or actual model fits. Consequently if you reload a saved CSV file the*
-*ability to View Fits will be lost.*
-
-Parameter Plots
-^^^^^^^^^^^^^^^
-
-Any column of *numeric* parameter values can be plotted against another using
-the *Grid Window*. Simply select one column at the time and click the *Add*
-button next to the required *X/Y-axis Selection Range* text box. When both
-the X and Y axis boxes have been completed, click the *Plot* button.
-
-When the *Add* button is clicked, *SasView* also automatically completes the
-*X/Y-axis Label* text box with the heading from Row 1 of the selected table,
-but different labels and units can be entered manually.
-
-.. image:: plot_button.png
-
-The *X/Y-axis Selection Range* can be edited manually. The text control box
-recognises the operators +, -, \*, /, or 'pow', and allows the following
-types of expression :
-
-  1) if an axis label range is a function of 1 or more *columns*, write
-     this type of expression
-
-     constant1 * column_name1 [minimum row index :  maximum  row index]
-     operator constant2 * column_name2 [minimum row index :  maximum  row index]
-
-     Example: radius [2 : 5] -3 * scale [2 : 5]
-
-  2) if only some *values* of a given column are needed but the range between
-     the first row and the last row used is not continuous, write this type of
-     expression
-
-     column_name1 [minimum row index1 :  maximum  row index1] , column_name1
-     [minimum row index2 :  maximum  row index2]
-
-     Example: radius [2 : 5] , radius [10 : 25]
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Combined Batch Fit Mode
------------------------
-
-The purpose of the Combined Batch Fit is to allow running two or more batch
-fits in sequence without overwriting the output table of results.  This may be
-of interest for example if one is fitting a series of data sets where there is
-a shape change occurring in the series that requires changing the model part
-way through the series; for example a sphere to rod transition.  Indeed the
-regular batch mode does not allow for multiple models and requires all the
-files in the series to be fit with single model and set of parameters.  While
-it is of course possible to just run part of the series as a batch fit using
-model one followed by running another batch fit on the rest of the series with
-model two (and/or model three etc), doing so will overwrite the table of
-outputs from the previous batch fit(s).  This may not be desirable if one is
-interested in comparing the parameters: for example the sphere radius of set
-one and the cylinder radius of set two.
-
-Method
-^^^^^^
-
-In order to use the *Combined Batch Fit*, first load all the data needed as
-described in :ref:`Loading_data`. Next start up two or more *BatchPage* fits
-following the instructions in :ref:`Batch_Fit_Mode` but **DO NOT PRESS FIT**.
-At this point the *Combine Batch Fit* menu item under the *Fitting menu* should
-be active (if there is one or no *BatchPage* the menu item will be greyed out
-and inactive).  Clicking on *Combine Batch Fit* will bring up a new panel,
-similar to the *Const & Simult Fit* panel. In this case there will be a
-checkbox for each *BatchPage* instead of each *FitPage* that should be included
-in the fit.  Once all are selected, click the Fit button on
-the *BatchPage* to run each batch fit in *sequence*
-
-.. image:: combine_batch_page.png
-
-The batch table will then pop up at the end as for the case of the simple Batch
-Fitting with the following caveats:
-
-.. note::
-   The order matters.  The parameters in the table will be taken from the model
-   used in the first *BatchPage* of the list.  Any parameters from the
-   second and later *BatchPage* s that have the same name as a parameter in the
-   first will show up allowing for plotting of that parameter across the
-   models. The other parameters will not be available in the grid.
-.. note::
-   a corralary of the above is that currently models created as a sum|multiply
-   model will not work as desired because the generated model parameters have a
-   p#_ appended to the beginning and thus radius and p1_radius will not be
-   recognized as the same parameter.
-
-.. image:: combine_batch_grid.png
-
-In the example shown above the data is a time series with a shifting peak.
-The first part of the series was fitted using the *broad_peak* model, while
-the rest of the data were fit using the *gaussian_peak* model. Unfortunately the
-time is not listed in the file but the file name contains the information. As
-described in :ref:`Grid_Window`, a column can be added manually, in this case
-called time, and the peak position plotted against time.
-
-.. image:: combine_batch_plot.png
-
-Note the discontinuity in the peak position.  This reflects the fact that the
-Gaussian fit is a rather poor model for the data and is not actually
-finding the peak.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Paul Butler, 10 September
-   2017
Index: src/sas/sasgui/perspectives/fitting/media/residuals_help.rst
===================================================================
--- src/sas/sasgui/perspectives/fitting/media/residuals_help.rst	(revision 99ded31b1523f79bd1cb6e2ce2af4d4f1200022d)
+++ 	(revision )
@@ -1,91 +1,0 @@
-.. residuals_help.rst
-
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. _Assessing_Fit_Quality:
-
-Assessing Fit Quality
----------------------
-
-When performing model-fits to some experimental data it is helpful to be able to
-gauge how good an individual fit is, how it compares to a fit of the *same model*
-*to another set of data*, or how it compares to a fit of a *different model to the*
-*same data*.
-
-One way is obviously to just inspect the graph of the experimental data and to
-see how closely (or not!) the 'theory' calculation matches it. But *SasView*
-also provides two other measures of the quality of a fit:
-
-*  $\chi^2$ (or 'Chi2'; pronounced 'chi-squared')
-*  *Residuals*
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Chi2
-^^^^
-
-$\chi^2$ is a statistical parameter that quantifies the differences between
-an observed data set and an expected dataset (or 'theory').
-
-When showing the a model with the data, *SasView* displays this parameter
-normalized to the number of data points, $N_\mathrm{pts}$ such that
-
-.. math::
-
-  \chi^2_N
-  =  \sum[(Y_i - \mathrm{theory}_i)^2 / \mathrm{error}_i^2] / N_\mathrm{pts}
-
-When performing a fit, *SasView* instead displays the reduced $\chi^2_R$,
-which takes into account the number of fitting parameters $N_\mathrm{par}$
-(to calculate the number of 'degrees of freedom'). This is computed as
-
-.. math::
-
-  \chi^2_R
-  =  \sum[(Y_i - \mathrm{theory}_i)^2 / \mathrm{error}_i^2]
-  / [N_\mathrm{pts} - N_\mathrm{par}]
-
-The normalized $\chi^2_N$ and the reduced $\chi^2_R$ are very close to each
-other when $N_\mathrm{pts} \gg N_\mathrm{par}$.
-
-For a good fit, $\chi^2_R$ tends to 1.
-
-$\chi^2_R$ is sometimes referred to as the 'goodness-of-fit' parameter.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Residuals
-^^^^^^^^^
-
-A residual is the difference between an observed value and an estimate of that
-value, such as a 'theory' calculation (whereas the difference between an
-observed value and its *true* value is its error).
-
-*SasView* calculates 'normalized residuals', $R_i$, for each data point in the
-fit:
-
-.. math::
-
-  R_i = (Y_i - \mathrm{theory}_i) / \mathrm{error}_i
-
-Think of each normalized residual as the number of standard deviations
-between the measured value and the theory.  For a good fit, 68% of $R_i$
-will be within one standard deviation, which will show up in the Residuals
-plot as $R_i$ values between $-1$ and $+1$.  Almost all the values should
-be between $-3$ and $+3$.
-
-Residuals values larger than $\pm 3$ indicate that the model
-is not fit correctly, the wrong model was chosen (e.g., because there is
-more than one phase in your system), or there are problems in
-the data reduction.  Since the goodness of fit is calculated from the
-sum-squared residuals, these extreme values will drive the choice of fit
-parameters.  Any uncertainties calculated for the fitting parameters will
-be meaningless.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-*Document History*
-
-| 2015-06-08 Steve King
-| 2017-09-28 Paul Kienzle
Index: src/sas/sasgui/perspectives/invariant/media/invariant_help.rst
===================================================================
--- src/sas/sasgui/perspectives/invariant/media/invariant_help.rst	(revision 094b9ebf28997d46b643648b6775fc6c6b14cb0d)
+++ 	(revision )
@@ -1,135 +1,0 @@
-.. invariant_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.
-
-Invariant Calculation
-=====================
-
-Description
------------
-
-The scattering, or Porod, invariant ($Q^*$) is a model-independent quantity that
-can be easily calculated from scattering data.
-
-For two phase systems, the scattering invariant is defined as the integral of
-the square of the wavevector transfer ($Q$) multiplied by the scattering cross section
-over the full range of $Q$ from zero to infinity, that is
-
-.. math::
-
-    Q^* = \int_0^\infty q^2I(q)\,dq
-
-in the case of pinhole geometry. For slit geometry the invariant is given by
-
-.. math::
-
-    Q^* = \Delta q_v \int_0^\infty qI(q)\,dq
-
-where $\Delta q_v$ is the slit height.
-
-The worth of $Q^*$  is that it can be used to determine the volume fraction and
-the specific area of a sample. Whilst these quantities are useful in their own
-right they can also be used in further analysis.
-
-The difficulty with using $Q^*$  arises from the fact that experimental data is
-never measured over the range $0 \le Q \le \infty$. At best, combining USAS and
-WAS data might cover the range $10^{-5} \le Q \le 10$ 1/\ |Ang| . Thus it is usually
-necessary to extrapolate the experimental data to low and high $Q$. For this
-
-High-\ $Q$ region (>= *Qmax* in data)
-
-*  The power law function $C/Q^4$ is used where the constant
-   $C = 2 \pi \Delta\rho S_v$ is to be found by fitting part of data
-   within the range $Q_{N-m}$ to $Q_N$ (where $m < N$).
-
-Low-\ $Q$ region (<= *Qmin* in data)
-
-*  The Guinier function $I_0 exp(-R_g^2 Q^2/3)$ where $I_0$
-   and $R_g$ are obtained by fitting as for the high-\ $Q$ region above.
-   Alternatively a power law can be used.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Using invariant analysis
-------------------------
-
-1) Select *Invariant* from the *Analysis* menu on the SasView toolbar.
-
-2) Load some data with the *Data Explorer*.
-
-3) Select a dataset and use the *Send To* button on the *Data Explorer* to load
-   the dataset into the *Invariant* panel.
-
-4) Use the *Customised Input* boxes on the *Invariant* panel to subtract
-   any background, specify the contrast (i.e. difference in SLDs - this must be
-   specified for the eventual value of $Q^*$  to be on an absolute scale), or to
-   rescale the data.
-
-5) Adjust the extrapolation range as necessary. In most cases the default
-   values will suffice.
-
-6) Click the *Compute* button.
-
-7) To include a lower and/or higher $Q$ range, check the relevant *Enable
-   Extrapolate* check boxes.
-
-   If power law extrapolations are chosen, the exponent can be either held
-   fixed or fitted. The number of points, Npts, to be used for the basis of the
-   extrapolation can also be specified.
-
-8) If the value of $Q^*$  calculated with the extrapolated regions is invalid, a
-   red warning will appear at the top of the *Invariant* panel.
-
-   The details of the calculation are available by clicking the *Details*
-   button in the middle of the panel.
-
-.. image:: image005.png
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Parameters
-----------
-
-Volume Fraction
-^^^^^^^^^^^^^^^
-
-The volume fraction $\phi$ is related to $Q^*$  by
-
-.. math::
-
-    \phi(1 - \phi) = \frac{Q^*}{2\pi^2(\Delta\rho)^2} \equiv A
-
-where $\Delta\rho$ is the SLD contrast.
-
-.. math::
-
-    \phi = \frac{1 \pm \sqrt{1 - 4A}}{2}
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Specific Surface Area
-^^^^^^^^^^^^^^^^^^^^^
-
-The specific surface area $S_v$ is related to $Q^*$  by
-
-.. math::
-
-    S_v = \frac{2\pi\phi(1-\phi)C_p}{Q^*} = \frac{2\pi A C_p}{Q^*}
-
-where $C_p$ is the Porod constant.
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-Reference
----------
-
-O. Glatter and O. Kratky
-Chapter 2 in *Small Angle X-Ray Scattering*
-Academic Press, New York, 1982
-
-http://web.archive.org/web/20110824105537/http://physchem.kfunigraz.ac.at/sm/Service/Glatter_Kratky_SAXS_1982.zip
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last changed by Steve King, 01May2015
Index: src/sas/sasgui/perspectives/invariant/media/report_template.html
===================================================================
--- src/sas/sasgui/perspectives/invariant/media/report_template.html	(revision d85c194ea2f78cb2b9b3de9c969e1b8ebea6b6d2)
+++ 	(revision )
@@ -1,201 +1,0 @@
-<html>
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator >
-</head>
-<body lang=EN-US>
-<div class=WordSection1>
-<font size='4'>
-<p class=MsoNormal><b><span >%s</span></b></p>
-<p class=MsoNormal><span >%s</span></p>
-</font>
-<font size='3'>
-<p class=MsoNormal><b><span > Input
-parameters</span></b></p>
-<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0>
- <tr>
-  <td width=170 valign=top>
-  <p class=MsoNormal > Parameter</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > Value</p>
-  </td>
-  <td width=170 valign=top >
-  <p class=MsoNormal > Unit</p>
-  </td>
- </tr>
- <tr>
-  <td width=170 valign=top >
-  <p class=MsoNormal > scale</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=170 valign=top >&nbsp;</p>
-  </td>
- </tr>
- <tr>
-  <td width=170 valign=top >
-  <p class=MsoNormal > porod constant</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=170 valign=top >&nbsp;</p>
-  </td>
- </tr>
- <tr>
-  <td width=170 valign=top>
-  <p class=MsoNormal > background</p>
-  </td>
-  <td width=170 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=170 valign=top ><span > cm<sup>-1</sup></span></p>
-  </td>
- </tr>
- <tr>
-  <td width=170 valign=top >
-  <p class=MsoNormal > contrast</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=170 valign=top >
-  <p class=MsoNormal ><span > A<sup>-2</sup></span></p>
-  </td>
- </tr>
-</table>
-<p class=MsoNormal><b><span > Extrapolation</span></b></p>
-<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0>
- <tr>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
- </tr>
- <tr>
-  <td width=213 valign=top >
-  <p class=MsoNormal > npts low = %s</p>
-  </td>
-  <td width=213 valign=top > npts high = %s</p>
-  </td>
- </tr>
- <tr>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=213 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
- </tr>
-</table>
-<p class=MsoNormal><b><span > Outputs</span></b></p>
-<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0>
- <tr>
-  <td width=110 valign=top >
-  <p class=MsoNormal s> Parameter</p>
-  </td>
-  <td width=150 valign=top >
-  <p class=MsoNormal >&nbsp;</p>
-  </td>
-  <td width=255 valign=top >
-  <p class=MsoNormal > Value</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal > Unit</p>
-  </td>
- </tr>
- <tr>
-  <td width=110 rowspan=4 >
-  <p class=MsoNormal > invariant (Q<sup>*</sup>)</p>
-  </td>
-  <td width=150 valign=top >
-  <p class=MsoNormal > low Q extrapolation</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal > (cmA)<sup>-1</sup></p>
-  </td>
- </tr>
- <tr>
-  <td width=150 valign=top >
-  <p class=MsoNormal > data</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal > (cmA)<sup>-1</sup></p>
-  </td>
- </tr>
- <tr>
-  <td width=150 valign=top >
-  <p class=MsoNormal > high Q extrapolation</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal > (cmA)<sup>-1</sup></p>
-  </td>
- </tr>
- <tr>
-  <td width=150 valign=top >
-  <p class=MsoNormal > total</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal > (cmA)<sup>-1</sup></p>
-  </td>
- </tr>
- <tr>
-  <td width=110 valign=top >
-  <p class=MsoNormal > volume fraction</p>
-  </td>
-  <td width=150 valign=top >
-  <p class=MsoNormal >&nbsp;</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal >&nbsp;</p>
-  </td>
- </tr>
- <tr>
-  <td width=110 valign=top >
-  <p class=MsoNormal > specific surface</p>
-  </td>
-  <td width=150 valign=top >
-  <p class=MsoNormal >&nbsp;</p>
-  </td>
-  <td width=230 valign=top >
-  <p class=MsoNormal > %s</p>
-  </td>
-  <td width=65 valign=top >
-  <p class=MsoNormal >&nbsp;</p>
-  </td>
- </tr>
-</table>
-</font>
-<p class=MsoNormal>&nbsp;</p>
-<font size=4>
-<br><b><span > Plot</span></b>
-<center>
-<br>Invariant Computation
-<br>Data: "%s"
-<img src="%s" height=400 width=550>
-</center>
-</font>
-</div>
-
-</body>
-
-</html>
Index: src/sas/sasgui/perspectives/pr/media/pr_help.rst
===================================================================
--- src/sas/sasgui/perspectives/pr/media/pr_help.rst	(revision 1abd19cf44dad3cb6ecf909cc6fc8c5be7075466)
+++ 	(revision )
@@ -1,78 +1,0 @@
-.. 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
-
-Reference
----------
-
-P.B. Moore
-*J. Appl. Cryst.*, 13 (1980) 168-175
-
-.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
-
-.. note::  This help document was last modified by Paul Butler, 05 September, 2016
