Changeset 6d6832e in sasview

Timestamp:

Apr 7, 2017 5:16:20 AM (8 years ago)

Author:

wojciech

Branches:

master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload

Children:

62af61fd, d1bee3f

Parents:

9d06728 (diff), 5ed76f8 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'ticket-510' of ​https://github.com/SasView/sasview into ticket-510

Files:

• src/sas/sascalc/calculator/sas_gen.py (modified) (1 diff)
• src/sas/sasgui/guiframe/media/graph_help.rst (modified) (9 diffs)
• src/sas/sasgui/perspectives/calculator/media/kiessig_calculator_help.rst (modified) (2 diffs)
• src/sas/sasgui/perspectives/calculator/media/resolution_calculator_help.rst (modified) (5 diffs)
• src/sas/sasgui/perspectives/calculator/media/sas_calculator_help.rst (modified) (8 diffs)
• src/sas/sasgui/perspectives/calculator/media/sld_calculator_help.rst (modified) (3 diffs)
• src/sas/sasgui/perspectives/calculator/media/slit_calculator_help.rst (modified) (2 diffs)
• src/sas/sasgui/perspectives/calculator/media/v_j.png (deleted)
• src/sas/sasgui/perspectives/fitting/media/fitting_help.rst (modified) (2 diffs)
• src/sas/sasgui/perspectives/fitting/media/mag_help.rst (modified) (7 diffs)
• src/sas/sasgui/perspectives/fitting/media/pd_help.rst (modified) (10 diffs)
• src/sas/sasgui/perspectives/fitting/media/residuals_help.rst (modified) (3 diffs)
• src/sas/sasgui/perspectives/fitting/media/sm_help.rst (modified) (12 diffs)
• src/sas/sasgui/perspectives/invariant/media/image001.png (deleted)
• src/sas/sasgui/perspectives/invariant/media/image002.png (deleted)
• src/sas/sasgui/perspectives/invariant/media/image003.png (deleted)
• src/sas/sasgui/perspectives/invariant/media/image004.png (deleted)
• src/sas/sasgui/perspectives/invariant/media/invariant_help.rst (modified) (4 diffs)
• docs/sphinx-docs/build_sphinx.py (modified) (2 diffs)

src/sas/sascalc/calculator/sas_gen.py

@@ -909 +909 @@
     def set_sldms(self, sld_mx, sld_my, sld_mz):
         r"""
-        Sets (\|m\|, m_theta, m_phi)
-        """
+        Sets mx, my, mz and abs(m).
+        """ # Note: escaping
         if sld_mx.__class__.__name__ == 'float':
             self.sld_mx = np.ones(len(self.pos_x)) * sld_mx

src/sas/sasgui/guiframe/media/graph_help.rst

@@ -9 +9 @@
 
 SasView generates three different types of graph window: one that displays *1D data*
-(ie, I(Q) vs Q), one that displays *1D residuals* (ie, the difference between the
-experimental data and the theory at the same Q values), and *2D color maps*.
+(i.e., $I(Q)$ vs $Q$), one that displays *1D residuals* (ie, the difference between the
+experimental data and the theory at the same $Q$ values), and *2D color maps*.
 
 Graph window options
@@ -42 +42 @@
 plot window.
 
-.. note:: 
+.. note::
     *If a residuals graph (when fitting data) is hidden, it will not show up
     after computation.*
@@ -138 +138 @@
 style and size. *Remove Text* will remove the last annotation added. To change
 the legend. *Window Title* allows a custom title to be entered instead of Graph
-x. 
+x.
 
 Changing scales
@@ -226 +226 @@
 ^^^^^^^^^^^^^^^^^^^
 
-Linear fit performs a simple ( y(x)=ax+b ) linear fit within the plot window.
+Linear fit performs a simple $y(x)=ax+b$ linear fit within the plot window.
 
 In the *Dataset Menu* (see Invoking_the_dataset_menu_), select *Linear Fit*. A
@@ -234 +234 @@
 
 This option is most useful for performing simple Guinier, XS Guinier, and
-Porod type analyses, for example, to estimate Rg, a rod diameter, or incoherent
+Porod type analyses, for example, to estimate $R_g$, a rod diameter, or incoherent
 background level, respectively.
 
@@ -319 +319 @@
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
-This operation will perform an average in constant Q-rings around the (x,y)
+This operation will perform an average in constant $Q$ rings around the (x,y)
 pixel location of the beam center.
 
@@ -331 +331 @@
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-This operation averages in constant Q-arcs.
-
-The width of the sector is specified in degrees (+/- |delta|\|phi|\) each side
-of the central angle (|phi|\).
-
-Annular average [|phi| View]
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-This operation performs an average between two Q-values centered on (0,0),
+This operation averages in constant $Q$ arcs.
+
+The width of the sector is specified in degrees ($\pm\delta|\phi|$) each side
+of the central angle $\phi$.
+
+Annular average [:math:`\phi`]
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This operation performs an average between two $Q$ values centered on (0,0),
 and averaged over a specified number of pixels.
 
-The data is returned as a function of angle (|phi|\) in degrees with zero
+The data is returned as a function of angle $\phi$ in degrees with zero
 degrees at the 3 O'clock position.
 
@@ -356 +356 @@
 ^^^^^^^^^^^^^^^^^^^
 
-This operation computes an average I(Qx) for the region of interest.
+This operation computes an average $I(Q_x)$ for the region of interest.
 
 When editing the slicer parameters, the user can control the length and the
 width the rectangular slicer. The averaged output is calculated from constant
-bins with rectangular shape. The resultant Q values are nominal values, that
+bins with rectangular shape. The resultant $Q$ values are nominal values, that
 is, the central value of each bin on the x-axis.
 
@@ -366 +366 @@
 ^^^^^^^^^^^^^^^^^^^
 
-This operation computes an average I(Qy) for the region of interest.
+This operation computes an average $I(Q_y)$ for the region of interest.
 
 When editing the slicer parameters, the user can control the length and the
 width the rectangular slicer. The averaged output is calculated from constant
-bins with rectangular shape. The resultant Q values are nominal values, that
+bins with rectangular shape. The resultant $Q$ values are nominal values, that
 is, the central value of each bin on the x-axis.
 

src/sas/sasgui/perspectives/calculator/media/kiessig_calculator_help.rst

@@ -10 +10 @@
 -----------
 
-This tool is approximately estimates the thickness of a layer or the diameter 
-of particles from the position of the Kiessig fringe/Bragg peak in NR/SAS data 
-using the relation
+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
 
-(thickness *or* size) = 2 * |pi| / (fringe_width *or* peak position)
-  
+.. 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
 
@@ -21 +26 @@
 --------------
 
-To get a rough thickness or particle size, simply type the fringe or peak 
+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 Steve King, 01May2015
-
+.. note::  This help document was last changed by Paul Kienzle, 05Apr2017

src/sas/sasgui/perspectives/calculator/media/resolution_calculator_help.rst

@@ -10 +10 @@
 -----------
 
-This tool is approximately estimates the resolution of Q from SAS instrumental 
-parameter values assuming that the detector is flat and normal to the 
+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.
 
@@ -23 +23 @@
 2) Select the source (Neutron or Photon) and source type (Monochromatic or TOF).
 
-   *NOTE! The computational difference between the sources is only the 
+   *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 
+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 (= 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 
+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 
+
+   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 
+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 
+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 
+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 
+
+   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 
 
-   [ie., Q < 2. |pi|\ .(beam block diameter) / (sample-to-detector distance) / |lambda|\_min] 
+   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 
+8) A summary of the calculation is written to the SasView *Console* at the
    bottom of the main SasView window.
 
@@ -76 +76 @@
 .. image:: q.png
 
-In the small-angle limit, the variance of Q is to a first-order 
+In the small-angle limit, the variance of $Q$ is to a first-order
 approximation
 
@@ -85 +85 @@
 .. image:: sigma_table.png
 
-Finally, a Gaussian function is used to describe the 2D weighting distribution 
-of the uncertainty in Q.
+Finally, a Gaussian function is used to describe the 2D weighting distribution
+of the uncertainty in $Q$.
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
@@ -93 +93 @@
 ----------
 
-D.F.R. Mildner and J.M. Carpenter 
+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 
+D.F.R. Mildner, J.M. Carpenter and D.L. Worcester
 *J. Appl. Cryst.* 19 (1986) 311-319
 

src/sas/sasgui/perspectives/calculator/media/sas_calculator_help.rst

@@ -19 +19 @@
 ------
 
-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*.
+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 
+Assuming that all the pixel sizes are the same, the elastic scattering
 intensity from the particle is
 
@@ -30 +30 @@
 Equation 1.
 
-where |beta|\ :sub:`j` and *r*\ :sub:`j` are the scattering length density and 
-the position of the j'th pixel respectively.
+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*
+The total volume $V$
 
-.. image:: v_j.png
+.. math::
 
-for |beta|\ :sub:`j` |noteql|\0 where *v*\ :sub:`j` is the volume of the j'th 
-pixel (or the j'th natural atomic volume (= atomic mass / (natural molar 
+    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. 
+$V$ 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|\ :sub:`j` *displayed in the GUI may be incorrect but this will not 
+*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 
+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.
 
@@ -54 +56 @@
 ^^^^^^^^^^^^^^^^^^^
 
-For magnetic scattering, only the magnetization component, *M*\ :sub:`perp`\ , 
-perpendicular to the scattering vector *Q* contributes to the magnetic 
+For magnetic scattering, only the magnetization component, $M_\perp$,
+perpendicular to the scattering vector $Q$ contributes to the magnetic
 scattering length.
 
@@ -64 +66 @@
 .. image:: dm_eq.png
 
-where the gyromagnetic ratio |gamma| = -1.913, |mu|\ :sub:`B` is the Bohr 
-magneton, *r*\ :sub:`0` is the classical radius of electron, and |sigma| is the 
+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 
+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 (- -)
@@ -79 +81 @@
 .. 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|\ :sub:`up` respectively (see above). Then, 
-depending upon the polarization (spin) state of neutrons, the scattering 
-length densities, including the nuclear scattering length density (|beta|\ :sub:`N`\ ) 
+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
 
@@ -105 +107 @@
 .. image:: mqy.png
 
-Here the *M0*\ :sub:`x`\ , *M0*\ :sub:`y` and *M0*\ :sub:`z` are the x, y and z 
-components of the magnetisation vector in the laboratory xyz frame. 
+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
@@ -115 +117 @@
 .. image:: gen_gui_help.png
 
-After computation the result will appear in the *Theory* box in the SasView  
+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 
+*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 
+*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 
+*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 
+*NOTE 3. For the nuclear scattering length density, only the real component
 is taken account.*
 
@@ -139 +141 @@
 
 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 
+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 
+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*\ :sub:`j` |beta|\ :sub:`j` |equiv| *b*\ :sub:`j` is the scattering 
-length of the j'th atom. The calculation output is passed to the *Data Explorer* 
+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.
 

src/sas/sasgui/perspectives/calculator/media/sld_calculator_help.rst

@@ -10 +10 @@
 -----------
 
-The neutron scattering length density (SLD) is defined as
+The neutron scattering length density (SLD, $\beta_N$) is defined as
 
-  SLD = (b_c1 + b_c2 + ... + b_cn) / Vm
+.. math::
 
-where b_ci is the bound coherent scattering length of ith of n atoms in a molecule
-with the molecular volume Vm
+  \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
@@ -22 +24 @@
 ----------------------------
 
-To calculate scattering length densities enter the empirical formula of a 
+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 
+Entering a wavelength value is optional (a default value of 6.0 |Ang| will
 be used).
 
@@ -38 +40 @@
 *  Parentheses can be nested, such as "(CaCO3(H2O)6)1".
 
-*  Isotopes are represented by their atomic number in *square brackets*, such 
+*  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 
+*  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 
+*  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 Steve King, 01May2015
+.. note::  This help document was last changed by Paul Kienzle, 05Apr2017
 

src/sas/sasgui/perspectives/calculator/media/slit_calculator_help.rst

@@ -11 +11 @@
 -----------
 
-This tool enables X-ray users to calculate the slit size (FWHM/2) for smearing 
+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*\ |TM|\  
-*software.*
+only been tested with beam profile data from Anton-Paar SAXSess:sup:`TM` software.*
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
@@ -27 +26 @@
 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 
+   *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 
+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 
+*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.*

src/sas/sasgui/perspectives/fitting/media/fitting_help.rst

@@ -381 +381 @@
 
 In the bottom left corner of the *Fit Page* is a box displaying the normalised value
-of the statistical |chi|\  :sup:`2` parameter returned by the optimiser.
+of the statistical $\chi^2$ parameter returned by the optimiser.
 
 Now check the box for another model parameter and click *Fit* again. Repeat this
@@ -387 +387 @@
 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 zero, and certainly <100. See :ref:`Assessing_Fit_Quality`.
+close to one, and certainly <100. See :ref:`Assessing_Fit_Quality`.
 
 SasView has a number of different optimisers (see the section :ref:`Fitting_Options`).

src/sas/sasgui/perspectives/fitting/media/mag_help.rst

@@ -20 +20 @@
 --------------------------------
 
-Magnetic scattering is implemented in five (2D) models 
+Magnetic scattering is implemented in five (2D) models
 
 *  *sphere*
@@ -28 +28 @@
 *  *parallelepiped*
 
-In general, the scattering length density (SLD, = |beta|) in each region where the
+In general, the scattering length density (SLD, = $\beta$) in each region where the
 SLD is uniform, is a combination of the nuclear and magnetic SLDs and, for polarised
 neutrons, also depends on the spin states of the neutrons.
 
-For magnetic scattering, only the magnetization component, *M*\ :sub:`perp`,
-perpendicular to the scattering vector *Q* contributes to the the magnetic
+For magnetic scattering, only the magnetization component, $M_\perp$,
+perpendicular to the scattering vector $Q$ contributes to the the magnetic
 scattering length.
 
@@ -42 +42 @@
 .. image:: dm_eq.png
 
-where |gamma| = -1.913 is the gyromagnetic ratio, |mu|\ :sub:`B` is the
-Bohr magneton, *r*\ :sub:`0` is the classical radius of electron, and |sigma|
+where $\gamma = -1.913$ is the gyromagnetic ratio, $\mu_B$ is the
+Bohr magneton, $r_0$ is the classical radius of electron, and $\sigma$
 is the Pauli spin.
 
@@ -55 +55 @@
 .. image:: M_angles_pic.png
 
-If the angles of the *Q* vector and the spin-axis (*x'*) to the *x*-axis are |phi|
-and |theta|\ :sub:`up`, respectively, then, depending on the spin state of the
+If the angles of the $Q$ vector and the spin-axis (*x'*) to the *x*-axis are $\phi$
+and $\theta_\text{up}$, respectively, then, depending on the spin state of the
 neutrons, the scattering length densities, including the nuclear scattering
-length density (|beta|\ :sub:`N`) are
+length density ($\beta_N$) are
 
 .. image:: sld1.png
@@ -78 +78 @@
 .. image:: mqy.png
 
-Here, *M*\ :sub:`0x`, *M*\ :sub:`0y` and *M*\ :sub:`0z` are the x, y and z components
-of the magnetization vector given in the laboratory xyz frame given by
+Here, $M_{0x}$, $M_{0y}$ and $M_{0z}$ are the $x$, $y$ and $z$ components
+of the magnetization vector given in the laboratory $xyz$ frame given by
 
 .. image:: m0x_eq.png
@@ -87 +87 @@
 .. image:: m0z_eq.png
 
-and the magnetization angles |theta|\ :sub:`M` and |phi|\ :sub:`M` are defined in
+and the magnetization angles $\theta_M$ and $\phi_M$ are defined in
 the figure above.
 
@@ -93 +93 @@
 
 ===========   ================================================================
- M0_sld        = *D*\ :sub:`M` *M*\ :sub:`0`
- Up_theta      = |theta|\ :sub:`up`
- M_theta       = |theta|\ :sub:`M`
- M_phi         = |phi|\ :sub:`M`
+ M0_sld        = $D_M M_0$
+ Up_theta      = $\theta_\text{up}$
+ M_theta       = $\theta_M$
+ M_phi         = $\phi_M$
  Up_frac_i     = (spin up)/(spin up + spin down) neutrons *before* the sample
  Up_frac_f     = (spin up)/(spin up + spin down) neutrons *after* the sample

src/sas/sasgui/perspectives/fitting/media/pd_help.rst

@@ -24 +24 @@
 form factor is normalized by the average particle volume such that
 
-*P(q) = scale* * \ <F*\F> / *V + bkg*
+.. math::
 
-where F is the scattering amplitude and the \<\> denote an average over the size
-distribution.
+    P(q) = \text{scale} \langle F^*F rangle V + \text{background}
+
+where $F$ is the scattering amplitude and $\langle\cdot\rangle$ denotes an average
+over the size distribution.
 
 Users should note that this computation is very intensive. Applying polydispersion
@@ -57 +59 @@
 .. image:: pd_image001.png
 
-where *xmean* is the mean of the distribution, *w* is the half-width, and *Norm* is a
-normalization factor which is determined during the numerical calculation.
+where $x_{mean}$ is the mean of the distribution, $w$ is the half-width, and $Norm$
+is a normalization factor which is determined during the numerical calculation.
 
-Note that the standard deviation and the half width *w* are different!
+Note that the standard deviation and the half width $w$ are different!
 
 The standard deviation is
@@ -81 +83 @@
 .. image:: pd_image005.png
 
-where *xmean* is the mean of the distribution and *Norm* is a normalization factor
+where $x_{mean}$ is the mean of the distribution and $Norm$ is a normalization factor
 which is determined during the numerical calculation.
 
@@ -100 +102 @@
 .. image:: pd_image007.png
 
-where |mu|\ =ln(*xmed*), *xmed* is the median value of the distribution, and
-*Norm* is a normalization factor which will be determined during the numerical
+where $\mu=\ln(x_{med})$, $x_{med}$ is the median value of the distribution, and
+$Norm$ is a normalization factor which will be determined during the numerical
 calculation.
 
@@ -107 +109 @@
 size parameter in the *FitPage*, for example, radius = 60.
 
-The polydispersity is given by |sigma|
+The polydispersity is given by $\sigma$
 
 .. image:: pd_image008.png
@@ -115 +117 @@
 .. image:: pd_image009.png
 
-The mean value is given by *xmean*\ =exp(|mu|\ +p\ :sup:`2`\ /2). The peak value
-is given by *xpeak*\ =exp(|mu|-p\ :sup:`2`\ ).
+The mean value is given by $x_{mean} =\exp(\mu + p^2 /2)$. The peak value
+is given by $x_{peak} =\exp(\mu-p^2)$.
 
 .. image:: pd_image010.jpg
 
-This distribution function spreads more, and the peak shifts to the left, as *p*
+This distribution function spreads more, and the peak shifts to the left, as $p$
 increases, requiring higher values of Nsigmas and Npts.
 
@@ -132 +134 @@
 .. image:: pd_image011.png
 
-where *xmean* is the mean of the distribution and *Norm* is a normalization factor
-which is determined during the numerical calculation, and *z* is a measure of the
+where $x_{mean}$ is the mean of the distribution and $Norm$ is a normalization factor
+which is determined during the numerical calculation, and $z$ is a measure of the
 width of the distribution such that
 
-z = (1-p\ :sup:`2`\ ) / p\ :sup:`2`
+.. math::
+
+    z = (1-p^2 ) / p^2
 
 The polydispersity is
@@ -156 +160 @@
 
 This user-definable distribution should be given as as a simple ASCII text file
-where the array is defined by two columns of numbers: *x* and *f(x)*. The *f(x)*
+where the array is defined by two columns of numbers: $x$ and $f(x)$. The $f(x)$
 will be normalized by SasView during the computation.
 
@@ -172 +176 @@
 
 SasView only uses these array values during the computation, therefore any mean
-value of the parameter represented by *x* present in the *FitPage*
+value of the parameter represented by $x$ present in the *FitPage*
 will be ignored.
 
@@ -181 +185 @@
 
 Many commercial Dynamic Light Scattering (DLS) instruments produce a size
-polydispersity parameter, sometimes even given the symbol *p*! This parameter is
+polydispersity parameter, sometimes even given the symbol $p$! This parameter is
 defined as the relative standard deviation coefficient of variation of the size
 distribution and is NOT the same as the polydispersity parameters in the Lognormal

src/sas/sasgui/perspectives/fitting/media/residuals_help.rst

@@ -18 +18 @@
 also provides two other measures of the quality of a fit:
 
-*  |chi|\  :sup:`2` (or 'Chi2'; pronounced 'chi-squared')
+*  $\chi^2$ (or 'Chi2'; pronounced 'chi-squared')
 *  *Residuals*
 
@@ -32 +32 @@
 *Npts* such that
 
-  *Chi2/Npts* = { SUM[(*Y_i* - *Y_theory_i*)^2 / (*Y_error_i*)^2] } / *Npts*
+.. math::
 
-This differs slightly from what is sometimes called the 'reduced chi-squared'
+  \chi^2/N_{pts} =  \sum[(Y_i - Y_{theory}_i)^2 / (Y_error_i)^2] } / N_{pts}
+
+This differs slightly from what is sometimes called the 'reduced $\chi^2$'
 because it does not take into account the number of fitting parameters (to
-calculate the number of 'degrees of freedom'), but the 'normalized chi-squared'
-and the 'reduced chi-squared' are very close to each other when *Npts* >> number of
-parameters.
+calculate the number of 'degrees of freedom'), but the 'normalized $\chi^2$
+and the 'reduced $\chi^2$ are very close to each other when $N_{pts} \gg
+\text{number of parameters}.
 
-For a good fit, *Chi2/Npts* tends to 0.
+For a good fit, $\chi^2/N_{pts}$ tends to 1.
 
-*Chi2/Npts* is sometimes referred to as the 'goodness-of-fit' parameter.
+$\chi^2/N_{pts}$ is sometimes referred to as the 'goodness-of-fit' parameter.
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
@@ -53 +55 @@
 value and its *true* value is its error).
 
-*SasView* calculates 'normalized residuals', *R_i*, for each data point in the
+*SasView* calculates 'normalized residuals', $R_i$, for each data point in the
 fit:
 
-  *R_i* = (*Y_i* - *Y_theory_i*) / (*Y_err_i*)
+.. math::
 
-For a good fit, *R_i* ~ 0.
+  R_i = (Y_i - Y_theory_i) / (Y_err_i)
+
+For a good fit, $R_i \sim 0$.
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ

src/sas/sasgui/perspectives/fitting/media/sm_help.rst

@@ -20 +20 @@
 ==================
 
-Sometimes the instrumental geometry used to acquire the experimental data has 
-an impact on the clarity of features in the reduced scattering curve. For 
-example, peaks or fringes might be slightly broadened. This is known as 
-*Q resolution smearing*. To compensate for this effect one can either try and 
-remove the resolution contribution - a process called *desmearing* - or add the 
-resolution contribution into a model calculation/simulation (which by definition 
-will be exact) to make it more representative of what has been measured 
+Sometimes the instrumental geometry used to acquire the experimental data has
+an impact on the clarity of features in the reduced scattering curve. For
+example, peaks or fringes might be slightly broadened. This is known as
+*Q resolution smearing*. To compensate for this effect one can either try and
+remove the resolution contribution - a process called *desmearing* - or add the
+resolution contribution into a model calculation/simulation (which by definition
+will be exact) to make it more representative of what has been measured
 experimentally - a process called *smearing*. SasView will do the latter.
 
-Both smearing and desmearing rely on functions to describe the resolution 
+Both smearing and desmearing rely on functions to describe the resolution
 effect. SasView provides three smearing algorithms:
 
@@ -36 +36 @@
 *  *2D Smearing*
 
-SasView also has an option to use Q resolution data (estimated at the time of 
+SasView also has an option to use $Q$ resolution data (estimated at the time of
 data reduction) supplied in a reduced data file: the *Use dQ data* radio button.
 
@@ -43 +43 @@
 dQ Smearing
 -----------
- 
-If this option is checked, SasView will assume that the supplied dQ values 
+
+If this option is checked, SasView will assume that the supplied $dQ$ values
 represent the standard deviations of Gaussian functions.
 
@@ -65 +65 @@
 **[Equation 1]**
 
-The functions |inlineimage004| and |inlineimage005|
-refer to the slit width weighting function and the slit height weighting 
-determined at the given *q* point, respectively. It is assumed that the weighting
+The functions $W_v(v)$ and $W_u(u)$
+refer to the slit width weighting function and the slit height weighting
+determined at the given $q$ point, respectively. It is assumed that the weighting
 function is described by a rectangular function, such that
 
@@ -80 +80 @@
 **[Equation 3]**
 
-so that |inlineimage008| |inlineimage009| for |inlineimage010| and *u*\ .
-
-Here |inlineimage011| and |inlineimage012| stand for
-the slit height (FWHM/2) and the slit width (FWHM/2) in *q* space.
+so that $\Delta q_\alpha = \int_0^\infty d\alpha W_\alpha(\alpha)$
+for $\alpha = v$ and $u$.
+
+Here $\Delta q_u$ and $\Delta q_v$ stand for
+the slit height (FWHM/2) and the slit width (FWHM/2) in $q$ space.
 
 This simplifies the integral in Equation 1 to
@@ -91 +92 @@
 **[Equation 4]**
 
-which may be solved numerically, depending on the nature of |inlineimage011| and |inlineimage012| .
+which may be solved numerically, depending on the nature of
+$\Delta q_u$ and $\Delta q_v$.
 
 Solution 1
 ^^^^^^^^^^
 
-**For** |inlineimage012| **= 0 and** |inlineimage011| **= constant.**
+**For $\Delta q_v= 0$ and $\Delta q_u = \text{constant}$.**
 
 .. image:: sm_image016.png
 
-For discrete *q* values, at the *q* values of the data points and at the *q*
-values extended up to *q*\ :sub:`N`\ = *q*\ :sub:`i` + |inlineimage011| the smeared
+For discrete $q$ values, at the $q$ values of the data points and at the $q$
+values extended up to $q_N = q_i + \Delta q_u$ the smeared
 intensity can be approximately calculated as
 
@@ -108 +110 @@
 **[Equation 5]**
 
-where |inlineimage018| = 0 for *I*\ :sub:`s` when *j* < *i* or *j* > *N-1*.
+where |inlineimage018| = 0 for $I_s$ when $j < i$ or $j > N-1$.
 
 Solution 2
 ^^^^^^^^^^
 
-**For** |inlineimage012| **= constant and** |inlineimage011| **= 0.**
+**For $\Delta q_v = \text{constant}$ and $\Delta q_u= 0$.**
 
 Similar to Case 1
 
-|inlineimage019| for *q*\ :sub:`p` = *q*\ :sub:`i` - |inlineimage012| and *q*\ :sub:`N` = *q*\ :sub:`i` + |inlineimage012|
+|inlineimage019| for $q_p = q_i - \Delta q_v$ and $q_N = q_i + \Delta q_v$
 
 **[Equation 6]**
 
-where |inlineimage018| = 0 for *I*\ :sub:`s` when *j* < *p* or *j* > *N-1*.
+where |inlineimage018| = 0 for $I_s$ when $j < p$ or $j > N-1$.
 
 Solution 3
 ^^^^^^^^^^
 
-**For** |inlineimage011| **= constant and** |inlineimage011| **= constant.**
+**For $\Delta q_u = \text{constant}$ and $\Delta q_v = \text{constant}$.**
 
 In this case, the best way is to perform the integration of Equation 1
@@ -142 +144 @@
 **[Equation 7]**
 
-for *q*\ :sub:`p` = *q*\ :sub:`i` - |inlineimage012| and *q*\ :sub:`N` = *q*\ :sub:`i` + |inlineimage012|
-
-where |inlineimage018| = 0 for *I*\ :sub:`s` when *j* < *p* or *j* > *N-1*.
+for *q_p = q_i - \Delta q_v$ and $q_N = q_i + \Delta q_v$
+where |inlineimage018| = 0 for *I_s$ when $j < p$ or $j > N-1$.
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
@@ -175 +176 @@
 **[Equation 9]**
 
-In Equation 9, *x*\ :sub:`0` = *q* cos(|theta|), *y*\ :sub:`0` = *q* sin(|theta|), and
-the primed axes, are all in the coordinate rotated by an angle |theta| about
-the z-axis (see the figure below) so that *x'*\ :sub:`0` = *x*\ :sub:`0` cos(|theta|) +
-*y*\ :sub:`0` sin(|theta|) and *y'*\ :sub:`0` = -*x*\ :sub:`0` sin(|theta|) +
-*y*\ :sub:`0` cos(|theta|). Note that the rotation angle is zero for a x-y symmetric
-elliptical Gaussian distribution. The *A* is a normalization factor.
+In Equation 9, $x_0 = q \cos(\theta)$, $y_0 = q \sin(\theta)$, and
+the primed axes, are all in the coordinate rotated by an angle $\theta$ about
+the z-axis (see the figure below) so that
+$x'_0 = x_0 \cos(\theta) + y_0 \sin(\theta)$ and
+$y'_0 = -x_0 \sin(\theta) + y_0 \cos(\theta)$.
+Note that the rotation angle is zero for a $xy$ symmetric
+elliptical Gaussian distribution. The $A$ is a normalization factor.
 
 .. image:: sm_image023.png
 
-Now we consider a numerical integration where each of the bins in |theta| and *R* are
-*evenly* (this is to simplify the equation below) distributed by |bigdelta|\ |theta|
-and |bigdelta|\ R, respectively, and it is further assumed that *I(x',y')* is constant
+Now we consider a numerical integration where each of the bins in $\theta$ and $R$ are
+*evenly* (this is to simplify the equation below) distributed by $\Delta \theta$
+and $\Delta R$, respectively, and it is further assumed that $I(x',y')$ is constant
 within the bins. Then
 
@@ -194 +196 @@
 
 Since the weighting factor on each of the bins is known, it is convenient to
-transform *x'-y'* back to *x-y* coordinates (by rotating it by -|theta| around the
-*z* axis).
+transform $x'y'$ back to $xy$ coordinates (by rotating it by $-\theta$ around the
+$z$ axis).
 
 Then, for a polar symmetric smear
@@ -207 +209 @@
 .. image:: sm_image026.png
 
-while for a *x-y* symmetric smear
+while for a $xy$ symmetric smear
 
 .. image:: sm_image027.png
@@ -225 +227 @@
 -------------------------
 
-In all the cases above, the weighting matrix *W* is calculated on the first call
-to a smearing function, and includes ~60 *q* values (finely and evenly binned)
-below (>0) and above the *q* range of data in order to smear all data points for
-a given model and slit/pinhole size. The *Norm*  factor is found numerically with the
-weighting matrix and applied on the computation of *I*\ :sub:`s`.
+In all the cases above, the weighting matrix $W$ is calculated on the first call
+to a smearing function, and includes ~60 $q$ values (finely and evenly binned)
+below (>0) and above the $q$ range of data in order to smear all data points for
+a given model and slit/pinhole size. The $Norm$  factor is found numerically with the
+weighting matrix and applied on the computation of $I_s$.
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ

src/sas/sasgui/perspectives/invariant/media/invariant_help.rst

@@ -10 +10 @@
 -----------
 
-The scattering, or Porod, invariant (Q*\) is a model-independent quantity that 
+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 wave transfer (Q) multiplied by the scattering cross section 
-over the full range of Q from zero to infinity, that is
+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
 
-.. image:: image001.png
+.. math::
 
-where *g = q* for pinhole geometry (SAS) and *g = q*\ :sub:`v` (the slit height) for  
-slit geometry (USAS).
+    Q^* = \int_0^\infty q^2I(q)\,dq
 
-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 
+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 =< *Q* =< infinity. At best, combining USAS and 
-WAS data might cover the range 1e-5 =< *Q* =< 10 1/\ |Ang| . Thus it is usually 
-necessary to extrapolate the experimental data to low and high *Q*. For this
+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)
+High-\ $Q$ region (>= *Qmax* in data)
 
-*  The power law function *C*/*Q*\ :sup:`4` is used where the constant 
-   *C* (= 2.\ |pi|\ .(\ |bigdelta|\ |rho|\ ).\ *Sv*\ ) is to be found by fitting part of data 
-   within the range *Q*\ :sub:`N-m` to *Q*\ :sub:`N` (where m < N).
+*  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)
+Low-\ $Q$ region (<= *Qmin* in data)
 
-*  The Guinier function *I0.exp(-Rg*\ :sup:`2`\ *Q*\ :sup:`2`\ */3)* where *I0* 
-   and *Rg* are obtained by fitting as for the high-*Q* region above. 
+*  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.
 
@@ -52 +59 @@
 2) Load some data with the *Data Explorer*.
 
-3) Select a dataset and use the *Send To* button on the *Data Explorer* to load 
+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 
+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 
+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 
+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 
+
+   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 
+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* 
+   The details of the calculation are available by clicking the *Details*
    button in the middle of the panel.
 
@@ -88 +95 @@
 ^^^^^^^^^^^^^^^
 
-The volume fraction |phi| is related to Q*\  by
+The volume fraction $\phi$ is related to $Q^*$  by
 
-.. image:: image002.png
+.. math::
 
-where |bigdelta|\ |rho| is the SLD contrast.
+    \phi(1 - \phi) = \frac{Q^*}{2\pi^2(\Delta\rho)^2} \equiv A
 
-.. image:: image003.png
+where $\Delta\rho$ is the SLD contrast.
+
+.. math::
+
+    \phi = \frac{1 \pm \sqrt{1 - 4A}}{2}
 
 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
@@ -101 +112 @@
 ^^^^^^^^^^^^^^^^^^^^^
 
-The specific surface area *Sv* is related to Q*\  by
+The specific surface area $S_v$ is related to $Q^*$  by
 
-.. image:: image004.png
+.. math::
 
-where *Cp* is the Porod constant.
+    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

docs/sphinx-docs/build_sphinx.py

@@ -373 +373 @@
     copy_tree(html, SASVIEW_DOCS)
 
-    print "=== Build Latex Docs from Rest Files ==="
-    subprocess.call(["sphinx-build",
+    #We are building latex doc on linux only
+    if "linux" in platform:
+        print "=== Build Latex Docs from Rest Files ==="
+        subprocess.call(["sphinx-build",
                      "-b", "latex", # Builder name. TODO: accept as arg to setup.py.
                      "-d", os.path.join(SPHINX_BUILD, "doctrees"),
@@ -380 +382 @@
                      os.path.join(SPHINX_BUILD, "latex")])
 
-    print "=== Copy Latex Docs to Build Directory ==="
-    latex = os.path.join(SPHINX_BUILD, "latex")
-    copy_tree(latex, SASVIEW_DOCS)
+        print "=== Copy Latex Docs to Build Directory ==="
+        latex = os.path.join(SPHINX_BUILD, "latex")
+        copy_tree(latex, SASVIEW_DOCS)
 
 def rebuild():