Merge remote-tracking branch 'origin/feature/9677_algs_and_fit_index'

mantidproject · Jun 27, 2014 · 2f584a7 · 2f584a7
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diff --git a/Code/Mantid/docs/source/fitfunctions/Abragam.rst b/Code/Mantid/docs/source/fitfunctions/Abragam.rst
@@ -1,7 +1,10 @@
+.. _func-Abragam:
+
 =======
 Abragam
 =======
 
+.. index:: Abragam
 
 Description
 -----------
@@ -10,4 +13,4 @@ Abragam fitting function for use by Muon scientists defined by
 
 .. math:: \mbox{A}\times cos( 2 \pi \times {Omega} \times {x} + {Phi} ) \times \exp(-{Sigma}^2 \times Tau^2 \times {x}^2 \times ( exp ( {x} / Tau ) - 1 + {x} / Tau ) )
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/BSpline.rst b/Code/Mantid/docs/source/fitfunctions/BSpline.rst
@@ -1,7 +1,10 @@
+.. _func-BSpline:
+
 =======
 BSpline
 =======
 
+.. index:: BSpline
 
 Description
 -----------
@@ -18,4 +21,4 @@ interpolation points. The parameter names have the form 'yi' where 'y'
 is letter 'y' and 'i' is the parameter's index starting from 0 and have
 the type double. Likewise, the attribute names have the form 'xi'.
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/BackToBackExponential.rst b/Code/Mantid/docs/source/fitfunctions/BackToBackExponential.rst
@@ -4,6 +4,7 @@
 BackToBackExponential
 =====================
 
+.. index:: BackToBackExponential
 
 Description
 -----------
@@ -49,4 +50,4 @@ Properties
 based on fitting a couple of peaks in a dataset collected on the ISIS's
 HRPD instrument.*
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/BivariateNormal.rst b/Code/Mantid/docs/source/fitfunctions/BivariateNormal.rst
@@ -4,6 +4,7 @@
 BivariateNormal
 ===============
 
+.. index:: BivariateNormal
 
 Description
 -----------
@@ -63,4 +64,4 @@ square or contiguous subregion of a panel
 The values for out in function1D are, for each pixel, the difference of
 V(see formula) and dataY(0).
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/Chebyshev.rst b/Code/Mantid/docs/source/fitfunctions/Chebyshev.rst
@@ -1,7 +1,10 @@
+.. _func-Chebyshev:
+
 =========
 Chebyshev
 =========
 
+.. index:: Chebyshev
 
 Description
 -----------
@@ -32,4 +35,4 @@ index starting from 0.
 The other two attributes are doubles 'StartX' and 'EndX' which define
 the expansion (fitting) interval.
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/ChudleyElliot.rst b/Code/Mantid/docs/source/fitfunctions/ChudleyElliot.rst
@@ -1,7 +1,11 @@
+.. _func-ChudleyElliot:
+
 ==============
 Chudley-Elliot
 ==============
 
+.. index:: Chudley-Elliot
+
 Description
 -----------
 
@@ -11,4 +15,4 @@ motions of molecules. The Chudley-Elliot Jump diffusion model (1961) has the for
 
 .. math:: Gamma(Q) = (1 - sin(Ql)/Ql)/tau
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/CompositeFunction.rst b/Code/Mantid/docs/source/fitfunctions/CompositeFunction.rst
@@ -4,6 +4,7 @@
 CompositeFunction
 =================
 
+.. index:: CompositeFunction
 
 Description
 -----------
@@ -64,4 +65,4 @@ inner one in brackets:
 
 ``name=LinearBackground;(composite=Convolution;name=Resolution;name=Lorentzian)``
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/Convolution.rst b/Code/Mantid/docs/source/fitfunctions/Convolution.rst
@@ -4,6 +4,7 @@
 Convolution
 ===========
 
+.. index:: Convolution
 
 Description
 -----------
@@ -41,4 +42,4 @@ Note that the box function is defined on interval [-5, 5]:
 
    Box.png
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/CubicSpline.rst b/Code/Mantid/docs/source/fitfunctions/CubicSpline.rst
@@ -1,7 +1,10 @@
+.. _func-CubicSpline:
+
 ===========
 CubicSpline
 ===========
 
+.. index:: CubicSpline
 
 Description
 -----------
@@ -18,4 +21,4 @@ interpolation points. The parameter names have the form 'yi' where 'y'
 is letter 'y' and 'i' is the parameter's index starting from 0 and have
 the type double. Likewise, the attribute names have the form 'xi'.
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/DSFInterp1DFit.rst b/Code/Mantid/docs/source/fitfunctions/DSFInterp1DFit.rst
@@ -1,46 +1,42 @@
+.. _func-DSFInterp1DFit:
+
 ==============
 DSFInterp1DFit
 ==============
 
+.. index:: DSFInterp1DFit
 
 Description
 ----------- 
 
-Given a set of parameter values :math: T_i and corresponding structure factors :math: S(Q,E,T_i), this
-fit function interpolates :math: S(Q,E,T) for any value of parameter T within the range spanned by the :math: T_i set in order to fit against a reference :math: S(Q,E).
+Given a set of parameter values :math:`T_i` and corresponding structure factors :math:`S(Q,E,T_i)`, this
+fit function interpolates :math:`S(Q,E,T)` for any value of parameter T within the range spanned by the :math:`T_i` set in order to fit against a reference :math:`S(Q,E)`.
 
-This fitting function is closely related to algorithm [[DSFinterp|DSFinterp]]. Please check the algorithm wiki page to learn about the details of the interpolator.
+This fitting function is closely related to algorithm :ref:`DSFinterp <algm-DSFinterp>`. Please check the algorithm wiki page to learn about the details of the interpolator.
 
 Atributes (non-fitting parameters)
 ----------------------------------
 
-+---------+------------------+-------------+-----------+-----------+------------------------------------------------------------------------------+
-| Order   | Name             | Direction   | Type      | Default   | Description                                                                  |
-+=========+==================+=============+===========+===========+==============================================================================+
-| 1       | InputWorkspaces  | Input       | str, list | Mandatory | list of input workspace names in a single string, separated by white spaces  |
-+---------+------------------+-------------+-----------+-----------+------------------------------------------------------------------------------+
-| 2       | LoadErrors       | Input       | bool      | True      | Do we load error data contained in the workspaces?                           |
-+---------+------------------+-------------+-----------+-----------+------------------------------------------------------------------------------+
-| 3       | ParameterValues  | Input       | dbl list  | Mandatory | list of input parameter values, as a single string separated by white spaces |
-+---------+------------------+-------------+-----------+-----------+------------------------------------------------------------------------------+
-| 4       | LocalRegression  | Input       | bool      | True      | Perform running local-regression?                                            |
-+---------+------------------+-------------+-----------+-----------+------------------------------------------------------------------------------+
-| 5       | RegressionWindow | Input       | number    | 6         | window size for the running local-regression                                 |
-+---------+------------------+-------------+-----------+-----------+------------------------------------------------------------------------------+
-| 6       | RegressionType   | Input       | str       | quadratic | type of local-regression; linear and quadratic are available                 |
-+---------+------------------+-------------+-----------+-----------+------------------------------------------------------------------------------+
+===== ================ ========= ========= ========= ===========================================================================
+Order Name             Direction Type      Default   Description
+===== ================ ========= ========= ========= ===========================================================================
+1     InputWorkspaces  Input     str list  Mandatory list of input workspace names in a single string, separated by white spaces
+2     LoadErrors       Input     bool      True      Do we load error data contained in the workspaces? 
+3     ParameterValues  Input     dbl list  Mandatory list of input parameter values, as a single string separated by white spaces
+4     LocalRegression  Input     bool      True      Perform running local-regression?
+5     RegressionWindow Input     number    6         window size for the running local-regression
+6     RegressionType   Input     str       quadratic type of local-regression; linear and quadratic are available
+===== ================ ========= ========= ========= ===========================================================================
 
 
 Fitting parameters
 ------------------
 
-+---------+------------------+-----------+-----------+-----------------------------------------------------------------------------------+
-| Order   | Name             | Type      | Default   | Description                                                                       |
-+=========+==================+===========+===========+===================================================================================+
-| 1       | Intensity        | dbl       | 1.0       | Multiplicative prefactor scaling the height or intensity of the structure factor  |
-+---------+------------------+-----------+-----------+-----------------------------------------------------------------------------------+
-| 2       | TargetParameter  | dbl       | 1.0       | Parameter value for which the interpolator is evaluated                           |
-+---------+------------------+-----------+-----------+-----------------------------------------------------------------------------------+
-
+===== =============== ==== ======= ================================================================================
+Order Name            Type Default Description
+===== =============== ==== ======= ================================================================================
+1     Intensity       dbl  1.0     Multiplicative prefactor scaling the height or intensity of the structure factor
+2     TargetParameter dbl  1.0     Parameter value for which the interpolator is evaluated
+===== =============== ==== ======= ================================================================================
 
-.. categories:: FitFunctions QuasiElastic
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/DiffRotDiscreteCircle.rst b/Code/Mantid/docs/source/fitfunctions/DiffRotDiscreteCircle.rst
@@ -1,7 +1,10 @@
+.. _func-DiffRotDiscreteCircle:
+
 =====================
 DiffRotDiscreteCircle
 =====================
 
+.. index:: DiffRotDiscreteCircle
 
 Description
 -----------
@@ -128,6 +131,4 @@ Properties
 | 3       | Decay       | 1.0       | inverse of the transition rate (ps if energy in meV; ns if energy in :math:`\mu`\ eV)   |
 +---------+-------------+-----------+-----------------------------------------------------------------------------------------+
 
-Category:Fit_functions
-
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/DiffSphere.rst b/Code/Mantid/docs/source/fitfunctions/DiffSphere.rst
@@ -1,7 +1,10 @@
+.. _func-DiffSphere:
+
 ==========
 DiffSphere
 ==========
 
+.. index:: DiffSphere
 
 Description
 -----------
@@ -62,6 +65,4 @@ Properties
 | 3       | Diffusion   | 0.05      | Diffusion constant [Å\ :math:`{}^2/ps \equiv 10 \cdot (10^{-5} cm^2/s)`]   |
 +---------+-------------+-----------+----------------------------------------------------------------------------+
 
-Category:Fit_functions
-
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/ExpDecay.rst b/Code/Mantid/docs/source/fitfunctions/ExpDecay.rst
@@ -1,7 +1,10 @@
+.. _func-ExpDecay:
+
 ========
 ExpDecay
 ========
 
+.. index:: ExpDecay
 
 Description
 -----------
@@ -10,4 +13,4 @@ Exponential decay function is defined by
 
 .. math:: \mbox{Height}\times \exp(-\frac{x}{\mbox{Lifetime}})
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/ExpDecayMuon.rst b/Code/Mantid/docs/source/fitfunctions/ExpDecayMuon.rst
@@ -1,7 +1,10 @@
+.. _func-ExpDecayMuon:
+
 ============
 ExpDecayMuon
 ============
 
+.. index:: ExpDecayMuon
 
 Description
 -----------
@@ -10,4 +13,4 @@ Exponential decay for use by Muon scientists defined by
 
 .. math:: \mbox{A}\times \exp(-{Lambda} \times {x})
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/ExpDecayOsc.rst b/Code/Mantid/docs/source/fitfunctions/ExpDecayOsc.rst
@@ -1,7 +1,10 @@
+.. _func-ExpDecayOsc:
+
 ===========
 ExpDecayOsc
 ===========
 
+.. index:: ExpDecayOsc
 
 Description
 -----------
@@ -10,4 +13,4 @@ Oscillation exponential decay function is defined by
 
 .. math:: \mbox{A}\times \exp(-{Lambda} \times {x}) \times cos( 2 \pi \times {Frequency} \times {x} + {Phi} )
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/FickDiffusion.rst b/Code/Mantid/docs/source/fitfunctions/FickDiffusion.rst
@@ -1,7 +1,10 @@
+.. _func-FickDiffusion:
+
 ==============
 Fick Diffusion
 ==============
 
+.. index:: Fick Diffusion
 
 Description
 -----------
@@ -12,4 +15,4 @@ motions of molecules. Fick's law for diffusion has the form:
 
 .. math:: Gamma(Q) = D*Q^2 where D=<l^2>*Q^2/6*tau
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/FlatBackground.rst b/Code/Mantid/docs/source/fitfunctions/FlatBackground.rst
@@ -1,7 +1,10 @@
+.. _func-FlatBackground:
+
 ==============
 FlatBackground
 ==============
 
+.. index:: FlatBackground
 
 Description
 -----------
@@ -10,4 +13,4 @@ A Flat background function is defined as:
 
 :math:`y = A_0`
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/GausDecay.rst b/Code/Mantid/docs/source/fitfunctions/GausDecay.rst
@@ -1,7 +1,10 @@
+.. _func-GausDecay:
+
 =========
 GausDecay
 =========
 
+.. index:: GausDecay
 
 Description
 -----------
@@ -10,4 +13,4 @@ Gaussian decay for use by Muon scientists defined by
 
 .. math:: \mbox{A}\times \exp(-{Sigma}^2 \times {x}^2 )
 
-.. categories:: FitFunctions
+.. categories::
diff --git a/Code/Mantid/docs/source/fitfunctions/GausOsc.rst b/Code/Mantid/docs/source/fitfunctions/GausOsc.rst
@@ -1,7 +1,10 @@
+.. _func-GausOsc:
+
 =======
 GausOsc
 =======
 
+.. index:: GausOsc
 
 Description
 -----------
@@ -10,4 +13,4 @@ Oscillating Gaussian decay for use by Muon scientists defined by
 
 .. math:: \mbox{A}\times \exp(-{Sigma}^2 \times {x}^2) \times cos( 2 \pi \times {Frequency} \times {x} + {Phi} )
 
-.. categories:: FitFunctions
+.. categories::