Merge remote-tracking branch 'origin/feature/9572_documentation_check'

Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/ModeratorTzeroLinear.h

@@ -71,14 +71,13 @@ class DLLExport ModeratorTzeroLinear : public API::Algorithm
   /// Virtual destructor
   virtual ~ModeratorTzeroLinear() {}
   /// Algorithm's name
-  virtual const std::string name() const { return "ModeratorTzeroLinear"; }
-    ///Summary of algorithms purpose
-    virtual const std::string summary() const {return " Corrects the time of flight of an indirect geometry instrument by a time offset that is linearly dependent on the wavelength of the neutron after passing through the moderator.";}
-
+  virtual const std::string name() const;
+  ///Summary of algorithms purpose
+  virtual const std::string summary() const;
   /// Algorithm's version
-  virtual int version() const { return (1); }
+  virtual int version() const;
   /// Algorithm's category for identification
-  virtual const std::string category() const { return "CorrectionFunctions\\InstrumentCorrections"; }
+  virtual const std::string category() const;
 
 private:
   //conversion constants applicable to histogram and event workspaces

Code/Mantid/Framework/Algorithms/src/ModeratorTzeroLinear.cpp

@@ -25,6 +25,26 @@ using namespace Mantid::DataObjects;
 // A reference to the logger is provided by the base class, it is called g_log.
 // It is used to print out information, warning and error messages
 
+const std::string ModeratorTzeroLinear::name() const
+{
+  return "ModeratorTzeroLinear";
+}
+
+const std::string ModeratorTzeroLinear::summary() const
+{
+  return "Corrects the time of flight of an indirect geometry instrument by a time offset that is linearly dependent on the wavelength of the neutron after passing through the moderator.";
+}
+
+int ModeratorTzeroLinear::version() const
+{
+  return 1;
+}
+
+const std::string ModeratorTzeroLinear::category() const
+{
+  return "CorrectionFunctions\\InstrumentCorrections";
+}
+
 void ModeratorTzeroLinear::init()
 {
   declareProperty(new WorkspaceProperty<MatrixWorkspace>("InputWorkspace","",Direction::Input,boost::make_shared<WorkspaceUnitValidator>("TOF")),

Code/Mantid/Framework/DataHandling/src/SetSampleMaterial.cpp

@@ -52,31 +52,7 @@ namespace Mantid
       declareProperty(
         new WorkspaceProperty<Workspace>("InputWorkspace","",Direction::InOut),
         "The workspace with which to associate the sample ");
-      declareProperty("ChemicalFormula", "", "ChemicalFormula or AtomicNumber must be given. "
-        "Enter a composition as a molecular formula of \n"
-        "elements or isotopes.  For example, basic "
-        "elements might be \"H\", \"Fe\" or \"Si\", etc. \n"
-        "A molecular formula of elements might be "
-        "\"H4-N2-C3\", which corresponds to a molecule \n"
-        "with 4 Hydrogen atoms, 2 Nitrogen atoms and "
-        "3 Carbon atoms.  Each element in a molecular \n"
-        "formula is followed by the number of the atoms "
-        "for that element, specified _without a hyphen_, \n"
-        "because each element is separated from other "
-        "elements using a hyphen.  The number of atoms \n"
-        "can be integer or float, but must start with "
-        "a digit, e.g. 0.6 is fine but .6 is not. \n"
-        "Isotopes may also be included in a material "
-        "composition, and can be specified alone \n"
-        "(as in \"Li7\"), or in a molecular formula "
-        "(as in \"(Li7)2-C-H4-N-Cl6\").  Note, however, \n"
-        "that No Spaces or Hyphens are allowed in an "
-        "isotope symbol specification.  Also Note \n"
-        "that for isotopes specified in a molecular "
-        "expression, the isotope must be enclosed \n"
-        "by parenthesis, except for two special "
-        "cases, D and T, which stand for H2 and H3, \n"
-        "respectively.");
+      declareProperty("ChemicalFormula", "", "ChemicalFormula or AtomicNumber must be given.");
       declareProperty("AtomicNumber", 0, "ChemicalFormula or AtomicNumber must be given");
       declareProperty("MassNumber", 0, "Mass number if ion (default is 0)");
       auto mustBePositive = boost::make_shared<BoundedValidator<double> >();

Code/Mantid/docs/source/algorithms/ApplyTransmissionCorrection-v1.rst

@@ -9,7 +9,7 @@
 Description
 -----------
 
-The transmission can be given as a MatrixWorkspace or given directly as
+The transmission can be given as a `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ or given directly as
 numbers. One or the other method must be used.
 
 See `SANS

Code/Mantid/docs/source/algorithms/CalibrateRectangularDetectors-v1.rst

@@ -12,25 +12,21 @@ Description
 Here are examples of input and output from PG3 and SNAP:
 
 .. figure:: /images/PG3_Calibrate.png
-   :alt: PG3_Calibrate.png
 
-   PG3\_Calibrate.png
 .. figure:: /images/SNAP_Calibrate.png
-   :alt: SNAP_Calibrate.png
 
-   SNAP\_Calibrate.png
--The purpose of this algorithm is to calibrate the detector pixels and
+The purpose of this algorithm is to calibrate the detector pixels and
 write a calibration file. The calibration file name contains the
 instrument, run number, and date of calibration. A binary Dspacemap file
 that converts from TOF to d-space including the calculated offsets is
-also an output option. For CrossCorrelation option: If one peak is not
+also an output option. For ``CrossCorrelation`` option: If one peak is not
 in the spectra of all the detectors, you can specify the first n
 detectors to be calibrated with one peak and the next n detectors to be
 calibrated with the second peak. If a color fill plot of the calibrated
 workspace does not look good, do a color fill plot of the workspace that
-ends in cc to see if the CrossCorrelationPoints and/or PeakHalfWidth
-should be increased or decreased. Also plot the reference spectra from
-the cc workspace.
+ends in cc (cross correlation) to see if the ``CrossCorrelationPoints``
+and/or ``PeakHalfWidth`` should be increased or decreased. Also plot the 
+reference spectra from the cc workspace.
 
 Features to improve performance of peak finding
 -----------------------------------------------
@@ -40,18 +36,17 @@ Define peak fit-window
 
 There are two exclusive approaches to define peak's fit-window.
 
-1. *PeakWindowMax*: All peaks will use this value to define their
-fitting range.
-
-2. *FitwindowTableWorkspace*: This is a table workspace by which each
-peak will have its individual fit window defined.
+- ``PeakWindowMax`` All peaks will use this value to define their fitting 
+  range.
+- ``FitwindowTableWorkspace`` This is a table workspace by which each peak 
+  will have its individual fit window defined.
 
 Define accepted range of peak's width
 #####################################
 
-Optional input property *DetectorResolutionWorkspace* is a matrix
+Optional input property ``DetectorResolutionWorkspace`` is a matrix
 workspace containing the detector resolution :math:`\Delta(d)/d` for
-each spectrum. Combining with property *AllowedResRange*, it defines the
+each spectrum. Combining with property ``AllowedResRange``, it defines the
 lower and upper limit for accepted fitted peak width.
 
 Let :math:`c_l = AllowedResRange[0]`, :math:`c_h = AllowedResRange[1]`

Code/Mantid/docs/source/algorithms/ChangePulsetime-v1.rst

@@ -9,8 +9,8 @@
 Description
 -----------
 
-Modifies the pulse time (wall-clock time) of all the events in the
-specified spectra of an EventWorkspace, by adding the given number of
-seconds.
+Modifies the pulse time (wall-clock time) of all the events in the specified 
+spectra of an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`__, by adding the given number 
+of seconds as specified with ``TimeOffset``.
 
 .. categories::

Code/Mantid/docs/source/algorithms/ClearMaskFlag-v1.rst

@@ -10,6 +10,7 @@ Description
 -----------
 
 This algorithm clears the mask flag/bit on all spectra of a workspace.
-It does not restore masked data.
+
+.. note:: It does not restore masked data.
 
 .. categories::

Code/Mantid/docs/source/algorithms/ConvertToEventWorkspace-v1.rst

@@ -9,22 +9,23 @@
 Description
 -----------
 
-This algorithm takes a Workspace2D with any binning or units as its
-input. An event is created for each bin of each histogram, except if the
-bin count is 0.0 (unless *GenerateZeros* is true). Infinity and NAN
-(not-a-number) values are always skipped.
+This algorithm takes a `Workspace2D <http://www.mantidproject.org/Workspace2D>`__ 
+with any binning or units as its input. An event is created for each 
+bin of each histogram, except if the bin count is 0.0 (unless 
+``GenerateZeros`` is true). Infinity and NAN (not-a-number) values 
+are always skipped.
 
 Each event is created with an X position (typically time-of-flight)
-equal to the \*\*center\*\* of the bin. The weight and error of the
+equal to the **center** of the bin. The weight and error of the
 event are taken from the histogram value.
 
-If the *GenerateMultipleEvents* option is set, then instead of a single
+If the ``GenerateMultipleEvents`` option is set, then instead of a single
 event per bin, a certain number of events evenly distributed along the X
 bin are generated. The number of events generated in each bin is
 calculated by N = (Y/E)^2. However, it is limited to a max of
-*MaxEventsPerBin* and a minimum of 1 event per bin.
+``MaxEventsPerBin`` and a minimum of 1 event per bin.
 
-Note that using *GenerateZeros* or *GenerateMultipleEvents* may use a
+Note that using ``GenerateZeros`` or ``GenerateMultipleEvents`` may use a
 lot of memory!
 
 .. categories::

Code/Mantid/docs/source/algorithms/ConvertToHistogram-v1.rst

@@ -9,9 +9,9 @@
 Description
 -----------
 
-The input workspace must contain point data.
+The ``InputWorkspace`` must contain point data.
 
-Once executed, the OutputWorkspace will contain histogram data where the
+Once executed, the ``OutputWorkspace`` will contain histogram data where the
 bin width is guessed from the spacing between the input X points.
 
 .. categories::

Code/Mantid/docs/source/algorithms/ConvertToPointData-v1.rst

@@ -9,8 +9,8 @@
 Description
 -----------
 
-The input workspace must contain histogram data. Once executed the
-OutputWorkspace will contain point data, where the X values are simply
+The ``InputWorkspace`` must contain histogram data. Once executed the
+``OutputWorkspace`` will contain point data, where the X values are simply
 the centre points of the input bins.
 
 .. categories::

Code/Mantid/docs/source/algorithms/FindPeakBackground-v1.rst

@@ -9,21 +9,27 @@
 Description
 -----------
 
-Algorithm written using this paper: J. Appl. Cryst. (2013). 46, 663-671
-
-Objective algorithm to separate signal from noise in a
-Poisson-distributed pixel data set
-
-T. Straaso/, D. Mueter, H. O. So/rensen and J. Als-Nielsen
-
-Synopsis: A method is described for the estimation of background level
-and separation of background pixels from signal pixels in a
-Poisson-distributed data set by statistical analysis. For each
-iteration, the pixel with the highest intensity value is eliminated from
-the data set and the sample mean and the unbiased variance estimator are
-calculated. Convergence is reached when the absolute difference between
-the sample mean and the sample variance of the data set is within k
-standard deviations of the variance, the default value of k being 1. The
-k value is called SigmaConstant in the algorithm input.
+Algorithm written using the paper referenced below which has a very good 
+description. 
+
+This algorithm estimates the background level and separates the background 
+from signal data in a Poisson-distributed data set by statistical analysis. 
+For each iteration, the bins/points with the highest intensity value are 
+eliminated from the data set and the sample mean and the unbiased variance 
+estimator are calculated. Convergence is reached when the absolute 
+difference between the sample mean and the sample variance of the data set 
+is within k standard deviations of the variance, the default value of k 
+being 1. The k value is called ``SigmaConstant`` in the algorithm input.
+
+References
+----------
+**Objective algorithm to separate signal from noise in a Poisson-distributed pixel data set**
+by T. |Straaso|, D. Mueter, H. O. |Sorensen| and J. Als-Nielsen Strass
+`J. Appl. Cryst. (2013). 46, 663-671 <http://dx.doi.org/10.1107/S0021889813006511>`__
+
+.. |Straaso| unicode:: Straas U+00F8 ..
+   :ltrim:
+.. |Sorensen| unicode:: S U+00F8 rensen ..
+   :trim:
 
 .. categories::

Code/Mantid/docs/source/algorithms/MaskDetectorsIf-v1.rst

@@ -12,6 +12,6 @@ Description
 Iterates over the input workspace evaluating the test for each single
 value spectrum. If the detectors should be masked it deselects all of
 the contributing detectors in the output calfile. All other aspects of
-the InputCalFile are copied over to the OutputCalFile.
+the ``InputCalFile`` are copied over to the ``OutputCalFile``.
 
 .. categories::

Code/Mantid/docs/source/algorithms/ModeratorTzero-v1.rst

@@ -9,64 +9,70 @@
 Description
 -----------
 
-| Corrects the time of flight (TOF) by a time offset that is dependent
+Corrects the time of flight (TOF) by a time offset that is dependent
 on the energy of the neutron after passing through the moderator. A
 heuristic formula for the correction is stored in the instrument
 definition file. Below is shown the entry in the instrument file for the
 VISION beamline:
-|  <!-- formula for t0 calculation. See
-http://muparser.sourceforge.net/mup\_features.html#idDef2 for available
-operators-->
-
-| `` <parameter name="t0_formula" type="string">``
-| ``  <value val="(incidentEnergy < 34.7332) ? 37.011296*incidentEnergy^(-0.052874) : (incidentEnergy < 88.7556) ? 124.267307*incidentEnergy^(-0.394282) : (incidentEnergy < 252.471) ? 963.775145*incidentEnergy^(-0.850919) : (incidentEnergy < 420.145) ? 33.225834*incidentEnergy^(-0.242105) : (incidentEnergy < 100000.0) ? 120.569231*incidentEnergy^(-0.455477) : 0.0" />``
-| ``</parameter>``
-
-| The recorded :math:`TOF = t_0 + t_i + t_f` with
-| :math:`t_0`: emission time from the moderator
-| :math:`t_1`: time from moderator to sample or monitor
-| :math:`t_2`: time from sample to detector
-| This algorithm will replace :math:`TOF` with
-:math:`TOF^* = TOF-t_0 = t_i+t_f`
-
-| For a direct geometry instrument, the incident energy :math:`E_1` is
+
+.. code-block:: xml
+
+  <!-- formula for t0 calculation. See http://muparser.sourceforge.net/mup_features.html#idDef2 for available operators-->
+  <parameter name="t0_formula" type="string">
+    <value val="(incidentEnergy < 34.7332) ? 37.011296*incidentEnergy^(-0.052874) : (incidentEnergy < 88.7556) ? 124.267307*incidentEnergy^(-0.394282) : (incidentEnergy < 252.471) ? 963.775145*incidentEnergy^(-0.850919) : (incidentEnergy < 420.145) ? 33.225834*incidentEnergy^(-0.242105) : (incidentEnergy < 100000.0) ? 120.569231*incidentEnergy^(-0.455477) : 0.0" />
+  </parameter>
+
+The recorded :math:`TOF = t_0 + t_i + t_f` with
+
+- :math:`t_0`: emission time from the moderator
+- :math:`t_1`: time from moderator to sample or monitor
+- :math:`t_2`: time from sample to detector
+
+This algorithm will replace :math:`TOF` with :math:`TOF^* = TOF-t_0 = t_i+t_f`
+
+For a direct geometry instrument, the incident energy :math:`E_1` is
 the same for all neutrons. Hence, the moderator emission time is the
 same for all neutrons. For an indirect geometry instrument, :math:`E_1`
 is different for each neutron and is not known. However, the final
 energy :math:`E_2` selected by the analyzers is known.
-| :math:`t_0 = func(E_1)` , a function of the incident energy
-| :math:`t_1 = L_1/v_1` with :math:`L_1` the distance from moderator to
-sample, and :math:`v_1` the initial unknown velocity (
-:math:`E_1=1/2*m*v_1^2`)
-| :math:`t_2 = L_2/v_2` with :math:`L_2` the distance from sample to
-detector, and :math:`v_2` is the final fixed velocity (
-:math:`E_2=1/2*m*v_2^2`)
-
-| **Note:** We obtain :math:`TOF^*` as an iterative process, taking into
-account the fact that the correction :math:`t_0` is much smaller than
-:math:`t_i+t_f`. Thus
-| :math:`TOF-t_0^{(n)} = L_1/v_1^{(n)} + L_2/v_2` , n=0, 1, 2,..
-| Set :math:`t_0^{(0)}=0` and obtain :math:`v_1^{(0)}` from the previous
-formula. From :math:`v_1^{(0)}` we obtain :math:`E_1^{(0)}`
-| Set :math:`t_0^{(1)}=func( E_1^{(0)} )` and repeat the steps until
-:math:`|t_0^{(n+1)} - t_0^{(n+1)}| < tolTOF`. With
-tolTOF=0.1microsecond, only one iteration is needed for convergence.
+
+- :math:`t_0 = func(E_1)` , a function of the incident energy
+- :math:`t_1 = L_1/v_1` with :math:`L_1` the distance from moderator to
+  sample, and :math:`v_1` the initial unknown velocity (:math:`E_1=1/2*m*v_1^2`)
+- :math:`t_2 = L_2/v_2` with :math:`L_2` the distance from sample to
+  detector, and :math:`v_2` is the final fixed velocity (:math:`E_2=1/2*m*v_2^2`)
+
+.. note:: We obtain :math:`TOF^*` as an iterative process,
+  taking into account the fact that the correction :math:`t_0` is much
+  smaller than :math:`t_i+t_f`. Thus
+  :math:`TOF-t_0^{(n)} = L_1/v_1^{(n)} + L_2/v_2` , :math:`n=0, 1, 2,..`
+  Set :math:`t_0^{(0)}=0` and obtain :math:`v_1^{(0)}` from the previous
+  formula. From :math:`v_1^{(0)}` we obtain :math:`E_1^{(0)}`
+  Set :math:`t_0^{(1)}=func( E_1^{(0)} )` and repeat the steps until
+  :math:`|t_0^{(n+1)} - t_0^{(n+1)}| < tolTOF`. With
+  :math:`tolTOF=0.1 microsecond`, only one iteration is needed for convergence.
 
 Here's the result of applying ModeratorTzero to both the event list and
 the histogrammed data of a run in the VISION beamline. The
 transformation of either events or histograms shifts the curve to
 smaller TOF's. The transformed curves are not supposed to be identical,
 but similar and differenciated from the original curve.
 
-+---------------------------------------------------------------------------------------+----------------+---------------------------------------------------------------------------------------+--------------+---------------------------------------------------------------------------------------+--------------+
-| Sumed Histogram                                                                       | Elastic Line   | Inelastic Peaks                                                                       |
-+=======================================================================================+================+=======================================================================================+==============+=======================================================================================+==============+
-| [[`File:ModeratorTzero\_Fig.1.jpeg\|200px <File:ModeratorTzero_Fig.1.jpeg|200px>`__   | center\|]]     | [[`File:ModeratorTzero\_Fig.2.jpeg\|200px <File:ModeratorTzero_Fig.2.jpeg|200px>`__   | center\|]]   | [[`File:ModeratorTzero\_Fig.3.jpeg\|200px <File:ModeratorTzero_Fig.3.jpeg|200px>`__   | center\|]]   |
-+---------------------------------------------------------------------------------------+----------------+---------------------------------------------------------------------------------------+--------------+---------------------------------------------------------------------------------------+--------------+
+.. figure:: /images/ModeratorTzero_Fig.1.jpeg
+   :width:  400px
+   :alt:    Summed Histogram
+
+.. figure:: /images/ModeratorTzero_Fig.2.jpeg
+   :width:  400px
+   :alt:    Elastic Line
+
+.. figure:: /images/ModeratorTzero_Fig.3.jpeg
+   :width:  400px
+   :alt:    Inelastic Peaks
 
 For indirect instruments featuring an incoming neutron flux having a
 sufficiently narrow distribution of energies, a linear relationship
-between t\_0 and the wavelength of the incoming neutron can be
+between :math:`t_0` and the wavelength of the incoming neutron can be
 established. This relation allows for coding of an algorithm with faster
 execution times. For indirect instruments that comply with these
 conditions, use of :ref:`algm-ModeratorTzeroLinear` is