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alg links to concepts, re #9923
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NickDraper committed Aug 1, 2014
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Expand Up @@ -50,8 +50,8 @@ Assumptions
This algorithm assumes that the (parallel) beam illuminates the entire
sample **unless** a 'gauge volume' has been defined using the
:ref:`algm-DefineGaugeVolume` algorithm (or by otherwise
adding a valid XML string `defining a
shape <http://www.mantidproject.org/HowToDefineGeometricShape>`_ to a `Run <http://www.mantidproject.org/Run>`_ property called
adding a valid XML string :ref:`defining a
shape <HowToDefineGeometricShape>` to a :ref:`Run <Run>` property called
"GaugeVolume"). In this latter case only scattering within this volume
(and the sample) is integrated, because this is all the detector can
'see'. The full sample is still used for the neutron paths. (**N.B.** If
Expand All @@ -64,7 +64,7 @@ Restrictions on the input workspace
###################################

The input workspace must have units of wavelength. The
`instrument <http://www.mantidproject.org/instrument>`_ associated with the workspace must be fully
:ref:`instrument <instrument>` associated with the workspace must be fully
defined because detector, source & sample position are needed.

.. |AbsorptionFlow.png| image:: /images/AbsorptionFlow.png
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2 changes: 1 addition & 1 deletion Code/Mantid/docs/source/algorithms/AlignDetectors-v1.rst
Expand Up @@ -25,7 +25,7 @@ Restrictions on the input workspace

The input workspace must contain histogram or event data where the X
unit is time-of-flight and the Y data is raw counts. The
`instrument <http://www.mantidproject.org/instrument>`__ associated with the workspace must be fully
:ref:`instrument <instrument>`_ associated with the workspace must be fully
defined because detector, source & sample position are needed.

Usage
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4 changes: 2 additions & 2 deletions Code/Mantid/docs/source/algorithms/AppendSpectra-v1.rst
Expand Up @@ -22,10 +22,10 @@ anyway, then you probably shouldn't be using this algorithm!).
Restrictions on the input workspace
###################################

For `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_, there are no restrictions on
For :ref:`EventWorkspaces <EventWorkspace>`, there are no restrictions on
the input workspaces if ValidateInputs=false.

For `Workspace2Ds <http://www.mantidproject.org/Workspace2D>`_, the number of bins must be the same
For :ref:`Workspace2Ds <Workspace2D>`, the number of bins must be the same
in both inputs.

If ValidateInputs is selected, then the input workspaces must also:
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Expand Up @@ -9,7 +9,7 @@
Description
-----------

The transmission can be given as a `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ or given directly as
The transmission can be given as a :ref:`MatrixWorkspace <MatrixWorkspace>`_ or given directly as
numbers. One or the other method must be used.

See `SANS
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6 changes: 3 additions & 3 deletions Code/Mantid/docs/source/algorithms/BinMD-v1.rst
Expand Up @@ -11,7 +11,7 @@ Description

This algorithm performs dense binning of the events in multiple
dimensions of an input `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`__ and
places them into a dense `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`__ with 1-4 dimensions.
places them into a dense :ref:`MDHistoWorkspace <MDHistoWorkspace>`_ with 1-4 dimensions.

The input `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`__ may have more dimensions than the number of
output dimensions. The names of the dimensions in the DimX, etc.
Expand Down Expand Up @@ -89,8 +89,8 @@ dimensions!
Binning a MDHistoWorkspace
##########################

It is possible to rebin a `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`__. Each
`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`__ holds a reference to the
It is possible to rebin a :ref:`MDHistoWorkspace <MDHistoWorkspace>`_. Each
:ref:`MDHistoWorkspace <MDHistoWorkspace>`_ holds a reference to the
`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`__ that created it, as well as the
coordinate transformation that was used. In this case, the rebinning is
actually performed on the original `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`__, after suitably
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2 changes: 1 addition & 1 deletion Code/Mantid/docs/source/algorithms/ChangePulsetime-v1.rst
Expand Up @@ -10,7 +10,7 @@ Description
-----------

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
spectra of an :ref:`EventWorkspace <EventWorkspace>`_, by adding the given number
of seconds as specified with ``TimeOffset``.

.. categories::
Expand Up @@ -17,7 +17,7 @@ also optionally check the axes (this includes the units), the
spectra-detector map, the instrument (the name and parameter map) and
any bin masking.

In the case of `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_, they are checked to
In the case of :ref:`EventWorkspaces <EventWorkspace>`, they are checked to
hold identical event lists. Comparisons between an EventList and a
Workspace2D always fail.

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2 changes: 1 addition & 1 deletion Code/Mantid/docs/source/algorithms/ClearUB-v1.rst
Expand Up @@ -10,7 +10,7 @@ Description
-----------

Clears the OrientedLattice of each ExperimentInfo attached to the intput
`Workspace <http://www.mantidproject.org/Workspace>`_. Works with both single ExperimentInfos and
:ref:`Workspace <Workspace>`. Works with both single ExperimentInfos and
MultipleExperimentInfo instances.

.. categories::
2 changes: 1 addition & 1 deletion Code/Mantid/docs/source/algorithms/CloneMDWorkspace-v1.rst
Expand Up @@ -11,7 +11,7 @@ Description

This algorithm will clones an existing
`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ or
`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ into a new one.
:ref:`MDHistoWorkspace <MDHistoWorkspace>` into a new one.

If the InputWorkspace is a file-backed MDEventWorkspace, then the
algorithm will copy the original file into a new one with the suffix
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4 changes: 2 additions & 2 deletions Code/Mantid/docs/source/algorithms/CloneWorkspace-v1.rst
Expand Up @@ -11,9 +11,9 @@ Description

This algorithm performs a deep copy of all of the information in the
workspace. It maintains events if the input is an
`EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_. It will call CloneMDWorkspace for a
:ref:`EventWorkspace <EventWorkspace>`. It will call CloneMDWorkspace for a
`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ or a
`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_. It can also clone a
:ref:`MDHistoWorkspace <MDHistoWorkspace>`. It can also clone a
`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_.

.. categories::
Expand Up @@ -10,7 +10,7 @@ Description
-----------

Compare two MDWorkspaces (`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ or
`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_) to see if they are the same.
:ref:`MDHistoWorkspace <MDHistoWorkspace>`) to see if they are the same.
This is mostly meant for testing/debugging use by developers.

**What is compared**: The dimensions, as well as the signal and error
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Expand Up @@ -9,7 +9,7 @@
Description
-----------

This algorithm takes a a `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`_ and
This algorithm takes a a :ref:`MatrixWorkspace <MatrixWorkspace>` and
converts it into a `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ that can be
viewed in the `SliceViewer <http://www.mantidproject.org/SliceViewer>`_.

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Expand Up @@ -9,7 +9,7 @@
Description
-----------

This algorithm takes a `Workspace2D <http://www.mantidproject.org/Workspace2D>`__
This algorithm takes a :ref:`Workspace2D <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
Expand Down
14 changes: 7 additions & 7 deletions Code/Mantid/docs/source/algorithms/ConvertToMD-v1.rst
Expand Up @@ -9,8 +9,8 @@
Description
-----------

The algorithm is used transform existing `Event <http://www.mantidproject.org/EventWorkspace>`_
or `Matrix <http://www.mantidproject.org/MatrixWorkspace>`_ workspace into
The algorithm is used transform existing :ref:`Event <EventWorkspace>`
or :ref:`Matrix <MatrixWorkspace>` workspace into
`Multidimensional workspace <http://www.mantidproject.org/MDEventWorkspace>`__ using
`MD Transformations Factory <http://www.mantidproject.org/MD_Transformation_factory>`_.

Expand All @@ -22,9 +22,9 @@ the **MD Events** are added to this workspace.
Used Subalgorithms
------------------

The algorithm uses `Unit Factory <http://www.mantidproject.org/Unit_Factory>`_ and existing unit
conversion procedures from the input Workspace `units <http://www.mantidproject.org/Unit_Factory>`__
to the `units <http://www.mantidproject.org/Unit_Factory>`__ , necessary
The algorithm uses :ref:`Unit Factory <Unit_Factory>` and existing unit
conversion procedures from the input Workspace :ref:`units <Unit_Factory>`_
to the :ref:`units <Unit_Factory>`_ , necessary
for transformation into correspondent **MD Event workspace**. It also uses
:ref:`algm-PreprocessDetectorsToMD` algorithm to help
with transformation to reciprocal space.
Expand All @@ -42,7 +42,7 @@ Notes
-----

#. For elastic analysis (:math:`dEAnalysisMode=Elastic`) the target
`unit <http://www.mantidproject.org/Unit_Factory>`_ is momentum :math:`k`.
:ref:`unit <Unit_Factory>` is momentum :math:`k`.
#. For no analysis (CopyToMD) mode, the units remain the one, previously
defined along the workspace's axes.
#. When units of input Matrix 2D workspace (Histogram workspace) are not
Expand All @@ -58,7 +58,7 @@ Notes
when one tries to process the results of inelastic scattering
experiment in elastic mode. This message is generated by units
conversion routine, which finds out that one of the workspace axis is
in `unit <http://www.mantidproject.org/Unit_Factory>`_ of DeltaE. These units can not be directly
in :ref:`unit <Unit_Factory>` of DeltaE. These units can not be directly
converted into momentum or energy, necessary for elastic mode. Select
Direct or Indirect mode and integrate over whole energy transfer
range to obtain MD workspace, which would correspond to an Elastic
Expand Down
4 changes: 2 additions & 2 deletions Code/Mantid/docs/source/algorithms/ConvertUnits-v1.rst
Expand Up @@ -9,7 +9,7 @@
Description
-----------

Changes the units in which the X values of a `workspace <http://www.mantidproject.org/Workspace>`__
Changes the units in which the X values of a :ref:`workspace <Workspace>`_
are represented. The available units are those registered with the `Unit
Factory <http://www.mantidproject.org/Units>`__. If the Y data is 'dimensioned' (i.e. has been
divided by the bin width), then this will be correctly handled, but at
Expand Down Expand Up @@ -38,7 +38,7 @@ Restrictions on the input workspace
known to the `Unit Factory <http://www.mantidproject.org/Units>`__.
- Only histograms, not point data, can be handled at present.
- The algorithm will also fail if the source-sample distance cannot be
calculated (i.e. the `instrument <http://www.mantidproject.org/instrument>`__ has not been
calculated (i.e. the :ref:`instrument <instrument>`_ has not been
properly defined).

Available units
Expand Down
2 changes: 1 addition & 1 deletion Code/Mantid/docs/source/algorithms/CorrectToFile-v1.rst
Expand Up @@ -15,7 +15,7 @@ the input data. The operations allowed for the correction are

Allowed correction files may contain one spectrum with many bins or many
spectra each with one bin. If the are many bins then the
FirstColumnValue must match the `units <http://www.mantidproject.org/Unit_Factory>`_ of the
FirstColumnValue must match the :ref:`units <Unit_Factory>` of the
(X-values on the) workspace on the InputWorkspace. When there are many
spectra (e.g. flood correction files) FirstColumnValue must be set to
"SpectrumNumber" and the number of spectra in the file and workspace
Expand Down
Expand Up @@ -11,7 +11,7 @@ Description

Creates a shape object that defines the sample and sets the sample for
the given workspace. Shapes are defined using XML descriptions that can
be found `here <http://www.mantidproject.org/HowToDefineGeometricShape>`_.
be found :ref:`here <HowToDefineGeometricShape>`.

Usage
-----
Expand Down
Expand Up @@ -36,7 +36,7 @@ Restrictions on the input workspace
###################################

The input workspace must have units of wavelength. The
`instrument <http://www.mantidproject.org/instrument>`__ associated with the workspace must be fully
:ref:`instrument <instrument>`_ associated with the workspace must be fully
defined because detector, source & sample position are needed. A sample
shape must have been defined using, e.g.,
:ref:`algm-CreateSampleShape` and the gauge volume must be
Expand Down
Expand Up @@ -37,7 +37,7 @@ Restrictions on the input workspace
###################################

The input workspace must have units of wavelength. The
`instrument <http://www.mantidproject.org/instrument>`__ associated with the workspace must be fully
:ref:`instrument <instrument>`_ associated with the workspace must be fully
defined because detector, source & sample position are needed.

References
Expand Down
4 changes: 2 additions & 2 deletions Code/Mantid/docs/source/algorithms/DefineGaugeVolume-v1.rst
Expand Up @@ -16,10 +16,10 @@ larger sample in the :ref:`algm-AbsorptionCorrection`
algorithm. The sample shape will also need to be defined using, e.g.,
the :ref:`algm-CreateSampleShape` algorithm. Shapes are
defined using XML descriptions that can be found
`here <http://www.mantidproject.org/HowToDefineGeometricShape>`__.
:ref:`here <HowToDefineGeometricShape>`_.

Internally, this works by attaching the XML string (after validating it)
to a property called "GaugeVolume" on the workspace's `Run <http://www.mantidproject.org/Run>`__
to a property called "GaugeVolume" on the workspace's :ref:`Run <Run>`_
object.


Expand Down
Expand Up @@ -10,14 +10,14 @@ Description
-----------

The probability of neutron detection by each detector in the
`workspace <http://www.mantidproject.org/workspace>`_ is calculated from the neutrons' kinetic
:ref:`workspace <workspace>` is calculated from the neutrons' kinetic
energy, angle between their path and the detector axis, detector gas
pressure, radius and wall thickness. The detectors must be cylindrical
and their :sup:`3`\ He partial pressure, wall thickness and radius
are attached to the instrument stored in the input workspace,
The first parameter is in atmospheres and the last two in metres.
That workspace then needs to be converted so that its
X-values are in `units <http://www.mantidproject.org/Unit_Factory>`_ of energy transfer, e.g. using
X-values are in :ref:`units <Unit_Factory>` of energy transfer, e.g. using
the :ref:`algm-ConvertUnits` algorithm.

To estimate the true number of neutrons that entered the detector the
Expand All @@ -37,7 +37,7 @@ detector and energy bin). They're calculated, in angstrom\ :sup:`-1`, as
where :math:`E_i` and :math:`\Delta E` are energies in meV, the inital
neutron kinetic energy and the energy lost to the sample respectively.

Note: it is not possible to use this `algorithm <http://www.mantidproject.org/algorithm>`_ to
Note: it is not possible to use this :ref:`algorithm <algorithm>` to
correct for the detector efficiency alone. One solution to this is to
divide the output of the algorithm by :math:`k_i/k_f` calculated as above.

Expand Down
Expand Up @@ -40,7 +40,7 @@ which is a `CalFile <http://www.mantidproject.org/CalFile>`_.
For EventWorkspaces
###################

The algorithm can be used with an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_
The algorithm can be used with an :ref:`EventWorkspace <EventWorkspace>`
input, and will create an EventWorkspace output if a different workspace
is specified.

Expand Down
2 changes: 1 addition & 1 deletion Code/Mantid/docs/source/algorithms/DivideMD-v1.rst
Expand Up @@ -9,7 +9,7 @@
Description
-----------

Divide two `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_'s or a
Divide two :ref:`MDHistoWorkspace <MDHistoWorkspace>`'s or a
MDHistoWorkspace and a scalar.

The error of :math:`f = a / b` is propagated with
Expand Down
4 changes: 2 additions & 2 deletions Code/Mantid/docs/source/algorithms/ExponentialMD-v1.rst
Expand Up @@ -9,15 +9,15 @@
Description
-----------

This executes the exponential function on a `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`__.
This executes the exponential function on a :ref:`MDHistoWorkspace <MDHistoWorkspace>`_.

The signal :math:`a` becomes :math:`f = e^a`

The error :math:`da` becomes :math:`df^2 = f^2 * da^2`

This algorithm cannot be run on a
`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`__. Its equivalent on a
`MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ is called
:ref:`MatrixWorkspace <MatrixWorkspace>`_ is called
:ref:`algm-Exponential`.

.. categories::
Expand Up @@ -9,7 +9,7 @@
Description
-----------

Extracts a single spectrum from a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ and
Extracts a single spectrum from a :ref:`Workspace2D <Workspace2D>` and
stores it in a new workspace.

Usage
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4 changes: 2 additions & 2 deletions Code/Mantid/docs/source/algorithms/FilterEvents-v1.rst
Expand Up @@ -10,8 +10,8 @@ Description
-----------

This algorithm filters events from an
`EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_ to one or multiple
`EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_ according to an input
:ref:`EventWorkspace <EventWorkspace>` to one or multiple
:ref:`EventWorkspaces <EventWorkspace>` according to an input
`SplittersWorkspace <http://www.mantidproject.org/SplittersWorkspace>`_ containing a series of
splitters (i.e., `SplittingIntervals <http://www.mantidproject.org/SplittingInterval>`_).

Expand Down
Expand Up @@ -10,10 +10,10 @@ Description
-----------

The LoadEventPreNeXus algorithm stores data from the pre-nexus neutron
event data file in an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_. The default
event data file in an :ref:`EventWorkspace <EventWorkspace>`. The default
histogram bin boundaries consist of a single bin able to hold all events
(in all pixels), and will have their `units <http://www.mantidproject.org/units>`_ set to
time-of-flight. Since it is an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_, it
time-of-flight. Since it is an :ref:`EventWorkspace <EventWorkspace>`, it
can be rebinned to finer bins with no loss of data.

Optional properties
Expand Down
8 changes: 4 additions & 4 deletions Code/Mantid/docs/source/algorithms/FindPeaksMD-v1.rst
Expand Up @@ -11,7 +11,7 @@ Description

This algorithm is used to find single-crystal peaks in a
multi-dimensional workspace (`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ or
`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_). It looks for high signal
:ref:`MDHistoWorkspace <MDHistoWorkspace>`). It looks for high signal
density areas, and is based on an algorithm designed by Dennis Mikkelson
for ISAW.

Expand All @@ -37,12 +37,12 @@ Each peak created is placed in the output
`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_, which can be a new workspace or
replace the old one.

This algorithm works on a `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_
This algorithm works on a :ref:`MDHistoWorkspace <MDHistoWorkspace>`
resulting from the :ref:`algm-BinMD` algorithm also. It works in the
same way, except that the center of each bin is used since the centroid
is not accessible. It may give better results on
`Workspace2D <http://www.mantidproject.org/Workspace2D>`_'s that were converted to
`MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_.
:ref:`Workspace2D <Workspace2D>`'s that were converted to
:ref:`MDWorkspaces <MDWorkspace>`.


Usage
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