diff --git a/Code/Mantid/docs/source/algorithms/AbsorptionCorrection-v1.rst b/Code/Mantid/docs/source/algorithms/AbsorptionCorrection-v1.rst
index a2124ea1f6b83c5f15df6a2d44510db45cd0eba6..9c2cc7626e1f497448f1f5667ec5acd8bc5b6074 100644
--- a/Code/Mantid/docs/source/algorithms/AbsorptionCorrection-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/AbsorptionCorrection-v1.rst
@@ -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
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/AlignDetectors-v1.rst b/Code/Mantid/docs/source/algorithms/AlignDetectors-v1.rst
index e0de33553a5e73432e854d7f5eaa9201bf985204..7456412a77e3a1700ba2aa314ad99c5cd2af0ed0 100644
--- a/Code/Mantid/docs/source/algorithms/AlignDetectors-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/AlignDetectors-v1.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/AppendSpectra-v1.rst b/Code/Mantid/docs/source/algorithms/AppendSpectra-v1.rst
index 684c742aee489b34f832aa3ee3fd31e839d57267..eb19376bd9cfb8255800c73c4f47dbac5a4bbf3d 100644
--- a/Code/Mantid/docs/source/algorithms/AppendSpectra-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/AppendSpectra-v1.rst
@@ -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:
diff --git a/Code/Mantid/docs/source/algorithms/ApplyTransmissionCorrection-v1.rst b/Code/Mantid/docs/source/algorithms/ApplyTransmissionCorrection-v1.rst
index dc3866c6b7e4d354fa1158394b95ddf5c3cfd175..1c77103dc9565c3df619139cc90d265d57198cef 100644
--- a/Code/Mantid/docs/source/algorithms/ApplyTransmissionCorrection-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ApplyTransmissionCorrection-v1.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/BinMD-v1.rst b/Code/Mantid/docs/source/algorithms/BinMD-v1.rst
index 711f93d8f2c35426e9d6bdee08f933d1bf0ffedc..884eca51296ebffa7f984526dc0a24dcbdf43cfe 100644
--- a/Code/Mantid/docs/source/algorithms/BinMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/BinMD-v1.rst
@@ -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.
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/ChangePulsetime-v1.rst b/Code/Mantid/docs/source/algorithms/ChangePulsetime-v1.rst
index f224896bace2bd193958a0ebd1a34b9029862390..08b9ca80ec5559f100ab50bcdc6b4a40905a366c 100644
--- a/Code/Mantid/docs/source/algorithms/ChangePulsetime-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ChangePulsetime-v1.rst
@@ -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::
diff --git a/Code/Mantid/docs/source/algorithms/CheckWorkspacesMatch-v1.rst b/Code/Mantid/docs/source/algorithms/CheckWorkspacesMatch-v1.rst
index 8aa5b8d7868a488afcd0cb9bc5ad54bee7104e39..bece0f67830342dc5e93f91deb9175c181823290 100644
--- a/Code/Mantid/docs/source/algorithms/CheckWorkspacesMatch-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CheckWorkspacesMatch-v1.rst
@@ -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.
diff --git a/Code/Mantid/docs/source/algorithms/ClearUB-v1.rst b/Code/Mantid/docs/source/algorithms/ClearUB-v1.rst
index 1dfc639a69ac98d746804b549e27604e2ed77c6d..418a5b87a596c73f976945097bb3cfe8f92d13dc 100644
--- a/Code/Mantid/docs/source/algorithms/ClearUB-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ClearUB-v1.rst
@@ -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::
diff --git a/Code/Mantid/docs/source/algorithms/CloneMDWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/CloneMDWorkspace-v1.rst
index a94d18b7491deb30a621d56af94138924d7da78d..5f02b9fd8bc557f7ec3c8b0c4cd54d2192002525 100644
--- a/Code/Mantid/docs/source/algorithms/CloneMDWorkspace-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CloneMDWorkspace-v1.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/CloneWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/CloneWorkspace-v1.rst
index 43f797bbd36d694490335f1238db7e5eb3c23b50..7f6ccb5b8cc17fbce1bdbdae358087296d57b128 100644
--- a/Code/Mantid/docs/source/algorithms/CloneWorkspace-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CloneWorkspace-v1.rst
@@ -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::
diff --git a/Code/Mantid/docs/source/algorithms/CompareMDWorkspaces-v1.rst b/Code/Mantid/docs/source/algorithms/CompareMDWorkspaces-v1.rst
index ffe7c24020e677e647805dd20eca1c5897ed2c52..be06d8d7be6e21b6124c832057246cecb3dc29a9 100644
--- a/Code/Mantid/docs/source/algorithms/CompareMDWorkspaces-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CompareMDWorkspaces-v1.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/ConvertToDetectorFaceMD-v1.rst b/Code/Mantid/docs/source/algorithms/ConvertToDetectorFaceMD-v1.rst
index a74dacd75cfe1912e8cc2886afb5b4994f84f9a6..7dbf4e39211ae398cab4152e7c087de78dabfe14 100644
--- a/Code/Mantid/docs/source/algorithms/ConvertToDetectorFaceMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ConvertToDetectorFaceMD-v1.rst
@@ -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>`_.
diff --git a/Code/Mantid/docs/source/algorithms/ConvertToEventWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/ConvertToEventWorkspace-v1.rst
index 7626297e736b0f9d877bb43690f4fb23ea29c167..773520f5adf68d27379942a6c9a78caa5dfdb53b 100644
--- a/Code/Mantid/docs/source/algorithms/ConvertToEventWorkspace-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ConvertToEventWorkspace-v1.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/ConvertToMD-v1.rst b/Code/Mantid/docs/source/algorithms/ConvertToMD-v1.rst
index a988c24278b4488cc0f638b1057cc47a7861c5d9..44737e203e1813bfc37651b9d271265e8f374730 100644
--- a/Code/Mantid/docs/source/algorithms/ConvertToMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ConvertToMD-v1.rst
@@ -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>`_.
@@ -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.
@@ -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
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/ConvertUnits-v1.rst b/Code/Mantid/docs/source/algorithms/ConvertUnits-v1.rst
index 3786e0389bcdf164c8cf58fbcd1dcb11da352676..21fd8afdd7b8b7432069d4f75a0c4b4e9944d077 100644
--- a/Code/Mantid/docs/source/algorithms/ConvertUnits-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ConvertUnits-v1.rst
@@ -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
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/CorrectToFile-v1.rst b/Code/Mantid/docs/source/algorithms/CorrectToFile-v1.rst
index 502fd37acb0938177a3f376ad0777a2d420ca736..5f88acbb8a8c47119e6d4684a3191f1256462fca 100644
--- a/Code/Mantid/docs/source/algorithms/CorrectToFile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CorrectToFile-v1.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/CreateSampleShape-v1.rst b/Code/Mantid/docs/source/algorithms/CreateSampleShape-v1.rst
index 50223df96eaa77dc3b1f359a6660217e12d9fa53..8ff6c6c7532e338a76f68bb8a5ba813f68813c76 100644
--- a/Code/Mantid/docs/source/algorithms/CreateSampleShape-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CreateSampleShape-v1.rst
@@ -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
-----
diff --git a/Code/Mantid/docs/source/algorithms/CuboidGaugeVolumeAbsorption-v1.rst b/Code/Mantid/docs/source/algorithms/CuboidGaugeVolumeAbsorption-v1.rst
index 42494a3bd0afa4beb2223a156e568fb0a421eb80..3670660cfb9a11f9c862dbd9fb98edadebc24a6c 100644
--- a/Code/Mantid/docs/source/algorithms/CuboidGaugeVolumeAbsorption-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CuboidGaugeVolumeAbsorption-v1.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/CylinderAbsorption-v1.rst b/Code/Mantid/docs/source/algorithms/CylinderAbsorption-v1.rst
index 7e8e448a8bbf9ad17cf92f485243289888094ddc..7767dc183bfefc84e94dbd99dd5b2aaed9aadb7b 100644
--- a/Code/Mantid/docs/source/algorithms/CylinderAbsorption-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/CylinderAbsorption-v1.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/DefineGaugeVolume-v1.rst b/Code/Mantid/docs/source/algorithms/DefineGaugeVolume-v1.rst
index 50ff5f8b9d8f1daccc0f0caacfb84668cf982ebd..8cfc3968380d17c242adec69a66435fb12741209 100644
--- a/Code/Mantid/docs/source/algorithms/DefineGaugeVolume-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/DefineGaugeVolume-v1.rst
@@ -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.
diff --git a/Code/Mantid/docs/source/algorithms/DetectorEfficiencyCor-v1.rst b/Code/Mantid/docs/source/algorithms/DetectorEfficiencyCor-v1.rst
index 72f48ed6c973dbc364508df2afccba42322f407d..79526dcee9dc6abc300f47722d691a7e065eec35 100644
--- a/Code/Mantid/docs/source/algorithms/DetectorEfficiencyCor-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/DetectorEfficiencyCor-v1.rst
@@ -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
@@ -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.
diff --git a/Code/Mantid/docs/source/algorithms/DiffractionFocussing-v1.rst b/Code/Mantid/docs/source/algorithms/DiffractionFocussing-v1.rst
index 6ffd784802d3e6e8fd8ccc9e94b605283e396f30..006090cf2b35bde38cf5c93258283cafcb2b274c 100644
--- a/Code/Mantid/docs/source/algorithms/DiffractionFocussing-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/DiffractionFocussing-v1.rst
@@ -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.
diff --git a/Code/Mantid/docs/source/algorithms/DivideMD-v1.rst b/Code/Mantid/docs/source/algorithms/DivideMD-v1.rst
index 8b796bb3254bf745c460ae8868da8c034ad6d26b..e3c2e2c9c575d05cdf461a7983831baf61fdad5e 100644
--- a/Code/Mantid/docs/source/algorithms/DivideMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/DivideMD-v1.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/ExponentialMD-v1.rst b/Code/Mantid/docs/source/algorithms/ExponentialMD-v1.rst
index 021f257ccabde08b862da3841ea965ee7cb97ab2..34fb2140c0932f6f363111901d88517d01827960 100644
--- a/Code/Mantid/docs/source/algorithms/ExponentialMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ExponentialMD-v1.rst
@@ -9,7 +9,7 @@
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`
@@ -17,7 +17,7 @@ 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::
diff --git a/Code/Mantid/docs/source/algorithms/ExtractSingleSpectrum-v1.rst b/Code/Mantid/docs/source/algorithms/ExtractSingleSpectrum-v1.rst
index d58e7378cfa0d4b524864c693fd37909e5c92da2..36b141c527a68393e69d1efd7d8b0462e51f63ba 100644
--- a/Code/Mantid/docs/source/algorithms/ExtractSingleSpectrum-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ExtractSingleSpectrum-v1.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/FilterEvents-v1.rst b/Code/Mantid/docs/source/algorithms/FilterEvents-v1.rst
index 353c1272ed9333e1e14b1b5511ad84b2ad748674..bdaa11f3444a2866d9b8a2953eeb2ed9a8fdb54d 100644
--- a/Code/Mantid/docs/source/algorithms/FilterEvents-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FilterEvents-v1.rst
@@ -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>`_).
diff --git a/Code/Mantid/docs/source/algorithms/FilterEventsByLogValuePreNexus-v2.rst b/Code/Mantid/docs/source/algorithms/FilterEventsByLogValuePreNexus-v2.rst
index f77b7d42fb04092f3162e1b9527be53208262cb0..62c7c96e4b35247f59f8aeba3e46ea63f2870ecd 100644
--- a/Code/Mantid/docs/source/algorithms/FilterEventsByLogValuePreNexus-v2.rst
+++ b/Code/Mantid/docs/source/algorithms/FilterEventsByLogValuePreNexus-v2.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/FindPeaksMD-v1.rst b/Code/Mantid/docs/source/algorithms/FindPeaksMD-v1.rst
index 125f310bba458ed1cf1611183498a873a2deb337..c3aa69ab50c5ec0cc0f63f7d72924f3cba8235c2 100644
--- a/Code/Mantid/docs/source/algorithms/FindPeaksMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FindPeaksMD-v1.rst
@@ -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.
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/Fit-v1.rst b/Code/Mantid/docs/source/algorithms/Fit-v1.rst
index 51a86574f4e4f835d89f82cf722103774b24482f..121c1e461b54067a724be88ca20eb596b0b57a62 100644
--- a/Code/Mantid/docs/source/algorithms/Fit-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/Fit-v1.rst
@@ -13,7 +13,7 @@ Additional properties for a 1D function and a MatrixWorkspace
#############################################################
If Function defines a one-dimensional function and InputWorkspace is a
-`MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`_ the algorithm will have these
+:ref:`MatrixWorkspace <MatrixWorkspace>` the algorithm will have these
additional properties:
+------------------+-------------+-----------+-------------------------+---------------------------------------------------------------------+
@@ -31,7 +31,7 @@ Overview
This is a generic algorithm for fitting data in a Workspace with a
function. The workspace must have the type supported by the algorithm.
-Currently supported types are: `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`_ for
+Currently supported types are: :ref:`MatrixWorkspace <MatrixWorkspace>` for
fitting with a `IFunction1D <http://www.mantidproject.org/IFunction1D>`_ and
`IMDWorkspace <http://www.mantidproject.org/IMDWorkspace>`_ for fitting with
`IFunctionMD <http://www.mantidproject.org/IFunctionMD>`_. After Function and InputWorkspace
@@ -151,7 +151,7 @@ Parameters can be constrained to be above a lower boundary and/or below
an upper boundary. If a constraint is violated a penalty to the fit is
applied which should result the parameters satisfying the constraint.
The penalty applied is described in more detail
-`here <http://www.mantidproject.org/FitConstraint>`_. Use Constraints property to set any
+:ref:`here <FitConstraint>`. Use Constraints property to set any
constraints. In case of a simple function the parameter names are used
as variables in the constraint expressions. For example
@@ -186,7 +186,7 @@ Output
Setting the Output property defines the names of the two output
workspaces. One of them is a `TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_ with
the fitted parameter values. The other is a
-`Workspace2D <http://www.mantidproject.org/Workspace2D>`_ which compares the fit with the original
+:ref:`Workspace2D <Workspace2D>` which compares the fit with the original
data. It has three spectra. The first (index 0) contains the original
data, the second one the data simulated with the fitting function and
the third spectrum is the difference between the first two. For example,
diff --git a/Code/Mantid/docs/source/algorithms/FlatPlateAbsorption-v1.rst b/Code/Mantid/docs/source/algorithms/FlatPlateAbsorption-v1.rst
index 46f9764380f771838cd66b47d6857477d9c1040d..ef8c3987d973f04d30e33861ad46dfcdf0a7fa73 100644
--- a/Code/Mantid/docs/source/algorithms/FlatPlateAbsorption-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FlatPlateAbsorption-v1.rst
@@ -27,7 +27,7 @@ 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.
diff --git a/Code/Mantid/docs/source/algorithms/GenerateEventsFilter-v1.rst b/Code/Mantid/docs/source/algorithms/GenerateEventsFilter-v1.rst
index 38f682d5dc4bc4411864c34a4fc0879f22e8c098..4f3ec49ab74f0a45250403629e23833f87c1acf7 100644
--- a/Code/Mantid/docs/source/algorithms/GenerateEventsFilter-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/GenerateEventsFilter-v1.rst
@@ -12,10 +12,10 @@ Description
This algorithm is able to generate event splitters according to user's
requirement for filtering events. The generated time splitters are
stored either in a `SplittersWorkspace <http://www.mantidproject.org/SplittersWorkspace>`_ or a
-`MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`_. Both of them will be used by
+:ref:`MatrixWorkspace <MatrixWorkspace>`. Both of them will be used by
algorithm :ref:`FilterEvents <algm-FilterEvents>`
to filter events from an
-`EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_.
+:ref:`EventWorkspace <EventWorkspace>`.
This algorithm is designed as a general-purposed event splitter
generator. Combined with :ref:`FilterEvents <algm-FilterEvents>`,
@@ -45,7 +45,7 @@ event splitters that are supported by this algorithm.
time, stop time and target workspace for events within start time and
stop time. This type of workspace is appropriate for the case that
the amount of generated event splitters are not huge;
-- `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`_: It uses X-axis to store time
+- :ref:`MatrixWorkspace <MatrixWorkspace>`: It uses X-axis to store time
stamp in total nanoseconds and Y-axis to store target workspace. For
example, x\_i, x\_i+1 and y\_i construct an event filter as start
time is x\_i, stop time is x\_i+1, and target workspace is y\_i-th
@@ -53,7 +53,7 @@ event splitters that are supported by this algorithm.
between time x\_i and x\_i+1 will be discarded. This type of
workspace is appropriate for the case that the amount of generated
event splitters are huge, because processing a
- `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`_ is way faster than a
+ :ref:`MatrixWorkspace <MatrixWorkspace>` is way faster than a
`TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_ in Mantid.
Functionalities
@@ -136,7 +136,7 @@ Usage
.. include:: ../usagedata-note.txt
The following is a contrived example to show how one would use the algorithm to split
-up an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_ by a temperature
+up an :ref:`EventWorkspace <EventWorkspace>` by a temperature
log. The resulting workspaces would then be fed to
:ref:`FilterEvents <algm-FilterEvents>`
for further processing.
diff --git a/Code/Mantid/docs/source/algorithms/HRPDSlabCanAbsorption-v1.rst b/Code/Mantid/docs/source/algorithms/HRPDSlabCanAbsorption-v1.rst
index 60823dfecf6f7ff5ef69a404ed6b769930342b03..416c898e3348b6f80a7391a824962baf43065ac3 100644
--- a/Code/Mantid/docs/source/algorithms/HRPDSlabCanAbsorption-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/HRPDSlabCanAbsorption-v1.rst
@@ -34,7 +34,7 @@ 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.
ChildAlgorithms used
diff --git a/Code/Mantid/docs/source/algorithms/ImportMDHistoWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/ImportMDHistoWorkspace-v1.rst
index cc5d67392dd04c804c7f29b6cfe65139d305d78e..2c6cb12f8efaafd98042024b24f0bde16a6d8019 100644
--- a/Code/Mantid/docs/source/algorithms/ImportMDHistoWorkspace-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ImportMDHistoWorkspace-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
This algorithm takes a text file (.txt extension) containing two columns
-and converts it into an `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_.
+and converts it into an :ref:`MDHistoWorkspace <MDHistoWorkspace>`.
Details
#######
diff --git a/Code/Mantid/docs/source/algorithms/IntegrateEllipsoids-v1.rst b/Code/Mantid/docs/source/algorithms/IntegrateEllipsoids-v1.rst
index b764682349a2f033d7b8d07fb8701127962ba022..713c57f5c5ab7beb6ed24a79e535e63583dea0d1 100644
--- a/Code/Mantid/docs/source/algorithms/IntegrateEllipsoids-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/IntegrateEllipsoids-v1.rst
@@ -44,7 +44,7 @@ Explanation of Inputs
#####################
- The event data to be integrated is obtained from an ordinary
- `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_
+ :ref:`EventWorkspace <EventWorkspace>`
with an X-axis in time-of-flight, as loaded from a
NeXus event file. This algorithm maps the events to reciprocal space
using *PeaksWorkwpace* with indexed peaks to determine the parameters
@@ -101,7 +101,7 @@ Detailed Algorithm Description
This algorithm will integrate a list of indexed single-crystal
diffraction peaks from a *PeaksWorkspace*, using events from an
-( `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_ ).
+( :ref:`EventWorkspace <EventWorkspace>` ).
The indexed peaks are first used to determine a UB
matrix. The inverse of that UB matrix is then used to form lists of
events that are close to peaks in reciprocal space. An event will be
diff --git a/Code/Mantid/docs/source/algorithms/IntegratePeaksHybrid-v1.rst b/Code/Mantid/docs/source/algorithms/IntegratePeaksHybrid-v1.rst
index 74aa957cdc8eed319c2f155686925fbccab93314..5b8097dd6b8ac99580b10c9c0821ad035fcec62e 100644
--- a/Code/Mantid/docs/source/algorithms/IntegratePeaksHybrid-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/IntegratePeaksHybrid-v1.rst
@@ -13,10 +13,10 @@ This is a hybrid between :ref:`algm-IntegratePeaksMD` and :ref:`algm-IntegratePe
The NumberOfBins and BackgroundOuterRadius are global to all Peaks. The actual background threshold is calculated independently for each peak based on NumberOfBins, BackgroundOuterRadius and the signal values in that region. This algorithm is in general faster than :ref:`algm-IntegratePeaksUsingClusters` and has a better ability to distinguish peaks from the background because each peak is treated independently.
Integrates arbitary shaped single crystal peaks defined on an
-`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ using connected component
+:ref:`MDHistoWorkspace <MDHistoWorkspace>` using connected component
analysis to determine regions of interest around each peak of the
`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_. The output is an integrated
-`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_ as well as a group of images `WorkspaceGroup <http://www.mantidproject.org/WorkspaceGroup>`_ of `MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_ containing the
+`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_ as well as a group of images :ref:`WorkspaceGroup <WorkspaceGroup>` of :ref:`MDWorkspaces <MDWorkspace>` containing the
labels assigned to each cluster for diagnostic and visualisation
purposes.
@@ -51,7 +51,7 @@ No Cluster Corresponding to Peak
This is because the input `PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_ has peaks
that do not align with peaks in the image. The error could either be on
the side of the input PeaksWorkspace (spurious peaks), or of the
-`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ generated as part of processing.
+:ref:`MDHistoWorkspace <MDHistoWorkspace>` generated as part of processing.
One thing to verify is that the combination of Threshold and
Normalization input parameters are not so low that they are treating
genuine peaks in the image as background.
diff --git a/Code/Mantid/docs/source/algorithms/IntegratePeaksUsingClusters-v1.rst b/Code/Mantid/docs/source/algorithms/IntegratePeaksUsingClusters-v1.rst
index f4ae300277f71eb3879cf8e6b259f7bf5b772e8c..8cd1fce12292e732969121cbe658a2b18298231c 100644
--- a/Code/Mantid/docs/source/algorithms/IntegratePeaksUsingClusters-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/IntegratePeaksUsingClusters-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
Integrates arbitary shaped single crystal peaks defined on an
-`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ using connected component
+:ref:`MDHistoWorkspace <MDHistoWorkspace>` using connected component
analysis to determine regions of interest around each peak of the
`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_. The output is an integrated
`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_ as well as an image containing the
@@ -72,7 +72,7 @@ No Cluster Corresponding to Peak
This is because the input `PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_ has peaks
that do not align with peaks in the image. The error could either be on
the side of the input PeaksWorkspace (spurious peaks), or of the
-`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ generated as part of processing.
+:ref:`MDHistoWorkspace <MDHistoWorkspace>` generated as part of processing.
One thing to verify is that the combination of Threshold and
Normalization input parameters are not so low that they are treating
genuine peaks in the image as background.
diff --git a/Code/Mantid/docs/source/algorithms/Integration-v1.rst b/Code/Mantid/docs/source/algorithms/Integration-v1.rst
index 036ce35cb271a6744b3116106fd52ed44e24bfc9..095419ce4e1e8c71aea89feeab9c5f1e1dceb979 100644
--- a/Code/Mantid/docs/source/algorithms/Integration-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/Integration-v1.rst
@@ -9,8 +9,8 @@
Description
-----------
-Integration sums up spectra in a `Workspace <http://www.mantidproject.org/Workspace>`__ and outputs a
-`Workspace <http://www.mantidproject.org/Workspace>`__ that contains only 1 value per spectrum (i.e.
+Integration sums up spectra in a :ref:`Workspace <Workspace>`_ and outputs a
+:ref:`Workspace <Workspace>`_ that contains only 1 value per spectrum (i.e.
the sum). The associated errors are added in quadrature. The two X
values per spectrum are set to the limits of the range over which the
spectrum has been integrated. By default, the entire range is integrated
@@ -37,8 +37,8 @@ workspace.
EventWorkspaces
###############
-If an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`__ is used as the input, the
-output will be a `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__.
+If an :ref:`EventWorkspace <EventWorkspace>`_ is used as the input, the
+output will be a :ref:`MatrixWorkspace <MatrixWorkspace>`_.
:ref:`algm-Rebin` is recommended if you want to keep the workspace as an
EventWorkspace.
diff --git a/Code/Mantid/docs/source/algorithms/LoadAscii-v1.rst b/Code/Mantid/docs/source/algorithms/LoadAscii-v1.rst
index e37b44bbb6f0120997a10b26c94fd4649db91134..e48be06f873c3d6571eb71cfbc0af23f9336e7be 100644
--- a/Code/Mantid/docs/source/algorithms/LoadAscii-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadAscii-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
The LoadAscii algorithm reads in spectra data from a text file and
-stores it in a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ as data points. The data in
+stores it in a :ref:`Workspace2D <Workspace2D>` as data points. The data in
the file must be organized in columns separated by commas, tabs, spaces,
colons or semicolons. Only one separator type can be used throughout the
file; use the "Separator" property to tell the algorithm which to use.
diff --git a/Code/Mantid/docs/source/algorithms/LoadEmptyInstrument-v1.rst b/Code/Mantid/docs/source/algorithms/LoadEmptyInstrument-v1.rst
index d2444a17abef32b4940af14d4f57b073f3cf382c..eea21194a955985a5badb7a3c3521d4edb87028b 100644
--- a/Code/Mantid/docs/source/algorithms/LoadEmptyInstrument-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadEmptyInstrument-v1.rst
@@ -11,7 +11,7 @@ Description
This algorithm is to enable you to look at an instrument without having
to load a full data file. Instead of loading a data file, it loads the
-`InstrumentDefinitionFile <http://www.mantidproject.org/InstrumentDefinitionFile>`_ for the
+:ref:`InstrumentDefinitionFile <InstrumentDefinitionFile>` for the
instrument, which has information about the instrument. The instrument
is referred to as being empty because there is no data associated with
it.
diff --git a/Code/Mantid/docs/source/algorithms/LoadEventNexus-v1.rst b/Code/Mantid/docs/source/algorithms/LoadEventNexus-v1.rst
index 2fa8a0150998dde628065c16b52233758684d6e0..35480cbad8c61b88a13ef8142ed5366f93c5e233 100644
--- a/Code/Mantid/docs/source/algorithms/LoadEventNexus-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadEventNexus-v1.rst
@@ -10,10 +10,10 @@ Description
-----------
The LoadEventNeXus algorithm loads data from an EventNexus file into an
-`EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_. The default histogram bin
+: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 can be rebinned
+Since it is an :ref:`EventWorkspace <EventWorkspace>`, it can be rebinned
to finer bins with no loss of data.
Sample logs, such as motor positions or e.g. temperature vs time, are
diff --git a/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v1.rst b/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v1.rst
index ff1b35aa72fab08601f0d215a7b4acae4651d890..435a520cc65addbf67570519e89dde660800a51b 100644
--- a/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v1.rst
@@ -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
diff --git a/Code/Mantid/docs/source/algorithms/LoadILL-v1.rst b/Code/Mantid/docs/source/algorithms/LoadILL-v1.rst
index 441d2c7130d6ac374c1cf79ea24830fe2b5d5017..25137cb7405f37e41a3704f13cfe7c67b8dd3498 100644
--- a/Code/Mantid/docs/source/algorithms/LoadILL-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadILL-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads an ILL TOF NeXus file into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ with
+Loads an ILL TOF NeXus file into a :ref:`Workspace2D <Workspace2D>` with
the given name.
This loader calculates the elastic peak position (EPP) on the fly. In
diff --git a/Code/Mantid/docs/source/algorithms/LoadILLIndirect-v1.rst b/Code/Mantid/docs/source/algorithms/LoadILLIndirect-v1.rst
index 0f887cdd567192e2f79ef4223aee49fadd93cbab..ac1a29d18dd968218cbd87f3d6f44b3b63036c97 100644
--- a/Code/Mantid/docs/source/algorithms/LoadILLIndirect-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadILLIndirect-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads an ILL Back Scattering NeXus file into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ with
+Loads an ILL Back Scattering NeXus file into a :ref:`Workspace2D <Workspace2D>` with
the given name.
The Units axis is defined with *empty* units. The main purpose of this loader is to be used with the **Indirect Load** interface.
diff --git a/Code/Mantid/docs/source/algorithms/LoadILLSANS-v1.rst b/Code/Mantid/docs/source/algorithms/LoadILLSANS-v1.rst
index d2cccc197c02ae1cb27c9a69ff9ec86fb5693e33..767a999dd78c211ddcf4cd43ef81065860674e10 100644
--- a/Code/Mantid/docs/source/algorithms/LoadILLSANS-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadILLSANS-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads an ILL D33 nexus file into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ with
+Loads an ILL D33 nexus file into a :ref:`Workspace2D <Workspace2D>` with
the given name.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/LoadInstrument-v1.rst b/Code/Mantid/docs/source/algorithms/LoadInstrument-v1.rst
index 65b46d2b0e63bea04477a133a25fb615a02985ee..16e10305d6f5dcd6a6c25b8d53e0c729ef31b109 100644
--- a/Code/Mantid/docs/source/algorithms/LoadInstrument-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadInstrument-v1.rst
@@ -9,11 +9,11 @@
Description
-----------
-Loads an instrument definition file (`IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`_)
+Loads an instrument definition file (:ref:`IDF <InstrumentDefinitionFile>`)
into a workspace, which contains information about detector positions,
their geometric shape, slit properties, links between values stored in
ISIS log-files and components of the instrument and so on. For more on
-IDFs see: `InstrumentDefinitionFile <http://www.mantidproject.org/InstrumentDefinitionFile>`_.
+IDFs see: :ref:`InstrumentDefinitionFile <InstrumentDefinitionFile>`.
By default the algorithm will write a 1:1 map between the spectrum
number and detector ID. Any custom loading algorithm that calls this as
diff --git a/Code/Mantid/docs/source/algorithms/LoadLLB-v1.rst b/Code/Mantid/docs/source/algorithms/LoadLLB-v1.rst
index 320f0206029594ff2b2bd83e955f4dc58a02e92a..b1f35cb4afdf0db9aceb32d1be1401ab01d05131 100644
--- a/Code/Mantid/docs/source/algorithms/LoadLLB-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadLLB-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads an LLB MIBEMOL TOF NeXus file into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_
+Loads an LLB MIBEMOL TOF NeXus file into a :ref:`Workspace2D <Workspace2D>`
with the given name.
This loader calculates the elastic peak position (EPP) on the fly.
diff --git a/Code/Mantid/docs/source/algorithms/LoadLiveData-v1.rst b/Code/Mantid/docs/source/algorithms/LoadLiveData-v1.rst
index ff520ef735e1b8d470103547466a7a28d7f351a5..771161dfa44ee055ff9e8fb1412e0c77d19158c5 100644
--- a/Code/Mantid/docs/source/algorithms/LoadLiveData-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadLiveData-v1.rst
@@ -25,7 +25,7 @@ Data Processing
`LiveListener <http://www.mantidproject.org/LiveListener>`_.
- This consists of all the data collected since the previous call.
- - The data is saved in a temporary `workspace <http://www.mantidproject.org/workspace>`_.
+ - The data is saved in a temporary :ref:`workspace <workspace>`.
- You have two options on how to process this workspace:
@@ -76,7 +76,7 @@ A Warning About Events
######################
Beware! If you select *PreserveEvents* and your processing keeps the
-data as `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_, you may end up creating
+data as :ref:`EventWorkspaces <EventWorkspace>`, you may end up creating
**very large** EventWorkspaces in long runs. Most plots require
re-sorting the events, which is an operation that gets much slower as
the list gets bigger (Order of N\*log(N)). This could cause Mantid to
diff --git a/Code/Mantid/docs/source/algorithms/LoadMappingTable-v1.rst b/Code/Mantid/docs/source/algorithms/LoadMappingTable-v1.rst
index 71b1c294c5a948f32b3e695254904e4a34263b6b..3f4b50338cf98ed10d28ad49eb398f6c9359b479 100644
--- a/Code/Mantid/docs/source/algorithms/LoadMappingTable-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadMappingTable-v1.rst
@@ -12,9 +12,9 @@ Description
Loads the mapping table between spectra and `IDetector <http://www.mantidproject.org/IDetector>`__
from a RAW file. It fills the
`SpectraToDetectorMap <http://www.mantidproject.org/SpectraToDetectorMap>`__ object contained in a
-`workspace <http://www.mantidproject.org/workspace>`__. This algorithm will fail if the
-`workspace <http://www.mantidproject.org/workspace>`__ does not already point to a full
-`instrument <http://www.mantidproject.org/instrument>`__ `geometry <http://www.mantidproject.org/geometry>`__ (which usually means
+:ref:`workspace <workspace>`_. This algorithm will fail if the
+:ref:`workspace <workspace>`_ does not already point to a full
+:ref:`instrument <instrument>`_ :ref:`geometry <geometry>`_ (which usually means
it must be run after
:ref:`algm-LoadInstrument`/:ref:`algm-LoadInstrumentFromRaw`).
diff --git a/Code/Mantid/docs/source/algorithms/LoadMcStasNexus-v1.rst b/Code/Mantid/docs/source/algorithms/LoadMcStasNexus-v1.rst
index 169522064cbe5e4565b8ddb35e11a96c4ca111ae..2678e81e93bdb8478e50da7f8afaf35141af5681 100644
--- a/Code/Mantid/docs/source/algorithms/LoadMcStasNexus-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadMcStasNexus-v1.rst
@@ -11,7 +11,7 @@ Description
Reads a McStas NeXus file into a Mantid WorkspaceGroup with a
user-supplied name. Data generated by McStas monitor components are
-stored in workspaces of type `Workspace2D <http://www.mantidproject.org/Workspace2D>`_. All data
+stored in workspaces of type :ref:`Workspace2D <Workspace2D>`. All data
sets are numbered and nested within the WorkspaceGroup. This algorithm
is under development. To date it has been tested with the following
instrument files from the McStas 2.0 instrument suite: templateDIFF,
diff --git a/Code/Mantid/docs/source/algorithms/LoadNexusMonitors-v1.rst b/Code/Mantid/docs/source/algorithms/LoadNexusMonitors-v1.rst
index 35dc09d2c9b3a7e2be07e94b60fc943aea58b56c..f37398bd745665bf8cf1ee3b11635754a7699113 100644
--- a/Code/Mantid/docs/source/algorithms/LoadNexusMonitors-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadNexusMonitors-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
This algorithm loads all monitors found in a NeXus file into a single
-`Workspace2D <http://www.mantidproject.org/Workspace2D>`_. The algorithm
+:ref:`Workspace2D <Workspace2D>`. The algorithm
assumes that all of the
monitors are histograms and have the same bin boundaries. **NOTE:** The
entry is assumed to be in SNS format, so the loader is currently not
diff --git a/Code/Mantid/docs/source/algorithms/LoadParameterFile-v1.rst b/Code/Mantid/docs/source/algorithms/LoadParameterFile-v1.rst
index eb53c17ad839d534382af7be8c283e4ef37c4cf7..bdc7a3bc4650429c702de29306e0c0abd32f431f 100644
--- a/Code/Mantid/docs/source/algorithms/LoadParameterFile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadParameterFile-v1.rst
@@ -13,12 +13,12 @@ Description
:class: highlight
This algorithm allows instrument parameters to be specified in a
-separate file from the `IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`__. The required
+separate file from the :ref:`IDF <InstrumentDefinitionFile>`_. The required
format for this file is identical to that used for defining parameters
through :xml:`<component-link>` tags in an
-`IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`_. Below is an example of how to define a parameter
+:ref:`IDF <InstrumentDefinitionFile>`. Below is an example of how to define a parameter
named 'test' to be associated with a component named 'bank\_90degnew'
-defined in the `IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`_ of the HRPD instrument:
+defined in the :ref:`IDF <InstrumentDefinitionFile>` of the HRPD instrument:
.. code-block:: xml
diff --git a/Code/Mantid/docs/source/algorithms/LoadRKH-v1.rst b/Code/Mantid/docs/source/algorithms/LoadRKH-v1.rst
index dc5417360d7cc16cefd40f8219410a218cb18b4f..aa39a2c3fad45bcbe56fd5f9e5df5afcbf1acd55 100644
--- a/Code/Mantid/docs/source/algorithms/LoadRKH-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadRKH-v1.rst
@@ -11,7 +11,7 @@ Description
Loads the given file in the RKH text format, which can be a file with
three columns of numbers. If the FirstColumnValue is a recognised
-`Mantid unit <http://www.mantidproject.org/Unit_Factory>`_ the workspace is created with just one
+:ref:`Mantid unit <Unit_Factory>` the workspace is created with just one
spectrum. Alteratively if FirstColumnValue is set to 'SpectrumNumber'
then the workspace can have many spectra with the spectrum ID's equal to
the first column in the file.
diff --git a/Code/Mantid/docs/source/algorithms/LoadRawSpectrum0-v1.rst b/Code/Mantid/docs/source/algorithms/LoadRawSpectrum0-v1.rst
index d0b0059e8c888bfe751b6b2100770727c26602df..5fda9ead37d087d9ed0c0230dc479c0383242042 100644
--- a/Code/Mantid/docs/source/algorithms/LoadRawSpectrum0-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadRawSpectrum0-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
The LoadRawSpectrum0 algorithm stores spectrum zero data from the
-selected `RAW <http://www.mantidproject.org/RAW_File>`_ file in a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_.
+selected :ref:`RAW <RAW_File>` file in a :ref:`Workspace2D <Workspace2D>`.
Usage
-----
diff --git a/Code/Mantid/docs/source/algorithms/LoadSINQFocus-v1.rst b/Code/Mantid/docs/source/algorithms/LoadSINQFocus-v1.rst
index b4568ab145ea59be8d360d01aba6bd2d4cafa05c..80dd8a38d2aa5fe286a838d9ce15c62a3aa30380 100644
--- a/Code/Mantid/docs/source/algorithms/LoadSINQFocus-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadSINQFocus-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads a SINQ (PSI) nexus file into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ with
+Loads a SINQ (PSI) nexus file into a :ref:`Workspace2D <Workspace2D>` with
the given name.
To date this algorithm only supports: FOCUS
diff --git a/Code/Mantid/docs/source/algorithms/LoadSPE-v1.rst b/Code/Mantid/docs/source/algorithms/LoadSPE-v1.rst
index 3a9a203af328cdcbf8b34889e3c925f6e01f29f9..ca76d0666c9a7cd473c920195c058a019ab0bb12 100644
--- a/Code/Mantid/docs/source/algorithms/LoadSPE-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadSPE-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads the file given into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ with the given name. The file should be in the SPE format, which is described `here <Media:Spe_file_format.pdf>`__. The workspace will have X units of `Energy transfer <http://www.mantidproject.org/Unit_Factory>`_. The other axis will be binned and have units of either `Momentum transfer / Q <Unit_Factory>`__ or degrees, depending on the label in the input file. The workspace will be flagged as a distribution.
+Loads the file given into a :ref:`Workspace2D <Workspace2D>` with the given name. The file should be in the SPE format, which is described `here <Media:Spe_file_format.pdf>`__. The workspace will have X units of :ref:`Energy transfer <Unit_Factory>`. The other axis will be binned and have units of either `Momentum transfer / Q <Unit_Factory>`__ or degrees, depending on the label in the input file. The workspace will be flagged as a distribution.
File Format
###########
diff --git a/Code/Mantid/docs/source/algorithms/LoadSassena-v1.rst b/Code/Mantid/docs/source/algorithms/LoadSassena-v1.rst
index f3a12706e2c6354a5227813152cee69b95c3ba0c..1fd55481f0c57e4c4b047ce9852e8399f3ff63dd 100644
--- a/Code/Mantid/docs/source/algorithms/LoadSassena-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadSassena-v1.rst
@@ -12,8 +12,8 @@ Description
The Sassena application `1 <http://sassena.org>`__ generates
intermediate scattering factors from molecular dynamics trajectories.
This algorithm reads Sassena output and stores all data in workspaces of
-type `Workspace2D <http://www.mantidproject.org/Workspace2D>`_, grouped under a single
-`WorkspaceGroup <http://www.mantidproject.org/WorkspaceGroup>`_.
+type :ref:`Workspace2D <Workspace2D>`, grouped under a single
+:ref:`WorkspaceGroup <WorkspaceGroup>`.
Sassena ouput files are in HDF5 format
`2 <http://www.hdfgroup.org/HDF5>`__, and can be made up of the
diff --git a/Code/Mantid/docs/source/algorithms/LoadSpec-v1.rst b/Code/Mantid/docs/source/algorithms/LoadSpec-v1.rst
index cd234f79be9301b169c45386e8381b69948d7276..fe484052b94801259924e4730517dc076961d241 100644
--- a/Code/Mantid/docs/source/algorithms/LoadSpec-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadSpec-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
The LoadSpec algorithm reads in spectra data from a text file and stores
-it in a `Workspace2D <http://www.mantidproject.org/Workspace2D>`__ as data points.
+it in a :ref:`Workspace2D <Workspace2D>`_ as data points.
The data in the file must be organized by set of 3 columns (separated by any number of spaces). The
first column has to be the X values, the second column the Y values and
the third column the error values.
@@ -38,7 +38,7 @@ LoadSpec:
5.0 25.0 3.2
6.0 30.0 4.2
-This will create a `Workspace2D <http://www.mantidproject.org/Workspace2D>`__ with 1 spectrum.
+This will create a :ref:`Workspace2D <Workspace2D>`_ with 1 spectrum.
*Example 2:*
@@ -71,6 +71,6 @@ This will create a `Workspace2D <http://www.mantidproject.org/Workspace2D>`__ wi
2.0 210.0 3.0
3.0 215.0 4.0
-This text file will create a `Workspace2D <http://www.mantidproject.org/Workspace2D>`__ with 3 spectra.
+This text file will create a :ref:`Workspace2D <Workspace2D>`_ with 3 spectra.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/LogarithmMD-v1.rst b/Code/Mantid/docs/source/algorithms/LogarithmMD-v1.rst
index beea139ce0b28cfaf6b6647ce469fce98d5e6c1a..60167e8f5fdbc4a9b1c7b200e106b1ccd307fc10 100644
--- a/Code/Mantid/docs/source/algorithms/LogarithmMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LogarithmMD-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-This executes the natural logarithm operation on a `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`__.
+This executes the natural logarithm operation on a :ref:`MDHistoWorkspace <MDHistoWorkspace>`_.
The signal :math:`a` becomes :math:`f = log(a)`
@@ -17,7 +17,7 @@ The error :math:`da` becomes :math:`df^2 = a^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-Logarithm`.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/MaskDetectors-v1.rst b/Code/Mantid/docs/source/algorithms/MaskDetectors-v1.rst
index f048db69e441d952f540ca193bf150193777c3f1..8b025bfb6fd1c01312670ea49272bacfa7dbd243 100644
--- a/Code/Mantid/docs/source/algorithms/MaskDetectors-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MaskDetectors-v1.rst
@@ -58,7 +58,7 @@ mask detectors, including
- Spectra
- Detectors
- `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__
-- General `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ other than
+- General :ref:`MatrixWorkspace <MatrixWorkspace>`_ other than
`MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__ (In this case, the mask will be
extracted from this workspace)
@@ -69,13 +69,13 @@ Here are the rules for input information for masking
1. At least one of the inputs must be specified.
2. Workspace indices and Spectra cannot be given at the same time.
-3. `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__ and general `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ cannot be given at the same time.
-4. When a general `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ is specified, then all detectors in a spectrum are treated as masked if the effective detector of that spectrum is masked.
+3. `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__ and general :ref:`MatrixWorkspace <MatrixWorkspace>`_ cannot be given at the same time.
+4. When a general :ref:`MatrixWorkspace <MatrixWorkspace>`_ is specified, then all detectors in a spectrum are treated as masked if the effective detector of that spectrum is masked.
5. The masks specified from
a) workspace indices/spectra
b) detectors
- c) `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__ /general `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ will be combined by the *plus* operation.
+ c) `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__ /general :ref:`MatrixWorkspace <MatrixWorkspace>`_ will be combined by the *plus* operation.
Operations Involved in Masking
##############################
@@ -90,7 +90,7 @@ Implementation
In the plan, the workflow to mask detectors should be
-1. Convert input detectors, workspace indices or spectra, and general `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ to a `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__.
+1. Convert input detectors, workspace indices or spectra, and general :ref:`MatrixWorkspace <MatrixWorkspace>`_ to a `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__.
2. Mask detectors according to `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__.
3. Clear data on all spectra, which have at least one detector that is masked.
diff --git a/Code/Mantid/docs/source/algorithms/MaskDetectorsInShape-v1.rst b/Code/Mantid/docs/source/algorithms/MaskDetectorsInShape-v1.rst
index e2dc6541e80b82a1315e765c3ce49fd35b32eb5e..f44542100f09c6136cdabb310cba6b969079120a 100644
--- a/Code/Mantid/docs/source/algorithms/MaskDetectorsInShape-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MaskDetectorsInShape-v1.rst
@@ -17,7 +17,7 @@ instrument and masks any detector detectors that in contained within it.
A detector is considered to be contained it its central location point
is contained within the shape.
-`This page <http://www.mantidproject.org/HowToDefineGeometricShape>`_
+:ref:`This page <HowToDefineGeometricShape>`
provides a description of the syntax of ShapeXML string.
ChildAlgorithms used
diff --git a/Code/Mantid/docs/source/algorithms/MaskMD-v1.rst b/Code/Mantid/docs/source/algorithms/MaskMD-v1.rst
index 0984a1f2784e50ea09b91a773e61da9d4f14a743..77a149eb2b72d95156b1596369a68063449acacb 100644
--- a/Code/Mantid/docs/source/algorithms/MaskMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MaskMD-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-This algorithm masks a `MDWorkspace <http://www.mantidproject.org/MDWorkspace>`__ in-situ.
+This algorithm masks a :ref:`MDWorkspace <MDWorkspace>`_ in-situ.
This algorithm will first clear-out any existing masking and then apply
the new masking.
diff --git a/Code/Mantid/docs/source/algorithms/MergeMD-v1.rst b/Code/Mantid/docs/source/algorithms/MergeMD-v1.rst
index 0621096d27f3f2e07ef67f3a3a3b5c350d852224..7847a044b08c2530bab99a097c4a67c8b632892c 100644
--- a/Code/Mantid/docs/source/algorithms/MergeMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MergeMD-v1.rst
@@ -9,11 +9,11 @@
Description
-----------
-This algorithm merges several `MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_ together
+This algorithm merges several :ref:`MDWorkspaces <MDWorkspace>` together
into one by adding their events together.
The algorithm starts by going through the list of
-`MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_ to find the extents that fully encompass
+:ref:`MDWorkspaces <MDWorkspace>` to find the extents that fully encompass
all input workspaces in each dimension. The number and names of
dimensions must match for all input workspaces.
diff --git a/Code/Mantid/docs/source/algorithms/MinusMD-v1.rst b/Code/Mantid/docs/source/algorithms/MinusMD-v1.rst
index 71830673666001045ee73acfa994ff0859317096..dffb8e271d8046f5a1af475589c67f1310e59070 100644
--- a/Code/Mantid/docs/source/algorithms/MinusMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MinusMD-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Subtract two `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_'s or a
+Subtract two :ref:`MDHistoWorkspace <MDHistoWorkspace>`'s or a
MDHistoWorkspace and a scalar.
- **MDHistoWorkspace - MDHistoWorkspace**
diff --git a/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst b/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst
index 9beab7ac1ca59dc8e2551c22acbb80a3336dc136..6d9c53e8857540a0ab014ca785be7a4715c95dc6 100644
--- a/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst
@@ -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.
At a minimum, the input workspace must have a sample shape defined.
diff --git a/Code/Mantid/docs/source/algorithms/MultiplyMD-v1.rst b/Code/Mantid/docs/source/algorithms/MultiplyMD-v1.rst
index f48bcbe024b70058bd91ea2754046c10a106bc06..272f359d5e9859a17395a4fa1b3cba4dbd9cdb67 100644
--- a/Code/Mantid/docs/source/algorithms/MultiplyMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MultiplyMD-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Multiply two `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_'s or a
+Multiply two :ref:`MDHistoWorkspace <MDHistoWorkspace>`'s or a
MDHistoWorkspace and a scalar.
The error of :math:`f = a * b` is propagated with
diff --git a/Code/Mantid/docs/source/algorithms/NormaliseByCurrent-v1.rst b/Code/Mantid/docs/source/algorithms/NormaliseByCurrent-v1.rst
index cc32b76ddd4649a976aa3df6088c249340a5f561..9b04cc2624e251f551bdde730b1a0c107465c1de 100644
--- a/Code/Mantid/docs/source/algorithms/NormaliseByCurrent-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/NormaliseByCurrent-v1.rst
@@ -29,7 +29,7 @@ property.
EventWorkspaces
###############
-If the input workspace is an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_, then
+If the input workspace is an :ref:`EventWorkspace <EventWorkspace>`, then
the output will be as well. Weighted events are used to scale by the
current (see the :ref:`algm-Divide` algorithm, which is a child
algorithm being used).
diff --git a/Code/Mantid/docs/source/algorithms/NotMD-v1.rst b/Code/Mantid/docs/source/algorithms/NotMD-v1.rst
index f85a197efdfff7bfec908800ed6731090d58c8d0..7399891c2c82aeab95198124ccc62aeaf5726e4a 100644
--- a/Code/Mantid/docs/source/algorithms/NotMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/NotMD-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
Perform the Not (negation) boolean operation on a
-`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_. The not operation is performed
+:ref:`MDHistoWorkspace <MDHistoWorkspace>`. The not operation is performed
element-by-element. Any 0.0 signal is changed to 1.0 (meaning true). Any
non-zero signal is changed to 0.0 (meaning false).
diff --git a/Code/Mantid/docs/source/algorithms/OneStepMDEW-v1.rst b/Code/Mantid/docs/source/algorithms/OneStepMDEW-v1.rst
index 335f26e86cb369c8692b592fcf260b9b435c7077..85792476505fb5f11d0b991a462cd599b873f4e9 100644
--- a/Code/Mantid/docs/source/algorithms/OneStepMDEW-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/OneStepMDEW-v1.rst
@@ -13,7 +13,7 @@ This algorithm is used in the Paraview event nexus loader to both load
an event nexus file and convert it into a `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ for use in visualization.
The :ref:`algm-LoadEventNexus` algorithm is called with default
-parameters to load into an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_.
+parameters to load into an :ref:`EventWorkspace <EventWorkspace>`.
After, that, :ref:`algm-ConvertToDiffractionMDWorkspace` algorithm is called with the new
EventWorkspace as input. The parameters are set to convert to **Q** in the lab frame,
diff --git a/Code/Mantid/docs/source/algorithms/PeakIntensityVsRadius-v1.rst b/Code/Mantid/docs/source/algorithms/PeakIntensityVsRadius-v1.rst
index 8b718123f3437c98f355cecc85f92f33f2870b87..429c9d09f2e197dea9b7a140f52e0fe3f7701d72 100644
--- a/Code/Mantid/docs/source/algorithms/PeakIntensityVsRadius-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/PeakIntensityVsRadius-v1.rst
@@ -17,14 +17,14 @@ correct integration radius for each peak.
:alt: {Integrated peak intensity vs integration radius for 3 SCD peaks}
-The algorithm requires a `MDWorkspace <http://www.mantidproject.org/MDWorkspace>`__ of SCD data in
+The algorithm requires a :ref:`MDWorkspace <MDWorkspace>`_ of SCD data in
reciprocal space; generated by e.g.
:ref:`algm-ConvertToDiffractionMDWorkspace`.
Also, you will need a `PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`__ as the list of
peaks to integrate. This can be generated using
:ref:`algm-FindPeaksMD`, for example.
-The output will be a `Workspace2D <http://www.mantidproject.org/Workspace2D>`__ with one spectrum per
+The output will be a :ref:`Workspace2D <Workspace2D>`_ with one spectrum per
peak, where:
- X = peak radius
diff --git a/Code/Mantid/docs/source/algorithms/PlotPeakByLogValue-v1.rst b/Code/Mantid/docs/source/algorithms/PlotPeakByLogValue-v1.rst
index 3e84930fb65bd9eebef86403998a431f86d3f891..a9af17f2f656fbf28c9fa38942f7ab5876015df6 100644
--- a/Code/Mantid/docs/source/algorithms/PlotPeakByLogValue-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/PlotPeakByLogValue-v1.rst
@@ -16,7 +16,7 @@ defined in the Input property. The Input property expects a list of
spectra identifiers separated by semicolons (;). An identifier is itself
a comma-separated list of values. The first value is the name of the
source. It can be either a workspace name or a name of a file (RAW or
-Nexus). If it is a name of a `WorkspaceGroup <http://www.mantidproject.org/WorkspaceGroup>`_ all its
+Nexus). If it is a name of a :ref:`WorkspaceGroup <WorkspaceGroup>` all its
members will be included in the fit. The second value selects a spectrum
within the workspace or file. It is an integer number with a prefix
defining the meaning of the number: "sp" for a spectrum number, "i" for
diff --git a/Code/Mantid/docs/source/algorithms/Plus-v1.rst b/Code/Mantid/docs/source/algorithms/Plus-v1.rst
index 394b74a279dfc9fd0dee1def7e39e71fae29e067..5410ac828102b5c5946d6851411553d0db9d7f40 100644
--- a/Code/Mantid/docs/source/algorithms/Plus-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/Plus-v1.rst
@@ -20,7 +20,7 @@ Description
EventWorkspace note
###################
-For `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_, the event lists at each
+For :ref:`EventWorkspaces <EventWorkspace>`, the event lists at each
workspace index are concatenated to create the output event list at the
same workspace index. Note that in some (rare :sup:`\*`) cases, these
event lists might be from different detectors; this is not checked
diff --git a/Code/Mantid/docs/source/algorithms/PlusMD-v1.rst b/Code/Mantid/docs/source/algorithms/PlusMD-v1.rst
index 7c19cb1c465d87f7c0c01f8563711bb842733c17..1afcf0f9a232ed9011696da148c12653f098cbe4 100644
--- a/Code/Mantid/docs/source/algorithms/PlusMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/PlusMD-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-This algorithm sums two `MDHistoWorkspaces <http://www.mantidproject.org/MDHistoWorkspace>`_ or
+This algorithm sums two :ref:`MDHistoWorkspaces <MDHistoWorkspace>` or
merges two `MDEventWorkspaces <http://www.mantidproject.org/MDEventWorkspace>`_ together.
MDHistoWorkspaces
@@ -28,7 +28,7 @@ MDEventWorkspaces
#################
This algorithm operates similary to calling Plus on two
-`EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_: it combines the events from the
+:ref:`EventWorkspaces <EventWorkspace>`: it combines the events from the
two workspaces together to form one large workspace.
Note for file-backed workspaces
diff --git a/Code/Mantid/docs/source/algorithms/PowerMD-v1.rst b/Code/Mantid/docs/source/algorithms/PowerMD-v1.rst
index b11dc3a0dbee7b1c7900d134b36b21375f9b3e1e..0615c96973751e52e712960e80942d14995fb9ef 100644
--- a/Code/Mantid/docs/source/algorithms/PowerMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/PowerMD-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-This executes the power function on a `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`__.
+This executes the power function on a :ref:`MDHistoWorkspace <MDHistoWorkspace>`_.
The signal :math:`a` becomes :math:`f = a^b`
@@ -17,6 +17,6 @@ The error :math:`da` becomes :math:`df^2 = f^2 * b^2 * (da^2 / a^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:`algm-Power`.
+:ref:`MatrixWorkspace <MatrixWorkspace>`_ is called :ref:`algm-Power`.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/Q1D-v2.rst b/Code/Mantid/docs/source/algorithms/Q1D-v2.rst
index bf129c67b5343faf93eb36d0692d691cd01a344c..462076924ac3a3f04a047f0c838d5e892e655bf6 100644
--- a/Code/Mantid/docs/source/algorithms/Q1D-v2.rst
+++ b/Code/Mantid/docs/source/algorithms/Q1D-v2.rst
@@ -37,7 +37,7 @@ neutrons are all travelling in horizontal at sample, and that
Normalized Intensity
####################
-This `algorithm <http://www.mantidproject.org/Algorithm>`_ takes a workspace of number of neutron
+This :ref:`algorithm <Algorithm>` takes a workspace of number of neutron
counts against `wavelength <http://www.mantidproject.org/Units>`_ and creates a workspace of cross
section against Q. The output Q bins boundaries are defined by setting
the property OutputBinning.
@@ -92,7 +92,7 @@ takes any `bin masking <http://www.mantidproject.org/MaskBins>`_ into account.
Although the units on the y-axis of the output workspace space are
quoted in 1/cm note that conversion to a cross section requires scaling
-by an `instrument <http://www.mantidproject.org/instrument>`_ dependent absolute units constant.
+by an :ref:`instrument <instrument>` dependent absolute units constant.
Resolution and Cutoffs
######################
diff --git a/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst b/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst
index 8747274b51d8aae61d362d6b6df07cd461fec7e4..0285523b040cf9b9b8aa5972165e1ee46f0391fe 100644
--- a/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst
@@ -12,7 +12,7 @@ Description
RadiusSum sums the counts in rings against radius.
Below, there is an example of the execution of the RadiusSum to a
-`Workspace2D <http://www.mantidproject.org/Workspace2D>`__
+:ref:`Workspace2D <Workspace2D>`_
where the position of the pixels are not associated to detector
positions, but it is derived from the Axes.
@@ -31,7 +31,7 @@ one with :math:`width = BinSize` for
The algorithm applies a rudimentary calculation to define the bin for
each that each pixel or detector in the
-`Workspace2D <http://www.mantidproject.org/Workspace2D>`__,
+:ref:`Workspace2D <Workspace2D>`_,
but taking its center point. If the center point belongs to one bin, it
is considered that the whole pixel belongs to the bin. The picture
below, shows what does this means. An ideal solution for RadiusSum is
@@ -41,7 +41,7 @@ the left image, while the right image is what is current implemented.
:width: 300px
Although the images were applied to an image
-`Workspace2D <http://www.mantidproject.org/Workspace2D>`__, the
+:ref:`Workspace2D <Workspace2D>`_, the
image below shows that it is possible to apply this algorithm to
Workspaces attached to instruments.
diff --git a/Code/Mantid/docs/source/algorithms/RawFileInfo-v1.rst b/Code/Mantid/docs/source/algorithms/RawFileInfo-v1.rst
index 6ec1d8eea8481b8a155f2a44343acba0c3d20024..8dcc7391b3652d46c945dd6b9b53ef3c5f9604e3 100644
--- a/Code/Mantid/docs/source/algorithms/RawFileInfo-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/RawFileInfo-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Extracts run parameters from the `RAW <http://www.mantidproject.org/RAW_File>`__ file given as an
+Extracts run parameters from the :ref:`RAW <RAW_File>`_ file given as an
input property. If the ``GetRunParameters`` argument is ``True`` then a
`TableWorkspace <http://www.mantidproject.org/TableWorkspace>`__ is created that contains a
column for each value of the ``RPB_STRUCT``, i.e. column names such as ``r_dur``, ``r_goodfrm``
diff --git a/Code/Mantid/docs/source/algorithms/Rebin-v1.rst b/Code/Mantid/docs/source/algorithms/Rebin-v1.rst
index 3079cf8041444803068bd5c2fcd0181a10ebac8c..e501900321a3e90810d37cb782923482f218f444 100644
--- a/Code/Mantid/docs/source/algorithms/Rebin-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/Rebin-v1.rst
@@ -46,7 +46,7 @@ only be requested as needed, for example, when plotting or displaying
the data.
If "Preserve Events" is false., then the output workspace will be
-created as a `Workspace2D <http://www.mantidproject.org/Workspace2D>`__, with fixed histogram bins,
+created as a :ref:`Workspace2D <Workspace2D>`_, with fixed histogram bins,
and all Y data will be computed immediately. All event-specific data is
lost at that point.
diff --git a/Code/Mantid/docs/source/algorithms/RingProfile-v1.rst b/Code/Mantid/docs/source/algorithms/RingProfile-v1.rst
index 5a2d9b52f9048837a6dbca79dc76a093bac33e5c..c8d7a3c22c9f948e20a2406e51c98d82e2a247a9 100644
--- a/Code/Mantid/docs/source/algorithms/RingProfile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/RingProfile-v1.rst
@@ -12,7 +12,7 @@ Description
RingProfile sums the counts against a ring.
Below, there is an example of the execution of the RingProfile to a
-`Workspace2D <http://www.mantidproject.org/Workspace2D>`_ where the position of the pixels are not
+:ref:`Workspace2D <Workspace2D>` where the position of the pixels are not
associated to detector positions, but it is derived from the
`Axes <Interacting_with_Matrix_Workspaces#Axes>`__.
diff --git a/Code/Mantid/docs/source/algorithms/SassenaFFT-v1.rst b/Code/Mantid/docs/source/algorithms/SassenaFFT-v1.rst
index eee338e6b4e564a4e4ec6c45acadc0e99817df2f..dee3bd40d988361b59bf7d587b9414eaaebf3026 100644
--- a/Code/Mantid/docs/source/algorithms/SassenaFFT-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SassenaFFT-v1.rst
@@ -12,8 +12,8 @@ Description
The `Sassena <http://sassena.org>`__ application generates
intermediate scattering factors from molecular dynamics trajectories.
This algorithm reads Sassena output and stores all data in workspaces of
-type `Workspace2D <http://www.mantidproject.org/Workspace2D>`_, grouped under a single
-`WorkspaceGroup <http://www.mantidproject.org/WorkspaceGroup>`_. It is implied that the time unit is
+type :ref:`Workspace2D <Workspace2D>`, grouped under a single
+:ref:`WorkspaceGroup <WorkspaceGroup>`. It is implied that the time unit is
one **picosecond**.
Sassena ouput files are in `HDF5 <http://www.hdfgroup.org/HDF5>`__ format, and can be made up of the
diff --git a/Code/Mantid/docs/source/algorithms/SaveMD-v1.rst b/Code/Mantid/docs/source/algorithms/SaveMD-v1.rst
index e4163565ea991446f76a38aea15bcf73cc08926a..2f58ba31b373adcbff21435dabc55257441931fe 100644
--- a/Code/Mantid/docs/source/algorithms/SaveMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SaveMD-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
Save an `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ or a
-`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ to a .nxs file. The
+:ref:`MDHistoWorkspace <MDHistoWorkspace>` to a .nxs file. The
workspace's current box structure and entire list of events is
preserved. The resulting file can be loaded via :ref:`LoadMD <algm-LoadMD>`.
diff --git a/Code/Mantid/docs/source/algorithms/SaveMask-v1.rst b/Code/Mantid/docs/source/algorithms/SaveMask-v1.rst
index c398c9b829b52e0b22f14ee3ea51baef3716fbfc..1a40fa2b8039c4e6bb2473b43a51c935c09d59d3 100644
--- a/Code/Mantid/docs/source/algorithms/SaveMask-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SaveMask-v1.rst
@@ -23,7 +23,7 @@ There are two types of mask workspace that can serve as input.
In this case, :ref:`algm-SaveMask` will read Y values to determine
which detectors are masked;
-2. A non-\ `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__ `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ containing `Instrument <http://www.mantidproject.org/Instrument>`__
+2. A non-\ `MaskWorkspace <http://www.mantidproject.org/MaskWorkspace>`__ :ref:`MatrixWorkspace <MatrixWorkspace>`_ containing :ref:`Instrument <Instrument>`_
################################################################################################################################################################################################################
In this case, :ref:`algm-SaveMask` will scan through all detectors to
diff --git a/Code/Mantid/docs/source/algorithms/SaveNexusProcessed-v1.rst b/Code/Mantid/docs/source/algorithms/SaveNexusProcessed-v1.rst
index 51718572c8556aa4886f672ac9178d61ab3320e8..5dead787512b7125fb002fad3dc8862958c69b9d 100644
--- a/Code/Mantid/docs/source/algorithms/SaveNexusProcessed-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SaveNexusProcessed-v1.rst
@@ -36,7 +36,7 @@ loaded at present.
EventWorkspaces
###############
-This algorithm will save `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_ with full
+This algorithm will save :ref:`EventWorkspaces <EventWorkspace>` with full
event data, unless you uncheck *PreserveEvents*, in which case the
histogram version of the workspace is saved.
diff --git a/Code/Mantid/docs/source/algorithms/SaveZODS-v1.rst b/Code/Mantid/docs/source/algorithms/SaveZODS-v1.rst
index 846bc38edd070200ecb88c8fbda028779e7989bb..40294a5eec0aa0cd25a0925c8d64d6e1a4883d3d 100644
--- a/Code/Mantid/docs/source/algorithms/SaveZODS-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SaveZODS-v1.rst
@@ -11,7 +11,7 @@ Description
Saves a HDF5 file to the ZODS (Zurich Oak Ridge Disorder Simulation
program) format. This format consists of a slice of a
-`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`__ and some information about its
+:ref:`MDHistoWorkspace <MDHistoWorkspace>`_ and some information about its
location.
**You must be in HKL space for the output of this algorithm to make
diff --git a/Code/Mantid/docs/source/algorithms/SetMDUsingMask-v1.rst b/Code/Mantid/docs/source/algorithms/SetMDUsingMask-v1.rst
index 2d1f41b14ac8da04bbb3f5dceccf827e71e18637..65bc95bd65d8ca7669c9500c373efc97738de4b8 100644
--- a/Code/Mantid/docs/source/algorithms/SetMDUsingMask-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SetMDUsingMask-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
This algorithm is used to replace values in a
-`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ but only at particular points.
+:ref:`MDHistoWorkspace <MDHistoWorkspace>` but only at particular points.
A mask MDHistoWorkspace is provided, where non-zero values indicate
'true'. At these points, the corresponding value in the ValueWorkspace
diff --git a/Code/Mantid/docs/source/algorithms/SetSpecialCoordinates-v1.rst b/Code/Mantid/docs/source/algorithms/SetSpecialCoordinates-v1.rst
index 998506051fa6c207967feb00de869ba48beb5319..d218db752e69743c08f25a25b098d259928ea202 100644
--- a/Code/Mantid/docs/source/algorithms/SetSpecialCoordinates-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SetSpecialCoordinates-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
`MDEventWorkspaces <http://www.mantidproject.org/MDEventWorkspace>`_ and
-`MDHistoWorkspaces <http://www.mantidproject.org/MDHistoWorkspace>`_ can be used with any type of
+:ref:`MDHistoWorkspaces <MDHistoWorkspace>` can be used with any type of
coordinate system. On the other hand
`PeaksWorkspaces <http://www.mantidproject.org/PeaksWorkspace>`_ may be plotted either in QLab,
QSample or HKL. There is an inherent link between a PeaksWorkspace and a
diff --git a/Code/Mantid/docs/source/algorithms/SignalOverError-v1.rst b/Code/Mantid/docs/source/algorithms/SignalOverError-v1.rst
index 31c783f5e9a54fe70533e6f727cfe4e4c569eabf..f3d6ddfebb07929ca802df25e224c56a3c237309 100644
--- a/Code/Mantid/docs/source/algorithms/SignalOverError-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SignalOverError-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Take a `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`__ as input, and replaces the
+Take a :ref:`MatrixWorkspace <MatrixWorkspace>`_ as input, and replaces the
Y values by Y/E (signal divided by error)
diff --git a/Code/Mantid/docs/source/algorithms/SliceMD-v1.rst b/Code/Mantid/docs/source/algorithms/SliceMD-v1.rst
index 38066391d7607dc59831b62bc99ba852dd33a4b7..f3967560a5eb20f622215bef3aa91b5e1f8ba43d 100644
--- a/Code/Mantid/docs/source/algorithms/SliceMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SliceMD-v1.rst
@@ -48,7 +48,7 @@ in every other dimension - that way, boxes will only be split along the
Slicing a MDHistoWorkspace
##########################
-It is possible to slice a `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_. Each
+It is possible to slice a :ref:`MDHistoWorkspace <MDHistoWorkspace>`. Each
MDHistoWorkspace holds a reference to the
`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ that created it, as well as the
coordinate transformation that was used.
diff --git a/Code/Mantid/docs/source/algorithms/SofQW2-v1.rst b/Code/Mantid/docs/source/algorithms/SofQW2-v1.rst
index 82006b7f7067242a0ed73618512a2eddf4c07ea7..50a81a1173c26595349a6800f00b84ac5e6efb1f 100644
--- a/Code/Mantid/docs/source/algorithms/SofQW2-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SofQW2-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Converts a 2D workspace in `units <http://www.mantidproject.org/Unit_Factory>`_
+Converts a 2D workspace in :ref:`units <Unit_Factory>`
of spectrum number/**energy transfer** to
the intensity as a function of momentum transfer
:math:`Q` and energy transfer :math:`\Delta E`.
diff --git a/Code/Mantid/docs/source/algorithms/SofQW3-v1.rst b/Code/Mantid/docs/source/algorithms/SofQW3-v1.rst
index abe76ab07e2c811133cf5e699afbc2ee058f9c10..459dca030c644beac28b8c26bc9c86b3a2042a80 100644
--- a/Code/Mantid/docs/source/algorithms/SofQW3-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SofQW3-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Converts a 2D workspace from `units <http://www.mantidproject.org/Unit_Factory>`_
+Converts a 2D workspace from :ref:`units <Unit_Factory>`
of spectrum number/**energy transfer**
to the intensity as a function of **momentum transfer** :math:`Q`
and **energy transfer** :math:`\Delta E`. The rebinning is done as a
diff --git a/Code/Mantid/docs/source/algorithms/SortEvents-v1.rst b/Code/Mantid/docs/source/algorithms/SortEvents-v1.rst
index 9bd498464229484c931f58482f4ced844077082f..6ede713908b102fe3724e146bb7fe778967497f3 100644
--- a/Code/Mantid/docs/source/algorithms/SortEvents-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SortEvents-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-In an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_, event binning is performed on
+In an :ref:`EventWorkspace <EventWorkspace>`, event binning is performed on
the fly. The algorithm for binning requires a list of events sorted by
time of flight, so it will perform a sort (once) on each pixel -
however, this is done on request and without using multiple CPUs). To
diff --git a/Code/Mantid/docs/source/algorithms/SortXAxis-v1.rst b/Code/Mantid/docs/source/algorithms/SortXAxis-v1.rst
index 4ed00ad71d915c851c30406f2eb169fe6c50b667..da6bc94738d7bfeef220d18d79c5c25022c9d38a 100644
--- a/Code/Mantid/docs/source/algorithms/SortXAxis-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SortXAxis-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Clones the input `Matrix Workspaces <http://www.mantidproject.org/MatrixWorkspace>`_ and orders the
+Clones the input :ref:`Matrix Workspaces <MatrixWorkspace>` and orders the
x-axis in an ascending fashion. Ensures that the y-axis and error data
is sorted in a consistent way with the x-axis. All x-values of the input
workspace MUST be in either a descending or ascending fashion before
diff --git a/Code/Mantid/docs/source/algorithms/Stitch1D-v3.rst b/Code/Mantid/docs/source/algorithms/Stitch1D-v3.rst
index c72bbb4ce755893b21039e118f7bb1c9c2f86d60..38e8cc8afd4bdceb0e1dde0f2dc9a3210272dd12 100644
--- a/Code/Mantid/docs/source/algorithms/Stitch1D-v3.rst
+++ b/Code/Mantid/docs/source/algorithms/Stitch1D-v3.rst
@@ -9,7 +9,7 @@
Description
-----------
-Stitches single histogram `Matrix Workspaces <http://www.mantidproject.org/MatrixWorkspace>`_
+Stitches single histogram :ref:`Matrix Workspaces <MatrixWorkspace>`
together outputting a stitched Matrix Workspace. Either the
right-hand-side or left-hand-side workspace can be chosen to be scaled.
Users must provide a Param step (single value), but the binning start
diff --git a/Code/Mantid/docs/source/algorithms/Stitch1DMany-v1.rst b/Code/Mantid/docs/source/algorithms/Stitch1DMany-v1.rst
index 8efe758f4b424c4fe3098656056f295aef1f0943..ba774fc4cfb43cbb9f2a060c73cc71e44617fc71 100644
--- a/Code/Mantid/docs/source/algorithms/Stitch1DMany-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/Stitch1DMany-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Stitches single histogram `Matrix Workspaces <http://www.mantidproject.org/MatrixWorkspace>`_
+Stitches single histogram :ref:`Matrix Workspaces <MatrixWorkspace>`
together outputting a stitched Matrix Workspace. This algorithm is a
wrapper over :ref:`algm-Stitch1D`.
diff --git a/Code/Mantid/docs/source/algorithms/SumNeighbours-v1.rst b/Code/Mantid/docs/source/algorithms/SumNeighbours-v1.rst
index 53364591a600eda199a49d756dadcb48b97f00e2..3ed231648c937b7584b64c27021d30c93e14a3db 100644
--- a/Code/Mantid/docs/source/algorithms/SumNeighbours-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SumNeighbours-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-The algorithm looks through the `Instrument <http://www.mantidproject.org/Instrument>`__ to find all
+The algorithm looks through the :ref:`Instrument <Instrument>`_ to find all
the `RectangularDetectors <http://www.mantidproject.org/RectangularDetector>`__ defined. For each
detector, the SumX\*SumY neighboring event lists are summed together and
saved in the output workspace as a single spectrum. Therefore, the
diff --git a/Code/Mantid/docs/source/algorithms/TransformMD-v1.rst b/Code/Mantid/docs/source/algorithms/TransformMD-v1.rst
index 9e56e6fd6cb6d6169abcb228b4e14853f81d17ec..7171af5bd9dac00ee582f01d26fe506290b2b2c5 100644
--- a/Code/Mantid/docs/source/algorithms/TransformMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/TransformMD-v1.rst
@@ -10,8 +10,8 @@ Description
-----------
This algorithm applies a simple linear transformation to a
-`MDWorkspace <http://www.mantidproject.org/MDWorkspace>`_ or
-`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_. This could be used, for
+:ref:`MDWorkspace <MDWorkspace>` or
+:ref:`MDHistoWorkspace <MDHistoWorkspace>`. This could be used, for
example, to scale the Energy dimension to different units.
Each coordinate is tranformed so that :math:`x'_d = (x_d * s_d) + o_d`
@@ -29,9 +29,9 @@ Notes
#####
The relationship between the workspace and the original
-`MDWorkspace <http://www.mantidproject.org/MDWorkspace>`_, for example when the MDHistoWorkspace is
+:ref:`MDWorkspace <MDWorkspace>`, for example when the MDHistoWorkspace is
the result of :ref:`algm-BinMD`, is lost. This means that you cannot
-re-bin a transformed `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_.
+re-bin a transformed :ref:`MDHistoWorkspace <MDHistoWorkspace>`.
No units are not modified by this algorithm.
@@ -41,12 +41,12 @@ Performance Notes
- Performing the operation in-place (input=output) is always faster
because the first step of the algorithm if NOT in-place is to clone
the original workspace.
-- For `MDHistoWorkspaces <http://www.mantidproject.org/MDHistoWorkspace>`_ done in-place,
+- For :ref:`MDHistoWorkspaces <MDHistoWorkspace>` done in-place,
TransformMD is very quick (no data is modified, just the
coordinates).
-- For `MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_, every event's coordinates gets
+- For :ref:`MDWorkspaces <MDWorkspace>`, every event's coordinates gets
modified, so this may take a while for large workspaces.
-- For file-backed `MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_, you will find much
+- For file-backed :ref:`MDWorkspaces <MDWorkspace>`, you will find much
better performance if you perform the change in-place (input=output),
because the data gets written out to disk twice otherwise.
diff --git a/Code/Mantid/docs/source/algorithms/UnGroupWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/UnGroupWorkspace-v1.rst
index 4726bcff117829499ebcad40412204271bcdd711..99da598df31c853ef377cce9a234984fd4084315 100644
--- a/Code/Mantid/docs/source/algorithms/UnGroupWorkspace-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/UnGroupWorkspace-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Takes a `WorkspaceGroup <http://www.mantidproject.org/WorkspaceGroup>`_ as input and ungroups it
+Takes a :ref:`WorkspaceGroup <WorkspaceGroup>` as input and ungroups it
into several workspaces. You can perform this from the MantidPlot GUI by
selecting the WorkspaceGroup and clicking "Ungroup".
diff --git a/Code/Mantid/docs/source/algorithms/UpdateInstrumentFromFile-v1.rst b/Code/Mantid/docs/source/algorithms/UpdateInstrumentFromFile-v1.rst
index ffa5a2283cb00047fbc6b772a7e1be7e70ad947e..e4987aae5d15a37518729f5d6f5f33379f39e7f3 100644
--- a/Code/Mantid/docs/source/algorithms/UpdateInstrumentFromFile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/UpdateInstrumentFromFile-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Some instrument definition file (`IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`_)
+Some instrument definition file (:ref:`IDF <InstrumentDefinitionFile>`)
positions are only approximately correct and the true positions are
located within data files. This algorithm reads the detector positioning
from the supplied file and updates the instrument accordingly. It
diff --git a/Code/Tools/scripts/CorrectConceptLinksinAlgPages.py b/Code/Tools/scripts/CorrectConceptLinksinAlgPages.py
new file mode 100644
index 0000000000000000000000000000000000000000..0cb7836d03b552f79c49924a960a25e2e86132fa
--- /dev/null
+++ b/Code/Tools/scripts/CorrectConceptLinksinAlgPages.py
@@ -0,0 +1,78 @@
+import os, re
+import urllib2
+
+concepts = ['Algorithm',
+'Analysis_Data_Service',
+'categories',
+'Create_an_IDF',
+'Data_Service',
+'Dynamic_Factory',
+'Error_Propagation',
+'EventWorkspace',
+'Facilities_File',
+'FitConstraint',
+'Framework_Manager',
+'Geometry',
+'Geometry_of_Position',
+'Geometry_of_Shape',
+'HowToDefineGeometricShape',
+'index',
+'Instrument',
+'InstrumentDefinitionFile',
+'InstrumentParameterFile',
+'Instrument_Data_Service',
+'Lattice',
+'LET_Sample_IDF',
+'MatrixWorkspace',
+'MDHistoWorkspace',
+'MDWorkspace',
+'Nexus_file',
+'Plugin',
+'Project',
+'Properties',
+'Properties_File',
+'RAW_File',
+'Run',
+'SANS2D_Sample_IDF',
+'Shared_Pointer',
+'Table_Workspaces',
+'Unit_Factory',
+'UserAlgorithms',
+'Workflow_Algorithm',
+'Workspace',
+'Workspace2D',
+'WorkspaceGroup']
+
+
+def outputError(alg, algVersion, description, notes=""):
+ print "%s, %i, %s, %s" % (alg, algVersion, description, notes)
+
+rstdir = r"C:\Mantid\Code\Mantid\docs\source\algorithms"
+conceptsPattern = {}
+for concept in concepts:
+ #conceptsPattern[concept] = re.compile(concept, re.IGNORECASE)
+ conceptsPattern[concept] = re.compile(r'`([\w\s]+?)\s*<http:\/\/www\.mantidproject\.org\/(' + concept + r')\s*>`_', re.IGNORECASE)
+ #print r'`([\w\s]+?)\s*<http:\/\/www\.mantidproject\.org\/' + concept + r'\s*>`_'
+
+
+algs = AlgorithmFactory.getRegisteredAlgorithms(True)
+for alg in algs:
+ algVersion = algs[alg][0]
+ fileFound = False
+ filename = os.path.join(rstdir,alg + "-v" + str(algVersion) + ".rst")
+ if os.path.exists(filename):
+ algText = ""
+ with open (filename, "r") as algRst:
+ fileFound = True
+ algText = algRst.read()
+ for concept in concepts:
+ regex = conceptsPattern[concept]
+ while (regex.search(algText) != None):
+ outputError(alg, algVersion, "found", concept)
+ algText = regex.sub(r":ref:`\1 <\2>`",algText)
+ with open (filename, "w") as algRst:
+ algRst.write(algText)
+
+ if fileFound==False:
+ outputError(alg, algVersion, "File not found")
+