Commit 99a5861d authored by Nick Draper's avatar Nick Draper
Browse files

alg links to concepts, re #9923

parent 41f17308
......@@ -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
......
......@@ -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
......
......@@ -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:
......
......@@ -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
......
......@@ -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
......
......@@ -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::
......@@ -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.
......
......@@ -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::
......@@ -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
......
......@@ -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::
......@@ -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
......
......@@ -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>`_.
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
-----
......
......@@ -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
......
......@@ -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
......
......@@ -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.
......
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