Commit 570935b7 authored by Nick Draper's avatar Nick Draper
Browse files

re #9734 3rd pass of the links

parent 16917ab7
......@@ -12,6 +12,6 @@ Description
Abort a job that has been submitted to a remote compute resource.
For more details, see the `remote job submission API
docs <Remote_Job_Submission_API>`__.
docs <http://www.mantidproject.org/Remote_Job_Submission_API>`_.
.. categories::
......@@ -51,7 +51,7 @@ 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 <HowToDefineGeometricShape>`__ to a `Run <Run>`__ property called
shape <http://www.mantidproject.org/HowToDefineGeometricShape>`_ to a `Run <http://www.mantidproject.org/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 <instrument>`__ associated with the workspace must be fully
`instrument <http://www.mantidproject.org/instrument>`_ associated with the workspace must be fully
defined because detector, source & sample position are needed.
.. |AbsorptionFlow.png| image:: /images/AbsorptionFlow.png
......
......@@ -22,10 +22,10 @@ anyway, then you probably shouldn't be using this algorithm!).
Restrictions on the input workspace
###################################
For `EventWorkspaces <EventWorkspace>`__, there are no restrictions on
For `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_, there are no restrictions on
the input workspaces if ValidateInputs=false.
For `Workspace2Ds <Workspace2D>`__, the number of bins must be the same
For `Workspace2Ds <http://www.mantidproject.org/Workspace2D>`_, the number of bins must be the same
in both inputs.
If ValidateInputs is selected, then the input workspaces must also:
......
......@@ -15,7 +15,7 @@ updated as absolute positions and so this update can be repeated.
The PositionTable must have columns *Detector ID* and *Detector
Position*. The entries of the *Detector ID* column are integer referring
to the Detector ID and the enties of the *Detector Position* are
`V3Ds <V3D>`__ referring to the position of the detector whose ID is in
`V3Ds <http://www.mantidproject.org/V3D>`_ referring to the position of the detector whose ID is in
same row.
.. categories::
......@@ -13,6 +13,6 @@ Authenticate to the remote compute resource. This must be executed
before calling any other remote algorithms.
For more details, see the `remote job submission API
docs <Remote_Job_Submission_API>`__.
docs <http://www.mantidproject.org/Remote_Job_Submission_API>`_.
.. categories::
......@@ -12,7 +12,7 @@ Description
Calculates the probability of a neutron being transmitted through the
sample using detected counts from two monitors, one in front and one
behind the sample. A data workspace can be corrected for transmission by
`dividing <Divide>`__ by the output of this algorithm.
`dividing <http://www.mantidproject.org/Divide>`_ by the output of this algorithm.
| Because the detection efficiency of the monitors can be different the
transmission calculation is done using two runs, one run with the sample
......@@ -36,7 +36,7 @@ the data to be corrected.
ChildAlgorithms used
####################
Uses the algorithm `linear <linear>`__ to fit to the calculated
Uses the algorithm `linear <http://www.mantidproject.org/linear>`_ to fit to the calculated
transmission fraction.
.. 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 <EventWorkspace>`__, they are checked to
In the case of `EventWorkspaces <http://www.mantidproject.org/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 <Workspace>`__. Works with both single ExperimentInfos and
`Workspace <http://www.mantidproject.org/Workspace>`_. Works with both single ExperimentInfos and
MultipleExperimentInfo instances.
.. categories::
......@@ -10,8 +10,8 @@ Description
-----------
This algorithm will clones an existing
`MDEventWorkspace <MDEventWorkspace>`__ or
`MDHistoWorkspace <MDHistoWorkspace>`__ into a new one.
`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ or
`MDHistoWorkspace <http://www.mantidproject.org/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 <EventWorkspace>`__. It will call CloneMDWorkspace for a
`MDEventWorkspace <MDEventWorkspace>`__ or a
`MDHistoWorkspace <MDHistoWorkspace>`__. It can also clone a
`PeaksWorkspace <PeaksWorkspace>`__.
`EventWorkspace <http://www.mantidproject.org/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
`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_.
.. categories::
......@@ -9,14 +9,14 @@
Description
-----------
Compare two MDWorkspaces (`MDEventWorkspace <MDEventWorkspace>`__ or
`MDHistoWorkspace <MDHistoWorkspace>`__) to see if they are the same.
Compare two MDWorkspaces (`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ or
`MDHistoWorkspace <http://www.mantidproject.org/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
for each bin of each workspace will be compared.
**`MDEventWorkspace <MDEventWorkspace>`__**: the events in each box will
**`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_**: the events in each box will
be compared if the *CheckEvents* option is checked. The events would
need to be in the same order to match.
......
......@@ -12,7 +12,7 @@ Description
Used Subalgorithms
------------------
The algorithm uses `Unit Factory <Unit_Factory>`__ and existing unit
The algorithm uses `Unit Factory <http://www.mantidproject.org/Unit_Factory>`_ and existing unit
conversion procedures from input Workspace Units to the Units, necessary
for transformation into correspondent MD Event workspace. It also uses
:ref:`algm-PreprocessDetectorsToMD` algorithm to help
......@@ -29,7 +29,7 @@ Notes
-----
#. For elastic analysis (:math:`dEAnalysisMode=Elastic`) the target
`unit <units>`__ is momentum :math:`k`.
`unit <http://www.mantidproject.org/units>`_ 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
......@@ -45,7 +45,7 @@ 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 <units>`__ of DeltaE. These units can not be directly
in `unit <http://www.mantidproject.org/units>`_ 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
......
......@@ -11,11 +11,11 @@ Description
Use data from the supplied file, written in the RKH format, to correct
the input data. The operations allowed for the correction are
`multiply <multiply>`__ and `divide <divide>`__.
`multiply <http://www.mantidproject.org/multiply>`_ and `divide <http://www.mantidproject.org/divide>`_.
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 <Unit_Factory>`__ of the
FirstColumnValue must match the `units <http://www.mantidproject.org/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
......
......@@ -13,12 +13,12 @@ Description
:alt: Instrument Tree
Instrument Tree
Create a `calibration file <CalFile>`__ for diffraction focusing based
Create a `calibration file <http://www.mantidproject.org/CalFile>`_ for diffraction focusing based
on list of names of the instrument tree.
If a new file name is specified then offsets in the file are all sets to
zero and all detectors are selected. If a valid calibration file already
exists at the location specified by the `GroupingFileName <CalFile>`__
exists at the location specified by the `GroupingFileName <http://www.mantidproject.org/CalFile>`_
then any existing offsets and selection values will be maintained and
only the grouping values changed.
......
......@@ -13,7 +13,7 @@ Description
:alt: Instrument Tree
Instrument Tree
Create a dummy `calibration file <CalFile>`__ for diffraction focusing
Create a dummy `calibration file <http://www.mantidproject.org/CalFile>`_ for diffraction focusing
with one group.
Offsets in the file are all sets to zero and all detectors are selected.
......
......@@ -9,7 +9,7 @@
Description
-----------
A `GroupingWorkspace <GroupingWorkspace>`__ is a simple workspace with
A `GroupingWorkspace <http://www.mantidproject.org/GroupingWorkspace>`_ is a simple workspace with
one value per detector pixel; this value corresponds to the group number
that will be used when focussing or summing another workspace.
......
......@@ -9,12 +9,12 @@
Description
-----------
Create an empty `PeaksWorkspace <PeaksWorkspace>`__. Use
Create an empty `PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_. Use
:ref:`algm-LoadIsawPeaks` or :ref:`algm-FindPeaksMD` to
create a peaks workspace with peaks.
This workspace can serve as a starting point for modifying the
`PeaksWorkspace <PeaksWorkspace>`__, using the GUI or python scripting,
`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_, using the GUI or python scripting,
for example.
Usage
......
......@@ -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 <HowToDefineGeometricShape>`__.
be found `here <http://www.mantidproject.org/HowToDefineGeometricShape>`_.
Usage
-----
......
......@@ -10,13 +10,13 @@ Description
-----------
The probability of neutron detection by each detector in the
`workspace <workspace>`__ is calculated from the neutrons' kinetic
`workspace <http://www.mantidproject.org/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
stored in the input workspace, the first in atmospheres and the last two
in metres. That workspace then needs to be converted so that its
X-values are in `units <Unit_Factory>`__ of energy transfer, e.g. using
X-values are in `units <http://www.mantidproject.org/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
......@@ -35,7 +35,7 @@ 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 <algorithm>`__ to
Note: it is not possible to use this `algorithm <http://www.mantidproject.org/algorithm>`_ to
correct for the detector efficiency alone. One solution to this is to
divide the output algorithm by :math:`k_i/k_f` calculated as above.
......
......@@ -22,7 +22,7 @@ following:
#. All histograms are read and rebinned to the new grid for their group.
#. A new workspace with N histograms is created.
Within the `CalFile <CalFile>`__ any detectors with the 'select' flag
Within the `CalFile <http://www.mantidproject.org/CalFile>`_ any detectors with the 'select' flag
can be set to zero or with a group number of 0 or -ve groups are not
included in the analysis.
......@@ -30,17 +30,17 @@ Since the new X boundaries depend on the group and not the entire
workspace, this focusing algorithm does not create overestimated X
ranges for multi-group instruments. However it is important to remember
that this means that this algorithm outputs a `ragged
workspace <Ragged_Workspace>`__. Some 2D and 3D plots will not display
workspace <http://www.mantidproject.org/Ragged_Workspace>`_. Some 2D and 3D plots will not display
the data correctly.
The DiffractionFocussing algorithm uses GroupDetectors algorithm to
combine data from several spectra according to GroupingFileName file
which is a `CalFile <CalFile>`__.
which is a `CalFile <http://www.mantidproject.org/CalFile>`_.
For EventWorkspaces
###################
The algorithm can be used with an `EventWorkspace <EventWorkspace>`__
The algorithm can be used with an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_
input, and will create an EventWorkspace output if a different workspace
is specified.
......
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