Re-organised Indirect Data Analysis docs Re #27840

docs/source/interfaces/Indirect Analysis.rst

+.. _Elwin-iqt-ref:
+
+Elwin and IQt
+=============
+
+.. contents:: Table of Contents
+  :local:
+
+Elwin
+-----
+
+Provides an interface for the :ref:`ElasticWindow <algm-ElasticWindow>`
+algorithm, with the option of selecting the range to integrate over as well as
+the background range. An on-screen plot is also provided.
+
+For workspaces that have a sample log or have a sample log file available in the
+Mantid data search paths that contains the sample environment information the
+ELF workspace can also be normalised to the lowest temperature run in the range
+of input files.
+
+.. interface:: Data Analysis
+  :width: 450
+  :widget: tabElwin
+
+Elwin Options
+~~~~~~~~~~~~~
+
+Input File
+  Specify a range of input files that are either reduced (*_red.nxs*) or
+  :math:`S(Q, \omega)`.
+
+Group Input
+  The :ref:`ElasticWindowMultiple <algm-ElasticWindowMultiple>` algorithm is performed on the input files and returns a group
+  workspace as the output. This option, if unchecked, will ungroup these output workspaces.
+
+Load History
+  If unchecked the input workspace will be loaded without it's history.
+
+Integration Range
+  The energy range over which to integrate the values.
+
+Background Subtraction
+  If checked a background will be calculated and subtracted from the raw data.
+
+Background Range
+  The energy range over which a background is calculated which is subtracted from
+  the raw data.
+
+Normalise to Lowest Temp
+  If checked the raw files will be normalised to the run with the lowest
+  temperature, to do this there must be a valid sample environment entry in the
+  sample logs for each of the input files.
+
+SE log name
+  The name of the sample environment log entry in the input files sample logs
+  (defaults to ‘sample’).
+
+SE log value
+  The value to be taken from the "SE log name" data series (defaults to the
+  specified value in the instrument parameters file, and in the absence of such
+  specification, defaults to "last value")
+
+Preview File
+  The workspace currently active in the preview plot.
+
+Spectrum
+  Changes the spectrum displayed in the preview plot.
+
+Plot Current Preview
+  Plots the currently selected preview plot in a separate external window
+
+Run
+  Runs the processing configured on the current tab.
+
+Plot Spectra
+  If enabled, it will plot the selected workspace indices in the selected output workspace.
+
+Save Result
+  Saves the result in the default save directory.
+
+.. _elwin-example-workflow:
+
+Elwin Example Workflow
+~~~~~~~~~~~~~~~~~~~~~~
+The Elwin tab operates on ``_red`` and ``_sqw`` files. The files used in this workflow can
+be produced using the run numbers 104371-104375 on the
+:doc:`Indirect Data Reduction <Indirect Data Reduction>` interface in the ISIS Energy
+Transfer tab. The instrument used to produce these files is OSIRIS, the analyser is graphite
+and the reflection is 002.
+
+1. Untick the **Load History** checkbox next to the file selector if you want to load your data
+   without history.
+
+2. Click **Browse** and select the files ``osiris104371_graphite002_red``,
+   ``osiris104372_graphite002_red``, ``osiris104373_graphite002_red``, ``osiris104374_graphite002_red``
+   and ``osiris104375_graphite002_red``. Load these files and they will be plotted in the mini-plot
+   automatically.
+
+3. The workspace and spectrum displayed in the mini-plot can be changed using the combobox and
+   spinbox seen directly above the mini-plot.
+
+4. You may opt to change the x range of the mini-plot by changing the **Integration Range**, or
+   by sliding the blue lines seen on the mini-plot using the cursor. For the purpose of this
+   demonstration, use the default x range.
+
+5. Tick **Normalise to Lowest Temp**. This option will produce an extra workspace with end suffix
+   _elt. However, for this to work the input workspaces must have a temperature. See the
+   description above for more information.
+
+6. Click **Plot Current Preview** if you want a larger plot of the mini-plot.
+
+7. Click **Run** and wait for the interface to finish processing. This should generate four
+   workspaces ending in _eq, _eq2, _elf and _elt.
+
+8. In the **Output** section, select the workspace ending with _eq and then choose some workspace
+   indices (e.g. 0-2,4). Click **Plot Spectra** to plot the spectrum from the selected workspace.
+
+9. Choose a default save directory and then click **Save Result** to save the output workspaces.
+   The workspace ending in _eq will be used in the :ref:`msdfit-example-workflow`.
+
+I(Q, t)
+-------
+
+Given sample and resolution inputs, carries out a fit as per the theory detailed
+in the :ref:`TransformToIqt <algm-TransformToIqt>` algorithm.
+
+.. interface:: Data Analysis
+  :width: 450
+  :widget: tabIqt
+
+I(Q, t) Options
+~~~~~~~~~~~~~~~
+
+Sample
+  Either a reduced file (*_red.nxs*) or workspace (*_red*) or an :math:`S(Q,
+  \omega)` file (*_sqw.nxs*) or workspace (*_sqw*).
+
+Resolution
+  Either a resolution file (_res.nxs) or workspace (_res) or an :math:`S(Q,
+  \omega)` file (*_sqw.nxs*) or workspace (*_sqw*).
+
+ELow, EHigh
+  The rebinning range.
+
+SampleBinning
+  The number of neighbouring bins are summed.
+
+Symmetric Energy Range
+  Untick to allow an asymmetric energy range.
+
+Spectrum
+  Changes the spectrum displayed in the preview plot.
+
+Plot Current Preview
+  Plots the currently selected preview plot in a separate external window
+
+Calculate Errors
+  The calculation of errors using a Monte Carlo implementation can be skipped by unchecking
+  this option.
+
+Number Of Iterations
+  The number of iterations to perform in the Monte Carlo routine for error calculation 
+  in I(Q,t). 
+
+Run
+  Runs the processing configured on the current tab.
+
+Plot Spectra
+  If enabled, it will plot the selected workspace indices in the selected output workspace.
+
+Plot Tiled
+  It will plot a tiled plot containing the selected workspace indices. It accessed via the down
+  arrow on the **Plot Spectra** button.
+
+Save Result
+  Saves the result workspace in the default save directory.
+
+.. _iqt-example-workflow:
+
+I(Q, t) Example Workflow
+~~~~~~~~~~~~~~~~~~~~~~~~
+The I(Q, t) tab allows ``_red`` and ``_sqw`` for it's sample file, and allows ``_red``, ``_sqw`` and
+``_res`` for the resolution file. The sample file used in this workflow can be produced using the run
+number 26176 on the :doc:`Indirect Data Reduction <Indirect Data Reduction>` interface in the ISIS
+Energy Transfer tab. The resolution file is created in the ISIS Calibration tab using the run number
+26173. The instrument used to produce these files is IRIS, the analyser is graphite
+and the reflection is 002.
+
+1. Click **Browse** for the sample and select the file ``iris26176_graphite002_red``. Then click **Browse**
+   for the resolution and select the file ``iris26173_graphite002_res``.
+
+2. Change the **SampleBinning** variable to be 5. Changing this will calculate values for the **EWidth**,
+   **SampleBins** and **ResolutionBins** variables automatically by using the
+   :ref:`TransformToIqt <algm-TransformToIqt>` algorithm where the **BinReductionFactor** is given by the
+   **SampleBinning** value. The **SampleBinning** value must be low enough for the **ResolutionBins** to be
+   at least 5. A description of this option can be found in the :ref:`a-note-on-binning` section.
+
+3. Untick **Calculate Errors** if you do not want to calculate the errors for the output workspace which
+   ends with the suffix _iqt.
+
+4. Click **Run** and wait for the interface to finish processing. This should generate a workspace ending
+   with a suffix _iqt.
+
+5. In the **Output** section, select some workspace indices (e.g.0-2,4,6) for a tiled plot and then click
+   the down arrow on the **Plot Spectra** button before clicking **Plot Tiled**.
+
+6. Choose a default save directory and then click **Save Result** to save the _iqt workspace.
+   This workspace will be used in the :ref:`iqtfit-example-workflow`.
+
+.. _a-note-on-binning:
+
+A note on Binning
+~~~~~~~~~~~~~~~~~
+  
+The bin width is determined by the energy range and the sample binning factor. The number of bins is automatically 
+calculated based on the **SampleBinning** specified. The width is determined by the width of the range divided 
+by the number of bins.
+
+The following binning parameters are not enterable by the user and are instead automatically calculated through
+the :ref:`TransformToIqt <algm-TransformToIqt>` algorithm once a valid resolution file has been loaded. The calculated 
+binning parameters are displayed alongside the binning options:
+
+EWidth
+  The calculated bin width.
+
+SampleBins
+  The number of bins in the sample after rebinning.
+
+ResolutionBins
+  The number of bins in the resolution after rebinning. Typically this should be at
+  least 5 and a warning will be shown if it is less.
+
+.. categories:: Interfaces Indirect