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# Indirect Data Manipulation¶

## Overview¶

The Indirect Data Manipulation interface provides Processes for manipulating reduced data from Indirect Data Reduction and converting reduced instrument data to S(Q, w), or moments for analysis in the Indirect Data Analysis and Indirect Bayes interfaces.

### Action Buttons¶

Settings

Opens the Settings GUI which allows you to customize the settings for the Indirect interfaces.

?

Opens this help page.

Py

Exports a Python script which will replicate the processing done by the current tab.

Manage Directories

Opens the Manage Directories dialog allowing you to change your search directories and default save directory and enable/disable data archive search.

## Symmetrise¶

This tab allows you to take an asymmetric reduced file (_red.nxs) and symmetrise it about the Y axis.

The curve is symmetrised such that the range of positive values between $$EMin$$ and $$EMax$$ are reflected about the Y axis and replaces the negative values in the range $$-EMax$$ to $$-EMin$$, the curve between $$-EMin$$ and $$EMin$$ is not modified.

### Symmetrise Options¶

Input

Allows you to select a reduced NeXus file (_red.nxs) or workspace (_red) as the input to the algorithm.

EMin & EMax

Sets the energy range that is to be reflected about $$y=0$$.

Spectrum No

Changes the spectrum shown in the preview plots.

XRange

Changes the range of the preview plot, this can be useful for inspecting the curve before running the algorithm.

Preview

This button will update the preview plot and parameters under the Preview section.

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

If enabled the result will be saved as a NeXus file in the default save directory.

### Preview¶

The preview section shows what a given spectra in the input will look like after it has been symmetrised and gives an idea of how well the value of EMin fits the curve on both sides of the peak.

Negative Y

The value of $$y$$ at $$x=-EMin$$.

Positive Y

The value of $$y$$ at $$x=EMin$$.

Delta Y

The difference between Negative and Positive Y. Typically this should be as close to zero as possible.

### Symmetrise Example Workflow¶

The Symmetrise tab operates on _red files. The file used in this workflow can be produced using the 26176 run number on the ISIS Energy Transfer tab. The instrument used to produce this file is IRIS, the analyser is graphite and the reflection is 002. See the ISIS Energy Transfer Example Workflow.

1. In the Input box, load the file named iris26176_graphite002_red. This will automatically plot the data on the first mini-plot.

2. Move the green slider located at x = -0.5 to be at x = -0.4.

3. Click Preview. This will update the Preview properties and the neighbouring mini-plot.

4. Click Run and wait for the interface to finish processing. This will run the Symmetrise algorithm. The output workspace is called iris26176_graphite002_sym_red.

5. Click Plot Spectra to produce a spectra plot of the output workspace. Other indices can be plotted by entering indices in the box next to the Plot Spectra button. For example, entering indices 0-2,4,6-7 will plot the spectra with workspace indices 0, 1, 2, 4, 6 and 7.

Go to the S(Q, w) Example Workflow.

## S(Q, w)¶

Provides an interface for running the SofQW algorithm.

### Instrument Options¶

Instrument

Used to select the instrument on which the data being reduced was created on.

Analyser

The analyser bank that was active when the experiment was run, or for which you are interested in seeing the results of.

Reflection

The reflection plane of the instrument set up.

Tip

If you need clarification as to the instrument setup you should use please speak to the instrument scientist who dealt with your experiment.

### S(Q, w) Options¶

Input

Allows you to select a reduced NeXus file (_red.nxs) or workspace (_red) as the input to the algorithm. An automatic contour plot of _rqw will be plotted in the preview plot once a file has finished loading.

Q Low, Q Width & Q High

Q binning parameters that are passed to the SofQW algorithm. The low and high values can be determined using the neighbouring contour plot.

Rebin in Energy

If enabled the data will first be rebinned in energy before being passed to the SofQW algorithm.

E Low, E Width & E High

The energy rebinning parameters. The low and high values can be determined using the neighbouring contour plot.

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 Contour

If enabled, it will plot the selected output workspace as a contour plot.

Save Result

If enabled the result will be saved as a NeXus file in the default save directory.

### S(Q, w) Example Workflow¶

The S(Q, w) tab operates on _red files. The file used in this workflow can be produced using the 26176 run number on the ISIS Energy Transfer tab. The instrument used to produce this file is IRIS, the analyser is graphite and the reflection is 002. See the ISIS Energy Transfer Example Workflow.

1. In the Input box, load the file named iris26176_graphite002_red. This will automatically plot the data as a contour plot within the interface.

2. Set the Q Low, Q Width and Q High to be 0.5, 0.05 and 1.8. These values are read from the contour plot.

3. Tick Rebin in Energy.

4. Set the E Low, E Width and E High to be -0.5, 0.005 and 0.5. Again, these values should be read from the contour plot.

5. Click Run and wait for the interface to finish processing. This will perform an energy rebin before performing the SofQW algorithm. The output workspace ends with suffix _sqw and is called iris26176_graphite002_sqw.

6. Enter a list of workspace indices in the output options (e.g. 0-2,4,6-7) and then click Plot Spectra to plot spectra from the output workspace.

1. Click the down arrow on the Plot Spectra button, and select Plot Contour. This will produce a contour plot of the output workspace.

2. Choose a default save directory and then click Save Result to save the output workspace. The _sqw file is used in the Moments Example Workflow.

## Moments¶

This interface uses the SofQWMoments algorithm to calculate the $$n^{th}$$ moment of an $$S(Q, \omega)$$ workspace created by the SofQW tab.

### Moments Options¶

Input

Allows you to select an $$S(Q, \omega)$$ file (_sqw.nxs) or workspace (_sqw) as the input to the algorithm.

Scale By

Used to set an optional scale factor by which to scale the output of the algorithm.

EMin & EMax

Used to set the energy range of the sample that the algorithm will use for processing.

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

If enabled the result will be saved as a NeXus file in the default save directory.

### Moments Example Workflow¶

The Moments tab operates on _sqw files. The file used in this workflow is produced during the S(Q, w) Example Workflow.

1. In the Input box, load the file named irs26176_graphite002_sqw. This will automatically plot the data in the first mini-plot.

2. Drag the blue sliders on the mini-plot so they are x=-0.4 and x=0.4.

3. Click Run and wait for the interface to finish processing. This will run the SofQWMoments algorithm. The output workspace ends with suffix _moments and is called iris26176_graphite002_moments.

## Elwin¶

Provides an interface for the 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.

### Elwin Options¶

File or Workspace

Choose to load data from a file or a workspace by using this dropdown menu. See image below for demonstration of how to load files using either option.

Input File

Specify a range of input files that are either reduced (_red.nxs) or $$S(Q, \omega)$$.

Group Input

The 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.

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¶

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 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 I(Q, t) Fit.

## I(Q, t)¶

Given sample and resolution inputs, carries out a fit as per the theory detailed in the TransformToIqt algorithm.

### I(Q, t) Options¶

Sample

Either a reduced file (_red.nxs) or workspace (_red) or an $$S(Q, \omega)$$ file (_sqw.nxs) or workspace (_sqw).

Resolution

Either a resolution file (_res.nxs) or workspace (_res) or an $$S(Q, \omega)$$ 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

Generates a tiled plot containing the selected workspace indices. This option is accessed via the down arrow on the Plot Spectra button.

Save Result

Saves the result workspace in the default save directory.

### 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 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 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 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 I(Q, t) Fit Example Workflow.

### A note on Binning¶

The bin width is determined from the energy range and the sample binning factor. The number of bins is automatically calculated based on the SampleBinning specified. The width is determined from the width of the range divided by the number of bins.

The following binning parameters cannot be modified by the user and are instead automatically calculated through the 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