Indirect Data Analysis¶

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.

Elwin Options¶

Input File

Specify a range of input files that are either reduced (_red.nxs) or .

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.

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¶

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 MSD Fit Example Workflow.

MSD Fit Options¶

Sample

A file with extension _eq.nxs that has been created using the Elwin tab with an axis of . Alternatively, a workspace may be provided.

Single Input/Multiple Input

Choose between loading a single workspace or multiple workspaces.

Function Browser

This is used to decide the details of your fit including the fit type and minimizer used. It is possible to un-dock this browser.

Mini Plots

The top plot displays the sample data, guess and fit. The bottom plot displays the difference between the sample data and fit. It is possible to un-dock these plots.

Plot Spectrum

Changes the spectrum displayed in the mini plots.

Fit Single Spectrum

This will Fit a single spectrum selected by the neighboring Plot Spectrum spinbox.

Plot Current Preview

Plots the currently selected preview plot in a separate external window

Plot Guess

This will a plot a guess of your fit based on the information selected in the Function Browser.

Fit Spectra

Choose a range or discontinuous list of spectra to be fitted.

Mask X Range

Energy ranges may be excluded from a fit by selecting a spectrum next to the ‘Mask X Range of Spectrum’ label and then providing a comma-separated list of pairs, where each pair designates a range to exclude from the fit.

Run

Runs the processing configured on the current tab.

Plot

Plots the selected parameter stored in the result workspace.

Save Result

Saves the workspaces from the _Results group workspace in the default save directory.

MSD Fit Example Workflow¶

The MSD Fit tab operates on _eq files. The files used in this workflow are produced on the Elwin tab as seen in the Elwin Example Workflow.

1. Click Browse and select the file osi104371-104375_graphite002_red_elwin_eq. Load this file and it will be automatically plotted in the upper mini-plot.
2. Change the Plot Spectrum spinbox seen underneath the mini-plots to change the spectrum displayed in the upper mini-plot.
3. Change the EndX variable to be around 0.8 in order to change the Q range over which the fit shall take place. Alternatively, drag the EndX blue line seen on the mini-plot using the cursor.
4. Choose the Fit Type to be Gaussian. The parameters for this function can be seen if you expand the row labelled f0-MsdGauss. Choose appropriate starting values for these parameters. It is possible to constrain one of the parameters by right clicking a parameter and selecting Constrain.
5. Tick Plot Guess to get a prediction of what your fit will look like.
6. Click Run and wait for the interface to finish processing. This should generate a _Parameters table workspace and two group workspaces with end suffixes _Results and _Workspaces. The mini-plots should also update, with the upper plot displaying the calculated fit and the lower mini-plot displaying the difference between the input data and the fit.
7. Alternatively, you can click Fit Single Spectrum to perform a fit only for the spectrum currently displayed in the upper mini-plot. Do not click this for the purposes of this demonstration.
8. In the Output section, select the Msd parameter and then click Plot. This plots the Msd parameter which can be found within the _Results group workspace.

Go to the I(Q, t) Example Workflow.

I(Q, t) Options¶

Sample

Either a reduced file (_red.nxs) or workspace (_red) or an file (_sqw.nxs) or workspace (_sqw).

Resolution

Either a resolution file (_res.nxs) or workspace (_res) or an 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.

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 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 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.

I(Q, t) Fit Options¶

Sample

Either a file (_iqt.nxs) or workspace (_iqt) that has been created using the Iqt tab.

Single Input/Multiple Input

Choose between loading a single workspace or multiple workspaces.

Function Browser

This is used to decide the details of your fit including the fit type and minimizer used. Further options are seen below. It is possible to un-dock this browser.

Constrain Intensities

Check to ensure that the sum of the background and intensities is always equal to 1.

Make Beta Global

Check to use a multi-domain fitting function with the value of beta constrained - the IqtFitSimultaneous will be used to perform this fit.

Extract Members

If checked, each individual member of the fit (e.g. exponential functions), will be extracted.

Mini Plots

The top plot displays the sample data, guess and fit. The bottom plot displays the difference between the sample data and fit. It is possible to un-dock these plots.

Plot Spectrum

Changes the spectrum displayed in the mini plots.

Fit Single Spectrum

This will Fit a single spectrum selected by the neighboring Plot Spectrum spinbox.

Plot Current Preview

Plots the currently selected preview plot in a separate external window

Plot Guess

This will a plot a guess of your fit based on the information selected in the Function Browser.

Fit Spectra

Choose a range or discontinuous list of spectra to be fitted.

Mask X Range

Energy ranges may be excluded from a fit by selecting a spectrum next to the ‘Mask X Range of Spectrum’ label and then providing a comma-separated list of pairs, where each pair designates a range to exclude from the fit.

Run

Runs the processing configured on the current tab.

Plot

Plots the selected parameter stored in the result (or PDF) workspace.

Edit Result

Allows you to replace values within your _Results workspace using the IndirectReplaceFitResult algorithm. See below for more detail.

Save Result

Saves the workspaces from the _Results group workspace in the default save directory.

I(Q, t) Fit Example Workflow¶

The I(Q, t) Fit tab operates on _iqt files. The files used in this workflow are produced on the I(Q, t) tab as seen in the I(Q, t) Example Workflow.

1. Click Browse and select the file irs26176_graphite002_iqt.
2. Change the EndX variable to be around 0.2 in order to change the time range. Alternatively, drag the EndX blue line seen on the upper mini-plot using the cursor.
3. Choose the number of Exponentials to be 1. Select a Flat Background.
4. Change the Fit Spectra to go from 0 to 7. This will ensure that only the spectra within the input workspace with workspace indices between 0 and 7 are fitted.
5. Click Run and wait for the interface to finish processing. This should generate a _Parameters table workspace and two group workspaces with end suffixes _Results and _Workspaces. The mini-plots should also update, with the upper plot displaying the calculated fit and the lower mini-plot displaying the difference between the input data and the fit.
6. In the Output section, you can choose which parameter you want to plot.
7. Click Fit Single Spectrum to produce a fit result for the first spectrum.
8. In the Output section, click Edit Result and then select the _Result workspace containing multiple fits (1), and in the second combobox select the _Result workspace containing the single fit (2). Choose an output name and click Replace Fit Result. This will replace the corresponding fit result in (1) with the fit result found in (2). See the IndirectReplaceFitResult algorithm for more details. Note that the output workspace is inserted into the group workspace in which (1) is found.

Go to the ConvFit Example Workflow.

Conv Fit Options¶

Sample

Either a reduced file (_red.nxs) or workspace (_red) or an file (_sqw.nxs, _sqw.dave) or workspace (_sqw).

Resolution

Either a resolution file (_res.nxs) or workspace (_res) or an file (_sqw.nxs, _sqw.dave) or workspace (_sqw).

Single Input/Multiple Input

Choose between loading a single workspace or multiple workspaces.

Function Browser

This is used to decide the details of your fit including the fit type and minimizer used. Further options are seen below. It is possible to un-dock this browser.

Use Delta Function

Found under ‘Custom Function Groups’. Enables use of a delta function.

Extract Members

If checked, each individual member of the fit (e.g. exponential functions), will be extracted into a <result_name>_Members group workspace.

Use Temperature Correction

Adds the custom user function for temperature correction to the fit function.

Background Options

Flat Background: Adds a flat background to the composite fit function. Linear Background: Adds a linear background to the composite fit function.

Mini Plots

The top plot displays the sample data, guess and fit. The bottom plot displays the difference between the sample data and fit. It is possible to un-dock these plots.

Plot Spectrum

Changes the spectrum displayed in the mini plots.

Fit Single Spectrum

This will Fit a single spectrum selected by the neighboring Plot Spectrum spinbox.

Plot Current Preview

Plots the currently selected preview plot in a separate external window

Plot Guess

This will a plot a guess of your fit based on the information selected in the Function Browser.

Fit Spectra

Choose a range or discontinuous list of spectra to be fitted.

Mask X Range

Energy ranges may be excluded from a fit by selecting a spectrum next to the ‘Mask X Range of Spectrum’ label and then providing a comma-separated list of pairs, where each pair designates a range to exclude from the fit.

Run

Runs the processing configured on the current tab.

Plot

Plots the selected parameter stored in the result (or PDF) workspace.

Edit Result

Allows you to replace values within your _Results workspace using the IndirectReplaceFitResult algorithm. See below for more detail.

Save Result

Saves the workspaces from the _Results group workspace in the default save directory.

ConvFit Example Workflow¶

The Conv Fit tab allows _red and _sqw for its 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. Choose the Fit Type to be One Lorentzian. Tick the Delta Function checkbox. Set the background to be a Flat Background.
3. Expand the variables called f0-Lorentzian and f1-DeltaFunction. To tie the delta functions Centre to the PeakCentre of the Lorentzian, right click on the Centre parameter and go to Tie->Custom Tie and then enter f0.PeakCentre.
4. Tick Plot Guess to get a prediction of what your fit will look like.
5. Click Run and wait for the interface to finish processing. This should generate a _Parameters table workspace and two group workspaces with end suffixes _Results and _Workspaces. The mini-plots should also update, with the upper plot displaying the calculated fit and the lower mini-plot displaying the difference between the input data and the fit.
6. Choose a default save directory and then click Save Result to save the _result workspaces found inside of the group workspace ending with _Results. The saved workspace will be used in the F(Q) Fit Example Workflow.

Theory¶

For more on the theory of Conv Fit see the Conv Fit concept page.

F(Q) Fit Options¶

Sample

A sample workspace created with either ConvFit or Quasi.

Single Input/Multiple Input

Choose between loading a single workspace or multiple workspaces.

Fit Parameter

This allows you to select the type of parameter displayed in the neighbouring combobox to its right (see option below). The allowed types are ‘Width’ and ‘EISF’. Changing this combobox will also change the available Fit types in the Function Browser.

Width/EISF

Next to the ‘Fit Parameter’ menu, will be either a ‘Width’ or ‘EISF’ menu, depending on which was selected. This menu can be used to select the specific width/EISF parameter to be fit. Selecting one of these parameters will automatically set the active spectrum index of the loaded workspace in which this parameter is located.

Function Browser

This is used to decide the details of your fit including the fit type and minimizer used. Further options are seen below. It is possible to un-dock this browser.

Mini Plots

The top plot displays the sample data, guess and fit. The bottom plot displays the difference between the sample data and fit. It is possible to un-dock these plots.

Plot Spectrum

Changes the spectrum displayed in the mini plots.

Fit Single Spectrum

This will Fit a single spectrum selected by the neighboring Plot Spectrum spinbox.

Plot Current Preview

Plots the currently selected preview plot in a separate external window

Plot Guess

This will a plot a guess of your fit based on the information selected in the Function Browser.

Fit Spectra

Choose a range or discontinuous list of spectra to be fitted.

Mask X Range

Energy ranges may be excluded from a fit by selecting a spectrum next to the ‘Mask X Range of Spectrum’ label and then providing a comma-separated list of pairs, where each pair designates a range to exclude from the fit.

Run

Runs the processing configured on the current tab.

Plot

Plots the selected parameter stored in the result workspace.

Save Result

Saves the workspaces from the _Results group workspace in the default save directory.

F(Q) Fit Example Workflow¶

The F(Q) Fit tab operates on _result files which can be produced on the ConvFit tab. The sample file used in this workflow is produced on the Conv Fit tab as seen in the ConvFit Example Workflow.

1. Click Browse and select the file irs26176_graphite002_conv_Delta1LFitF_s0_to_9_Result.
2. Change the mini-plot data by choosing the type of Fit Parameter you want to display. For the purposes of this demonstration select EISF. The combobox immediately to the right can be used to choose which EISF you want to see in the mini-plot. In this example there is only one available.
3. Change the Fit Parameter back to Width.
4. Choose the Fit Type to be TeixeiraWater.
5. Click Run and wait for the interface to finish processing. This should generate a _Parameters table workspace and two group workspaces with end suffixes _Results and _Workspaces. The mini-plots should also update, with the upper plot displaying the calculated fit and the lower mini-plot displaying the difference between the input data and the fit.
6. In the Output section, you can choose which parameter you want to plot. In this case the plotting option is disabled as the output workspace ending in _Result only has one data point to plot.

Single & Multiple Input¶

Each interface provides the option to choose between selecting one or multiple data files to be fit. The selected mode can be changed by clicking either the ‘Single Input’ tab or ‘Multiple Input’ tab at the the top of the interface to switch between selecting one or multiple data files respectively. Data may either be provided as a file, or selected from workspaces which have already been loaded.

When selecting ‘Multiple Input’, a table along with two buttons ‘Add Workspace’ and ‘Remove’ will be displayed. Clicking ‘Add Workspace’ will allow you to add a new data-set to be fit (this will bring up a menu allowing you to select a file/workspace and the spectra to load). Once data has been loaded, it will be displayed in the table. Highlighting data in the table and selecting ‘Remove’ will allow you to remove data from the fit. Above the preview plots will be a drop-down menu with which you can select the active data-set, which will be shown in the plots.

Custom Function Groups¶

Under ‘Custom Function Groups’, you will find utility options for quick selection of common fit functions, specific to each fitting interface.

The ‘Fit Type’ drop-down menu will be available here in each of the QENS fitting interfaces – which is useful for selecting common fit functions but not mandatory.

Fitting Range¶

Under ‘Fitting Range’, you may select the start and end -values (‘StartX’ and ‘EndX’) to be used in the fit.

Functions¶

Under ‘Functions’, you can view the selected model and associated parameters as well as make modifications. Right-clicking on ‘Functions’ and selecting ‘Add Function’ will allow you to add any function from Mantid’s library of fitting functions. It is also possible to right-click on a composite function and select ‘Add Function’ to add a function to the composite.

Parameters may be tied by right-clicking on a parameter and selecting either ‘Tie > To Function’ when creating a tie to a parameter of the same name in a different function or by selecting ‘Tie > Custom Tie’ to tie to parameters of different names and for providing mathematical expressions. Parameters can be constrained by right-clicking and using the available options under ‘Constrain’.

Upon performing a fit, the parameter values will be updated here to display the result of the fit for the selected spectrum.

Settings¶

Minimizer

The minimizer which will be used in the fit (defaults to Levenberg-Marquadt).

Ignore invalid data

Whether to ignore invalid (infinity/NaN) values when performing the fit.

Cost function

The cost function to be used in the fit (defaults to Least Squares).

Max Iterations

The maximum number of iterations used to perform the fit of each spectrum.

Preview Plots¶

Two preview plots are included in each of the fitting interfaces. The top preview plot displays the sample, guess and fit curves. The bottom preview plot displays the difference curve.

The preview plots will display the curves for the selected spectrum (‘Plot Spectrum’) of the selected data-set (when in multiple input mode, a drop-down menu will be available above the plots to select the active data-set).

The ‘Plot Spectrum’ option can be used to select the active/displayed spectrum.

A button labelled ‘Fit Single Spectrum’ is found under the preview plots and can be used to perform a fit of the selected specturm.

‘Plot Current Preview’ can be used to plot the sample, fit and difference curves of the selected spectrum in a separate plotting window.

The ‘Plot Guess’ check-box can be used to enable/disable the guess curve in the top preview plot.

Output¶

The results of the fit may be plotted and saved under the ‘Output’ section of the fitting interfaces.

Next to the ‘Plot’ label, you can select a parameter to plot and then click ‘Plot’ to plot it with error bars across the fit spectra (if multiple data-sets have been used, a separate plot will be produced for each data-set). The ‘Plot Output’ options will be disabled after a fit if there is only one data point for the parameters.

During a sequential fit, the parameters calculated for one spectrum become the start parameters for the next spectrum to be fitted. Although this normally yields better parameter values for the later spectra, it can also lead to poorly fitted parameters if the next spectrum is not ‘related’ to the previous spectrum. It may be useful to replace this poorly fitted spectrum with the results from a single fit using the ‘Edit Result’ option. Clicking the ‘Edit Result’ button will allow you to modify the data within your _Results workspace using results produced from a singly fit spectrum. See the algorithm IndirectReplaceFitResult.

Clicking the ‘Save Result’ button will save the result of the fit to your default save location.

Spectrum Selection¶

Below the preview plots, the spectra to be fit can be selected. The ‘Fit Spectra’ drop-down menu allows for selecting either ‘Range’ or ‘String’. If ‘Range’ is selected, you are able to select a range of spectra to fit by providing the upper and lower bounds. If ‘String’ is selected you can provide the spectra to fit in a text form. When selecting spectra using text, you can use ‘-‘ to identify a range and ‘,’ to separate each spectrum/range.

-Ranges may be excluded from the fit by selecting a spectrum next to the ‘Mask Bins of Spectrum’ label and then providing a comma-separated list of pairs, where each pair designates a range to exclude from the fit.