Indirect Data Analysis¶

Table of Contents

Overview ¶

The Indirect Data Analysis interface is a collection of tools within MantidPlot for analysing reduced data from indirect geometry spectrometers, such as IRIS and OSIRIS.

The majority of the functions used within this interface can be used with both reduced files (_red.nxs) and workspaces (_red) created using the Indirect Data Reduction interface or using $S(Q, \omega)$ files (_sqw.nxs) and workspaces (_sqw) created using either the Indirect Data Reduction interface or taken from a bespoke algorithm or auto reduction.

Four of the available tabs are QENS fitting interfaces and share common features and layout. These common factors are documented in the QENS Fitting Interfaces Features section of this document.

These interfaces do not support GroupWorkspace as input.

Action Buttons ¶

?: 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 ¶

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.

../_images/Data_Analysis_tabElwin_widget.png

Options ¶

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.
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 Spectrum: If enabled it will plot the spectrum represented by the workspace index in the neighbouring spin box. This workspace index is the index of the spectrum within the workspace selected in the combobox.
Save Result: Saves the result in the default save directory.

MSD Fit ¶

Given either a saved NeXus file or workspace generated using the Elwin tab, this tab fits $intensity$ vs. $Q$ with one of three functions for each run specified to give the Mean Square Displacement (MSD). It then plots the MSD as function of run number. This is done by means of the QENSFitSequential algorithm.

MSDFit searches for the log files named <runnumber>_sample.txt in your chosen raw file directory (the name ‘sample’ is for OSIRIS). These log files will exist if the correct temperature was loaded using SE-log-name in the Elwin tab. If they exist the temperature is read and the MSD is plotted versus temperature; if they do not exist the MSD is plotted versus run number (last 3 digits).

The fitted parameters for all runs are in _msd_Table and the <u2> in _msd. To run the Sequential fit a workspace named <inst><first-run>_to_<last-run>_eq is created of $intensity$ v. $Q$ for all runs. A contour or 3D plot of this may be of interest.

A sequential fit is run by clicking the Run button at the bottom of the tab, a single fit can be done using the Fit Single Spectrum button underneath the preview plot.

The Peters model [1] reduces to a Gaussian at large (towards infinity) beta. The Yi Model [2] reduces to a Gaussian at sigma equal to zero.

../_images/Data_Analysis_tabMSD_widget.png

Options ¶

Sample: A file with extension _eq.nxs that has been created using the Elwin tab with an $x$ axis of $Q$ . 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.

See also

Common options are detailed in the QENS Fitting Interfaces Features section.

See also

Sequential fitting is available, options are detailed in the Sequential Fitting section.

I(Q, t)¶

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

../_images/Data_Analysis_tabIqt_widget.png

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.
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 Spectrum: If enabled will plot the spectrum selected by the neighbouring spinbox.
Tiled Plot: Produces a tiled plot of spectra included within the range for the output workspaces generated. There is a maximum of 18 spectra allowed for a tiled plot.
Save Result: Saves the result workspace in the default save directory.

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 ¶

I(Q, t) Fit provides a simplified interface for controlling various fitting functions (see the Fit algorithm for more info). The functions are also available via the fit wizard.

The fit types available for use in IqtFit are Exponentials and Stretched Exponential.

../_images/Data_Analysis_tabIqtFit_widget.png

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.

See also

Common options are detailed in the QENS Fitting Interfaces Features section.

See also

Sequential fitting is available, options are detailed in the Sequential Fitting section.

Conv Fit ¶

ConvFit provides a simplified interface for controlling various fitting functions (see the Fit algorithm for more info). The functions are also available via the fit wizard.

Additionally, in the bottom-right of the interface there are options for doing a sequential fit. This is where the program loops through each spectrum in the input workspace, using the fitted values from the previous spectrum as input values for fitting the next. This is done by means of the ConvolutionFitSequential algorithm.

A sequential fit is run by clicking the Run button at the bottom of the tab, a single fit can be done using the Fit Single Spectrum button underneath the preview plot.

The fit types available in ConvFit are One Lorentzian, Two Lorentzian, TeixeiraWater (SQE), InelasticDiffSphere, InelasticDiffRotDiscreteCircle, ElasticDiffSphere, ElasticDiffRotDiscreteCircle and StretchedExpFT.

../_images/Data_Analysis_tabConvFit_widget.png

Options ¶

See also

Common options are detailed in the QENS Fitting Interfaces Features section.

See also

Sequential fitting is available, options are detailed in the Sequential Fitting section.

Sample: Either a reduced file (_red.nxs) or workspace (_red) or an $S(Q, \omega)$ file (_sqw.nxs, _sqw.dave) or workspace (_sqw).
Resolution: Either a resolution file (_res.nxs) or workspace (_res) or an $S(Q, \omega)$ 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.

Theory ¶

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

F(Q) Fit ¶

One of the models used to interpret diffusion is that of jump diffusion in which it is assumed that an atom remains at a given site for a time $\tau$ ; and then moves rapidly, that is, in a time negligible compared to $\tau$ .

This interface can be used for a jump diffusion fit as well as fitting across EISF. This is done by means of the QENSFitSequential algorithm.

The fit types available in F(Q)Fit are ChudleyElliot, HallRoss, FickDiffusion, TeixeiraWater, EISFDiffCylinder, EISFDiffSphere and EISFDiffSphereAlkyl.

../_images/Data_Analysis_tabJumpFit_widget.png

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.

See also

Common options are detailed in the QENS Fitting Interfaces Features section.

QENS Fitting Interfaces Features ¶

There are four QENS fitting interfaces:

MSD Fit
I(Q,t) Fit,
Conv Fit
F(Q)

These fitting interfaces share common features, with a few unique options in each.

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 $x$ -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.

Bayesian (FABADA minimizer)¶

There is the option to perform Bayesian data analysis on the I(Q, t) Fit ConvFit tabs on this interface by using the FABADA fitting minimizer, however in order to to use this you will need to use better starting parameters than the defaults provided by the interface.

You may also experience issues where the starting parameters may give a reliable fit on one spectra but not others, in this case the best option is to reduce the number of spectra that are fitted in one operation.

In both I(Q, t) Fit and ConvFit the following options are available when fitting using FABADA:

Output Chain: Select to enable output of the FABADA chain when using FABADA as the fitting minimizer.
Chain Length: Number of further steps carried out by fitting algorithm once parameters have converged (see ChainLength is FABADA documentation)
Convergence Criteria: The minimum variation in the cost function before the parameters are considered to have converged (see ConvergenceCriteria in FABADA documentation)
Acceptance Rate: The desired percentage acceptance of new parameters (see JumpAcceptanceRate in FABADA documentation)

The FABADA minimizer can output a PDF group workspace when the PDF option is ticked. If this happens, then it is possible to plot this PDF data using the output options at the bottom of the tabs.

Sequential Fitting ¶

Three of the fitting interfaces allow sequential fitting of several spectra:

MSD Fit
I(Q, T) Fit
ConvFit

At the bottom of the interface there are options for doing a sequential fit. This is where the program loops through each spectrum in the input workspace, using the fitted values from the previous spectrum as input values for fitting the next. This is done by means of the IqtFitSequential algorithm.

A sequential fit is run by clicking the Run button seen just above the output options, a single fit can be done using the Fit Single Spectrum button underneath the preview plot.

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.

$X$ -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.

ConvFit fitting model ¶

The model used to perform fitting in ConvFit is described in the following tree, note that everything under the Model section is optional and determined by the Fit Type and Use Delta Function options in the interface.

CompositeFunction
- LinearBackground
- Convolution
  - Resolution
  - Model (CompositeFunction)
    - DeltaFunction
    - ProductFunction (One Lorentzian)
      - Lorentzian
      - Temperature Correction
    - ProductFunction (Two Lorentzians)
      - Lorentzian
      - Temperature Correction
    - ProductFunction (InelasticDiffSphere)
      - Inelastic Diff Sphere
      - Temperature Correction
    - ProductFunction (InelasticDiffRotDiscreteCircle)
      - Inelastic Diff Rot Discrete Circle
      - Temperature Correction
    - ProductFunction (ElasticDiffSphere)
      - Elastic Diff Sphere
      - Temperature Correction
    - ProductFunction (ElasticDiffRotDiscreteCircle)
      - Elastic Diff Rot Discrete Circle
      - Temperature Correction
    - ProductFunction (StretchedExpFT)
      - StretchedExpFT
      - Temperature Correction

The Temperature Correction is a UserFunction with the formula $((x * 11.606) / T) / (1 - exp(-((x * 11.606) / T)))$ where $T$ is the temperature in Kelvin.

References

Peters & Kneller, Journal of Chemical Physics, 139, 165102 (2013)
Yi et al, J Phys Chem B 116, 5028 (2012)

Categories: Interfaces | Indirect