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Indirect Data Analysis.rst 18.59 KiB

Indirect Data Analysis

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 :ref:`qens-fitting-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.
Run
Runs the processing configured on 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.
Plot Current Preview
Takes the data currently plotted in the preview plot and puts it in a separate external plot

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.

Options

Input File
Specify a range of input files that are either reduced (_red.nxs) or S(Q, \omega).
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 intrument parameters file, and in the absence of such specification, defaults to "last value")
Plot Result
If enabled will plot the result as a spectra plot.
Save Result
If enabled the result will be saved as a NeXus file in the default save directory.

MSD Fit

Given either a saved NeXus file or workspace generated using the Elwin tab, this tab fits log(intensity) vs. Q with a straight line 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 :ref:`QENSFitSequential <algm-QENSFitSequential>` algorithm.

MSDFit searches for the log files named <runnumber>_sample.txt in your chosen raw file directory (the name ‘sample’ is for OSIRIS). 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>_lnI is created of ln(I) 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.

Options

Sample
A file that has been created using the Elwin tab with an x axis of Q. Alternatively, a workspace may be provided.

I(Q, t)

Given sample and resolution inputs, carries out a fit as per the theory detailed in the :ref:`TransformToIqt <algm-TransformToIqt>` algorithm.

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 rebiinning range.
SampleBinning
The ratio at which to decrease the number of bins by merging of intensities from neighbouring bins.
Plot Result
If enabled will plot the result as a spectra plot.
Save Result
If enabled the result will be saved as a NeXus file in the default save directory.
Tiled Plot
Produces a tiled plot of the output workspaces generated.
Monte Carlo Error Calculation - Number Of Iterations
The number of iterations to perform in the Monte Carlo routine for error calculation in I(Q,t)

A note on Binning

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

The calculated binning parameters are displayed alongside the binning options:

EWidth
The calculated bin width.
SampleBins
Number of bins in the sample after rebinning.
ResolutionBins
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 :ref:`Fit <algm-Fit>` algorithm for more info). The functions are also available via the fit wizard.

Options

Sample
Either a file (_iqt.nxs) or workspace (_iqt) that has been created using the Iqt tab.
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 :ref:`IqtFitSimultaneous <algm-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.

Background Options

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

Conv Fit

ConvFit provides a simplified interface for controlling various fitting functions (see the :ref:`Fit <algm-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 :ref:`ConvolutionFitSequential <algm-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.

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).
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.

Theory

For more on the theory of Conv Fit see the :ref:`ConvFitConcept` 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 :ref:`QENSFitSequential <algm-QENSFitSequential>` algorithm.

Options

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 plot and saved under the 'Output' section of the fitting interfaces.

Next to the 'Plot Output' label, you can select a parameter to plot and then click 'Plot' to plot it across the fit spectra (if multiple data-sets have been used, a separate plot will be produced for each data-set).

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 :ref:`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 :ref:`FABADA` documentation)
Convergence Criteria
The minimum variation in the cost function before the parameters are considered to have converged (see ConvergenceCriteria in :ref:`FABADA` documentation)
Acceptance Rate
The desired percentage acceptance of new parameters (see JumpAcceptanceRate in :ref:`FABADA` documentation)

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 :ref:`IqtFitSequential <algm-IqtFitSequential>` 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.

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.

  • :ref:`CompositeFunction <func-CompositeFunction>`
    • :ref:`LinearBackground <func-LinearBackground>`
    • :ref:`Convolution <func-Convolution>`
      • Resolution
      • Model (:ref:`CompositeFunction <func-CompositeFunction>`)
        • DeltaFunction
        • :ref:`ProductFunction <func-ProductFunction>` (One Lorentzian)
          • :ref:`Lorentzian <func-Lorentzian>`
          • Temperature Correction
        • :ref:`ProductFunction <func-ProductFunction>` (Two Lorentzians)
          • :ref:`Lorentzian <func-Lorentzian>`
          • Temperature Correction
        • :ref:`ProductFunction <func-ProductFunction>` (InelasticDiffSphere)
          • :ref:`Inelastic Diff Sphere <func-DiffSphere>`
          • Temperature Correction
        • :ref:`ProductFunction <func-ProductFunction>` (InelasticDiffRotDiscreteCircle)
          • :ref:`Inelastic Diff Rot Discrete Circle <func-DiffRotDiscreteCircle>`
          • Temperature Correction
        • :ref:`ProductFunction <func-ProductFunction>` (ElasticDiffSphere)
          • :ref:`Elastic Diff Sphere <func-DiffSphere>`
          • Temperature Correction
        • :ref:`ProductFunction <func-ProductFunction>` (ElasticDiffRotDiscreteCircle)
          • :ref:`Elastic Diff Rot Discrete Circle <func-DiffRotDiscreteCircle>`
          • Temperature Correction
        • :ref:`ProductFunction <func-ProductFunction>` (StretchedExpFT)
          • :ref:`StretchedExpFT <func-StretchedExpFT>`
          • Temperature Correction

The Temperature Correction is a :ref:`UserFunction <func-UserFunction>` with the formula ((x * 11.606) / T) / (1 - exp(-((x * 11.606) / T))) where T is the temperature in Kelvin.