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ReflectometryReductionOneAuto v3¶

Summary ¶

Reduces a single TOF/Lambda reflectometry run into a mod Q vs I/I0 workspace attempting to pick instrument parameters for missing properties

Properties ¶

Name	Direction	Type	Default	Description
InputWorkspace	Input	MatrixWorkspace	Mandatory	Input run in TOF or wavelength
SummationType	Input	string	SumInLambda	The type of summation to perform. Allowed values: [‘SumInLambda’, ‘SumInQ’]
ReductionType	Input	string	Normal	The type of reduction to perform when summing in Q. Allowed values: [‘Normal’, ‘DivergentBeam’, ‘NonFlatSample’]
IncludePartialBins	Input	boolean	False	If true then partial bins at the beginning and end of the output range are included
AnalysisMode	Input	string	PointDetectorAnalysis	Analysis mode. This property is only used when ProcessingInstructions is not set. Allowed values: [‘PointDetectorAnalysis’, ‘MultiDetectorAnalysis’]
ProcessingInstructions	Input	string		Grouping pattern of spectrum numbers to yield only the detectors of interest. See GroupDetectors for syntax.
ThetaIn	Input	number	Optional	Angle in degrees
ThetaLogName	Input	string		The name ThetaIn can be found in the run log as
CorrectDetectors	Input	boolean	True	Moves detectors to twoTheta if ThetaIn or ThetaLogName is given
DetectorCorrectionType	Input	string	VerticalShift	When correcting detector positions, this determines whether detectorsshould be shifted vertically or rotated around the sample position. Allowed values: [‘RotateAroundSample’, ‘VerticalShift’]
WavelengthMin	Input	number	Optional	Wavelength Min in angstroms
WavelengthMax	Input	number	Optional	Wavelength Max in angstroms
I0MonitorIndex	Input	number	Optional	I0 monitor workspace index
MonitorBackgroundWavelengthMin	Input	number	Optional	Wavelength minimum for monitor background subtraction in angstroms.
MonitorBackgroundWavelengthMax	Input	number	Optional	Wavelength maximum for monitor background subtraction in angstroms.
MonitorIntegrationWavelengthMin	Input	number	Optional	Wavelength minimum for integration in angstroms.
MonitorIntegrationWavelengthMax	Input	number	Optional	Wavelength maximum for integration in angstroms.
NormalizeByIntegratedMonitors	Input	boolean	True	Normalize by dividing by the integrated monitors.
SubtractBackground	Input	boolean	False	If true then perform background subtraction
BackgroundProcessingInstructions	Input	string		These processing instructions will be passed to the background subtraction algorithm
BackgroundCalculationMethod	Input	string	PerDetectorAverage	The type of background reduction to perform. Allowed values: [‘PerDetectorAverage’, ‘Polynomial’, ‘AveragePixelFit’]
DegreeOfPolynomial	Input	number	0	Degree of the fitted polynomial.
CostFunction	Input	string	Least squares	The cost function to be passed to the Fit algorithm. Allowed values: [‘Least squares’, ‘Unweighted least squares’]
FirstTransmissionRun	Input	MatrixWorkspace		First transmission run, or the low wavelength transmission run if SecondTransmissionRun is also provided.
SecondTransmissionRun	Input	MatrixWorkspace		Second, high wavelength transmission run. Optional. Causes the FirstTransmissionRun to be treated as the low wavelength transmission run.
Params	Input	dbl list		A comma separated list of first bin boundary, width, last bin boundary. These parameters are used for stitching together transmission runs. Values are in wavelength (angstroms). This input is only needed if a SecondTransmission run is provided.
StartOverlap	Input	number	Optional	Start wavelength for stitching transmission runs together. Only used if a second transmission run is provided.
EndOverlap	Input	number	Optional	End wavelength (angstroms) for stitching transmission runs together. Only used if a second transmission run is provided.
ScaleRHSWorkspace	Input	boolean	True	Scale the right-hand-side or left-hand-side workspace. Only used if a second transmission run is provided.
TransmissionProcessingInstructions	Input	string		These processing instructions will be passed to the transmission workspace algorithm
CorrectionAlgorithm	Input	string	AutoDetect	The type of correction to perform. Allowed values: [‘None’, ‘AutoDetect’, ‘PolynomialCorrection’, ‘ExponentialCorrection’]
Polynomial	Input	dbl list		Coefficients to be passed to the PolynomialCorrection algorithm.
C0	Input	number	0	C0 value to be passed to the ExponentialCorrection algorithm.
C1	Input	number	0	C1 value to be passed to the ExponentialCorrection algorithm.
MomentumTransferMin	Input	number	Optional	Minimum Q value in IvsQ Workspace. Used for Rebinning the IvsQ Workspace
MomentumTransferStep	Input	number	Optional	Resolution value in IvsQ Workspace. Used for Rebinning the IvsQ Workspace. This value will be made minus to apply logarithmic rebinning. If you wish to have linear bin-widths then please provide a negative value.
MomentumTransferMax	Input	number	Optional	Maximum Q value in IvsQ Workspace. Used for Rebinning the IvsQ Workspace
ScaleFactor	Input	number	Optional	Factor you wish to scale Q workspace by.
PolarizationAnalysis	Input	boolean	False	Apply polarization corrections
FloodCorrection	Input	string	Workspace	The way to apply flood correction: Workspace - use FloodWorkspace property to get the flood workspace, ParameterFile - use parameters in the parameter file to construct and apply flood correction workspace. Allowed values: [‘Workspace’, ‘ParameterFile’]
FloodWorkspace	Input	MatrixWorkspace		A flood workspace to apply; if empty and FloodCorrection is ‘Workspace’ then no correction is applied.
Debug	Input	boolean	False	Whether to enable the output of extra workspaces.
Diagnostics	Input	boolean	False	Whether to enable the output of interim workspaces for debugging purposes.
OutputWorkspaceBinned	Output	MatrixWorkspace		Output workspace in Q (rebinned workspace)
OutputWorkspace	Output	MatrixWorkspace		Output workspace in Q (native binning)
OutputWorkspaceWavelength	Output	MatrixWorkspace		Output workspace in wavelength
OutputWorkspaceTransmission	Output	MatrixWorkspace		Output transmissison workspace in wavelength
OutputWorkspaceFirstTransmission	Output	MatrixWorkspace		First transmissison workspace in wavelength
OutputWorkspaceSecondTransmission	Output	MatrixWorkspace		Second transmissison workspace in wavelength
PolarizationEfficiencies	Input	MatrixWorkspace		A workspace to be used for polarization analysis that contains the efficiency factors as histograms: P1, P2, F1 and F2 in the Wildes method and Pp, Ap, Rho and Alpha for Fredrikze.

This algorithm is a facade over ReflectometryReductionOne v2 (see ReflectometryReductionOne v2 for more information on the wrapped algorithm). It optionally corrects the detector position and then pulls numeric parameters out of the instrument parameter file where possible. These automatically applied defaults can be overridden by providing your own values. In addition, it outputs a rebinned workspace in Q, and it optionally performs polarization analysis if the input workspace is a workspace group. The input and transmission workspaces can also be optionally corrected for flood using ApplyFloodWorkspace v1 algorithm. The flood workspace either can be provided in FloodWorkspace property or it is created on the fly with the CreateFloodWorkspace v1 algorithm using properties stored in the instrument parameter file.

First, if ThetaIn is given the algorithm will try to correct the detector position. For this, it uses ProcessingInstructions, which corresponds to the grouping pattern of workspace indices that define the detectors of interest. Only the detectors of interest will be corrected, the rest of the instrument components will remain in the original position. Note that when ProcessingInstructions is not set, its value is inferred from other properties, depending on the value of AnalysisMode:

If AnalysisMode = PointDetectorAnalaysis the algorithm will search for PointDetectorStart and PointDetectorStop in the parameter file, and ProcessingInstructions will be set to PointDetectorStart:PointDetectorEnd.
If AnalysisMode = MultiDetectorAnalaysis the algorithm will search for MultiDetectorStart in the parameter file and all of the spectra from this value onwards will be used.

Note that ProcessingInstructions are workspace indices, not detector IDs. The first few workspaces may correspond to monitors, rather than detectors of interest. For the syntax of this property, see GroupDetectors v2.

theta is calculated using SpecularReflectionCalculateTheta. This is passed through to ReflectometryReductionOne and 2 * theta is passed through to CalculateResolution. theta can be overridden by setting ThetaIn or ThetaLogName (ThetaIn takes precedence if both are given). If CorrectDetectors is also true, then the algorithm corrects the positions of the detectors of interest to 2 * theta using SpecularReflectionPositionCorrect v2. The detectors are moved either by shifting them vertically, or by rotating them around the sample position, as specified by DetectorCorrectionType.

Next, the algorithm will try to populate input properties which have not been set. Specifically, it will search for LambdaMin, LambdaMax, I0MonitorIndex, MonitorBackgroundMin, MonitorBackgroundMax, MonitorIntegralMin and MonitorIntegralMin in the parameter file to populate WavelengthMin, WavelengthMax, I0MonitorIndex, MonitorBackgroundWavelengthMin, MonitorBackgroundWavelengthMax, MonitorIntegrationWavelengthMin and MonitorIntegrationWavelengthMax respectively. The first two properties will be used by ReflectometryReductionOne v2 to crop the workspace in wavelength, whereas the rest of the properties refer to monitors and are used to create a temporary monitor workspace by which the detectors of interest will be normalized. Note that there is an additional property referring to monitors, NormalizeByIntegratedMonitors, which can be used to specify whether or not integrated monitors should be considered.

The rest of the input properties are not inferred from the parameter file, and must be specified manually. RegionOfDirectBeam is an optional property that allows users to specify a region of direct beam that will be used to normalize the detector signal. The region of direct beam is specified by workspace indices. For instance, RegionOfDirectBeam='2-3' means that spectra with workspace indices 2 and 3 will be summed and the resulting workspace will be used as the direct beam workspace.

Transmission corrections can be optionally applied by providing either one or two transmission runs or polynomial corrections. Polynomial correction is enabled by setting the CorrectionAlgorithm property. If set to AutoDetect, the algorithm looks at the instrument parameters for the correction parameter. If this parameter is set to polynomial, then polynomial correction is performed using the PolynomialCorrection v1 algorithm, with the polynomial string taken from the instrument’s polystring parameter. If the correction parameter is set to exponential instead, then the ExponentialCorrection v1 algorithm is used, with C0 and C1 taken from the instrument parameters, C0 and C1. All these values can be specified manually by setting the CorrectionAlgorithm to either PolynomialCorrection or ExponentialCorrection and setting Polynomial or C0 and C1 properties accordingly. Note that when using a correction algorithm, monitors will not be integrated, even if NormalizeByIntegratedMonitors was set to true.

OutputWorkspace is scaled to ScaleFactor and cropped to MomentumTransferMin and/or MomentumTransferMax, if they are given.

OutputWorkspaceBinned is rebinned to the resolution specified by MomentumTransferStep, if it is given; otherwise the algorithm attempts to determine the bin width using NRCalculateSlitResolution v1 (note that to calculate the resolution this way, a slit component with a vertical gap must be defined in the instrument definition file - if it cannot be found, rebinning will not be done and a warning will be logged). MomentumTransferMin and MomentumTransferMax are used for the rebin if provided; otherwise the original min/max in Q is retained.

See ReflectometryReductionOne v2 for more information on how the input properties are used by the wrapped algorithm.

Workspace Groups ¶

If a workspace group is provided as input, each workspace in the group will be reduced independently and sequentially using ReflectometryReductionOne v2. Each of these individual reductions will produce three output workspaces: an output workspace in wavelength, an output workspace in Q with native binning, and a rebinned workspace in Q. Output workspaces in wavelength will be grouped together to produce an output workspace group in wavelength, and output workspaces in Q will be grouped together to produce an output workspace group in Q. The diagram below illustrates this process (note that, for the sake of clarity, the rebinned output workspace in Q, OutputWorkspaceBinned, is not represented but it is handled analogously to OutputWorkspace and OutputWorkspaceWavelength):

../_images/ReflectometryReductionOneAuto-v2-Groups_wkflw.svg

Note that if transmission runs are given in the form of a workspace group, then the first element in the group will be used on every input workspace. If transmission runs are provided as matrix workspaces the specified runs will be used for all members of the input workspace group.

Polarization Analysis ¶

If PolarizationAnalysis is set to false the reduction stops. This is regardless of whether or not a value has been provided for the PolarizationEfficiencies parameter. If PolarizationAnalysis is set to true, the reduction continues and polarization corrections will be applied to the workspace that was output in wavelength.

If a PolarizationEfficiencies workspace is provided then the values from this workspace are used to run either the PolarizationCorrectionFredrikze v1 or PolarizationCorrectionWildes v1 methods. The method to run is determined from the efficiency factor axes labels specified in the workspace. Providing an efficiencies workspace is only supported where the input workspace is a group of size 2 or 4. For the Fredrikze algorithm, the polarization mode will be PNR if the input workspace group has a size of 2 and PA if the size is 4. For Wildes, a workspace group of size 2 will use flipper configuration '0, 1', while a group of size 4 will use configuration '00, 01, 10, 11'.

If a workspace is not provided for the PolarizationEfficiencies parameter then the method and values specified in the parameters file are used instead.

The result of polarization analysis is a new workspace in wavelength, which will override the previous one. This will then be used as an input to re-run ReflectometryReductionOne v2 to calculate the new output workspaces in Q, which in turn will override the existing workspaces in Q. Note that when run with a workspace that is already summed and converted to wavelength, algm-ReflectometryReductionOne will not re-run these steps, so it is only the conversion to Q that is run again. Transmission and algorithm corrections are also skipped on the second run through because they have already been applied.

Previous Versions ¶

This is version 3 of the algorithm. For version 2, please see here and for version 1, please see here.

Usage ¶

Note

To run these usage examples please first download the usage data, and add these to your path. In Mantid this is done using Manage User Directories.

Example - Basic reduction with no transmission run, polynomial corrections will be automatically applied

run = Load(Filename='INTER00013460.nxs')
IvsQ, IvsQ_unbinned = ReflectometryReductionOneAuto(InputWorkspace=run, ThetaIn=0.7)

print("{:.5f}".format(IvsQ_unbinned.readY(0)[106]))
print("{:.5f}".format(IvsQ_unbinned.readY(0)[107]))
print("{:.5f}".format(IvsQ.readY(0)[13]))
print("{:.5f}".format(IvsQ.readY(0)[14]))

Output:

Example - Basic reduction with a transmission run

run = Load(Filename='INTER00013460.nxs')
trans = Load(Filename='INTER00013463.nxs')
IvsQ, IvsQ_unbinned, IvsLam, TRANS = ReflectometryReductionOneAuto(InputWorkspace=run, FirstTransmissionRun=trans, ThetaIn=0.7)

print("{:.5f}".format(IvsQ_unbinned.readY(0)[96]))
print("{:.5f}".format(IvsQ_unbinned.readY(0)[97]))
print("{:.5f}".format(IvsQ.readY(0)[5]))
print("{:.5f}".format(IvsQ.readY(0)[6]))

Output:

Example - Reduction overriding some default values

run = Load(Filename='INTER00013460.nxs')
IvsQ, IvsQ_unbinned = ReflectometryReductionOneAuto(InputWorkspace=run, ThetaIn=0.7, DetectorCorrectionType="RotateAroundSample", MonitorBackgroundWavelengthMin=0.0, MonitorBackgroundWavelengthMax=1.0)

print("{:.5f}".format(IvsQ_unbinned.readY(0)[106]))
print("{:.5f}".format(IvsQ_unbinned.readY(0)[107]))
print("{:.5f}".format(IvsQ.readY(0)[5]))
print("{:.5f}".format(IvsQ.readY(0)[6]))

Output:

Categories: AlgorithmIndex | Reflectometry\ISIS

Source ¶

C++ header: ReflectometryReductionOneAuto3.h

C++ source: ReflectometryReductionOneAuto3.cpp

ReflectometryReductionOneAuto v3¶

Summary ¶

See Also ¶

Properties ¶

Description ¶

Workspace Groups ¶

Polarization Analysis ¶

Previous Versions ¶

Usage ¶

Source ¶