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SingleCrystalDiffuseReduction v1

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Summary

Single Crystal Diffuse Scattering Reduction, normalisation, symmetry and background substraction

See Also

ConvertToMD, MDNormSCDPreprocessIncoherent, MDNorm

Properties

Name	Direction	Type	Default	Description
Filename	Input	list of str lists	Mandatory	Files to combine in reduction. Allowed extensions: [‘_event.nxs’, ‘.nxs.h5’, ‘.nxs’]
Background	Input	string		Background run. Allowed extensions: [‘_event.nxs’, ‘.nxs.h5’, ‘.nxs’]
BackgroundScale	Input	number	1	The background will be scaled by this number before being subtracted.
FilterByTofMin	Input	number	Optional	Optional: To exclude events that do not fall within a range of times-of-flight. This is the minimum accepted value in microseconds. Keep blank to load all events.
FilterByTofMax	Input	number	Optional	Optional: To exclude events that do not fall within a range of times-of-flight. This is the maximum accepted value in microseconds. Keep blank to load all events.
ReuseSAFlux	Input	boolean	True	If True then if a previous SolidAngle and Flux has been loaded it will be reused otherwise it will be loaded.
SolidAngle	Input	string	Mandatory	An input workspace containing momentum integrated vanadium (a measure of the solid angle). See MDNormSCDPreprocessIncoherent for details. Allowed extensions: [‘.nxs’]
Flux	Input	string	Mandatory	An input workspace containing momentum dependent flux. See MDnormSCD for details. Allowed extensions: [‘.nxs’]
MomentumMin	Input	number	Optional	Minimum value in momentum. The max of this value and the flux momentum minimum will be used.
MomentumMax	Input	number	Optional	Maximum value in momentum. The min of this value and the flux momentum maximum will be used.
UBMatrix	Input	list of str lists	Mandatory	Path to an ISAW-style UB matrix text file. See LoadIsawUB. Allowed extensions: [‘.mat’, ‘.ub’, ‘.txt’]
SetGoniometer	Input	boolean	False	Set which Goniometer to use. See SetGoniometer
Goniometers	Input	string	None, Specify Individually	Set the axes and motor names according to goniometers that we define in the code (Universal defined for SNS). Allowed values: [‘None, Specify Individually’, ‘Universal’]
Axis0	Input	string		Axis0: name, x,y,z, 1/-1 (1 for ccw, -1 for cw rotation). A number of degrees can be used instead of name. Leave blank for no axis
Axis1	Input	string		Axis1: name, x,y,z, 1/-1 (1 for ccw, -1 for cw rotation). A number of degrees can be used instead of name. Leave blank for no axis
Axis2	Input	string		Axis2: name, x,y,z, 1/-1 (1 for ccw, -1 for cw rotation). A number of degrees can be used instead of name. Leave blank for no axis
OmegaOffset	Input	dbl list		Offset to apply to the omega rotation of the Goniometer. Need to provide one value for every run.
LoadInstrument	Input	string		Load a different instrument IDF onto the data from a file. See LoadInstrument. Allowed extensions: [‘.xml’]
ApplyCalibration	Input	TableWorkspace		Calibration will be applied using this TableWorkspace using ApplyCalibration.
DetCal	Input	string		Load an ISAW DetCal calibration onto the data from a file. See LoadIsawDetCal. Allowed extensions: [‘.detcal’]
CopyInstrumentParameters	Input	MatrixWorkspace		The input workpsace from which CopyInstrumentParameters will copy parameters to data
MaskFile	Input	string		Masking file for masking. Supported file format is XML and ISIS ASCII. See LoadMask. Allowed extensions: [‘.xml’, ‘.msk’]
SymmetryOperations	Input	string		If specified the symmetry will be applied, can be space group name, point group name, or list individual symmetries.
QDimension0	Input	dbl list	1,0,0	The first Q projection axis
QDimension1	Input	dbl list	0,1,0	The second Q projection axis
QDimension2	Input	dbl list	0,0,1	The third Q projection axis
Dimension0Binning	Input	dbl list		Binning for the 0th dimension. - Leave blank for complete integration - One value is interpreted as step - Two values are interpreted integration interval - Three values are interpreted as min, step, max
Dimension1Binning	Input	dbl list		Binning for the 1th dimension. - Leave blank for complete integration - One value is interpreted as step - Two values are interpreted integration interval - Three values are interpreted as min, step, max
Dimension2Binning	Input	dbl list		Binning for the 2th dimension. - Leave blank for complete integration - One value is interpreted as step - Two values are interpreted integration interval - Three values are interpreted as min, step, max
KeepTemporaryWorkspaces	Input	boolean	False	If True the normalization and data workspaces in addition to the normalized data will be outputted
OutputWorkspace	Output	Workspace	Mandatory	Output Workspace. If background is subtracted _data and _background workspaces will also be made.

Description

Developed for CORELLI but should work on any instrument. This workflow algorithm loops over a series of runs combining them with correct normalisation, subtract the background and apply symmetry. The resulting workspace is a MDHistoWorkspace containing a volume of scattering.

The input filename follows the syntax from MultipleFileProperty

This workflow makes use of ConvertToMD and MDNorm so these should be reviewed to better understand all the options. An example of creating the Solid Angle and Flux workspaces are included in MDNormSCD. MDNormSCDPreprocessIncoherent can be used to process Vanadium data for the Solid Angle and Flux workspaces.

The resulting workspaces can be saved and loaded with SaveMD and LoadMD respectively.

Masking

The mask from the solid angle workspace is copied to the data. Additional masking is provided by a masking file. A masking file can be created my masking a data file then saving it using SaveMask.

Background

The background is processed the same as the data except that the Goniometer is copied from the data before setting the UB matrix. If a background is included three workspaces are create. If “OutputWorkspace” is set to “ws” you will get the following.

“ws_normalizedBackground” containing the normalised background.

“ws_normalizedData” containing the normalised data.

And “ws” where

\[ws = ws\_normalizedData - ws\_normalizedBackground * BackgroundScale\]

Should the background scale not be correct this allows you to redo the background subtraction without rerunning the reduction.

If no background is used then the “ws” is just the normalised data.

Symmetries

The SymmetryOperations parameters can either be defined as a point or space group were all the symmetries for that group is applied, or you can specify individual symmetries to apply.

For example setting SymmetryOperations to space group “P 31 2 1”, point group “321” or “x,y,z; -y,x-y,z; -x+y,-x,z; y,x,-z; x-y,-y,-z; -x,-x+y,-z” are equivalent. Note these symmetries are on the real lattice not reciprocal.

Temporary Workspaces

If the KeepTemporaryWorkspaces option is True the data and the normalization in addition to the nomalized data will be outputted. This allows you to run separate instances of SingleCrystalDiffuseReduction and combine the results. They will have names “ws_data” and “ws_normalization” respectively.

Where

\[ws\_normalizedData = \frac{ws\_data}{ws\_normalization}\]

If background is subtracted there will be similar “ws_background_data” and “ws_background_normalization” for the background.

Where

\[ws\_normalizedBackground = \frac{ws\_background\_data}{ws\_backgournd\_normalization}\]

Workflow

diagram generation was disabled

Usage

Single file

SingleCrystalDiffuseReduction(Filename='CORELLI_29782',
                              SolidAngle='/SNS/CORELLI/shared/Vanadium/2016B/SolidAngle20160720NoCC.nxs',
                              Flux='/SNS/CORELLI/shared/Vanadium/2016B/Spectrum20160720NoCC.nxs',
                              UBMatrix="/SNS/CORELLI/IPTS-15526/shared/benzil_Hexagonal.mat",
                              OutputWorkspace='output',
                              SetGoniometer=True,
                              Axis0="BL9:Mot:Sample:Axis1,0,1,0,1",
                              Dimension0Binning='-10.05,0.1,10.05',
                              Dimension1Binning='-10.05,0.1,10.05',
                              Dimension2Binning='-0.1,0.1')

Multiple files

SingleCrystalDiffuseReduction(Filename='CORELLI_29782:29817:10',
                              SolidAngle='/SNS/CORELLI/shared/Vanadium/2016B/SolidAngle20160720NoCC.nxs',
                              Flux='/SNS/CORELLI/shared/Vanadium/2016B/Spectrum20160720NoCC.nxs',
                              UBMatrix="/SNS/CORELLI/IPTS-15526/shared/benzil_Hexagonal.mat",
                              OutputWorkspace='output',
                              SetGoniometer=True,
                              Axis0="BL9:Mot:Sample:Axis1,0,1,0,1",
                              Dimension0Binning='-10.05,0.1,10.05',
                              Dimension1Binning='-10.05,0.1,10.05',
                              Dimension2Binning='-0.1,0.1')

Single file with symmetry

SingleCrystalDiffuseReduction(Filename='CORELLI_29782',
                              SolidAngle='/SNS/CORELLI/shared/Vanadium/2016B/SolidAngle20160720NoCC.nxs',
                              Flux='/SNS/CORELLI/shared/Vanadium/2016B/Spectrum20160720NoCC.nxs',
                              UBMatrix="/SNS/CORELLI/IPTS-15526/shared/benzil_Hexagonal.mat",
                              OutputWorkspace='output',
                              SetGoniometer=True,
                              Axis0="BL9:Mot:Sample:Axis1,0,1,0,1",
                              Dimension0Binning='-10.05,0.1,10.05',
                              Dimension1Binning='-10.05,0.1,10.05',
                              Dimension2Binning='-0.1,0.1',
                              SymmetryOperations="P 31 2 1")

Multiple files with symmetry

SingleCrystalDiffuseReduction(Filename='CORELLI_29782:29817:10',
                              SolidAngle='/SNS/CORELLI/shared/Vanadium/2016B/SolidAngle20160720NoCC.nxs',
                              Flux='/SNS/CORELLI/shared/Vanadium/2016B/Spectrum20160720NoCC.nxs',
                              UBMatrix="/SNS/CORELLI/IPTS-15526/shared/benzil_Hexagonal.mat",
                              OutputWorkspace='output',
                              SetGoniometer=True,
                              Axis0="BL9:Mot:Sample:Axis1,0,1,0,1",
                              Dimension0Binning='-10.05,0.1,10.05',
                              Dimension1Binning='-10.05,0.1,10.05',
                              Dimension2Binning='-0.1,0.1',
                              SymmetryOperations="P 31 2 1")

Multiple files with symmetry and background substraction

SingleCrystalDiffuseReduction(Filename='CORELLI_29782:29817:10',
                              Background='CORELLI_28124',
                              BackgroundScale=0.95,
                              SolidAngle='/SNS/CORELLI/shared/Vanadium/2016B/SolidAngle20160720NoCC.nxs',
                              Flux='/SNS/CORELLI/shared/Vanadium/2016B/Spectrum20160720NoCC.nxs',
                              UBMatrix="/SNS/CORELLI/IPTS-15526/shared/benzil_Hexagonal.mat",
                              OutputWorkspace='output',
                              SetGoniometer=True,
                              Axis0="BL9:Mot:Sample:Axis1,0,1,0,1",
                              Dimension0Binning='-10.05,0.1,10.05',
                              Dimension1Binning='-10.05,0.1,10.05',
                              Dimension2Binning='-0.1,0.1',
                              SymmetryOperations="P 31 2 1")

Reading in elastic Corelli autoreduced data

SingleCrystalDiffuseReduction(Filename=','.join('/SNS/CORELLI/IPTS-15526/shared/autoreduce/CORELLI_'+str(run)+'_elastic.nxs' for run in range(29782,29818,10)),
                              Background='/SNS/CORELLI/IPTS-15796/shared/autoreduce/CORELLI_28124_elastic.nxs',
                              BackgroundScale=0.95,
                              SolidAngle='/SNS/CORELLI/shared/Vanadium/2016B/SolidAngle20160720NoCC.nxs',
                              Flux='/SNS/CORELLI/shared/Vanadium/2016B/Spectrum20160720NoCC.nxs',
                              UBMatrix="/SNS/CORELLI/IPTS-15526/shared/benzil_Hexagonal.mat",
                              OutputWorkspace='output',
                              SetGoniometer=True,
                              Axis0="BL9:Mot:Sample:Axis1,0,1,0,1",
                              Dimension0Binning='-10.05,10.05,0.1',
                              Dimension1Binning='-10.05,10.05,0.1',
                              Dimension2Binning='-0.1,0.1',
                              SymmetryOperations="P 31 2 1")

Defining the axis to be [H,H,0], [H,-H,0], [0,0,L]

SingleCrystalDiffuseReduction(Filename='CORELLI_29782:29817:10',
                              Background='CORELLI_28124',
                              BackgroundScale=0.95,
                              SolidAngle='/SNS/CORELLI/shared/Vanadium/2016B/SolidAngle20160720NoCC.nxs',
                              Flux='/SNS/CORELLI/shared/Vanadium/2016B/Spectrum20160720NoCC.nxs',
                              UBMatrix="/SNS/CORELLI/IPTS-15526/shared/benzil_Hexagonal.mat",
                              OutputWorkspace='output',
                              SetGoniometer=True,
                              Axis0="BL9:Mot:Sample:Axis1,0,1,0,1",
                              QDimension0='1,1,0',
                              QDimension1='1,-1,0',
                              QDimension2='0,0,1',
                              Dimension0Binning='-7.5375,0.075,7.5375',
                              Dimension1Binning='-13.165625,0.13100125,13.165625',
                              Dimension2Binning='-0.1,0.1',
                              SymmetryOperations="P 31 2 1")

import matplotlib.pyplot as plt
from mantid import plots
fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
c = ax.pcolormesh(mtd['output'],vmin=0, vmax=1e-5)
fig.colorbar(c)
plt.show()

Related Algorithms

MDNormSCD is the algorithm performing the normalisation of a single file.

DeltaPDF3D calculates the 3D-ΔPDF from the resulting workspace of this algorithm.

Categories: AlgorithmIndex | Diffraction\Reduction

Source

Python: SingleCrystalDiffuseReduction.py