6.3

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PDCalibration v1

../_images/PDCalibration-v1_dlg.png

PDCalibration dialog.

Summary

Calibrate the detector pixels and create a calibration table

Properties

Name Direction Type Default Description
InputWorkspace InOut MatrixWorkspace Mandatory Input signal workspace
TofBinning Input dbl list Mandatory Min, Step, and Max of time-of-flight bins. Logarithmic binning is used if Step is negative.
PreviousCalibrationFile Input string   Previous calibration file. Allowed extensions: [‘.h5’, ‘.cal’]
PreviousCalibrationTable Input TableWorkspace   Previous calibration table. This overrides results from previous file.
PeakFunction Input string Gaussian Allowed values: [‘BackToBackExponential’, ‘Gaussian’, ‘Lorentzian’, ‘PseudoVoigt’, ‘IkedaCarpenterPV’]
BackgroundType Input string Linear Type of Background. Allowed values: [‘Flat’, ‘Linear’, ‘Quadratic’]
PeakPositions Input dbl list Mandatory Comma delimited d-space positions of reference peaks.
PeakWindow Input dbl list 0.1 Window over which to fit a peak in d-spacing (if a single value is supplied it will used as half the window width for all peaks, otherwise a comma delimited list of boundaries).
PeakWidthPercent Input number Optional The estimated peak width as a percent of the peakcenter value, in d-spacing or TOF units.
MinimumPeakHeight Input number 2 Minimum peak height such that all the fitted peaks with height under this value will be excluded.
MaxChiSq Input number 100 Maximum chisq value for individual peak fit allowed. (Default: 100)
ConstrainPeakPositions Input boolean False If true, peak centers will be constrained by estimated positions (highest Y value position) and the peak width will either be estimated by observation or calculated.
CalibrationParameters Input string DIFC Select calibration parameters to fit. Allowed values: [‘DIFC’, ‘DIFC+TZERO’, ‘DIFC+TZERO+DIFA’]
TZEROrange Input dbl list   Range for allowable TZERO from calibration (default is all)
DIFArange Input dbl list   Range for allowable DIFA from calibration (default is all)
UseChiSq Input boolean False By default the square of the peak height is used as weights in the least-squares fit to find the diffractometer constants, if UseChiSq is true then the inverse square of the error on the fitted peak centres will be used instead.
OutputCalibrationTable Output TableWorkspace Mandatory Output table workspace containing the calibration
DiagnosticWorkspaces Output WorkspaceGroup Mandatory Workspaces to promote understanding of calibration results

Description

This algorithm calibrates the detector pixels and creates a diffraction calibration workspace. Unlike CalibrateRectangularDetectors the peak fitting and calibration is done in TOF not d spacing. The peak d values are converted to TOF based on either the old calibration or the instrument geometry. The InputWorkspace contains the data from a standard sample. The results are then fitted with up to (in order) difc, t_zero, and difa. These values are described in detail in AlignDetectors v1.

The peak fitting properties are explained in more detail in FitPeaks v1. This is used to perform a refinement of peaks using as much information as is provided as possible. Each input spectrum is calibrated separately following the same basic steps:

  1. The PeakPositions are used to determine fit windows in combination with PeakWindow. The windows are half the distance between the provided peak positions, with a maximum size of PeakWindow.
  2. The positions and windows are converted to time-of-flight for the spectrum using either the previous calibration information or the spectrum’s geometry.
  3. For each peak, the background is estimated from the first and last ten points in the fit window.
  4. For each peak, the nominal center is selected by locating the highest point near the expected position. The height is used as the initial guess as well.
  5. For each peak, the width is estimated by multiplying the peak center position with PeakWidthPercent or by calculating the second moment of the data in the window.
  6. For each peak, the peak fit parameters are refined.
  7. All of the fitted peak centers are used to fit the calibration constants, weighted by peak height.

If more than one constant is requested, the result that has the lowest reduced chi-squared value is returned. This favors using less parameters.

A mask workspace is created, named “OutputCalibrationTable” + ‘_mask’, with uncalibrated pixels masked.

The resulting calibration table can be saved with SaveDiffCal v1, loaded with LoadDiffCal v1 and applied to a workspace with AlignDetectors v1. There are also three workspaces placed in the DiagnosticWorkspace group. They are:

  • evaluated fit functions (_fitted)
  • raw peak fit values (_fitparam)
  • contain the fitted positions in dspace( _dspacing)
  • peak widths (_width)
  • peak heights (_height)
  • instrument resolution (delta-d/d _resolution)

Since multiple peak shapes can be used, see the documentation for the individual fit functions to see how they relate to the effective values displayed in the diagnostic tables. For Gaussian and Lorentzian, the widths and resolution are converted to values that can be directly compared with the results of EstimateResolutionDiffraction v1.

Usage

Example - PDCalibration

# If you have an old calibration it can be used as the starting point
oldCal = 'NOM_calibrate_d72460_2016_05_23.h5'

# list of d values for diamond
dvalues = (0.3117,0.3257,0.3499,0.4205,0.4645,0.4768,0.4996,0.5150,0.5441,0.5642,0.5947,0.6307,.6866,.7283,.8185,.8920,1.0758,1.2615,2.0599)

LoadEventNexus(Filename='NOM_72460', OutputWorkspace='NOM_72460')
PDCalibration(InputWorkspace='NOM_72460',
              TofBinning=[300,-.001,16666.7],
              PreviousCalibrationFile=oldCal,
              PeakPositions=dvalues,
              PeakWidthPercent=.008,
              OutputCalibrationTable='cal',
              DiagnosticWorkspaces='diag')

# Print the result
print("The calibrated difc at detid {detid} is {difc}".format(**mtd['cal'].row(40000)))

Output:

The calibrated difc at detid 40896 is 5523.060327692842

Example - PDCalibration with BackToBackExponential fit function

The following example shows how to use PDCalibration with the BackToBackExponential fit function. The fit works best if sensible initial values for the parameters are specified in an instrument definition or parameter file (for more details, see the fitting parameters documentation):

Load(Filename=r'ENGINX00193749.nxs', OutputWorkspace='193749')
dpks = (1.913220892, 1.631600313,
        1.562138267, 1.352851554, 1.104598643)

# initial values for GSAS parameters A, B, S are in ENGINX parameters .xml
# use log binning
PDCalibration(InputWorkspace='193749',
              TofBinning=[10000,-0.0005,46000],
              PeakPositions=dpks,
              PeakWindow = 0.03,
              MinimumPeakHeight = 0.5,
              PeakFunction = 'BackToBackExponential',
              CalibrationParameters = 'DIFC',
              OutputCalibrationTable='cal_B2B_DIFC_chisqTrue',
              DiagnosticWorkspaces = 'diag_B2B_DIFC_chisqTrue',
              UseChiSq = True)

# Print the result
print("The calibrated difc at detid {detid} is {difc}".format(**mtd['cal_B2B_DIFC_chisqTrue'].row(1000)))

Output:

The calibrated difc at detid 108041 is 16834.952770921267

Categories: AlgorithmIndex | Diffraction\Calibration

Source

C++ header: PDCalibration.h

C++ source: PDCalibration.cpp