Single Crystal Profile fit in Mantid corrections

[Vickie Lynch]

First data point is 0 which skews background. Profiles should be written in Art's format so they can be fitted with his code and fitting parameters for each peak should be saved in file. Fitting option with one exponential does not fit most peaks well. Gaussian Quadrature should be used for integration of profile with summing left as an option. Directory for output of png files should be specified.

[Vickie Lynch]

Refs #7432 fix first point zero

Changeset: bc7c199c2c86e0653756e69e71026d982e1bbc4b

[Vickie Lynch]

Refs #7432 find center of peak

Changeset: 0646b8c3581c75396176feb302457e6bc45e957b

[Vickie Lynch]

Refs #7432 profiles output files added

Changeset: 13f2ba999689e06e7c5914129f032cbaccde91cd

[Vickie Lynch]

Refs #7432 write file of optimized fitting parameters

Changeset: 0e51e62fc3d7d666f65923f05267944e42cdd0b9

[Vickie Lynch]

Refs #7432 fix Mac builds

Changeset: f5f1600a591a233870bed46d2d5541a3c803b704

[Vickie Lynch]

Refs #7432 use function for evaluation

Changeset: 0585d1d6eff3e66b151c31228fb5c31bc8f90ae5

[Vickie Lynch]

Refs #7432 function for evaluation

Changeset: 67996985eda093010f404b05e80052069a9fc1a9

[Vickie Lynch]

Refs #7432 use gsl integration instead of sum

Changeset: 6b4425273727dfdd58c968ec09dd363db32ebb5b

[Vickie Lynch]

Refs #7432 add gsl header file

Changeset: aea50515297b5cfe82e035b467b0c72354137aa2

[Vickie Lynch]

Refs #7432 options for integration of profile

Changeset: 1346465cf62e6206c602b0f1512a7a6caf14290a

[Vickie Lynch]

Here is script I used for testing. Puts all files in directories in your home area for checking. I removed ConvolutionExpGaussian option since it did not work well. Users would like plots put in directories without plotting in MantidPlot window but could not find a way to do this.

import os
Home = "/home/vel"
Load(Filename='TOPAZ_6674_event.nxs',OutputWorkspace='TOPAZ_6674_event',FilterByTofMin='2000',FilterByTofMax='16500',LoadMonitors='1',MonitorsAsEvents='1')
ConvertToDiffractionMDWorkspace(InputWorkspace='TOPAZ_6674_event',OutputWorkspace='TOPAZ_6674_MD',OutputDimensions='Q (sample frame)',SplitThreshold='50',MaxRecursionDepth='11')
FindPeaksMD(InputWorkspace='TOPAZ_6674_MD',PeakDistanceThreshold='0.471',MaxPeaks='100',OutputWorkspace='peaks_ws')
CentroidPeaksMD(InputWorkspace='TOPAZ_6674_MD',PeaksWorkspace='peaks_ws',OutputWorkspace='peaks_ws')
FindUBUsingFFT(PeaksWorkspace='peaks_ws',MinD='4',MaxD='12',Tolerance='0.12')
IndexPeaks(PeaksWorkspace='peaks_ws',Tolerance='0.12')
SelectCellOfType(PeaksWorkspace='peaks_ws',CellType='Rhombohedral',Centering='R')
IntegratePeaksMD(InputWorkspace='TOPAZ_6674_MD',CoordinatesToUse='Q (sample frame)',PeakRadius='0.1',PeaksWorkspace='peaks_ws',OutputWorkspace='peaks_ws_sphere')
IntegratePeaksMD(InputWorkspace='TOPAZ_6674_MD',CoordinatesToUse='Q (sample frame)',PeakRadius='0.1',PeaksWorkspace='peaks_ws',OutputWorkspace='peaks_ws_cylinder',
Cylinder='1',CylinderLength='0.4',PercentBackground='20',ProfileFunction='NoFit')

IntegratePeaksMD(InputWorkspace='TOPAZ_6674_MD',CoordinatesToUse='Q (sample frame)',PeakRadius='0.1',PeaksWorkspace='peaks_ws',OutputWorkspace='peaks_ws_cylinder_gauss',
Cylinder='1',CylinderLength='0.4',PercentBackground='20',ProfileFunction='Gaussian',ProfilesFile=Home+'/new.profiles')
os.system("mkdir ~/ProfileGauss")
for wi in xrange(mtd["ProfilesData"].getNumberHistograms()):
        graph_spec = plotSpectrum ("ProfilesData", wi, False, 1)
        l = graph_spec.activeLayer()
        l.insertCurve("ProfilesFit", wi)
        l.insertCurve("ProfilesFitDiff", wi)
        graph_spec.export(Home+"/ProfileGauss/ProfileGauss"+mtd["ProfilesData"].getAxis(1).label(wi)+".png")
        #Remove next 2 lines to keep plots in window
        graph_spec.confirmClose(False)
        graph_spec.close()

IntegratePeaksMD(InputWorkspace='TOPAZ_6674_MD',CoordinatesToUse='Q (sample frame)',PeakRadius='0.1',PeaksWorkspace='peaks_ws',OutputWorkspace='peaks_ws_cylinder_gauss_sum',
Cylinder='1',CylinderLength='0.4',PercentBackground='20',ProfileFunction='Gaussian',IntegrationOption="Sum")
os.system("mkdir ~/ProfileGauss_Sum")
for wi in xrange(mtd["ProfilesData"].getNumberHistograms()):
        graph_spec = plotSpectrum ("ProfilesData", wi, False, 1)
        l = graph_spec.activeLayer()
        l.insertCurve("ProfilesFit", wi)
        l.insertCurve("ProfilesFitDiff", wi)
        graph_spec.export(Home+"/ProfileGauss_Sum/ProfileGauss"+mtd["ProfilesData"].getAxis(1).label(wi)+".png")
        #Remove next 2 lines to keep plots in window
        graph_spec.confirmClose(False)
        graph_spec.close()

IntegratePeaksMD(InputWorkspace='TOPAZ_6674_MD',CoordinatesToUse='Q (sample frame)',PeakRadius='0.1',PeaksWorkspace='peaks_ws',OutputWorkspace='peaks_ws_cylinder_b2b',
Cylinder='1',CylinderLength='0.4',PercentBackground='20',ProfileFunction='ConvolutionBackToBackGaussian')
os.system("mkdir ~/ProfileB2B")
for wi in xrange(mtd["ProfilesData"].getNumberHistograms()):
        graph_spec = plotSpectrum ("ProfilesData", wi, False, 1)
        l = graph_spec.activeLayer()
        l.insertCurve("ProfilesFit", wi)
        l.insertCurve("ProfilesFitDiff", wi)
        graph_spec.export(Home+"/ProfileB2B/ProfileB2B"+mtd["ProfilesData"].getAxis(1).label(wi)+".png")
        #Remove next 2 lines to keep plots in window
        graph_spec.confirmClose(False)
        graph_spec.close()

IntegratePeaksMD(InputWorkspace='TOPAZ_6674_MD',CoordinatesToUse='Q (sample frame)',PeakRadius='0.1',PeaksWorkspace='peaks_ws',OutputWorkspace='peaks_ws_cylinder_b2b_sum',
Cylinder='1',CylinderLength='0.4',PercentBackground='20',ProfileFunction='ConvolutionBackToBackGaussian',IntegrationOption="Sum")
os.system("mkdir ~/ProfileB2B_Sum")
for wi in xrange(mtd["ProfilesData"].getNumberHistograms()):
        graph_spec = plotSpectrum ("ProfilesData", wi, False, 1)
        l = graph_spec.activeLayer()
        l.insertCurve("ProfilesFit", wi)
        l.insertCurve("ProfilesFitDiff", wi)
        graph_spec.export(Home+"/ProfileB2B_Sum/ProfileB2B"+mtd["ProfilesData"].getAxis(1).label(wi)+".png")
        #Remove next 2 lines to keep plots in window
        graph_spec.confirmClose(False)
        graph_spec.close()

[Andrei Savici]

Merge remote-tracking branch 'origin/feature/7432_profile_fit2'

[Stuart Campbell]

This ticket has been transferred to github issue ​8278