def Find_Peaks(rnum, long_cell, threshold, MaxPeaks, centroid_radius, edge_pixel):
mantid.PeakDistanceThreshold = 0.9 * 3.14 / long_cell
mantid.FindPeaksMD(InputWorkspace='WISH000' + str(rnum) + '_MD', PeakDistanceThreshold=PeakDistanceThreshold,
MaxPeaks=MaxPeaks, DensityThresholdFactor=threshold,
OutputWorkspace='WISH000' + str(rnum) + '_find_peaks', EdgePixels=edge_pixel)
mantid.CentroidPeaksMD(InputWorkspace='WISH000' + str(rnum) + '_MD', PeakRadius=centroid_radius,
PeaksWorkspace='WISH000' + str(rnum) + '_find_peaks',
OutputWorkspace='WISH000' + str(rnum) + '_find_peaks')
# Spherical Absorption and Lorentz Corrections
ws = mantid.AnvredCorrection(InputWorkspace=ws,
LinearScatteringCoef=0.451,
LinearAbsorptionCoef=0.993,
Radius=0.14)
# Convert to Q space
LabQ = mantid.ConvertToDiffractionMDWorkspace(InputWorkspace=ws,
LorentzCorrection='0',
OutputDimensions='Q (lab frame)',
SplitInto=2,
SplitThreshold=150)
# Find peaks
PeaksLattice = mantid.FindPeaksMD(InputWorkspace=LabQ, MaxPeaks=100)
# 3d integration to centroid peaks
PeaksLattice = mantid.CentroidPeaksMD(InputWorkspace=LabQ,
PeakRadius=0.12,
PeaksWorkspace=PeaksLattice)
# Find the UB matrix using the peaks and known lattice parameters
mantid.FindUBUsingLatticeParameters(PeaksWorkspace=PeaksLattice,
a=10.3522,
b=6.0768,
c=4.7276,
alpha=90,
beta=90,
gamma=90,
NumInitial=20,
def find_peak(self, exp_number, scan_number, pt_number):
""" Find 1 peak in sample Q space for UB matrix
:param scan_number:
:param pt_number:
:return:tuple as (boolean, object) such as (false, error message) and (true, PeakInfo object)
This part will be redo as 11847_Load_HB3A_Experiment
"""
# Check
assert isinstance(exp_number, int)
assert isinstance(scan_number, int)
assert isinstance(pt_number, int)
# Download or make sure data are there
status_sp, err_msg_sp = self.download_spice_file(exp_number,
scan_number,
over_write=False)
status_det, err_msg_det = self.download_spice_xml_file(scan_number,
pt_number,
exp_number,
overwrite=False)
if status_sp is False or status_det is False:
return False, 'Unable to access data (1) %s (2) %s' % (err_msg_sp,
err_msg_det)
# Collect reduction information: example
exp_info_ws_name = get_pt_info_ws_name(exp_number, scan_number)
virtual_instrument_info_table_name = get_virtual_instrument_table_name(
exp_number, scan_number, pt_number)
api.CollectHB3AExperimentInfo(
ExperimentNumber=exp_number,
GenerateVirtualInstrument=False,
ScanList=[scan_number],
PtLists=[-1, pt_number],
DataDirectory=self._dataDir,
GetFileFromServer=False,
Detector2ThetaTolerance=0.01,
OutputWorkspace=exp_info_ws_name,
DetectorTableWorkspace=virtual_instrument_info_table_name)
# Load XML file to MD
pt_md_ws_name = get_single_pt_md_name(exp_number, scan_number,
pt_number)
api.ConvertCWSDExpToMomentum(InputWorkspace=exp_info_ws_name,
CreateVirtualInstrument=False,
OutputWorkspace=pt_md_ws_name,
Directory=self._dataDir)
# Find peak in Q-space
pt_peak_ws_name = get_single_pt_peak_ws_name(exp_number, scan_number,
pt_number)
api.FindPeaksMD(InputWorkspace=pt_md_ws_name,
MaxPeaks=10,
DensityThresholdFactor=0.01,
OutputWorkspace=pt_peak_ws_name)
peak_ws = AnalysisDataService.retrieve(pt_peak_ws_name)
pt_md_ws = AnalysisDataService.retrieve(pt_md_ws_name)
self._myPtMDDict[(exp_number, scan_number, pt_number)] = pt_md_ws
num_peaks = peak_ws.getNumberPeaks()
if num_peaks != 1:
err_msg = 'Find %d peak from scan %d pt %d. ' \
'For UB matrix calculation, 1 and only 1 peak is allowed' % (num_peaks, scan_number, pt_number)
return False, err_msg
else:
self._add_ub_peak_ws(exp_number, scan_number, pt_number, peak_ws)
status, ret_obj = self.add_peak_info(exp_number, scan_number,
pt_number)
if status is True:
pass
# peak_info = ret_obj
# peak_info.set_md_ws(pt_md_ws)
else:
err_msg = ret_obj
return False, err_msg
return True, ''
#
# A lower SplitThreshold, with a reasonable bound on the recursion depth, helps find weaker peaks at higher Q.
#
QLab = mantid.ConvertToDiffractionMDWorkspace(InputWorkspace='SXD23767',
OutputDimensions='Q (lab frame)',
SplitThreshold=50,
LorentzCorrection='1',
MaxRecursionDepth='13',
Extents='-15,15,-15,15,-15,15')
#
# NaCl has a relatively small unit cell, so the distance between peaks is relatively large. Setting the PeakDistanceThreshold
# higher avoids finding high count regions on the sides of strong peaks as separate peaks.
#
peaks_qLab = mantid.FindPeaksMD(InputWorkspace='QLab',
MaxPeaks=300,
DensityThresholdFactor=10,
PeakDistanceThreshold=1.0)
#
# Fewer peaks index if Centroiding is used. This indicates that there may be an error in the centroiding algorithm,
# since the peaks seem to be less accurate.
#
# peaks_qLab = CentroidPeaksMD(InputWorkspace='QLab',PeaksWorkspace=peaks_qLab)
use_fft = True
use_cubic_lat_par = False
use_Niggli_lat_par = False
#
# Note: Reduced tolerance on FindUBUsingFFT will omit peaks not near the lattice. This seems to help
# find the Niggli cell correctly, with all angle 60 degrees, and all sides 3.99