New Python Algorithm: RefineSingleCrystalGoniometer

[ktactac-ornl]

Description of work

Summary of work

Introduces a new python algorithm RefineSingleCrystalGoniometer to handle a special case where FindUBUsingIndexedPeaks did not index all peaks.

Purpose of work

# import mantid algorithms, numpy and matplotlib
from mantid.simpleapi import *
import matplotlib.pyplot as plt
import numpy as np

from scipy.spatial.transform import Rotation
import scipy.optimize

filename = '/SNS/TOPAZ/IPTS-33878/shared/RFMBA2PbI4/RFMBA2PbI4_mantid_295K_find_peaks/RFMBA2PbI4_Monoclinic_P_5sig.integrate'

LoadIsawPeaks(Filename=filename, OutputWorkspace='peaks')

FindUBUsingIndexedPeaks(PeaksWorkspace='peaks', Tolerance=0.12)
IndexPeaks(PeaksWorkspace='peaks'', Tolerance=0.12)

The above script shows peculiar behavior. Running FindUBUsingIndexedPeaks only indexes about half the peaks. Running index peaks right after indexes nearly all of them. It seems the FindUBUsingIndexedPeaks algorithm is not working properly.

The problem is actually with the goniometer settings of the requested angles not reflecting reality.

The solution is a new mantid algorithm that refines the UB-matrix and goniometer offsets simultaneously. This improves the indexing of the peaks for those cases when there is sample misorientation.

Fixes 9593: [Story] RefineSingleCrystalGoniometer: FindUBUsingIndexed peaks only indexes half the number of reflections as IndexPeaks.

Further detail of work

To test:

PYTHONPATH=/path/to/build/bin python3 /path/to/src/Framework/PythonInterface/test/python/plugins/algorithms/RefineSingleCrystalGoniometerTest.py

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[sf1919]

The Linux Systems Test and Windows Test failures are genuine. Please ignore OSX. I won't re-run though as there will be further commit(s) to fix the failing tests.

[zjmorgan]

Use Mantid-like variable names

tol -> Tolerance
cell -> Cell
n_iter - NumIterations

[zjmorgan]

Add a check for an oriented lattice. Don't run without the UB/oriented lattice

Error in execution of algorithm RefineSingleCrystalGoniometer:
Sample::getOrientedLattice - No OrientedLattice has been defined.
  at line 76 in '/home/zgf/git/mantid/Framework/PythonInterface/plugins/algorithms/RefineSingleCrystalGoniometer.py'

[zjmorgan]

Once the test passes, It should be good to approve

[zjmorgan]

Looks good and works well for the dataset provided.