.. algorithm::

.. summary::

.. relatedalgorithms::

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Description
-----------

The purpose of this algorithm is to improve the indexing of peaks in special cases where ``FindUBUsingIndexedPeaks`` does not index all peaks due to sample misorientation.

The example below demonstrates a case where ``FindUBUsingIndexedPeaks`` is insufficient:

.. code-block:: python

    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)

This code will only index about half of the peaks.

The solution is to use this algorithm that refines the UB-matrix and goniometer offsets simultaneously.

.. code-block:: python

    from mantid.simpleapi import mtd, RefineSingleCrystalGoniometer, LoadIsawPeaks, FindUBUsingIndexedPeaks, IndexPeaks

    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")
    IndexPeaks(PeaksWorkspace="peaks", CommonUBForAll=True)

    RefineSingleCrystalGoniometer("peaks", tol=0.25, cell="Monoclinic", n_iter=5)
    IndexPeaks(PeaksWorkspace="peaks", CommonUBForAll=True)

This will result in a better indexing of the peaks.

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