SaveHKLCW.py

# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2020 ISIS Rutherford Appleton Laboratory UKRI,
#   NScD Oak Ridge National Laboratory, European Spallation Source,
#   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
# SPDX - License - Identifier: GPL - 3.0 +

import numpy as np
from mantid.api import (AlgorithmFactory, PythonAlgorithm, FileAction, FileProperty,
                        IPeaksWorkspaceProperty)
from mantid.kernel import Direction, logger


class SaveHKLCW(PythonAlgorithm):
    def category(self):
        return 'Diffraction\\DataHandling'

    def summary(self):
        """
        summary of the algorithm
        :return:
        """
        return "Save a PeaksWorkspace to SHELX76 format required by WINGX"

    def name(self):
        return "SaveHKLCW"

    def seeAlso(self):
        return ["SaveHKL"]

    def PyInit(self):
        self.declareProperty(IPeaksWorkspaceProperty('Workspace', '', direction=Direction.Input),
                             doc='PeaksWorkspace to be saved')
        self.declareProperty(FileProperty('OutputFile',
                                          '',
                                          action=FileAction.Save,
                                          extensions=['hkl', 'int'],
                                          direction=Direction.Input),
                             doc='Output File.')
        self.declareProperty('Header',
                             True,
                             direction=Direction.Input,
                             doc='If to include the header in the output')
        self.declareProperty('DirectionCosines',
                             False,
                             direction=Direction.Input,
                             doc='If to include the direction cosines output')

    def PyExec(self):

        peak_ws = self.getProperty('Workspace').value
        outFile = self.getPropertyValue('OutputFile')
        header = self.getProperty('Header').value
        directionCosines = self.getProperty('DirectionCosines').value

        with open(outFile, 'w') as f:
            if header:
                f.write("Single crystal data\n")
                if directionCosines:
                    f.write("(3i4,2f8.2,i4,6f8.5)\n")
                else:
                    f.write("(3i4,2f8.2,i4)\n")
                wavelengths = [p.getWavelength() for p in peak_ws]
                if np.std(wavelengths) > 0.01:
                    logger.warning(
                        "Large variation of wavelengths, this doesn't look like constant wavelength"
                    )
                wavelength = np.mean([p.getWavelength() for p in peak_ws])
                f.write(f"{wavelength:.5f}  0   0\n")

            if directionCosines:
                U = peak_ws.sample().getOrientedLattice().getU()
                for p in peak_ws:
                    ki_n = p.getReferenceFrame().vecPointingAlongBeam()
                    R = p.getGoniometerMatrix()
                    RU = np.dot(R, U)
                    ki = ki_n * (2 * np.pi / p.getWavelength())
                    kf_n = ki - p.getQLabFrame()  # direction of scattered wavevector
                    kf_n = kf_n * (1. / kf_n.norm())
                    dir_cos_1 = np.dot(RU.T, -ki_n)  # notice ki direction is reversed
                    dir_cos_2 = np.dot(RU.T, kf_n)
                    f.write(
                        "{:4.0f}{:4.0f}{:4.0f}{:8.2f}{:8.2f}{:4d}{:8.5f}{:8.5f}{:8.5f}{:8.5f}{:8.5f}{:8.5f}\n"
                        .format(p.getH(), p.getK(), p.getL(), p.getIntensity(),
                                p.getSigmaIntensity(), 1, dir_cos_1[0], dir_cos_2[0], dir_cos_1[1],
                                dir_cos_2[1], dir_cos_1[2], dir_cos_2[2]))
            else:
                for p in peak_ws:
                    f.write("{:4.0f}{:4.0f}{:4.0f}{:8.2f}{:8.2f}{:4d}\n".format(
                        p.getH(), p.getK(), p.getL(), p.getIntensity(), p.getSigmaIntensity(), 1))


AlgorithmFactory.subscribe(SaveHKLCW)