Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
# 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()
sample_pos = peak_ws.getInstrument().getSample().getPos()
source_pos = peak_ws.getInstrument().getSource().getPos()
ki_n = sample_pos - source_pos # direction of incident wavevector
ki_n = ki_n * (1. / ki_n.norm())
for p in peak_ws:
if directionCosines:
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:
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)