def readIdxrefLp(pathToIdxrefLp, resultXDSIndexing=None):
if resultXDSIndexing is None:
resultXDSIndexing = {}
if pathToIdxrefLp.exists():
with open(str(pathToIdxrefLp)) as f:
listLines = f.readlines()
indexLine = 0
doParseParameters = False
doParseLattice = False
while indexLine < len(listLines):
if "DIFFRACTION PARAMETERS USED AT START OF INTEGRATION" in listLines[
indexLine]:
doParseParameters = True
doParseLattice = False
elif "DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE" in listLines[
indexLine]:
doParseParameters = False
doParseLattice = True
if doParseParameters:
if "MOSAICITY" in listLines[indexLine]:
resultXDSIndexing['mosaicity'] = float(
listLines[indexLine].split()[-1])
elif "DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM" in listLines[
indexLine]:
resultXDSIndexing['xBeam'] = float(
listLines[indexLine].split()[-1])
resultXDSIndexing['yBeam'] = float(
listLines[indexLine].split()[-2])
elif "CRYSTAL TO DETECTOR DISTANCE" in listLines[
indexLine]:
resultXDSIndexing['distance'] = float(
listLines[indexLine].split()[-1])
elif doParseLattice:
if listLines[indexLine].startswith(
" * ") and not listLines[indexLine +
1].startswith(" * "):
listLine = listLines[indexLine].split()
latticeCharacter = int(listLine[1])
bravaisLattice = listLine[2]
spaceGroup = UtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(
bravaisLattice)
spaceGroupNumber = UtilsSymmetry.getITNumberFromSpaceGroupName(
spaceGroup)
qualityOfFit = float(listLine[3])
resultXDSIndexing.update({
'latticeCharacter': latticeCharacter,
'spaceGroupNumber': spaceGroupNumber,
'qualityOfFit': qualityOfFit,
'a': float(listLine[4]),
'b': float(listLine[5]),
'c': float(listLine[6]),
'alpha': float(listLine[7]),
'beta': float(listLine[8]),
'gamma': float(listLine[9])
})
indexLine += 1
return resultXDSIndexing
def test_getMinimumSymmetrySpaceGroupFromBravaisLattice(self):
"""
Testing retrieving the lowest symmetry space group from all Bravais Lattices
"""
listBravaisLattice = [
"aP",
"mP",
"mC",
"mI",
"oP",
"oA",
"oB",
"oC",
"oS",
"oF",
"oI",
"tP",
"tC",
"tI",
"tF",
"hP",
"hR",
"cP",
"cF",
"cI",
]
listSpaceGroup = [
"P1",
"P2",
"C2",
"C2",
"P222",
"C222",
"C222",
"C222",
"C222",
"F222",
"I222",
"P4",
"P4",
"I4",
"I4",
"P3",
"H3",
"P23",
"F23",
"I23",
]
for index in range(len(listBravaisLattice)):
self.assertEqual(
listSpaceGroup[index],
UtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(
listBravaisLattice[index]),
)
def parseLattice(indexLine, listLines, resultXDSIndexing):
if listLines[indexLine].startswith(
" * ") and not listLines[indexLine + 1].startswith(" * "):
listLine = listLines[indexLine].split()
latticeCharacter = int(listLine[1])
bravaisLattice = listLine[2]
spaceGroup = UtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(
bravaisLattice)
spaceGroupNumber = UtilsSymmetry.getITNumberFromSpaceGroupName(
spaceGroup)
qualityOfFit = float(listLine[3])
resultXDSIndexing.update({
"latticeCharacter": latticeCharacter,
"spaceGroupNumber": spaceGroupNumber,
"qualityOfFit": qualityOfFit,
"a": float(listLine[4]),
"b": float(listLine[5]),
"c": float(listLine[6]),
"alpha": float(listLine[7]),
"beta": float(listLine[8]),
"gamma": float(listLine[9]),
})