def test_creation_rotation(self):
symOpPlus = SymmetryOperationFactory.createSymOp("-y,x-y,z")
symElePlus = SymmetryElementFactory.createSymElement(symOpPlus)
self.assertEquals(symElePlus.getRotationSense(), SymmetryElement.RotationSense.Positive)
symOpMinus = SymmetryOperationFactory.createSymOp("-x+y,-x,z")
symEleMinus = SymmetryElementFactory.createSymElement(symOpMinus)
self.assertEquals(symEleMinus.getRotationSense(), SymmetryElement.RotationSense.Negative)
def test_creation_rotation(self):
symOpPlus = SymmetryOperationFactory.createSymOp("-y,x-y,z")
symElePlus = SymmetryElementFactory.createSymElement(symOpPlus)
self.assertEqual(symElePlus.getRotationSense(), SymmetryElement.RotationSense.Positive)
symOpMinus = SymmetryOperationFactory.createSymOp("-x+y,-x,z")
symEleMinus = SymmetryElementFactory.createSymElement(symOpMinus)
self.assertEqual(symEleMinus.getRotationSense(), SymmetryElement.RotationSense.Negative)
def test_creation_axis(self):
symOp = SymmetryOperationFactory.createSymOp("x,y,-z")
symEle = SymmetryElementFactory.createSymElement(symOp)
self.assertEquals(symEle.getHMSymbol(), "m")
self.assertEquals(symEle.getAxis(), V3D(0,0,1))
rotation = SymmetryOperationFactory.createSymOp("x,-y,-z")
rotationElement = SymmetryElementFactory.createSymElement(rotation)
self.assertEquals(rotationElement.getHMSymbol(), "2")
self.assertEquals(rotationElement.getAxis(), V3D(1,0,0))
def test_creation_axis(self):
symOp = SymmetryOperationFactory.createSymOp("x,y,-z")
symEle = SymmetryElementFactory.createSymElement(symOp)
self.assertEquals(symEle.getHMSymbol(), "m")
self.assertEquals(symEle.getAxis(), V3D(0, 0, 1))
rotation = SymmetryOperationFactory.createSymOp("x,-y,-z")
rotationElement = SymmetryElementFactory.createSymElement(rotation)
self.assertEquals(rotationElement.getHMSymbol(), "2")
self.assertEquals(rotationElement.getAxis(), V3D(1, 0, 0))
def _generate_UBList(self):
CreateSingleValuedWorkspace(OutputWorkspace='__ub')
LoadIsawUB('__ub', self.getProperty("UBMatrix").value)
ub = mtd['__ub'].sample().getOrientedLattice().getUB().copy()
DeleteWorkspace(Workspace='__ub')
symOps = self.getProperty("SymmetryOps").value
if symOps:
try:
symOps = SpaceGroupFactory.subscribedSpaceGroupSymbols(
int(symOps))[0]
except ValueError:
pass
if SpaceGroupFactory.isSubscribedSymbol(symOps):
symOps = SpaceGroupFactory.createSpaceGroup(
symOps).getSymmetryOperations()
else:
symOps = SymmetryOperationFactory.createSymOps(symOps)
logger.information('Using symmetries: ' +
str([sym.getIdentifier() for sym in symOps]))
ub_list = []
for sym in symOps:
UBtrans = np.zeros((3, 3))
UBtrans[0] = sym.transformHKL([1, 0, 0])
UBtrans[1] = sym.transformHKL([0, 1, 0])
UBtrans[2] = sym.transformHKL([0, 0, 1])
UBtrans = np.matrix(UBtrans.T)
ub_list.append(ub * UBtrans)
return ub_list
else:
return [ub]
def _generate_UBList(self):
CreateSingleValuedWorkspace(OutputWorkspace='__ub')
LoadIsawUB('__ub',self.getProperty("UBMatrix").value)
ub=mtd['__ub'].sample().getOrientedLattice().getUB().copy()
DeleteWorkspace(Workspace='__ub')
symOps = self.getProperty("SymmetryOps").value
if symOps:
try:
symOps = SpaceGroupFactory.subscribedSpaceGroupSymbols(int(symOps))[0]
except ValueError:
pass
if SpaceGroupFactory.isSubscribedSymbol(symOps):
symOps = SpaceGroupFactory.createSpaceGroup(symOps).getSymmetryOperations()
else:
symOps = SymmetryOperationFactory.createSymOps(symOps)
logger.information('Using symmetries: '+str([sym.getIdentifier() for sym in symOps]))
ub_list=[]
for sym in symOps:
UBtrans = np.zeros((3,3))
UBtrans[0] = sym.transformHKL([1,0,0])
UBtrans[1] = sym.transformHKL([0,1,0])
UBtrans[2] = sym.transformHKL([0,0,1])
UBtrans=np.matrix(UBtrans.T)
ub_list.append(ub*UBtrans)
return ub_list
else:
return [ub]
def test_apply(self):
symOp = SymmetryOperationFactory.createSymOp("x,y,-z")
hkl1 = V3D(1, 1, 1)
hkl2 = symOp.apply(hkl1)
self.assertEquals(hkl2, V3D(1, 1, -1))
self.assertEquals(symOp.transformHKL(hkl2), hkl1)
def test_apply(self):
symOp = SymmetryOperationFactory.createSymOp("x,y,-z")
hkl1 = V3D(1, 1, 1)
hkl2 = symOp.apply(hkl1)
self.assertEquals(hkl2, V3D(1, 1, -1))
self.assertEquals(symOp.transformHKL(hkl2), hkl1)
def validateInputs(self):
issues = dict()
if self.getProperty("SymmetryOps").value:
syms=self.getProperty("SymmetryOps").value
try:
if not SpaceGroupFactory.isSubscribedNumber(int(syms)):
issues["SymmetryOps"] = 'Space group number '+syms+' is not valid'
except ValueError:
if not SpaceGroupFactory.isSubscribedSymbol(syms):
for sym in syms.split(';'):
if not SymmetryOperationFactory.exists(sym):
issues["SymmetryOps"] = sym+' is not valid symmetry or space group name'
return issues
def validateInputs(self):
issues = dict()
if self.getProperty("SymmetryOps").value:
syms=self.getProperty("SymmetryOps").value
try:
if not SpaceGroupFactory.isSubscribedNumber(int(syms)):
issues["SymmetryOps"] = 'Space group number '+syms+' is not valid'
except ValueError:
if not SpaceGroupFactory.isSubscribedSymbol(syms):
for sym in syms.split(';'):
if not SymmetryOperationFactory.exists(sym):
issues["SymmetryOps"] = sym+' is not valid symmetry or space group name'
return issues
def _symmetrize_by_generators(self, mdws, axisAligned, basis0, basis1, basis2, basis3, normalizeBasisVectors, translation, outputExtents, outputBins, numOp, symOp1, symOp2, symOp3, symOp4, symOp5): unit0, basisVec0 = self._destringify(basis0) unit1, basisVec1 = self._destringify(basis1) unit2, basisVec2 = self._destringify(basis2) unit3, basisVec3 = self._destringify(basis3) symOpList = [symOp1, symOp2, symOp3, symOp4, symOp5] for i in range(numOp): basisVec0_str = None basisVec1_str = None basisVec2_str = None basisVec3_str = None symOp = SymmetryOperationFactory.createSymOp(symOpList[i]) if basisVec0 is not None: coordinatesPrime = symOp.transformCoordinates(basisVec0) basisVec0_str = unit0[0] + ',' + unit0[1] + ',' + str(coordinatesPrime.getX()) \ + ',' + str(coordinatesPrime.getY()) + ',' + str(coordinatesPrime.getZ()) + ',' + '0' if basisVec1 is not None: coordinatesPrime = symOp.transformCoordinates(basisVec1) basisVec1_str = unit1[0] + ',' + unit1[1] + ',' + str(coordinatesPrime.getX()) \ + ',' + str(coordinatesPrime.getY()) + ',' + str(coordinatesPrime.getZ()) + ',' + '0' if basisVec2 is not None: coordinatesPrime = symOp.transformCoordinates(basisVec2) basisVec2_str = unit2[0] + ',' + unit2[1] + ',' + str(coordinatesPrime.getX()) \ + ',' + str(coordinatesPrime.getY()) + ',' + str(coordinatesPrime.getZ()) + ',' + '0' if basisVec3 is not None: coordinatesPrime = symOp.transformCoordinates(basisVec3) basisVec3_str = unit3[0] + ',' + unit3[1] + ',' + str(coordinatesPrime.getX()) \ + ',' + str(coordinatesPrime.getY()) + ',' + str(coordinatesPrime.getZ()) + ',' + '0' self._binned_ws += BinMD(InputWorkspace=mdws, AxisAligned=axisAligned, BasisVector0=basisVec0_str, BasisVector1=basisVec1_str, BasisVector2=basisVec2_str, BasisVector3=basisVec3_str, NormalizeBasisVectors=normalizeBasisVectors, Translation=translation, OutputExtents=outputExtents, OutputBins=outputBins) return
Filename=
'/SNS/CORELLI/shared/Calibration/CORELLI_Definition_cal_20160310.xml',
OutputWorkspace='ub')
LoadIsawUB(InputWorkspace='ub', Filename=UBfile)
ub = mtd['ub'].sample().getOrientedLattice().getUB()
print "Starting UB :"
print ub
#DTO Fd-3m (227) general position has 192 symmety operations.
symOps = SymmetryOperationFactory.createSymOps(\
"x,y,z; -x,-y,z; -x,y,-z; x,-y,-z;\
z,x,y; z,-x,-y; -z,-x,y; -z,x,-y;\
y,z,x; -y,z,-x; y,-z,-x; -y,-z,x;\
y,x,-z; -y,-x,-z; y,-x,z; -y,x,z;\
x,z,-y; -x,z,y; -x,-z,-y; x,-z,y;\
z,y,-x; z,-y,x; -z,y,x; -z,-y,-x;\
-x,-y,-z; x,y,-z; x,-y,z; -x,y,z;\
-z,-x,-y; -z,x,y; z,x,-y; z,-x,y;\
-y,-z,-x; y,-z,x; -y,z,x; y,z,-x;\
-y,-x,z; y,x,z; -y,x,-z; y,-x,-z;\
-x,-z,y; x,-z,-y; x,z,y; -x,z,-y;\
-z,-y,x; -z,y,-x; z,-y,-x; z,y,x" )
ub_list = []
for sym in symOps:
UBtrans = np.zeros((3, 3))
UBtrans[0] = sym.transformHKL([1, 0, 0])
UBtrans[1] = sym.transformHKL([0, 1, 0])
UBtrans[2] = sym.transformHKL([0, 0, 1])
UBtrans = np.matrix(UBtrans.T)
new_ub = ub * UBtrans
def test_creation_no_rotation(self):
symOpNone = SymmetryOperationFactory.createSymOp("-x,-y,-z")
symEleNone = SymmetryElementFactory.createSymElement(symOpNone)
self.assertEquals(symEleNone.getRotationSense(), SymmetryElement.RotationSense.NoRotation)
def test_creation(self):
self.assertRaises(RuntimeError, SymmetryOperationFactory.createSymOp, "none")
SymmetryOperationFactory.createSymOp("x,y,-z")
def test_creation_no_axis(self):
symOp = SymmetryOperationFactory.createSymOp("-x,-y,-z")
symEle = SymmetryElementFactory.createSymElement(symOp)
self.assertEquals(symEle.getHMSymbol(), "-1")
self.assertEquals(symEle.getAxis(), V3D(0,0,0))
def test_creation_no_rotation(self):
symOpNone = SymmetryOperationFactory.createSymOp("-x,-y,-z")
symEleNone = SymmetryElementFactory.createSymElement(symOpNone)
self.assertEquals(symEleNone.getRotationSense(),
SymmetryElement.RotationSense.NoRotation)
def test_getInfo(self):
symOp = SymmetryOperationFactory.createSymOp("x, y, -z")
self.assertEquals(symOp.getOrder(), 2)
self.assertEquals(symOp.getIdentifier(), "x,y,-z")
from mantid.geometry import SymmetryOperationFactory
import numpy as np
# Get UBs
LoadEmptyInstrument(
Filename=
'/SNS/CORELLI/shared/Calibration/CORELLI_Definition_cal_20160310.xml',
OutputWorkspace='ub')
LoadIsawUB(InputWorkspace='ub',
Filename="/SNS/users/rwp/benzil/benzil_Hexagonal.mat")
ub = mtd['ub'].sample().getOrientedLattice().getUB()
print "Starting UB :"
print ub
symOps = SymmetryOperationFactory.createSymOps(
"x,y,z; -y,x-y,z+1/3; -x+y,-x,z+2/3; y,x,-z; x-y,-y,-z+2/3; -x,-x+y,-z+1/3"
)
ub_list = []
for sym in symOps:
UBtrans = np.zeros((3, 3))
UBtrans[0] = sym.transformHKL([1, 0, 0])
UBtrans[1] = sym.transformHKL([0, 1, 0])
UBtrans[2] = sym.transformHKL([0, 0, 1])
UBtrans = np.matrix(UBtrans.T)
new_ub = ub * UBtrans
print "Symmetry transform for " + sym.getIdentifier()
print UBtrans
print "New UB:"
print new_ub
ub_list.append(new_ub)
from mantid.simpleapi import *
from mantid.geometry import SymmetryOperationFactory
import numpy as np
# Get UBs
LoadEmptyInstrument(Filename='/SNS/CORELLI/shared/Calibration/CORELLI_Definition_cal_20160310.xml', OutputWorkspace='ub')
LoadIsawUB(InputWorkspace='ub', Filename="/SNS/users/rwp/benzil/benzil_Hexagonal.mat")
ub=mtd['ub'].sample().getOrientedLattice().getUB()
print "Starting UB :"
print ub
symOps = SymmetryOperationFactory.createSymOps("x,y,z; -y,x-y,z+1/3; -x+y,-x,z+2/3; y,x,-z; x-y,-y,-z+2/3; -x,-x+y,-z+1/3")
ub_list=[]
for sym in symOps:
UBtrans = np.zeros((3,3))
UBtrans[0] = sym.transformHKL([1,0,0])
UBtrans[1] = sym.transformHKL([0,1,0])
UBtrans[2] = sym.transformHKL([0,0,1])
UBtrans=np.matrix(UBtrans.T)
new_ub = ub*UBtrans
print "Symmetry transform for "+sym.getIdentifier()
print UBtrans
print "New UB:"
print new_ub
ub_list.append(new_ub)
outputdir="/SNS/CORELLI/IPTS-15526/shared/"
LoadNexus(Filename='/SNS/CORELLI/shared/Vanadium/2016B/SolidAngle20160720NoCC.nxs', OutputWorkspace='sa')
LoadNexus(Filename='/SNS/CORELLI/shared/Vanadium/2016B/Spectrum20160720NoCC.nxs', OutputWorkspace='flux')
#MaskBTP(workspace='sa',Pixel='1-16,241-256')
#for op in symOps:
# print op.getIdentifier()
# three different symmetry operation expressions
#symOps='206'
#symOps='x,y,z; -y,x-y,z+1/3; -x+y,-x,z+2/3; y,x,-z; x-y,-y,-z+2/3; -x,-x+y,-z+1/3'
symOps = 'I a -3'
try:
symOps = SpaceGroupFactory.subscribedSpaceGroupSymbols(int(symOps))[0]
except ValueError:
pass
if SpaceGroupFactory.isSubscribedSymbol(symOps):
symOps = SpaceGroupFactory.createSpaceGroup(symOps).getSymmetryOperations()
else:
symOps = SymmetryOperationFactory.createSymOps(symOps)
#print "Number of operations:", len(symOps)
#print "Operations:"
#for op in symOps:
# print op.getIdentifier()
totcoordinate = []
coordinates = [0, 0, 0]
for op in symOps:
coordinatesPrime = op.transformCoordinates(coordinates)
print('{:<20s},{:10s}').format(op.getIdentifier(), coordinatesPrime)
if coordinatesPrime not in totcoordinate:
totcoordinate.append(coordinatesPrime)
unique_coordinate = np.unique(totcoordinate, axis=0)
def test_getInfo(self):
symOp = SymmetryOperationFactory.createSymOp("x, y, -z")
self.assertEquals(symOp.getOrder(), 2)
self.assertEquals(symOp.getIdentifier(), "x,y,-z")
def test_creation_no_axis(self):
symOp = SymmetryOperationFactory.createSymOp("-x,-y,-z")
symEle = SymmetryElementFactory.createSymElement(symOp)
self.assertEquals(symEle.getHMSymbol(), "-1")
self.assertEquals(symEle.getAxis(), V3D(0, 0, 0))
def test_creation(self):
self.assertRaises(RuntimeError, SymmetryOperationFactory.createSymOp,
"none")
SymmetryOperationFactory.createSymOp("x,y,-z")
LoadNexus(Filename='/SNS/CORELLI/shared/Vanadium/SolidAngle20161123_cc.nxs',
OutputWorkspace='sa')
# Get UBs
LoadEmptyInstrument(
Filename=
'/SNS/CORELLI/shared/Calibration/CORELLI_Definition_cal_20160310.xml',
OutputWorkspace='ub')
LoadIsawUB(InputWorkspace='ub', Filename=outputdir + UBname)
ub = mtd['ub'].sample().getOrientedLattice().getUB()
print "Starting UB :"
print ub
#symOps = SymmetryOperationFactory.createSymOps(" x, y, z; -x ,-y, z; -x,y,-z; x,-y,-z;-x,-y,-z; x,y,-z; x,-y,z; -x,y,z")
#symOps = SymmetryOperationFactory.createSymOps("x, y, z;x,-y,-z; x,y,-z; x,-y,z")
symOps = SymmetryOperationFactory.createSymOps("x, y, z") #;-x,-y,-z")
ub_list = []
for sym in symOps:
UBtrans = np.zeros((3, 3))
UBtrans[0] = sym.transformHKL([1, 0, 0])
UBtrans[1] = sym.transformHKL([0, 1, 0])
UBtrans[2] = sym.transformHKL([0, 0, 1])
UBtrans = np.matrix(UBtrans.T)
new_ub = ub * UBtrans
print "Symmetry transform for " + sym.getIdentifier()
print UBtrans
print "New UB:"
print new_ub
ub_list.append(new_ub)
if mtd.doesExist('normMD'):
