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 _punch_and_fill(self, signal, dimX, dimY, dimZ): # noqa
Xmin, Xmax, _, Xwidth = self._get_dim_params(dimX)
Ymin, Ymax, _, Ywidth = self._get_dim_params(dimY)
Zmin, Zmax, _, Zwidth = self._get_dim_params(dimZ)
X, Y, Z = self._get_XYZ_ogrid(dimX, dimY, dimZ)
size = self.getProperty("Size").value
if len(size) == 1:
size = np.repeat(size, 3)
size /= 2.0 # We want radii or half box width
cut_shape = self.getProperty("Shape").value
space_group = self.getProperty("SpaceGroup").value
if space_group:
check_space_group = True
try:
space_group = SpaceGroupFactory.subscribedSpaceGroupSymbols(
int(space_group))[0]
except ValueError:
pass
logger.information('Using space group: ' + space_group)
sg = SpaceGroupFactory.createSpaceGroup(space_group)
else:
check_space_group = False
if cut_shape == 'cube':
for h in range(int(np.ceil(Xmin)), int(Xmax) + 1):
for k in range(int(np.ceil(Ymin)), int(Ymax) + 1):
for l in range(int(np.ceil(Zmin)), int(Zmax) + 1):
if not check_space_group or sg.isAllowedReflection(
[h, k, l]):
signal[int((h - size[0] - Xmin) / Xwidth +
1):int((h + size[0] - Xmin) / Xwidth),
int((k - size[1] - Ymin) / Ywidth +
1):int((k + size[1] - Ymin) / Ywidth),
int((l - size[2] - Zmin) / Zwidth +
1):int((l + size[2] - Zmin) /
Zwidth)] = np.nan
else: # sphere
mask = ((X - np.round(X))**2 / size[0]**2 +
(Y - np.round(Y))**2 / size[1]**2 +
(Z - np.round(Z))**2 / size[2]**2 < 1)
# Unmask invalid reflections
if check_space_group:
for h in range(int(np.ceil(Xmin)), int(Xmax) + 1):
for k in range(int(np.ceil(Ymin)), int(Ymax) + 1):
for l in range(int(np.ceil(Zmin)), int(Zmax) + 1):
if not sg.isAllowedReflection([h, k, l]):
mask[int((h - 0.5 - Xmin) / Xwidth +
1):int((h + 0.5 - Xmin) / Xwidth),
int((k - 0.5 - Ymin) / Ywidth +
1):int((k + 0.5 - Ymin) / Ywidth),
int((l - 0.5 - Zmin) / Zwidth +
1):int((l + 0.5 - Zmin) /
Zwidth)] = False
signal[mask] = np.nan
return signal
def validateInputs(self):
issues = dict()
inWS = self.getProperty("InputWorkspace").value
dimX = inWS.getXDimension()
dimY = inWS.getYDimension()
dimZ = inWS.getZDimension()
if dimX.name != '[H,0,0]' or dimY.name != '[0,K,0]' or dimZ.name != '[0,0,L]':
issues[
'InputWorkspace'] = 'dimensions must be [H,0,0], [0,K,0] and [0,0,L]'
for d in range(inWS.getNumDims()):
dim = inWS.getDimension(d)
if not np.isclose(dim.getMaximum(), -dim.getMinimum(), atol=1e-5):
issues[
'InputWorkspace'] = 'dimensions must be centered on zero'
if self.getProperty("Convolution").value and self.getProperty(
"Method").value == 'Punch and fill':
try:
import astropy # noqa
except ImportError:
issues[
"Convolution"] = 'python-astropy required to do convolution'
size = self.getProperty("Size").value
if len(size) != 1 and len(size) != 3:
issues["Size"] = 'Must provide 1 or 3 sizes'
if self.getProperty("SpaceGroup").value:
space_group = self.getProperty("SpaceGroup").value
try:
if not SpaceGroupFactory.isSubscribedNumber(int(space_group)):
issues["SpaceGroup"] = 'Space group number is not valid'
except ValueError:
if not SpaceGroupFactory.isSubscribedSymbol(space_group):
issues["SpaceGroup"] = 'Space group name is not valid'
sphereMin = self.getProperty("SphereMin").value
if len(sphereMin) != 1 and len(sphereMin) != 3:
issues["SphereMin"] = 'Must provide 1 or 3 diameters'
sphereMax = self.getProperty("SphereMax").value
if len(sphereMax) != 1 and len(sphereMax) != 3:
issues["SphereMax"] = 'Must provide 1 or 3 diameters'
if self.getProperty("WindowFunction").value == 'Tukey':
try:
ssignal.tukey
except AttributeError:
issues[
"WindowFunction"] = 'Tukey window requires scipy >= 0.16.0'
return issues
def validateInputs(self):
issues = dict()
inWS = self.getProperty("InputWorkspace").value
dimX=inWS.getXDimension()
dimY=inWS.getYDimension()
dimZ=inWS.getZDimension()
if dimX.name != '[H,0,0]' or dimY.name != '[0,K,0]' or dimZ.name != '[0,0,L]':
issues['InputWorkspace'] = 'dimensions must be [H,0,0], [0,K,0] and [0,0,L]'
for d in range(inWS.getNumDims()):
dim = inWS.getDimension(d)
if not np.isclose(dim.getMaximum(), -dim.getMinimum(), atol=1e-5):
issues['InputWorkspace'] = 'dimensions must be centered on zero'
if self.getProperty("Convolution").value and self.getProperty("Method").value == 'Punch and fill':
try:
import astropy # noqa
except ImportError:
issues["Convolution"] = 'python-astropy required to do convolution'
size = self.getProperty("Size").value
if len(size) != 1 and len(size) != 3:
issues["Size"] = 'Must provide 1 or 3 sizes'
if self.getProperty("SpaceGroup").value:
space_group=self.getProperty("SpaceGroup").value
try:
if not SpaceGroupFactory.isSubscribedNumber(int(space_group)):
issues["SpaceGroup"] = 'Space group number is not valid'
except ValueError:
if not SpaceGroupFactory.isSubscribedSymbol(space_group):
issues["SpaceGroup"] = 'Space group name is not valid'
sphereMin = self.getProperty("SphereMin").value
if len(sphereMin) != 1 and len(sphereMin) != 3:
issues["SphereMin"] = 'Must provide 1 or 3 diameters'
sphereMax = self.getProperty("SphereMax").value
if len(sphereMax) != 1 and len(sphereMax) != 3:
issues["SphereMax"] = 'Must provide 1 or 3 diameters'
if self.getProperty("WindowFunction").value == 'Tukey':
try:
ssignal.tukey
except AttributeError:
issues["WindowFunction"] = 'Tukey window requires scipy >= 0.16.0'
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 _getSpaceGroupFromNumber(self, cifData):
spaceGroupNumber = [int(cifData[x]) for x in
[u'_space_group_it_number', u'_symmetry_int_tables_number'] if
x in cifData.keys()]
if len(spaceGroupNumber) == 0:
raise RuntimeError('No space group symbol in CIF.')
possibleSpaceGroupSymbols = SpaceGroupFactory.subscribedSpaceGroupSymbols(spaceGroupNumber[0])
if len(possibleSpaceGroupSymbols) != 1:
raise RuntimeError(
'Can not use space group number to determine space group for no. {0}'.format(spaceGroupNumber))
return SpaceGroupFactory.createSpaceGroup(possibleSpaceGroupSymbols[0]).getHMSymbol()
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 _getSpaceGroupFromNumber(self, cifData):
spaceGroupNumber = [int(cifData[x]) for x in
['_space_group_it_number', '_symmetry_int_tables_number'] if
x in cifData.keys()]
if len(spaceGroupNumber) == 0:
raise RuntimeError('No space group symbol in CIF.')
possibleSpaceGroupSymbols = SpaceGroupFactory.subscribedSpaceGroupSymbols(spaceGroupNumber[0])
if len(possibleSpaceGroupSymbols) != 1:
raise RuntimeError(
'Can not use space group number to determine space group for no. {0}'.format(spaceGroupNumber))
return SpaceGroupFactory.createSpaceGroup(possibleSpaceGroupSymbols[0]).getHMSymbol()
def test_isAllowedUnitCell_cubic(self):
cubic = UnitCell(6, 6, 6)
tetragonal = UnitCell(6, 6, 6.01)
sg = SpaceGroupFactory.createSpaceGroup('P m -3')
self.assertTrue(sg.isAllowedUnitCell(cubic))
self.assertFalse(sg.isAllowedUnitCell(tetragonal))
def test_equivalentPositions_Monoclinic(self):
wyckoffs = [([0.3, 0.4, 0.45], 8), ([0.0, 0.4, 0.25], 4),
([0.25, 0.25, 0.5], 4), ([0.25, 0.25, 0.0], 4),
([0.0, 0.5, 0.0], 4), ([0.0, 0.0, 0.0], 4)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("C 1 2/c 1")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def test_equivalentPositions_Trigonal(self):
wyckoffs = [([0.3, 0.4, 0.45], 36), ([0.3, 0.0, 0.25], 18),
([0.5, 0.0, 0.0], 18), ([0.0, 0.0, 0.45], 12),
([0.0, 0.0, 0.0], 6), ([0.0, 0.0, 0.25], 6)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("R -3 c")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def test_isAllowedUnitCell_cubic(self):
cubic = UnitCell(6, 6, 6)
tetragonal = UnitCell(6, 6, 6.01)
sg = SpaceGroupFactory.createSpaceGroup('P m -3')
self.assertTrue(sg.isAllowedUnitCell(cubic))
self.assertFalse(sg.isAllowedUnitCell(tetragonal))
def _punch_and_fill(self, signal, dimX, dimY, dimZ): # noqa
Xmin, Xmax, _, Xwidth = self._get_dim_params(dimX)
Ymin, Ymax, _, Ywidth = self._get_dim_params(dimY)
Zmin, Zmax, _, Zwidth = self._get_dim_params(dimZ)
X, Y, Z = self._get_XYZ_ogrid(dimX, dimY, dimZ)
size = self.getProperty("Size").value
if len(size)==1:
size = np.repeat(size, 3)
size/=2.0 # We want radii or half box width
cut_shape = self.getProperty("Shape").value
space_group = self.getProperty("SpaceGroup").value
if space_group:
check_space_group = True
try:
space_group=SpaceGroupFactory.subscribedSpaceGroupSymbols(int(space_group))[0]
except ValueError:
pass
logger.information('Using space group: '+space_group)
sg=SpaceGroupFactory.createSpaceGroup(space_group)
else:
check_space_group = False
if cut_shape == 'cube':
for h in range(int(np.ceil(Xmin)), int(Xmax)+1):
for k in range(int(np.ceil(Ymin)), int(Ymax)+1):
for l in range(int(np.ceil(Zmin)), int(Zmax)+1):
if not check_space_group or sg.isAllowedReflection([h,k,l]):
signal[int((h-size[0]-Xmin)/Xwidth+1):int((h+size[0]-Xmin)/Xwidth),
int((k-size[1]-Ymin)/Ywidth+1):int((k+size[1]-Ymin)/Ywidth),
int((l-size[2]-Zmin)/Zwidth+1):int((l+size[2]-Zmin)/Zwidth)]=np.nan
else: # sphere
mask=((X-np.round(X))**2/size[0]**2 + (Y-np.round(Y))**2/size[1]**2 + (Z-np.round(Z))**2/size[2]**2 < 1)
# Unmask invalid reflections
if check_space_group:
for h in range(int(np.ceil(Xmin)), int(Xmax)+1):
for k in range(int(np.ceil(Ymin)), int(Ymax)+1):
for l in range(int(np.ceil(Zmin)), int(Zmax)+1):
if not sg.isAllowedReflection([h,k,l]):
mask[int((h-0.5-Xmin)/Xwidth+1):int((h+0.5-Xmin)/Xwidth),
int((k-0.5-Ymin)/Ywidth+1):int((k+0.5-Ymin)/Ywidth),
int((l-0.5-Zmin)/Zwidth+1):int((l+0.5-Zmin)/Zwidth)]=False
signal[mask]=np.nan
return signal
def test_equivalentPositions_Cubic(self):
wyckoffs = [([0.3, 0.4, 0.45], 96), ([0.3, 0.25, 0.25], 48),
([0.3, 0.0, 0.0], 48), ([0.3, 0.3, 0.3], 32),
([0.25, 0.0, 0.0], 24), ([0.0, 0.25, 0.25], 24),
([0.25, 0.25, 0.25], 8), ([0.0, 0.0, 0.0], 8)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("F -4 3 c")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def test_equivalentPositions_Tetragonal(self):
wyckoffs = [([0.3, 0.4, 0.45], 32), ([0.3, 0.3, 0.25], 16),
([0.25, 0.4, 0.125], 16), ([0.0, 0.0, 0.45], 16),
([0.0, 0.25, 0.125], 16), ([0.0, 0.0, 0.25], 8),
([0.0, 0.0, 0.0], 8)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("I 41/a c d")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def test_isAllowedUnitCell_trigonal(self):
rhombohedral = UnitCell(5, 5, 5, 80, 80, 80)
hexagonal = UnitCell(5, 5, 4, 90, 90, 120)
sgRh = SpaceGroupFactory.createSpaceGroup('R -3 c :r')
sgHex = SpaceGroupFactory.createSpaceGroup('R -3 c')
sgP6m = SpaceGroupFactory.createSpaceGroup('P 6/m')
self.assertTrue(sgRh.isAllowedUnitCell(rhombohedral))
self.assertFalse(sgRh.isAllowedUnitCell(hexagonal))
self.assertTrue(sgHex.isAllowedUnitCell(hexagonal))
self.assertFalse(sgHex.isAllowedUnitCell(rhombohedral))
self.assertTrue(sgP6m.isAllowedUnitCell(hexagonal))
self.assertFalse(sgP6m.isAllowedUnitCell(rhombohedral))
def test_isAllowedUnitCell_trigonal(self):
rhombohedral = UnitCell(5, 5, 5, 80, 80, 80)
hexagonal = UnitCell(5, 5, 4, 90, 90, 120)
sgRh = SpaceGroupFactory.createSpaceGroup('R -3 c :r')
sgHex = SpaceGroupFactory.createSpaceGroup('R -3 c')
sgP6m = SpaceGroupFactory.createSpaceGroup('P 6/m')
self.assertTrue(sgRh.isAllowedUnitCell(rhombohedral))
self.assertFalse(sgRh.isAllowedUnitCell(hexagonal))
self.assertTrue(sgHex.isAllowedUnitCell(hexagonal))
self.assertFalse(sgHex.isAllowedUnitCell(rhombohedral))
self.assertTrue(sgP6m.isAllowedUnitCell(hexagonal))
self.assertFalse(sgP6m.isAllowedUnitCell(rhombohedral))
def test_equivalentPositions_Triclinic(self):
wyckoffs = [([0.3, 0.4, 0.45], 2), ([0.5, 0.5, 0.5], 1),
([0.0, 0.5, 0.5], 1), ([0.5, 0.0, 0.5], 1),
([0.5, 0.5, 0.0], 1), ([0.5, 0.0, 0.0], 1),
([0.0, 0.5, 0.0], 1), ([0.0, 0.0, 0.5], 1),
([0.0, 0.0, 0.0], 1)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("P -1")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def test_equivalentPositions_Orthorhombic(self):
wyckoffs = [([0.3, 0.4, 0.45], 16), ([0.3, 0.25, 0.45], 8),
([0.0, 0.4, 0.45], 8), ([0.25, 0.4, 0.25], 8),
([0.3, 0.0, 0.0], 8), ([0.0, 0.25, 0.45], 4),
([0.25, 0.25, 0.75], 4), ([0.25, 0.25, 0.25], 4),
([0.0, 0.0, 0.5], 4), ([0.0, 0.0, 0.0], 4)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("I m m a")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def test_interface(self):
spaceGroup = SpaceGroupFactory.createSpaceGroup("P -1")
self.assertEquals(spaceGroup.getHMSymbol(), "P -1")
self.assertEquals(spaceGroup.getOrder(), 2)
symOpStrings = spaceGroup.getSymmetryOperationStrings()
self.assertEqual(len(symOpStrings), 2)
self.assertTrue("x,y,z" in symOpStrings)
self.assertTrue("-x,-y,-z" in symOpStrings)
def test_equivalentPositions_Trigonal(self):
wyckoffs = [([0.3, 0.4, 0.45], 36),
([0.3, 0.0, 0.25], 18),
([0.5, 0.0, 0.0], 18),
([0.0, 0.0, 0.45], 12),
([0.0, 0.0, 0.0], 6),
([0.0, 0.0, 0.25], 6)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("R -3 c")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def test_equivalentPositions_Hexagonal(self):
wyckoffs = [([0.3, 0.4, 0.45], 24), ([0.3, 0.6, 0.45], 12),
([0.3, 0.4, 0.25], 12), ([0.3, 0.0, 0.0], 12),
([0.3, 0.6, 0.25], 6), ([0.5, 0.0, 0.0], 6),
([1. / 3., 2. / 3., 0.45], 4), ([0.0, 0.0, 0.45], 4),
([1. / 3, 2. / 3., 0.75], 2), ([1. / 3, 2. / 3., 0.25], 2),
([0.0, 0.0, 0.25], 2), ([0.0, 0.0, 0.0], 2)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("P 63/m m c")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def test_interface(self):
spaceGroup = SpaceGroupFactory.createSpaceGroup("P -1")
self.assertEquals(spaceGroup.getHMSymbol(), "P -1")
self.assertEquals(spaceGroup.getOrder(), 2)
symOpStrings = spaceGroup.getSymmetryOperationStrings()
self.assertEqual(len(symOpStrings), 2)
self.assertTrue("x,y,z" in symOpStrings)
self.assertTrue("-x,-y,-z" in symOpStrings)
def test_equivalentPositions_Monoclinic(self):
wyckoffs = [([0.3, 0.4, 0.45], 8),
([0.0, 0.4, 0.25], 4),
([0.25, 0.25, 0.5], 4),
([0.25, 0.25, 0.0], 4),
([0.0, 0.5, 0.0], 4),
([0.0, 0.0, 0.0], 4)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("C 1 2/c 1")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def test_creationFromPythonList(self):
spaceGroup = SpaceGroupFactory.createSpaceGroup("P 63/m m c")
# Construct python list of only certain symmetry operations
symOps = [x for x in spaceGroup.getSymmetryOperations() if x.getOrder() == 6]
group = Group(symOps)
self.assertEqual(group.getOrder(), len(symOps))
# But the constructed group is not actually a group
self.assertFalse(group.isGroup())
def test_creationFromPythonList(self):
spaceGroup = SpaceGroupFactory.createSpaceGroup("P 63/m m c")
# Construct python list of only certain symmetry operations
symOps = [x for x in spaceGroup.getSymmetryOperations() if x.getOrder() == 6]
group = Group(symOps)
self.assertEqual(group.getOrder(), len(symOps))
# But the constructed group is not actually a group
self.assertFalse(group.isGroup())
def test_equivalentPositions_Tetragonal(self):
wyckoffs = [([0.3, 0.4, 0.45], 32),
([0.3, 0.3, 0.25], 16),
([0.25, 0.4, 0.125], 16),
([0.0, 0.0, 0.45], 16),
([0.0, 0.25, 0.125], 16),
([0.0, 0.0, 0.25], 8),
([0.0, 0.0, 0.0], 8)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("I 41/a c d")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def test_to_string(self):
spaceGroup = SpaceGroupFactory.createSpaceGroup("F -4 3 c")
expected_str = "Space group with Hermann-Mauguin symbol: "\
"F -4 3 c"
expected_repr = "SpaceGroupFactory.createSpaceGroup(\"F -4 3 c\")"
self.assertEqual(expected_str, str(spaceGroup))
self.assertEqual(expected_repr, spaceGroup.__repr__())
newSpaceGroup = eval(spaceGroup.__repr__())
self.assertEqual(spaceGroup.getHMSymbol(), newSpaceGroup.getHMSymbol())
def test_to_string(self):
spaceGroup = SpaceGroupFactory.createSpaceGroup("F -4 3 c")
expected_str = "Space group with Hermann-Mauguin symbol: "\
"F -4 3 c"
expected_repr = "SpaceGroupFactory.createSpaceGroup(\"F -4 3 c\")"
self.assertEqual(expected_str, str(spaceGroup))
self.assertEqual(expected_repr, spaceGroup.__repr__())
newSpaceGroup = eval(spaceGroup.__repr__())
self.assertEqual(spaceGroup.getHMSymbol(), newSpaceGroup.getHMSymbol())
def test_equivalentPositions_Cubic(self):
wyckoffs = [([0.3, 0.4, 0.45], 96),
([0.3, 0.25, 0.25], 48),
([0.3, 0.0, 0.0], 48),
([0.3, 0.3, 0.3], 32),
([0.25, 0.0, 0.0], 24),
([0.0, 0.25, 0.25], 24),
([0.25, 0.25, 0.25], 8),
([0.0, 0.0, 0.0], 8)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("F -4 3 c")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def _getSpaceGroupFromString(self, cifData):
# Try two possibilities for space group symbol. If neither is present, throw a RuntimeError.
rawSpaceGroupSymbol = [str(cifData[x]) for x in
[u'_space_group_name_h-m_alt', u'_symmetry_space_group_name_h-m'] if
x in cifData.keys()]
if len(rawSpaceGroupSymbol) == 0:
raise RuntimeError('No space group symbol in CIF.')
cleanSpaceGroupSymbol = self._getCleanSpaceGroupSymbol(rawSpaceGroupSymbol[0])
# If the symbol is not registered, throw as well.
return SpaceGroupFactory.createSpaceGroup(cleanSpaceGroupSymbol).getHMSymbol()
def _getSpaceGroupFromString(self, cifData):
# Try two possibilities for space group symbol. If neither is present, throw a RuntimeError.
rawSpaceGroupSymbol = [str(cifData[x]) for x in
['_space_group_name_h-m_alt', '_symmetry_space_group_name_h-m'] if
x in cifData.keys()]
if len(rawSpaceGroupSymbol) == 0:
raise RuntimeError('No space group symbol in CIF.')
cleanSpaceGroupSymbol = self._getCleanSpaceGroupSymbol(rawSpaceGroupSymbol[0])
# If the symbol is not registered, throw as well.
return SpaceGroupFactory.createSpaceGroup(cleanSpaceGroupSymbol).getHMSymbol()
def test_equivalentPositions_Triclinic(self):
wyckoffs = [([0.3, 0.4, 0.45], 2),
([0.5, 0.5, 0.5], 1),
([0.0, 0.5, 0.5], 1),
([0.5, 0.0, 0.5], 1),
([0.5, 0.5, 0.0], 1),
([0.5, 0.0, 0.0], 1),
([0.0, 0.5, 0.0], 1),
([0.0, 0.0, 0.5], 1),
([0.0, 0.0, 0.0], 1)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("P -1")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def test_equivalentPositions_Orthorhombic(self):
wyckoffs = [([0.3, 0.4, 0.45], 16),
([0.3, 0.25, 0.45], 8),
([0.0, 0.4, 0.45], 8),
([0.25, 0.4, 0.25], 8),
([0.3, 0.0, 0.0], 8),
([0.0, 0.25, 0.45], 4),
([0.25, 0.25, 0.75], 4),
([0.25, 0.25, 0.25], 4),
([0.0, 0.0, 0.5], 4),
([0.0, 0.0, 0.0], 4)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("I m m a")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
def getReflectionFamily(row):
sg = SpaceGroupFactory.createSpaceGroup('P 32 2 1')
pg = sg.getPointGroup()
h = float(row['h'])
k = float(row['k'])
l = float(row['l'])
hklPlus = np.array([h, k, l])
hklMinus = np.array([-h, -k, -l])
refFamPlus = pg.getReflectionFamily(hklPlus)
refFamMinus = pg.getReflectionFamily(hklMinus)
checkIDX = (~np.equal(refFamPlus, refFamMinus)).argmax()
if refFamPlus[checkIDX] >= refFamMinus[checkIDX]:
return tuple(np.array(refFamPlus, dtype=int))
else: # refFamPlus[checkIDX] < refFamMinus[checkIDX]:
return tuple(np.array(refFamMinus, dtype=int))
def test_equivalentPositions_Hexagonal(self):
wyckoffs = [([0.3, 0.4, 0.45], 24),
([0.3, 0.6, 0.45], 12),
([0.3, 0.4, 0.25], 12),
([0.3, 0.0, 0.0], 12),
([0.3, 0.6, 0.25], 6),
([0.5, 0.0, 0.0], 6),
([1. / 3., 2. / 3., 0.45], 4),
([0.0, 0.0, 0.45], 4),
([1. / 3, 2. / 3., 0.75], 2),
([1. / 3, 2. / 3., 0.25], 2),
([0.0, 0.0, 0.25], 2),
([0.0, 0.0, 0.0], 2)]
spaceGroup = SpaceGroupFactory.createSpaceGroup("P 63/m m c")
self.checkWyckoffPositions(spaceGroup, wyckoffs)
if dim.getMaximum() != -dim.getMinimum():
print('Workspace dimensions must be centered on zero')
exit()
#dim_list.append((dim.getNBins(), (dim.getMaximum()-dim.getMinimum())/dim.getNBins()))
fft_dim = np.fft.fftshift(
np.fft.fftfreq(dim.getNBins(),
(dim.getMaximum() - dim.getMinimum()) / dim.getNBins()))
dim_list.append((fft_dim[0], fft_dim[-1]))
dimX = ws.getXDimension()
dimY = ws.getYDimension()
dimZ = ws.getZDimension()
signal = ws.getSignalArray().copy()
sg = SpaceGroupFactory.createSpaceGroup(space_group)
X = np.linspace(dimX.getMinimum(), dimX.getMaximum(), dimX.getNBins() + 1)
Y = np.linspace(dimY.getMinimum(), dimY.getMaximum(), dimY.getNBins() + 1)
Z = np.linspace(dimZ.getMinimum(), dimZ.getMaximum(), dimZ.getNBins() + 1)
box_width = 0.1 # in hkl dimensions
for h in range(int(np.ceil(dimX.getMinimum())),
int(np.floor(dimX.getMaximum())) + 1):
for k in range(int(np.ceil(dimY.getMinimum())),
int(np.floor(dimY.getMaximum())) + 1):
for l in range(int(np.ceil(dimZ.getMinimum())),
int(np.floor(dimZ.getMaximum())) + 1):
if sg.isAllowedReflection([h, k, l]):
x_min = np.searchsorted(X, h - box_width)
def test_creationFromVector(self):
spaceGroup = SpaceGroupFactory.createSpaceGroup("P 63/m m c")
symOps = spaceGroup.getSymmetryOperations()
group = Group(symOps)
self.assertEqual(group.getOrder(), spaceGroup.getOrder())
from mantid.simpleapi import *
from mantid.geometry import SymmetryOperationFactory, SpaceGroupFactory
import numpy as np
#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")
ws=CreateSingleValuedWorkspace()
LoadIsawUB(ws,"/SNS/users/rwp/benzil/benzil_Hexagonal.mat")
sg=SpaceGroupFactory.createSpaceGroup("P 31 2 1")
symOps = sg.getSymmetryOperations()
ub=ws.sample().getOrientedLattice().getUB()
print("Starting UB :")
print(ub)
for sym in symOps:
symTrans = np.array([sym.transformHKL([1,0,0]),
sym.transformHKL([0,1,0]),
sym.transformHKL([0,0,1])])
symTrans=np.matrix(symTrans.T)
print("Symmetry transform for "+sym.getIdentifier())
print(symTrans)
print("New UB:")
newUB = ub*symTrans
print(newUB)
print("To use SetUB(ws, UB=newUB)")
def runTest(self):
# Na Mn Cl3
# R -3 H (148)
# 6.592 6.592 18.585177 90 90 120
# UB/wavelength from /HFIR/HB3A/IPTS-25470/shared/autoreduce/HB3A_exp0769_scan0040.nxs
ub = np.array([[1.20297e-01, 1.70416e-01, 1.43000e-04],
[8.16000e-04, -8.16000e-04, 5.38040e-02],
[1.27324e-01, -4.05110e-02, -4.81000e-04]])
wavelength = 1.553
# create fake MDEventWorkspace, similar to what is expected from exp769 after loading with HB3AAdjustSampleNorm
MD_Q_sample = CreateMDWorkspace(
Dimensions='3',
Extents='-5,5,-5,5,-5,5',
Names='Q_sample_x,Q_sample_y,Q_sample_z',
Units='rlu,rlu,rlu',
Frames='QSample,QSample,QSample')
inst = LoadEmptyInstrument(InstrumentName='HB3A')
AddTimeSeriesLog(inst, 'omega', '2010-01-01T00:00:00', 0.)
AddTimeSeriesLog(inst, 'phi', '2010-01-01T00:00:00', 0.)
AddTimeSeriesLog(inst, 'chi', '2010-01-01T00:00:00', 0.)
MD_Q_sample.addExperimentInfo(inst)
SetUB(MD_Q_sample, UB=ub)
ol = OrientedLattice()
ol.setUB(ub)
sg = SpaceGroupFactory.createSpaceGroup("R -3")
hkl = []
sat_hkl = []
for h in range(0, 6):
for k in range(0, 6):
for l in range(0, 11):
if sg.isAllowedReflection([h, k, l]):
if h == k == l == 0:
continue
q = V3D(h, k, l)
q_sample = ol.qFromHKL(q)
if not np.any(np.array(q_sample) > 5):
hkl.append(q)
FakeMDEventData(
MD_Q_sample,
PeakParams='1000,{},{},{},0.05'.format(
*q_sample))
# satellite peaks at 0,0,+1.5
q = V3D(h, k, l + 1.5)
q_sample = ol.qFromHKL(q)
if not np.any(np.array(q_sample) > 5):
sat_hkl.append(q)
FakeMDEventData(
MD_Q_sample,
PeakParams='100,{},{},{},0.02'.format(
*q_sample))
# satellite peaks at 0,0,-1.5
q = V3D(h, k, l - 1.5)
q_sample = ol.qFromHKL(q)
if not np.any(np.array(q_sample) > 5):
sat_hkl.append(q)
FakeMDEventData(
MD_Q_sample,
PeakParams='100,{},{},{},0.02'.format(
*q_sample))
# Check that this fake workpsace gives us the expected UB
peaks = FindPeaksMD(MD_Q_sample,
PeakDistanceThreshold=1,
OutputType='LeanElasticPeak')
FindUBUsingFFT(peaks, MinD=5, MaxD=20)
ShowPossibleCells(peaks)
SelectCellOfType(peaks,
CellType='Rhombohedral',
Centering='R',
Apply=True)
OptimizeLatticeForCellType(peaks, CellType='Hexagonal', Apply=True)
found_ol = peaks.sample().getOrientedLattice()
self.assertAlmostEqual(found_ol.a(), 6.592, places=2)
self.assertAlmostEqual(found_ol.b(), 6.592, places=2)
self.assertAlmostEqual(found_ol.c(), 18.585177, places=2)
self.assertAlmostEqual(found_ol.alpha(), 90)
self.assertAlmostEqual(found_ol.beta(), 90)
self.assertAlmostEqual(found_ol.gamma(), 120)
# nuclear peaks
predict = HB3APredictPeaks(
MD_Q_sample,
Wavelength=wavelength,
ReflectionCondition='Rhombohedrally centred, obverse',
SatellitePeaks=True,
IncludeIntegerHKL=True)
predict = HB3AIntegratePeaks(MD_Q_sample, predict, 0.25)
self.assertEqual(predict.getNumberPeaks(), 66)
# check that the found peaks are expected
for n in range(predict.getNumberPeaks()):
HKL = predict.getPeak(n).getHKL()
self.assertTrue(HKL in hkl, msg=f"Peak {n} with HKL={HKL}")
# magnetic peaks
satellites = HB3APredictPeaks(
MD_Q_sample,
Wavelength=wavelength,
ReflectionCondition='Rhombohedrally centred, obverse',
SatellitePeaks=True,
ModVector1='0,0,1.5',
MaxOrder=1,
IncludeIntegerHKL=False)
satellites = HB3AIntegratePeaks(MD_Q_sample, satellites, 0.1)
self.assertEqual(satellites.getNumberPeaks(), 80)
# check that the found peaks are expected
for n in range(satellites.getNumberPeaks()):
HKL = satellites.getPeak(n).getHKL()
self.assertTrue(HKL in sat_hkl, msg=f"Peak {n} with HKL={HKL}")
import itertools
import numpy as np
from mantid.geometry import SpaceGroupFactory, CrystalStructure
# Parse command line
parser = argparse.ArgumentParser(
description='Output VAMPIRE unit cell to file')
parser.add_argument('filename', metavar='f', type=str)
args = parser.parse_args()
# String joins
s = ' '
t = ';'
# Space group taken from literature
sg = SpaceGroupFactory.createSpaceGroup("P b n m")
# Unit cell dimensions a, b, c
unit_dim = [5.3170, 5.8348, 7.4202]
# Atom positions
Tb_position = [0.9973, 0.0772, 0.25]
Mn_position = [0.5, 0.0, 0.0]
O1_position = [0.1108, 0.4685, 0.25]
O2_position = [0.7086, 0.3272, 0.0504]
# Generate fractional positions
Tb_equiv = sg.getEquivalentPositions(Tb_position)
Mn_equiv = sg.getEquivalentPositions(Mn_position)
# Generate all O in 3x3
def test_creationFromVector(self):
spaceGroup = SpaceGroupFactory.createSpaceGroup("P 63/m m c")
symOps = spaceGroup.getSymmetryOperations()
group = Group(symOps)
self.assertEqual(group.getOrder(), spaceGroup.getOrder())
def test_creation(self):
self.assertRaises(ValueError, SpaceGroupFactory.createSpaceGroup, "none")
SpaceGroupFactory.createSpaceGroup("I m -3 m")
from mantid.simpleapi import *
from mantid.geometry import SymmetryOperationFactory, SpaceGroupFactory
import numpy as np
#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")
sg = SpaceGroupFactory.createSpaceGroup("R 3 m")
symOps = sg.getSymmetryOperations()
for sym in symOps:
symTrans = np.array([
sym.transformHKL([1, 0, 0]),
sym.transformHKL([0, 1, 0]),
sym.transformHKL([0, 0, 1])
])
symTrans = np.matrix(symTrans.T)
print "Symmetry transform for " + sym.getIdentifier()
print symTrans
from mantid.geometry import SpaceGroupFactory, SymmetryOperationFactory
# symOp = SymmetryOperationFactory.createSymOp("x,y,-z")
#symOps = SymmetryOperationFactory.createSymOps("x,y,-z; -x,-y,-z; z,x,y")
#print "Number of operations:", len(symOps)
#print "Operations:"
#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:
def test_creation(self):
self.assertRaises(ValueError, SpaceGroupFactory.createSpaceGroup,
"none")
SpaceGroupFactory.createSpaceGroup("I m -3 m")
def PyExec(self): # noqa
progress = Progress(self, 0.0, 1.0, 5)
inWS = self.getProperty("InputWorkspace").value
signal = inWS.getSignalArray().copy()
dimX = inWS.getXDimension()
dimY = inWS.getYDimension()
dimZ = inWS.getZDimension()
Xmin = dimX.getMinimum()
Ymin = dimY.getMinimum()
Zmin = dimZ.getMinimum()
Xmax = dimX.getMaximum()
Ymax = dimY.getMaximum()
Zmax = dimZ.getMaximum()
Xbins = dimX.getNBins()
Ybins = dimY.getNBins()
Zbins = dimZ.getNBins()
Xwidth = dimX.getBinWidth()
Ywidth = dimY.getBinWidth()
Zwidth = dimZ.getBinWidth()
X = np.linspace(Xmin, Xmax, Xbins + 1)
Y = np.linspace(Ymin, Ymax, Ybins + 1)
Z = np.linspace(Zmin, Zmax, Zbins + 1)
X, Y, Z = np.ogrid[(dimX.getX(0) + dimX.getX(1)) /
2:(dimX.getX(Xbins) + dimX.getX(Xbins - 1)) /
2:Xbins * 1j, (dimY.getX(0) + dimY.getX(1)) /
2:(dimY.getX(Ybins) + dimY.getX(Ybins - 1)) /
2:Ybins * 1j, (dimZ.getX(0) + dimZ.getX(1)) /
2:(dimZ.getX(Zbins) + dimZ.getX(Zbins - 1)) /
2:Zbins * 1j]
if self.getProperty("RemoveReflections").value:
progress.report("Removing Reflections")
size = self.getProperty("Size").value
if len(size) == 1:
size = np.repeat(size, 3)
size /= 2.0 # We want radii or half box width
cut_shape = self.getProperty("Shape").value
space_group = self.getProperty("SpaceGroup").value
if space_group:
check_space_group = True
try:
space_group = SpaceGroupFactory.subscribedSpaceGroupSymbols(
int(space_group))[0]
except ValueError:
pass
logger.information('Using space group: ' + space_group)
sg = SpaceGroupFactory.createSpaceGroup(space_group)
else:
check_space_group = False
if cut_shape == 'cube':
for h in range(int(np.ceil(Xmin)), int(Xmax) + 1):
for k in range(int(np.ceil(Ymin)), int(Ymax) + 1):
for l in range(int(np.ceil(Zmin)), int(Zmax) + 1):
if not check_space_group or sg.isAllowedReflection(
[h, k, l]):
signal[int((h - size[0] - Xmin) / Xwidth +
1):int((h + size[0] - Xmin) /
Xwidth),
int((k - size[1] - Ymin) / Ywidth +
1):int((k + size[1] - Ymin) /
Ywidth),
int((l - size[2] - Zmin) / Zwidth +
1):int((l + size[2] - Zmin) /
Zwidth)] = np.nan
else: # sphere
mask = ((X - np.round(X))**2 / size[0]**2 +
(Y - np.round(Y))**2 / size[1]**2 +
(Z - np.round(Z))**2 / size[2]**2 < 1)
# Unmask invalid reflections
if check_space_group:
for h in range(int(np.ceil(Xmin)), int(Xmax) + 1):
for k in range(int(np.ceil(Ymin)), int(Ymax) + 1):
for l in range(int(np.ceil(Zmin)), int(Zmax) + 1):
if not sg.isAllowedReflection([h, k, l]):
mask[int((h - 0.5 - Xmin) / Xwidth +
1):int((h + 0.5 - Xmin) / Xwidth),
int((k - 0.5 - Ymin) / Ywidth +
1):int((k + 0.5 - Ymin) / Ywidth),
int((l - 0.5 - Zmin) / Zwidth +
1):int((l + 0.5 - Zmin) /
Zwidth)] = False
signal[mask] = np.nan
if self.getProperty("CropSphere").value:
progress.report("Cropping to sphere")
sphereMin = self.getProperty("SphereMin").value
if sphereMin[0] < Property.EMPTY_DBL:
if len(sphereMin) == 1:
sphereMin = np.repeat(sphereMin, 3)
signal[X**2 / sphereMin[0]**2 + Y**2 / sphereMin[1]**2 +
Z**2 / sphereMin[2]**2 < 1] = np.nan
sphereMax = self.getProperty("SphereMax").value
if sphereMax[0] < Property.EMPTY_DBL:
if len(sphereMax) == 1:
sphereMax = np.repeat(sphereMax, 3)
if self.getProperty("FillValue").value == Property.EMPTY_DBL:
fill_value = np.nan
else:
fill_value = self.getProperty("FillValue").value
signal[X**2 / sphereMax[0]**2 + Y**2 / sphereMax[1]**2 +
Z**2 / sphereMax[2]**2 > 1] = fill_value
if self.getProperty("Convolution").value:
progress.report("Convoluting signal")
signal = self._convolution(signal)
if self.getPropertyValue("IntermediateWorkspace"):
cloneWS_alg = self.createChildAlgorithm("CloneMDWorkspace",
enableLogging=False)
cloneWS_alg.setProperty("InputWorkspace", inWS)
cloneWS_alg.execute()
signalOutWS = cloneWS_alg.getProperty("OutputWorkspace").value
signalOutWS.setSignalArray(signal)
self.setProperty("IntermediateWorkspace", signalOutWS)
# Do FFT
progress.report("Running FFT")
# Replace any remaining nan's or inf's with 0
# Otherwise you end up with a lot of nan's
signal[np.isnan(signal)] = 0
signal[np.isinf(signal)] = 0
signal = np.fft.fftshift(np.fft.fftn(np.fft.ifftshift(signal)))
number_of_bins = signal.shape
# Do deconvolution
if self.getProperty("Convolution").value and self.getProperty(
"Deconvolution").value:
signal /= self._deconvolution(np.array(signal.shape))
# CreateMDHistoWorkspace expects Fortan `column-major` ordering
signal = signal.real.flatten('F')
createWS_alg = self.createChildAlgorithm("CreateMDHistoWorkspace",
enableLogging=False)
createWS_alg.setProperty("SignalInput", signal)
createWS_alg.setProperty("ErrorInput", signal**2)
createWS_alg.setProperty("Dimensionality", 3)
createWS_alg.setProperty("Extents", self._calc_new_extents(inWS))
createWS_alg.setProperty("NumberOfBins", number_of_bins)
createWS_alg.setProperty("Names", 'x,y,z')
createWS_alg.setProperty("Units", 'a,b,c')
createWS_alg.execute()
outWS = createWS_alg.getProperty("OutputWorkspace").value
# Copy first experiment info
if inWS.getNumExperimentInfo() > 0:
outWS.copyExperimentInfos(inWS)
progress.report()
self.setProperty("OutputWorkspace", outWS)
OutputWorkspace='flux')
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=UBfile)
ub = mtd['ub'].sample().getOrientedLattice().getUB()
print "Starting UB :"
print ub
#PMN pm-3m (227) general position has 48 symmety operations.
sg = SpaceGroupFactory.createSpaceGroup("P m -3 m")
symOps = sg.getSymmetryOperations()
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)
def PyExec(self): # noqa
progress = Progress(self, 0.0, 1.0, 5)
inWS = self.getProperty("InputWorkspace").value
signal = inWS.getSignalArray().copy()
dimX=inWS.getXDimension()
dimY=inWS.getYDimension()
dimZ=inWS.getZDimension()
Xmin=dimX.getMinimum()
Ymin=dimY.getMinimum()
Zmin=dimZ.getMinimum()
Xmax=dimX.getMaximum()
Ymax=dimY.getMaximum()
Zmax=dimZ.getMaximum()
Xbins=dimX.getNBins()
Ybins=dimY.getNBins()
Zbins=dimZ.getNBins()
Xwidth=dimX.getBinWidth()
Ywidth=dimY.getBinWidth()
Zwidth=dimZ.getBinWidth()
X=np.linspace(Xmin,Xmax,Xbins+1)
Y=np.linspace(Ymin,Ymax,Ybins+1)
Z=np.linspace(Zmin,Zmax,Zbins+1)
X, Y, Z = np.ogrid[(dimX.getX(0)+dimX.getX(1))/2:(dimX.getX(Xbins)+dimX.getX(Xbins-1))/2:Xbins*1j,
(dimY.getX(0)+dimY.getX(1))/2:(dimY.getX(Ybins)+dimY.getX(Ybins-1))/2:Ybins*1j,
(dimZ.getX(0)+dimZ.getX(1))/2:(dimZ.getX(Zbins)+dimZ.getX(Zbins-1))/2:Zbins*1j]
if self.getProperty("RemoveReflections").value:
progress.report("Removing Reflections")
size = self.getProperty("Size").value
if len(size)==1:
size = np.repeat(size, 3)
size/=2.0 # We want radii or half box width
cut_shape = self.getProperty("Shape").value
space_group = self.getProperty("SpaceGroup").value
if space_group:
check_space_group = True
try:
space_group=SpaceGroupFactory.subscribedSpaceGroupSymbols(int(space_group))[0]
except ValueError:
pass
logger.information('Using space group: '+space_group)
sg=SpaceGroupFactory.createSpaceGroup(space_group)
else:
check_space_group = False
if cut_shape == 'cube':
for h in range(int(np.ceil(Xmin)), int(Xmax)+1):
for k in range(int(np.ceil(Ymin)), int(Ymax)+1):
for l in range(int(np.ceil(Zmin)), int(Zmax)+1):
if not check_space_group or sg.isAllowedReflection([h,k,l]):
signal[int((h-size[0]-Xmin)/Xwidth+1):int((h+size[0]-Xmin)/Xwidth),
int((k-size[1]-Ymin)/Ywidth+1):int((k+size[1]-Ymin)/Ywidth),
int((l-size[2]-Zmin)/Zwidth+1):int((l+size[2]-Zmin)/Zwidth)]=np.nan
else: # sphere
mask=((X-np.round(X))**2/size[0]**2 + (Y-np.round(Y))**2/size[1]**2 + (Z-np.round(Z))**2/size[2]**2 < 1)
# Unmask invalid reflections
if check_space_group:
for h in range(int(np.ceil(Xmin)), int(Xmax)+1):
for k in range(int(np.ceil(Ymin)), int(Ymax)+1):
for l in range(int(np.ceil(Zmin)), int(Zmax)+1):
if not sg.isAllowedReflection([h,k,l]):
mask[int((h-0.5-Xmin)/Xwidth+1):int((h+0.5-Xmin)/Xwidth),
int((k-0.5-Ymin)/Ywidth+1):int((k+0.5-Ymin)/Ywidth),
int((l-0.5-Zmin)/Zwidth+1):int((l+0.5-Zmin)/Zwidth)]=False
signal[mask]=np.nan
if self.getProperty("CropSphere").value:
progress.report("Cropping to sphere")
sphereMin = self.getProperty("SphereMin").value
if sphereMin[0] < Property.EMPTY_DBL:
if len(sphereMin)==1:
sphereMin = np.repeat(sphereMin, 3)
signal[X**2/sphereMin[0]**2 + Y**2/sphereMin[1]**2 + Z**2/sphereMin[2]**2 < 1]=np.nan
sphereMax = self.getProperty("SphereMax").value
if sphereMax[0] < Property.EMPTY_DBL:
if len(sphereMax)==1:
sphereMax = np.repeat(sphereMax, 3)
if self.getProperty("FillValue").value == Property.EMPTY_DBL:
fill_value = np.nan
else:
fill_value = self.getProperty("FillValue").value
signal[X**2/sphereMax[0]**2 + Y**2/sphereMax[1]**2 + Z**2/sphereMax[2]**2 > 1]=fill_value
if self.getProperty("Convolution").value:
progress.report("Convoluting signal")
signal = self._convolution(signal)
if self.getPropertyValue("IntermediateWorkspace"):
cloneWS_alg = self.createChildAlgorithm("CloneMDWorkspace", enableLogging=False)
cloneWS_alg.setProperty("InputWorkspace",inWS)
cloneWS_alg.execute()
signalOutWS = cloneWS_alg.getProperty("OutputWorkspace").value
signalOutWS.setSignalArray(signal)
self.setProperty("IntermediateWorkspace", signalOutWS)
# Do FFT
progress.report("Running FFT")
# Replace any remaining nan's or inf's with 0
# Otherwise you end up with a lot of nan's
signal[np.isnan(signal)]=0
signal[np.isinf(signal)]=0
signal=np.fft.fftshift(np.fft.fftn(np.fft.ifftshift(signal)))
number_of_bins = signal.shape
# Do deconvolution
if self.getProperty("Convolution").value and self.getProperty("Deconvolution").value:
signal /= self._deconvolution(np.array(signal.shape))
# CreateMDHistoWorkspace expects Fortan `column-major` ordering
signal = signal.real.flatten('F')
createWS_alg = self.createChildAlgorithm("CreateMDHistoWorkspace", enableLogging=False)
createWS_alg.setProperty("SignalInput", signal)
createWS_alg.setProperty("ErrorInput", signal**2)
createWS_alg.setProperty("Dimensionality", 3)
createWS_alg.setProperty("Extents", self._calc_new_extents(inWS))
createWS_alg.setProperty("NumberOfBins", number_of_bins)
createWS_alg.setProperty("Names", 'x,y,z')
createWS_alg.setProperty("Units", 'a,b,c')
createWS_alg.execute()
outWS = createWS_alg.getProperty("OutputWorkspace").value
# Copy first experiment info
if inWS.getNumExperimentInfo() > 0:
outWS.copyExperimentInfos(inWS)
progress.report()
self.setProperty("OutputWorkspace", outWS)
#peaksFile = '%s%s/peaks_combined_good.integrate'%(workDir,descriptorTOF)
peaksFile = '%s%s/peaks_%i_%s.integrate'%(workDir,descriptorTOF, sampleRuns[-1], descriptorTOF)
ellipseFile = '/SNS/users/ntv/integrate/corelli_beryl/combined_hexagonal_indexedonly.integrate'
pg = PointGroupFactory.createPointGroup("6/mmm")
'''
#Beta lactamase mutant
sampleRuns = range(5921, 5931 + 1)
workDir = '/SNS/users/ntv/dropbox/'
descriptorBVG = 'beta_lac_3D_mbvg_mutant_newppl'
descriptorTOF = 'beta_lac_lab_highres_mut2'
peaksFile = '%s%s/peaks_combined_good.integrate' % (workDir, descriptorTOF)
#peaksFile = '%s%s/peaks_%i_%s.integrate'%(workDir,descriptorTOF, sampleRuns[-1], descriptorTOF)
#ellipseFile = '/SNS/users/ntv/integrate/mandi_betalactamase/MANDI_betalactamase_2.integrate'
#ellipseFile = '/SNS/users/ntv/integrate/mandi_betalactamase/combined_triclinic.integrate'
ellipseFile = '/SNS/users/ntv/integrate/mandi_beta_lactamase3/combined.integrate'
sg = SpaceGroupFactory.createSpaceGroup("P 32 2 1")
pg = PointGroupFactory.createPointGroupFromSpaceGroup(sg)
'''
#pth
sampleRuns = [870,872,873,874,875,876]
workDir = '/SNS/users/ntv/dropbox/'
descriptorBVG = 'pth_3d'
descriptorTOF = 'pth_tof_secondRun'
peaksFile = '%s%s/peaks_combined_good.integrate'%(workDir,descriptorTOF)
#peaksFile = '%s%s/peaks_%i_%s.integrate'%(workDir,descriptorTOF, sampleRuns[-1], descriptorTOF)
ellipseFile = '/SNS/users/ntv/integrate/mandi_pth/peaks_combined.integrate'
sg = SpaceGroupFactory.createSpaceGroup("P 61 2 2")
pg = PointGroupFactory.createPointGroupFromSpaceGroup(sg)
'''
'''
#gfp
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")
symOps = SpaceGroupFactory.createSpaceGroup('P 2 3').getSymmetryOperations()
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)
