def test_FileOneCompoundTwoAtoms(self):
# It's the same structure and the same reflections, just the structure factors are different
fileHelper = TemporaryFileHelper("""SiliconCarbon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: F d -3 m
Atoms: {
Si 0 0 0 0.9 0.05
C 0 0 0 0.1 0.05
}
# Comment
}""")
ws = PoldiCreatePeaksFromFile(fileHelper.getName(), 0.7, 10.0)
self.assertEqual(ws.getNumberOfEntries(), 1)
self.assertTrue(ws.contains("SiliconCarbon"))
ws_expected = PoldiCreatePeaksFromCell(
"F d -3 m",
"Si 0 0 0 0.9 0.05; C 0 0 0 0.1 0.05",
a=5.43,
LatticeSpacingMin=0.7)
si_ws = AnalysisDataService.retrieve("SiliconCarbon")
self._tablesAreEqual(si_ws, ws_expected)
# Clean up
self._cleanWorkspaces([ws, ws_expected])
def test_map_file(self):
temp_map = TemporaryFileHelper(SAMPLE_GROUPING_XML, extension='.xml')
calib_ws = ILLIN16BCalibration(Run='ILLIN16B_034745.nxs',
MirrorMode=True,
MapFile=temp_map.getName(),
PeakRange=[-0.001, 0.002])
self.assertEqual(calib_ws.getNumberHistograms(), 4)
self.assertEqual(calib_ws.blocksize(), 1)
def test_map_file(self):
temp_map = TemporaryFileHelper(SAMPLE_GROUPING_XML, extension='.xml')
calib_ws = ILLIN16BCalibration(Run='ILLIN16B_034745.nxs',
MirrorMode=True,
MapFile=temp_map.getName(),
PeakRange=[-0.001, 0.002])
self.assertEqual(calib_ws.getNumberHistograms(), 4)
self.assertEqual(calib_ws.blocksize(), 1)
def test_FileFaultyLatticeStrings(self):
fhLatticeMissing = TemporaryFileHelper("""Silicon {
Spacegroup: F d -3 m
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
fhNoLattice = TemporaryFileHelper("""Silicon {
Lattice:
Spacegroup: F d -3 m
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
fhInvalidLattice = TemporaryFileHelper("""Silicon {
Lattice: invalid
Spacegroup: F d -3 m
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile,
*(fhLatticeMissing.getName(), 0.7, 10.0, 'ws'))
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile,
*(fhNoLattice.getName(), 0.7, 10.0, 'ws'))
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile,
*(fhInvalidLattice.getName(), 0.7, 10.0, 'ws'))
def test_FileFaultySpaceGroupStrings(self):
fhSgMissing = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
fhSgInvalid = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: invalid
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhSgMissing.getName(), 0.7, 10.0, 'ws'))
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhSgInvalid.getName(), 0.7, 10.0, 'ws'))
def test_FileOneCompoundOneAtom(self):
fileHelper = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: F d -3 m
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
ws = PoldiCreatePeaksFromFile(fileHelper.getName(), 0.7, 10.0)
# Check output GroupWorkspace
self.assertEqual(ws.getNumberOfEntries(), 1)
self.assertTrue(ws.contains("Silicon"))
# Check that the ouput is identical to what's expected
ws_expected = PoldiCreatePeaksFromCell("F d -3 m", "Si 0 0 0 1.0 0.05", a=5.43, LatticeSpacingMin=0.7)
si_ws = AnalysisDataService.retrieve("Silicon")
self._tablesAreEqual(si_ws, ws_expected)
# Clean up
self._cleanWorkspaces([ws, ws_expected])
def test_FileOneCompoundOneAtom(self):
fileHelper = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: F d -3 m
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
ws = PoldiCreatePeaksFromFile(fileHelper.getName(), 0.7, 10.0)
# Check output GroupWorkspace
self.assertEquals(ws.getNumberOfEntries(), 1)
self.assertTrue(ws.contains("Silicon"))
# Check that the ouput is identical to what's expected
ws_expected = PoldiCreatePeaksFromCell("F d -3 m", "Si 0 0 0 1.0 0.05", a=5.43, LatticeSpacingMin=0.7)
si_ws = AnalysisDataService.retrieve("Silicon")
self._tablesAreEqual(si_ws, ws_expected)
# Clean up
self._cleanWorkspaces([ws, ws_expected])
def test_FileFaultyLatticeStrings(self):
fhLatticeMissing = TemporaryFileHelper("""Silicon {
Spacegroup: F d -3 m
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
fhNoLattice = TemporaryFileHelper("""Silicon {
Lattice:
Spacegroup: F d -3 m
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
fhInvalidLattice = TemporaryFileHelper("""Silicon {
Lattice: invalid
Spacegroup: F d -3 m
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhLatticeMissing.getName(), 0.7, 10.0, 'ws'))
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhNoLattice.getName(), 0.7, 10.0, 'ws'))
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhInvalidLattice.getName(), 0.7, 10.0, 'ws'))
def test_FileOneCompoundTwoAtoms(self):
# It's the same structure and the same reflections, just the structure factors are different
fileHelper = TemporaryFileHelper("""SiliconCarbon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: F d -3 m
Atoms: {
Si 0 0 0 0.9 0.05
C 0 0 0 0.1 0.05
}
# Comment
}""")
ws = PoldiCreatePeaksFromFile(fileHelper.getName(), 0.7, 10.0)
self.assertEqual(ws.getNumberOfEntries(), 1)
self.assertTrue(ws.contains("SiliconCarbon"))
ws_expected = PoldiCreatePeaksFromCell("F d -3 m", "Si 0 0 0 0.9 0.05; C 0 0 0 0.1 0.05", a=5.43,
LatticeSpacingMin=0.7)
si_ws = AnalysisDataService.retrieve("SiliconCarbon")
self._tablesAreEqual(si_ws, ws_expected)
# Clean up
self._cleanWorkspaces([ws, ws_expected])
def test_FileTwoCompounds(self):
# Using two imaginary structures to check that two compounds are parsed correctly as well
fileHelper = TemporaryFileHelper("""SiliconCarbon {
Lattice: 5.43 5.43 5.43 90.0 90.0 120.0
Spacegroup: P 63/m m c
Atoms: {
Si 0 0 0 0.9 0.05
C 0 0 0 0.1 0.05
}
}
Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: F d -3 m
Atoms: {
Si 1/2 1/2 0 1.0 0.05
}
}""")
ws = PoldiCreatePeaksFromFile(fileHelper.getName(), 0.7, 10.0)
self.assertEqual(ws.getNumberOfEntries(), 2)
self.assertTrue(ws.contains("SiliconCarbon"))
self.assertTrue(ws.contains("Silicon"))
self._cleanWorkspaces([ws])
def test_FileTwoCompounds(self):
# Using two imaginary structures to check that two compounds are parsed correctly as well
fileHelper = TemporaryFileHelper("""SiliconCarbon {
Lattice: 5.43 5.43 5.43 90.0 90.0 120.0
Spacegroup: P 63/m m c
Atoms: {
Si 0 0 0 0.9 0.05
C 0 0 0 0.1 0.05
}
}
Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: F d -3 m
Atoms: {
Si 1/2 1/2 0 1.0 0.05
}
}""")
ws = PoldiCreatePeaksFromFile(fileHelper.getName(), 0.7, 10.0)
self.assertEqual(ws.getNumberOfEntries(), 2)
self.assertTrue(ws.contains("SiliconCarbon"))
self.assertTrue(ws.contains("Silicon"))
self._cleanWorkspaces([ws])
def test_FileFaultyAtomStrings(self):
fhAtomsMissing = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: F d -3 m
}""")
fhAtomsNoBraces = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: invalid
Atoms:
Sis 0 0 0 1.0 0.05
}""")
fhAtomsEmpty = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: invalid
Atoms: { }
}""")
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhAtomsMissing.getName(), 0.7, 10.0, 'ws'))
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhAtomsNoBraces.getName(), 0.7, 10.0, 'ws'))
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhAtomsEmpty.getName(), 0.7, 10.0, 'ws'))
def test_FileFaultySpaceGroupStrings(self):
fhSgMissing = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
fhSgInvalid = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: invalid
Atoms: {
Si 0 0 0 1.0 0.05
}
}""")
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhSgMissing.getName(), 0.7, 10.0, 'ws'))
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhSgInvalid.getName(), 0.7, 10.0, 'ws'))
def test_FileFaultyAtomStrings(self):
fhAtomsMissing = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: F d -3 m
}""")
fhAtomsNoBraces = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: invalid
Atoms:
Sis 0 0 0 1.0 0.05
}""")
fhAtomsEmpty = TemporaryFileHelper("""Silicon {
Lattice: 5.43 5.43 5.43 90.0 90.0 90.0
Spacegroup: invalid
Atoms: { }
}""")
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhAtomsMissing.getName(), 0.7, 10.0, 'ws'))
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhAtomsNoBraces.getName(), 0.7, 10.0, 'ws'))
self.assertRaises(RuntimeError, PoldiCreatePeaksFromFile, *(fhAtomsEmpty.getName(), 0.7, 10.0, 'ws'))