def setUp(self):
unittest.TestCase.setUp(self)
testDataFolder = Files.getCurrentModulePath(__file__, 'testdata')
self.testTxtFilepath = os.path.join(testDataFolder, 'test_txtFile.txt')
self.txt = txtFile.txt(self.testTxtFilepath)
def setUp(self):
unittest.TestCase.setUp(self)
testDataFolder = Files.getCurrentModulePath(__file__, '')
self.testCprFilepath = os.path.join(testDataFolder, 'cprmaster.cpr')
self.cpr = cprFile.cpr(self.testCprFilepath)
def setUp(self):
unittest.TestCase.setUp(self)
testDataFolder = Files.getCurrentModulePath(__file__, '')
self.testCprFilepath = os.path.join(testDataFolder, 'cprmaster.cpr')
self.cpr = cprFile.cpr(self.testCprFilepath)
def setUp(self):
unittest.TestCase.setUp(self)
relativePath = os.path.join('..', 'testdata', 'pe-spect-01.dat')
filepath = Files.getCurrentModulePath(__file__, relativePath)
self.energies, self.intensities = self._read_spectrum(filepath)
def setUp(self):
unittest.TestCase.setUp(self)
relativePath = os.path.join('testdata', 'test_ctfFile.ctf')
filepath = Files.getCurrentModulePath(__file__, relativePath)
self.ctf = ctfFile.ctf(filepath)
def setUp(self):
unittest.TestCase.setUp(self)
testDataFolder = Files.getCurrentModulePath(__file__, 'testdata')
self.testTxtFilepath = os.path.join(testDataFolder, 'test_txtFile.txt')
self.txt = txtFile.txt(self.testTxtFilepath)
def setUp(self):
unittest.TestCase.setUp(self)
relativepath = os.path.join('..', 'testdata', 'goodconfiguration.cfg')
configurationfilepath = Files.getCurrentModulePath(__file__, relativepath)
self.scatter = scatteringfactors.ElasticAtomicScatteringFactors(configurationfilepath)
def setUp(self):
unittest.TestCase.setUp(self)
# Unit cell.
unitcell_fcc = unitcell.create_cubic_unitcell(5.43)
unitcell_bcc = unitcell.create_cubic_unitcell(2.87)
unitcell_hcp = unitcell.create_hexagonal_unitcell(3.21, 5.21)
# Atom sites.
atoms_fcc = atomsites.create_fcc_atomsites(14)
atoms_bcc = atomsites.create_bcc_atomsites(14)
atoms_hcp = atomsites.create_hcp_atomsites(14)
# Scattering factors
relativepath = os.path.join('..', 'testdata', 'goodconfiguration.cfg')
configurationfilepath = Files.getCurrentModulePath(__file__, relativepath)
scatter = scatteringfactors.ElasticAtomicScatteringFactors(configurationfilepath)
# Reflectors
self.refls_fcc = \
reflectors.Reflectors(unitcell_fcc, atoms_fcc, scatter, maxindice=2)
self.refls_bcc = \
reflectors.Reflectors(unitcell_bcc, atoms_bcc, scatter, maxindice=2)
self.refls_hcp = \
reflectors.Reflectors(unitcell_hcp, atoms_hcp, scatter, maxindice=2)
def setUp(self):
unittest.TestCase.setUp(self)
relativePath = os.path.join('..', 'testdata', 'aluminum.cif')
filepath = Files.getCurrentModulePath(__file__, relativePath)
self.cifAl = cif.Reader(filepath)
relativePath = os.path.join('..', 'testdata', 'iron.cif')
filepath = Files.getCurrentModulePath(__file__, relativePath)
self.cifFe = cif.Reader(filepath)
relativePath = os.path.join('..', 'testdata', 'zirconium.cif')
filepath = Files.getCurrentModulePath(__file__, relativePath)
self.cifZr = cif.Reader(filepath)
relativePath = os.path.join('..', 'testdata', 'rudimer.cif')
filepath = Files.getCurrentModulePath(__file__, relativePath)
self.cifRuDimer = cif.Reader(filepath)
def setUp(self):
unittest.TestCase.setUp(self)
relativePath = os.path.join('..', 'testdata', 'aluminum.cif')
filepath = Files.getCurrentModulePath(__file__, relativePath)
self.cifAl = cif.Reader(filepath)
relativePath = os.path.join('..', 'testdata', 'iron.cif')
filepath = Files.getCurrentModulePath(__file__, relativePath)
self.cifFe = cif.Reader(filepath)
relativePath = os.path.join('..', 'testdata', 'zirconium.cif')
filepath = Files.getCurrentModulePath(__file__, relativePath)
self.cifZr = cif.Reader(filepath)
relativePath = os.path.join('..', 'testdata', 'rudimer.cif')
filepath = Files.getCurrentModulePath(__file__, relativePath)
self.cifRuDimer = cif.Reader(filepath)
def __init__(self, configurationfilepath=None):
"""
Read scattering factors from tables.
Two implementations:
* :class:`ElasticAtomicScatteringFactors`
* :class:`XrayScatteringFactors`
"""
if configurationfilepath is None:
relativepath = os.path.join('..', 'ebsdtools.cfg')
configurationfilepath = Files.getCurrentModulePath(__file__, relativepath)
self._readconfiguration(configurationfilepath)
self._read()
def __init__(self, configurationfilepath=None):
"""
Return the elastic atomic scattering factors as given by the
Crystallography Tables.
The data is a exponential fit of the scattering factors.
It is calculated from :math:`s = \\frac{4\\pi\\sin\\theta}{\\lambda}`.
It is separated into two files: from 0 to 2 A^{-1} and 2 to 6 A^{-1}.
:arg configurationfilepath: file path of the configuration file for the
module. If ``None``, the default configuration file is loaded.
:type configurationfilepath: :class:`str`
**References**
International Tables For Crystallography, Volume C, p. 262 and 282-285
"""
if configurationfilepath is None:
relativepath = os.path.join('..', 'ebsdtools.cfg')
configurationfilepath = Files.getCurrentModulePath(__file__, relativepath)
self._readconfiguration(configurationfilepath)
self._read()
def setUp(self):
unittest.TestCase.setUp(self)
# Manual testing
self.cubic = unitcell.create_cubic_unitcell(2)
self.tetragonal = unitcell.create_tetragonal_unitcell(2, 3)
self.orthorhombic = unitcell.create_orthorhombic_unitcell(1, 2, 3)
self.trigonal = unitcell.create_trigonal_unitcell(2, 35.0 / 180 * pi)
self.hexagonal = unitcell.create_hexagonal_unitcell(2, 3)
self.monoclinic = unitcell.create_monoclinic_unitcell(1, 2, 3, 55.0 / 180 * pi)
self.triclinic = \
unitcell.create_triclinic_unitcell(1, 2, 3,
75.0 / 180 * pi, 55.0 / 180 * pi, 35.0 / 180 * pi)
self.planes = [plane.Plane(1, 0, 0),
plane.Plane(1, 1, 0),
plane.Plane(1, 1, 1),
plane.Plane(2, 0, 2),
plane.Plane(1, 2, 3),
plane.Plane(4, 5, 6),
plane.Plane(0, 9, 2)]
# Example 1.13 from Mathematical Crystallography (p.31-33)
self.L1 = unitcell.create_hexagonal_unitcell(4.914, 5.409)
self.atom1 = atomsite.AtomSite(8, (0.4141, 0.2681, 0.1188))
self.atom2 = atomsite.AtomSite(14, (0.4699, 0.0, 0.0))
self.atom3 = atomsite.AtomSite(14, (0.5301, 0.5301, 0.3333))
# Problem 1.13 from Mathematical Crystallography (p.34)
alpha = 93.11 / 180.0 * pi
beta = 115.91 / 180.0 * pi
gamma = 91.26 / 180.0 * pi
self.L2 = unitcell.create_triclinic_unitcell(8.173, 12.869, 14.165
, alpha, beta, gamma)
self.atom4 = atomsite.AtomSite(8, (0.3419, 0.3587, 0.1333))
self.atom5 = atomsite.AtomSite(14, (0.5041, 0.3204, 0.1099))
self.atom6 = atomsite.AtomSite(13, (0.1852, 0.3775, 0.1816))
# Example 2.16 and Problem 2.9 from Mathematical Crystallography (p.64-65)
alpha = 114.27 / 180.0 * pi
beta = 82.68 / 180.0 * pi
gamma = 94.58 / 180.0 * pi
self.L3 = unitcell.create_triclinic_unitcell(6.621, 7.551, 17.381
, alpha, beta, gamma)
# Problem 2.15 from Mathematical Crystallography (p.79)
alpha = 113.97 / 180.0 * pi
beta = 98.64 / 180.0 * pi
gamma = 67.25 / 180.0 * pi
self.L4 = unitcell.create_triclinic_unitcell(5.148, 7.251, 5.060
, alpha, beta, gamma)
# Scattering factors
relativepath = os.path.join('..', 'testdata', 'goodconfiguration.cfg')
configurationfilepath = Files.getCurrentModulePath(__file__, relativepath)
self.scatter = scatteringfactors.XrayScatteringFactors(configurationfilepath)
# Atom sites
self.atomsfcc = atomsites.AtomSites([atomsite.AtomSite(14, 0.5, 0.5, 0.0),
atomsite.AtomSite(14, 0.5, 0.0, 0.5),
atomsite.AtomSite(14, 0.0, 0.5, 0.5),
atomsite.AtomSite(14, 0.0, 0.0, 0.0)])
self.atomsbcc = atomsites.AtomSites([atomsite.AtomSite(14, 0.5, 0.5, 0.5),
atomsite.AtomSite(14, 0.0, 0.0, 0.0)])
self.atomshcp = atomsites.AtomSites([atomsite.AtomSite(14, 1 / 3.0, 2 / 3.0, 0.5),
atomsite.AtomSite(14, 0.0, 0.0, 0.0)])
def setUp(self):
unittest.TestCase.setUp(self)
# Manual testing
self.cubic = unitcell.create_cubic_unitcell(2)
self.tetragonal = unitcell.create_tetragonal_unitcell(2, 3)
self.orthorhombic = unitcell.create_orthorhombic_unitcell(1, 2, 3)
self.trigonal = unitcell.create_trigonal_unitcell(2, 35.0 / 180 * pi)
self.hexagonal = unitcell.create_hexagonal_unitcell(2, 3)
self.monoclinic = unitcell.create_monoclinic_unitcell(
1, 2, 3, 55.0 / 180 * pi)
self.triclinic = \
unitcell.create_triclinic_unitcell(1, 2, 3,
75.0 / 180 * pi, 55.0 / 180 * pi, 35.0 / 180 * pi)
self.planes = [
plane.Plane(1, 0, 0),
plane.Plane(1, 1, 0),
plane.Plane(1, 1, 1),
plane.Plane(2, 0, 2),
plane.Plane(1, 2, 3),
plane.Plane(4, 5, 6),
plane.Plane(0, 9, 2)
]
# Example 1.13 from Mathematical Crystallography (p.31-33)
self.L1 = unitcell.create_hexagonal_unitcell(4.914, 5.409)
self.atom1 = atomsite.AtomSite(8, (0.4141, 0.2681, 0.1188))
self.atom2 = atomsite.AtomSite(14, (0.4699, 0.0, 0.0))
self.atom3 = atomsite.AtomSite(14, (0.5301, 0.5301, 0.3333))
# Problem 1.13 from Mathematical Crystallography (p.34)
alpha = 93.11 / 180.0 * pi
beta = 115.91 / 180.0 * pi
gamma = 91.26 / 180.0 * pi
self.L2 = unitcell.create_triclinic_unitcell(8.173, 12.869, 14.165,
alpha, beta, gamma)
self.atom4 = atomsite.AtomSite(8, (0.3419, 0.3587, 0.1333))
self.atom5 = atomsite.AtomSite(14, (0.5041, 0.3204, 0.1099))
self.atom6 = atomsite.AtomSite(13, (0.1852, 0.3775, 0.1816))
# Example 2.16 and Problem 2.9 from Mathematical Crystallography (p.64-65)
alpha = 114.27 / 180.0 * pi
beta = 82.68 / 180.0 * pi
gamma = 94.58 / 180.0 * pi
self.L3 = unitcell.create_triclinic_unitcell(6.621, 7.551, 17.381,
alpha, beta, gamma)
# Problem 2.15 from Mathematical Crystallography (p.79)
alpha = 113.97 / 180.0 * pi
beta = 98.64 / 180.0 * pi
gamma = 67.25 / 180.0 * pi
self.L4 = unitcell.create_triclinic_unitcell(5.148, 7.251, 5.060,
alpha, beta, gamma)
# Scattering factors
relativepath = os.path.join('..', 'testdata', 'goodconfiguration.cfg')
configurationfilepath = Files.getCurrentModulePath(
__file__, relativepath)
self.scatter = scatteringfactors.XrayScatteringFactors(
configurationfilepath)
# Atom sites
self.atomsfcc = atomsites.AtomSites([
atomsite.AtomSite(14, 0.5, 0.5, 0.0),
atomsite.AtomSite(14, 0.5, 0.0, 0.5),
atomsite.AtomSite(14, 0.0, 0.5, 0.5),
atomsite.AtomSite(14, 0.0, 0.0, 0.0)
])
self.atomsbcc = atomsites.AtomSites([
atomsite.AtomSite(14, 0.5, 0.5, 0.5),
atomsite.AtomSite(14, 0.0, 0.0, 0.0)
])
self.atomshcp = atomsites.AtomSites([
atomsite.AtomSite(14, 1 / 3.0, 2 / 3.0, 0.5),
atomsite.AtomSite(14, 0.0, 0.0, 0.0)
])
def setUp(self):
unittest.TestCase.setUp(self)
filepath = Files.getCurrentModulePath(__file__, os.path.join('testdata', 'test.smp'))
self.reader = smp.reader(open(filepath, 'rb'))