def _import_photon_intensity(self, options, name, detector, path):
wxrresult = CharacteristicIntensity(path)
factor = self._get_normalization_factor(options, detector)
# Retrieve intensities
intensities = {}
for z, line in wxrresult.getAtomicNumberLines():
data = wxrresult.intensities[z][line]
transition = from_string("%s %s" % (symbol(z), line))
gnf = list(map(mul, data[WXRGENERATED], [factor] * 2))
enf = list(map(mul, data[WXREMITTED], [factor] * 2))
intensities[PhotonKey(transition, False, PhotonKey.P)] = gnf
intensities[PhotonKey(transition, True, PhotonKey.P)] = enf
return PhotonIntensityResult(intensities)
def _import_photon_intensity(self, options, name, detector, jobdir):
intensities_filepath = os.path.join(jobdir, 'intensities_%s.csv' % name)
if not os.path.exists(intensities_filepath):
raise ImporterException('Result file "intensites_%s.csv" not found in job directory (%s)' % \
(name, jobdir))
intensities = {}
with open(intensities_filepath, 'r') as fp:
reader = csv.DictReader(fp, delimiter=';')
try:
row = next(reader)
except StopIteration:
row = {}
for transition, intensity in row.items():
transition = from_string(transition.strip())
enf = (float(intensity.strip().replace(',', '.')), 0.0) # FIXME: Hack to handle locale problem
intensities[PhotonKey(transition, True, PhotonKey.P)] = enf
return PhotonIntensityResult(intensities)
def setUp(self):
TestCase.setUp(self)
self.t1 = Transition(29, 9, 4)
self.t2 = K_family(14)
self.t3 = Transition(29, siegbahn='La2')
intensities = {}
intensities[PhotonKey(self.t1, False, PhotonKey.P)] = (3.0, 0.3)
intensities[PhotonKey(self.t1, False, PhotonKey.C)] = (1.0, 0.1)
intensities[PhotonKey(self.t1, False, PhotonKey.B)] = (2.0, 0.2)
intensities[PhotonKey(self.t1, False, PhotonKey.T)] = (6.0, 0.4)
intensities[PhotonKey(self.t1, True, PhotonKey.P)] = (7.0, 0.7)
intensities[PhotonKey(self.t1, True, PhotonKey.C)] = (5.0, 0.5)
intensities[PhotonKey(self.t1, True, PhotonKey.B)] = (6.0, 0.6)
intensities[PhotonKey(self.t1, True, PhotonKey.T)] = (18.0, 0.8)
intensities[PhotonKey(self.t2, False, PhotonKey.P)] = (13.0, 0.3)
intensities[PhotonKey(self.t2, False, PhotonKey.C)] = (11.0, 0.1)
intensities[PhotonKey(self.t2, False, PhotonKey.B)] = (12.0, 0.2)
intensities[PhotonKey(self.t2, False, PhotonKey.T)] = (36.0, 0.4)
intensities[PhotonKey(self.t2, True, PhotonKey.P)] = (17.0, 0.7)
intensities[PhotonKey(self.t2, True, PhotonKey.C)] = (15.0, 0.5)
intensities[PhotonKey(self.t2, True, PhotonKey.B)] = (16.0, 0.6)
intensities[PhotonKey(self.t2, True, PhotonKey.T)] = (48.0, 0.8)
intensities[PhotonKey(self.t3, False, PhotonKey.P)] = (23.0, 0.3)
intensities[PhotonKey(self.t3, False, PhotonKey.C)] = (21.0, 0.1)
intensities[PhotonKey(self.t3, False, PhotonKey.B)] = (22.0, 0.2)
intensities[PhotonKey(self.t3, False, PhotonKey.T)] = (66.0, 0.4)
intensities[PhotonKey(self.t3, True, PhotonKey.P)] = (27.0, 0.7)
intensities[PhotonKey(self.t3, True, PhotonKey.C)] = (25.0, 0.5)
intensities[PhotonKey(self.t3, True, PhotonKey.B)] = (26.0, 0.6)
intensities[PhotonKey(self.t3, True, PhotonKey.T)] = (78.0, 0.8)
self.r = PhotonIntensityResult(intensities)
class TestPhotonIntensityResult(TestCase):
def setUp(self):
TestCase.setUp(self)
self.t1 = Transition(29, 9, 4)
self.t2 = K_family(14)
self.t3 = Transition(29, siegbahn='La2')
intensities = {}
intensities[PhotonKey(self.t1, False, PhotonKey.P)] = (3.0, 0.3)
intensities[PhotonKey(self.t1, False, PhotonKey.C)] = (1.0, 0.1)
intensities[PhotonKey(self.t1, False, PhotonKey.B)] = (2.0, 0.2)
intensities[PhotonKey(self.t1, False, PhotonKey.T)] = (6.0, 0.4)
intensities[PhotonKey(self.t1, True, PhotonKey.P)] = (7.0, 0.7)
intensities[PhotonKey(self.t1, True, PhotonKey.C)] = (5.0, 0.5)
intensities[PhotonKey(self.t1, True, PhotonKey.B)] = (6.0, 0.6)
intensities[PhotonKey(self.t1, True, PhotonKey.T)] = (18.0, 0.8)
intensities[PhotonKey(self.t2, False, PhotonKey.P)] = (13.0, 0.3)
intensities[PhotonKey(self.t2, False, PhotonKey.C)] = (11.0, 0.1)
intensities[PhotonKey(self.t2, False, PhotonKey.B)] = (12.0, 0.2)
intensities[PhotonKey(self.t2, False, PhotonKey.T)] = (36.0, 0.4)
intensities[PhotonKey(self.t2, True, PhotonKey.P)] = (17.0, 0.7)
intensities[PhotonKey(self.t2, True, PhotonKey.C)] = (15.0, 0.5)
intensities[PhotonKey(self.t2, True, PhotonKey.B)] = (16.0, 0.6)
intensities[PhotonKey(self.t2, True, PhotonKey.T)] = (48.0, 0.8)
intensities[PhotonKey(self.t3, False, PhotonKey.P)] = (23.0, 0.3)
intensities[PhotonKey(self.t3, False, PhotonKey.C)] = (21.0, 0.1)
intensities[PhotonKey(self.t3, False, PhotonKey.B)] = (22.0, 0.2)
intensities[PhotonKey(self.t3, False, PhotonKey.T)] = (66.0, 0.4)
intensities[PhotonKey(self.t3, True, PhotonKey.P)] = (27.0, 0.7)
intensities[PhotonKey(self.t3, True, PhotonKey.C)] = (25.0, 0.5)
intensities[PhotonKey(self.t3, True, PhotonKey.B)] = (26.0, 0.6)
intensities[PhotonKey(self.t3, True, PhotonKey.T)] = (78.0, 0.8)
self.r = PhotonIntensityResult(intensities)
def tearDown(self):
TestCase.tearDown(self)
def testintensity(self):
# Transition 1
val, err = self.r.intensity(self.t1)
self.assertAlmostEqual(18.0, val, 4)
self.assertAlmostEqual(0.8, err, 4)
val, err = self.r.intensity('Cu La1')
self.assertAlmostEqual(18.0, val, 4)
self.assertAlmostEqual(0.8, err, 4)
val, err = self.r.intensity(self.t1, absorption=False)
self.assertAlmostEqual(6.0, val, 4)
self.assertAlmostEqual(0.4, err, 4)
val, err = self.r.intensity(self.t1, fluorescence=False)
self.assertAlmostEqual(7.0, val, 4)
self.assertAlmostEqual(0.7, err, 4)
val, err = self.r.intensity(self.t1, absorption=False, fluorescence=False)
self.assertAlmostEqual(3.0, val, 4)
self.assertAlmostEqual(0.3, err, 4)
# Transition 2
val, err = self.r.intensity(self.t2)
self.assertAlmostEqual(48.0, val, 4)
self.assertAlmostEqual(0.8, err, 4)
val, err = self.r.intensity('Si K')
self.assertAlmostEqual(48.0, val, 4)
self.assertAlmostEqual(0.8, err, 4)
val, err = self.r.intensity(self.t2, absorption=False)
self.assertAlmostEqual(36.0, val, 4)
self.assertAlmostEqual(0.4, err, 4)
val, err = self.r.intensity(self.t2, fluorescence=False)
self.assertAlmostEqual(17.0, val, 4)
self.assertAlmostEqual(0.7, err, 4)
val, err = self.r.intensity(self.t2, absorption=False, fluorescence=False)
self.assertAlmostEqual(13.0, val, 4)
self.assertAlmostEqual(0.3, err, 4)
# Transition 1 + 3
val, err = self.r.intensity('Cu La')
self.assertAlmostEqual(78.0 + 18.0, val, 4)
self.assertAlmostEqual(1.1314, err, 4)
def testhas_transition(self):
self.assertTrue(self.r.has_transition(self.t1))
self.assertTrue(self.r.has_transition(self.t2))
self.assertTrue(self.r.has_transition(self.t3))
self.assertFalse(self.r.has_transition('U Ma'))
def testcharacteristic_fluorescence(self):
# Transition 1
val, err = self.r.characteristic_fluorescence(self.t1)
self.assertAlmostEqual(5.0, val, 4)
self.assertAlmostEqual(0.5, err, 4)
val, err = self.r.characteristic_fluorescence(self.t1, absorption=False)
self.assertAlmostEqual(1.0, val, 4)
self.assertAlmostEqual(0.1, err, 4)
# Transition 2
val, err = self.r.characteristic_fluorescence(self.t2)
self.assertAlmostEqual(15.0, val, 4)
self.assertAlmostEqual(0.5, err, 4)
val, err = self.r.characteristic_fluorescence(self.t2, absorption=False)
self.assertAlmostEqual(11.0, val, 4)
self.assertAlmostEqual(0.1, err, 4)
def testbremmstrahlung_fluorescence(self):
# Transition 1
val, err = self.r.bremsstrahlung_fluorescence(self.t1)
self.assertAlmostEqual(6.0, val, 4)
self.assertAlmostEqual(0.6, err, 4)
val, err = self.r.bremsstrahlung_fluorescence(self.t1, absorption=False)
self.assertAlmostEqual(2.0, val, 4)
self.assertAlmostEqual(0.2, err, 4)
# Transition 2
val, err = self.r.bremsstrahlung_fluorescence(self.t2)
self.assertAlmostEqual(16.0, val, 4)
self.assertAlmostEqual(0.6, err, 4)
val, err = self.r.bremsstrahlung_fluorescence(self.t2, absorption=False)
self.assertAlmostEqual(12.0, val, 4)
self.assertAlmostEqual(0.2, err, 4)
def testfluorescence(self):
# Transition 1
val, err = self.r.fluorescence(self.t1)
self.assertAlmostEqual(11.0, val, 4)
self.assertAlmostEqual(0.78102, err, 4)
val, err = self.r.fluorescence(self.t1, absorption=False)
self.assertAlmostEqual(3.0, val, 4)
self.assertAlmostEqual(0.2236, err, 4)
# Transition 2
val, err = self.r.fluorescence(self.t2)
self.assertAlmostEqual(31.0, val, 4)
self.assertAlmostEqual(0.78102, err, 4)
val, err = self.r.fluorescence(self.t2, absorption=False)
self.assertAlmostEqual(23.0, val, 4)
self.assertAlmostEqual(0.2236, err, 4)
def testabsorption(self):
# Transition 1
val, err = self.r.absorption(self.t1)
self.assertAlmostEqual(12.0, val, 4)
self.assertAlmostEqual(0.8944, err, 4)
val, err = self.r.absorption(self.t1, fluorescence=False)
self.assertAlmostEqual(4.0, val, 4)
self.assertAlmostEqual(0.7616, err, 4)
# Transition 2
val, err = self.r.absorption(self.t2)
self.assertAlmostEqual(12.0, val, 4)
self.assertAlmostEqual(0.8944, err, 4)
val, err = self.r.absorption(self.t2, fluorescence=False)
self.assertAlmostEqual(4.0, val, 4)
self.assertAlmostEqual(0.7616, err, 4)
def testiter_transitions(self):
self.assertEqual(3, len(list(self.r.iter_transitions())))
def testiter_intensities(self):
self.assertEqual(3, len(list(self.r.iter_intensities())))
def _import_photon_intensity(self, options, key, detector, path,
phdets_key_index, phdets_index_keys, *args):
def _read_intensities_line(line):
values = line.split()
try:
z = int(values[0])
src = Subshell(z, iupac=values[2].strip())
dst = Subshell(z, iupac=values[1].strip())
transition = Transition(z, src, dst)
except ValueError: # transition not supported
return None, 0.0, 0.0, 0.0, 0.0
nf = float(values[4]), float(values[5])
cf = float(values[6]), float(values[7])
bf = float(values[8]), float(values[9])
#tf = float(values[10]), float(values[11]) # skip not needed
t = float(values[12]), float(values[13])
return transition, cf, bf, nf, t
index = phdets_key_index[key] + 1
# Find data files
emitted_filepath = os.path.join(
path, 'pe-intens-%s.dat' % str(index).zfill(2))
if not os.path.exists(emitted_filepath):
raise ImporterException("Data file %s cannot be found" %
emitted_filepath)
generated_filepath = os.path.join(path, 'pe-gen-ph.dat')
if not os.path.exists(generated_filepath):
raise ImporterException("Data file %s cannot be found" %
generated_filepath)
# Load generated
intensities = {}
with open(generated_filepath, 'r') as fp:
for line in fp:
line = line.strip()
if line.startswith('#'): continue
transition, gcf, gbf, gnf, gt = _read_intensities_line(line)
if transition is None:
continue
intensities[PhotonKey(transition, False, PhotonKey.C)] = gcf
intensities[PhotonKey(transition, False, PhotonKey.B)] = gbf
intensities[PhotonKey(transition, False, PhotonKey.P)] = gnf
intensities[PhotonKey(transition, False, PhotonKey.T)] = gt
# Load emitted
with open(emitted_filepath, 'r') as fp:
for line in fp:
line = line.strip()
if line.startswith('#'): continue
transition, ecf, ebf, enf, et = _read_intensities_line(line)
if transition is None:
continue
intensities[PhotonKey(transition, True, PhotonKey.C)] = ecf
intensities[PhotonKey(transition, True, PhotonKey.B)] = ebf
intensities[PhotonKey(transition, True, PhotonKey.P)] = enf
intensities[PhotonKey(transition, True, PhotonKey.T)] = et
return PhotonIntensityResult(intensities)
