def setup_method(self, method):
beam_energy = 200
energy_resolution_MnKa = 130
energy_axis = {'units': 'keV', 'size': 1200, 'scale': 0.01,
'name': 'E'}
s1 = utils_eds.xray_lines_model(
elements=['Fe', 'Cr'], weight_percents=[30, 70],
beam_energy=beam_energy,
energy_resolution_MnKa=energy_resolution_MnKa,
energy_axis=energy_axis)
s2 = utils_eds.xray_lines_model(
elements=['Ga', 'As'], weight_percents=[50, 50],
beam_energy=beam_energy,
energy_resolution_MnKa=energy_resolution_MnKa,
energy_axis=energy_axis)
mix = np.linspace(0., 1., 4).reshape(2, 2)
mix_data = np.tile(s1.data, mix.shape + (1,))
s = s1._deepcopy_with_new_data(mix_data)
a = s.axes_manager._axes.pop(0).get_axis_dictionary()
s.axes_manager.create_axes([{'size': mix.shape[0],
'navigate': True}] * 2 + [a])
s.add_elements(s2.metadata.Sample.elements)
for d, m in zip(s._iterate_signal(), mix.flatten()):
d[:] = d * m + (1 - m) * s2.data
self.mix = mix
self.s = s
def setup_method(self, method):
beam_energy = 200
energy_resolution_MnKa = 130
energy_axis = {'units': 'keV', 'size': 1200, 'scale': 0.01,
'name': 'E'}
s1 = utils_eds.xray_lines_model(
elements=['Fe', 'Cr'], weight_percents=[30, 70],
beam_energy=beam_energy,
energy_resolution_MnKa=energy_resolution_MnKa,
energy_axis=energy_axis)
s2 = utils_eds.xray_lines_model(
elements=['Ga', 'As'], weight_percents=[50, 50],
beam_energy=beam_energy,
energy_resolution_MnKa=energy_resolution_MnKa,
energy_axis=energy_axis)
mix = np.linspace(0., 1., 4).reshape(2, 2)
mix_data = np.tile(s1.data, mix.shape + (1,))
s = s1._deepcopy_with_new_data(mix_data)
a = s.axes_manager._axes.pop(0).get_axis_dictionary()
s.axes_manager.create_axes([{'size': mix.shape[0],
'navigate': True}] * 2 + [a])
s.add_elements(s2.metadata.Sample.elements)
for d, m in zip(s._iterate_signal(), mix.flatten()):
d[:] = d * m + (1 - m) * s2.data
self.mix = mix
self.s = s
def setUp(self):
beam_energy = 200
energy_resolution_MnKa = 130
energy_axis = {"units": "keV", "size": 1200, "scale": 0.01, "name": "E"}
s1 = utils_eds.xray_lines_model(
elements=["Fe", "Cr"],
weight_percents=[30, 70],
beam_energy=beam_energy,
energy_resolution_MnKa=energy_resolution_MnKa,
energy_axis=energy_axis,
)
s2 = utils_eds.xray_lines_model(
elements=["Ga", "As"],
weight_percents=[50, 50],
beam_energy=beam_energy,
energy_resolution_MnKa=energy_resolution_MnKa,
energy_axis=energy_axis,
)
mix = np.linspace(0.0, 1.0, 4).reshape(2, 2)
mix_data = np.tile(s1.data, mix.shape + (1,))
s = s1._deepcopy_with_new_data(mix_data)
a = s.axes_manager._axes.pop(0).get_axis_dictionary()
s.axes_manager.create_axes([{"size": mix.shape[0], "navigate": True}] * 2 + [a])
s.add_elements(s2.metadata.Sample.elements)
for d, m in zip(s._iterate_signal(), mix.flatten()):
d[:] = d * m + (1 - m) * s2.data
self.mix = mix
self.s = s
def setUp(self):
s = utils_eds.xray_lines_model(
elements=["Fe", "Cr", "Zn"],
beam_energy=200,
weight_percents=[20, 50, 30],
energy_resolution_MnKa=130,
energy_axis={"units": "keV", "size": 400, "scale": 0.01, "name": "E", "offset": 5.0},
)
s = s + 0.002
self.s = s
def setup_method(self, method):
s = utils_eds.xray_lines_model(elements=['Fe', 'Cr', 'Zn'],
beam_energy=200,
weight_percents=[20, 50, 30],
energy_resolution_MnKa=130,
energy_axis={'units': 'keV',
'size': 400,
'scale': 0.01,
'name': 'E',
'offset': 5.})
s = s + 0.002
self.s = s
def test_calibrate_xray_weight(self):
s = self.s
s1 = utils_eds.xray_lines_model(
elements=["Co"],
weight_percents=[50],
energy_axis={"units": "keV", "size": 400, "scale": 0.01, "name": "E", "offset": 4.9},
)
s = s + s1 / 50
m = s.create_model()
m.fit()
with assert_warns(message="The X-ray line expected to be in the model " "was not found"):
m.calibrate_xray_lines(calibrate="sub_weight", xray_lines=["Fe_Ka"], bound=100)
nt.assert_true(np.allclose(0.0347, m["Fe_Kb"].A.value, atol=1e-3))
def test_calibrate_xray_weight(self):
s = self.s
s1 = utils_eds.xray_lines_model(
elements=['Co'],
weight_percents=[50],
energy_axis={'units': 'keV', 'size': 400,
'scale': 0.01, 'name': 'E',
'offset': 4.9})
s = (s + s1 / 50)
m = s.create_model()
m.fit()
with assert_warns(message='The X-ray line expected to be in the model '
'was not found'):
m.calibrate_xray_lines(calibrate='sub_weight',
xray_lines=['Fe_Ka'], bound=100)
np.testing.assert_allclose(0.0347, m['Fe_Kb'].A.value,
atol=1e-3)
def setup_method(self, method):
s = utils_eds.xray_lines_model(elements=['Al', 'Zn'],
weight_percents=[50, 50])
self.signal = s
def setup_method(self, method):
s = utils_eds.xray_lines_model(elements=['Al', 'Zn'],
weight_percents=[50, 50])
self.signal = s
from hyperspy.datasets.example_signals import EDS_TEM_Spectrum
from hyperspy.decorators import lazifyTestClass
from hyperspy.misc import utils
from hyperspy.misc.eds import utils as utils_eds
from hyperspy.misc.elements import elements as elements_db
# Create this outside the test class to
# reduce computation in test suite by ~10seconds
s = utils_eds.xray_lines_model(
elements=["Fe", "Cr", "Zn"],
beam_energy=200,
weight_percents=[20, 50, 30],
energy_resolution_MnKa=130,
energy_axis={
"units": "keV",
"size": 400,
"scale": 0.01,
"name": "E",
"offset": 5.0,
},
)
s = s + 0.002
@lazifyTestClass
class TestlineFit:
def setup_method(self, method):
self.s = s.deepcopy()
def setUp(self):
s = utils_eds.xray_lines_model(elements=["Al", "Zn"], weight_percents=[50, 50])
self.signal = s
def setUp(self):
s = utils_eds.xray_lines_model(elements=['Al', 'Zn'],
weight_percents=[50, 50])
self.spectrum = s
