def get_abs_corr_zeta(
weight_percent, mass_thickness,
take_off_angle): # take_off_angle, temporary value for testing
"""
Calculate absorption correction terms.
Parameters
----------
weight_percent: list of signal
Composition in weight percent.
mass_thickness: signal
Density-thickness map in kg/m^2
take_off_angle: float
X-ray take-off angle in degrees.
"""
from hyperspy.misc import material
toa_rad = np.radians(take_off_angle)
csc_toa = 1.0 / np.sin(toa_rad)
# convert from cm^2/g to m^2/kg
mac = stack(
material.mass_absorption_mixture(weight_percent=weight_percent),
show_progressbar=False) * 0.1
acf = mac.data * mass_thickness.data * csc_toa
acf = acf / (1.0 - np.exp(-(acf)))
return acf
def get_abs_corr_cross_section(
composition, number_of_atoms, take_off_angle,
probe_area): # take_off_angle, temporary value for testing
"""
Calculate absorption correction terms.
Parameters
----------
number_of_atoms: list of signal
Stack of maps with number of atoms per pixel.
take_off_angle: float
X-ray take-off angle in degrees.
"""
from hyperspy.misc import material
toa_rad = np.radians(take_off_angle)
Av = constants.Avogadro
elements = [
intensity.metadata.Sample.elements[0] for intensity in number_of_atoms
]
atomic_weights = np.array([
elements_db[element]['General_properties']['atomic_weight']
for element in elements
])
number_of_atoms = stack(number_of_atoms).data
#calculate the total_mass per pixel, or mass thicknessself.
total_mass = np.zeros_like(number_of_atoms[0], dtype='float')
for i, (weight) in enumerate(atomic_weights):
total_mass += (number_of_atoms[i] * weight / Av / probe_area / 1E-15)
# determine mass absorption coefficients and convert from cm^2/g to m^2/atom.
mac = stack(
material.mass_absorption_mixture(
weight_percent=material.atomic_to_weight(composition))) * 0.1
acf = np.zeros_like(number_of_atoms)
constant = 1 / (Av * math.sin(toa_rad) * probe_area * 1E-16)
#determine an absorption coeficcient per element per pixel.
for i, (weight) in enumerate(atomic_weights):
expo = (mac.data[i] * total_mass * constant)
acf[i] = expo / (1 - math.e**(-expo))
return acf