def mass_absorption_coefficient(element, energies):
"""
Mass absorption coefficient (mu/rho) of a X-ray absorbed in a pure
material.
The mass absorption is retrieved from the database of Chantler2005
Parameters
----------
element: str
The element symbol of the absorber, e.g. 'Al'.
energies: float or list of float or str or list of str
The energy or energies of the X-ray in keV, or the name of the X-rays,
e.g. 'Al_Ka'.
Return
------
mass absorption coefficient(s) in cm^2/g
Examples
--------
>>> hs.material.mass_absorption_coefficient(
>>> element='Al', energies=['C_Ka','Al_Ka'])
array([ 26330.38933818, 372.02616732])
See also
--------
hs.material.mass_absorption_mixture
Note
----
See http://physics.nist.gov/ffast
Chantler, C.T., Olsen, K., Dragoset, R.A., Kishore, A.R., Kotochigova,
S.A., and Zucker, D.S. (2005), X-Ray Form Factor, Attenuation and
Scattering Tables (version 2.1).
"""
energies_db = np.array(ffast_mac[element].energies_keV)
macs = np.array(ffast_mac[element].mass_absorption_coefficient_cm2g)
energies = copy.copy(energies)
if isinstance(energies, str):
energies = utils_eds._get_energy_xray_line(energies)
elif hasattr(energies, '__iter__'):
for i, energy in enumerate(energies):
if isinstance(energy, str):
energies[i] = utils_eds._get_energy_xray_line(energy)
index = np.searchsorted(energies_db, energies)
mac_res = np.exp(np.log(macs[index - 1]) +
np.log(macs[index] / macs[index - 1]) *
(np.log(energies / energies_db[index - 1]) /
np.log(energies_db[index] / energies_db[index - 1])))
return np.nan_to_num(mac_res)
def _get_line_energy(self, Xray_line, FWHM_MnKa=None):
"""
Get the line energy and the energy resolution of a Xray line.
The return values are in the same units than the signal axis
Parameters
----------
Xray_line : strings
Valid element X-ray lines e.g. Fe_Kb
FWHM_MnKa: {None, float, 'auto'}
The energy resolution of the detector in eV
if 'auto', used the one in
'self.metadata.Acquisition_instrument.SEM.Detector.EDS.energy_resolution_MnKa'
Returns
-------
float: the line energy, if FWHM_MnKa is None
(float,float): the line energy and the energy resolution, if FWHM_MnKa
is not None
"""
units_name = self.axes_manager.signal_axes[0].units
if FWHM_MnKa == 'auto':
if self.metadata.Signal.signal_type == 'EDS_SEM':
FWHM_MnKa = self.metadata.Acquisition_instrument.SEM.\
Detector.EDS.energy_resolution_MnKa
elif self.metadata.Signal.signal_type == 'EDS_TEM':
FWHM_MnKa = self.metadata.Acquisition_instrument.TEM.\
Detector.EDS.energy_resolution_MnKa
else:
raise NotImplementedError(
"This method only works for EDS_TEM or EDS_SEM signals. "
"You can use `set_signal_type(\"EDS_TEM\")` or"
"`set_signal_type(\"EDS_SEM\")` to convert to one of these"
"signal types.")
line_energy = utils_eds._get_energy_xray_line(Xray_line)
if units_name == 'eV':
line_energy *= 1000
if FWHM_MnKa is not None:
line_FWHM = utils_eds.get_FWHM_at_Energy(
FWHM_MnKa, line_energy / 1000) * 1000
elif units_name == 'keV':
if FWHM_MnKa is not None:
line_FWHM = utils_eds.get_FWHM_at_Energy(FWHM_MnKa,
line_energy)
else:
raise ValueError(
"%s is not a valid units for the energy axis. "
"Only `eV` and `keV` are supported. "
"If `s` is the variable containing this EDS spectrum:\n "
">>> s.axes_manager.signal_axes[0].units = \'keV\' \n"
% units_name)
if FWHM_MnKa is None:
return line_energy
else:
return line_energy, line_FWHM
def _get_line_energy(self, Xray_line, FWHM_MnKa=None):
"""
Get the line energy and the energy resolution of a Xray line.
The return values are in the same units than the signal axis
Parameters
----------
Xray_line : strings
Valid element X-ray lines e.g. Fe_Kb
FWHM_MnKa: {None, float, 'auto'}
The energy resolution of the detector in eV
if 'auto', used the one in
'self.metadata.Acquisition_instrument.SEM.Detector.EDS.energy_resolution_MnKa'
Returns
-------
float: the line energy, if FWHM_MnKa is None
(float,float): the line energy and the energy resolution, if FWHM_MnKa
is not None
"""
units_name = self.axes_manager.signal_axes[0].units
if FWHM_MnKa == 'auto':
if self.metadata.Signal.signal_type == "EDS_SEM":
FWHM_MnKa = self.metadata.Acquisition_instrument.SEM.\
Detector.EDS.energy_resolution_MnKa
elif self.metadata.Signal.signal_type == "EDS_TEM":
FWHM_MnKa = self.metadata.Acquisition_instrument.TEM.\
Detector.EDS.energy_resolution_MnKa
else:
raise NotImplementedError(
"This method only works for EDS_TEM or EDS_SEM signals. "
"You can use `set_signal_type(\"EDS_TEM\")` or"
"`set_signal_type(\"EDS_SEM\")` to convert to one of these"
"signal types.")
line_energy = utils_eds._get_energy_xray_line(Xray_line)
if units_name == 'eV':
line_energy *= 1000
if FWHM_MnKa is not None:
line_FWHM = utils_eds.get_FWHM_at_Energy(
FWHM_MnKa, line_energy / 1000) * 1000
elif units_name == 'keV':
if FWHM_MnKa is not None:
line_FWHM = utils_eds.get_FWHM_at_Energy(
FWHM_MnKa, line_energy)
else:
raise ValueError(
"%s is not a valid units for the energy axis. "
"Only `eV` and `keV` are supported. "
"If `s` is the variable containing this EDS spectrum:\n "
">>> s.axes_manager.signal_axes[0].units = \'keV\' \n" %
units_name)
if FWHM_MnKa is None:
return line_energy
else:
return line_energy, line_FWHM
