# -*- coding: UTF-8 -*-
"""
fluorescence_lines.py
Tools for fitting and simulating X-ray fluorescence lines.
"""
import numpy as np
import scipy as sp
import pylab as plt
from . import line_models
from .energy_calibration import STANDARD_FEATURES
from collections import OrderedDict
from mass.mathstat.special import voigt
import logging
LOG = logging.getLogger("mass")
FWHM_OVER_SIGMA = (8 * np.log(2))**0.5
_rng = np.random.default_rng()
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class SpectralLine:
"""An abstract base class for modeling spectral lines as a sum
of Voigt profiles (i.e., Gaussian-convolved Lorentzians).
Call addline to create a new subclass properly.
The API follows scipy.stats.stats.rv_continuous and is kind of like rv_frozen.
Calling this object with an argument evalutes the pdf at the argument, it does not
return an rv_frozen.
But so far we ony define `rvs` and `pdf`.
"""
def __init__(self, element, material, linetype, energies, lorentzian_fwhm, intrinsic_sigma, # noqa: PLR0917
reference_plot_instrument_gaussian_fwhm, reference_short, reference_amplitude, reference_amplitude_type,
normalized_lorentzian_integral_intensity, nominal_peak_energy, fitter_type, position_uncertainty,
reference_measurement_type, is_default_material):
"""Constructor needs two Gaussian widths (both default to zero):
`intrinsic_sigma` is the width (sigma) of any 'intrinsic Gaussian', as found (for example) in
the Fowler et al 2020 metrology shape estimation for the lanthanide L lines. Normally zero.
"""
self.element = element
self.material = material
self.linetype = linetype
self.energies = energies
self.lorentzian_fwhm = lorentzian_fwhm
self.intrinsic_sigma = intrinsic_sigma
self.reference_plot_instrument_gaussian_fwhm = reference_plot_instrument_gaussian_fwhm
self.reference_short = reference_short
self.reference_amplitude = reference_amplitude
self.reference_amplitude_type = reference_amplitude_type
self.reference_measurement_type = reference_measurement_type
self.normalized_lorentzian_integral_intensity = normalized_lorentzian_integral_intensity
self.nominal_peak_energy = nominal_peak_energy
self.fitter_type = fitter_type
self.position_uncertainty = position_uncertainty
self.reference_measurement_type = reference_measurement_type
self.is_default_material = is_default_material
self._peak_energy = np.nan
self.cumulative_amplitudes = self.normalized_lorentzian_integral_intensity.cumsum()
@property
def peak_energy(self):
# lazily calculate peak energy
if np.isnan(self._peak_energy):
try:
self._peak_energy = sp.optimize.brent(lambda x: -self.pdf(x, instrument_gaussian_fwhm=0),
brack=np.array((0.5, 1, 1.5)) * self.nominal_peak_energy)
except ValueError:
self._peak_energy = self.nominal_peak_energy
return self._peak_energy
def __call__(self, x, instrument_gaussian_fwhm):
"""Make the class callable, returning the same value as the self.pdf method."""
return self.pdf(x, instrument_gaussian_fwhm)
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def pdf(self, x, instrument_gaussian_fwhm):
"""Spectrum (units of fraction per eV) as a function of <x>, the energy in eV"""
gaussian_sigma = self._gaussian_sigma(instrument_gaussian_fwhm)
x = np.asarray(x, dtype=float)
result = np.zeros_like(x)
for energy, fwhm, ampl in zip(self.energies, self.lorentzian_fwhm,
self.normalized_lorentzian_integral_intensity):
result += ampl * voigt(x, energy, hwhm=fwhm * 0.5, sigma=gaussian_sigma)
# mass.voigt() is normalized to have unit integrated intensity
return result
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def components(self, x, instrument_gaussian_fwhm):
"""List of spectrum components as a function of <x>, the energy in eV"""
gaussian_sigma = self._gaussian_sigma(instrument_gaussian_fwhm)
x = np.asarray(x, dtype=float)
components = []
for energy, fwhm, ampl in zip(self.energies, self.lorentzian_fwhm,
self.normalized_lorentzian_integral_intensity):
components.append(ampl * voigt(x, energy, hwhm=fwhm * 0.5, sigma=gaussian_sigma))
return components
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def plot(self, x=None, instrument_gaussian_fwhm=0, axis=None, components=True, label=None, setylim=True):
"""Plot the spectrum.
x - np array of energy in eV to plot at (sensible default)
axis - axis to plot on (default creates new figure)
components - True plots each voigt component in addition to the spectrum
label - a string to label the plot with (optional)"""
gaussian_sigma = self._gaussian_sigma(instrument_gaussian_fwhm)
if x is None:
width = max(2 * gaussian_sigma, 3 * np.amax(self.lorentzian_fwhm))
lo = np.amin(self.energies) - width
hi = np.amax(self.energies) + width
x = np.linspace(lo, hi, 500)
if axis is None:
plt.figure()
axis = plt.gca()
if components:
for component in self.components(x, instrument_gaussian_fwhm):
axis.plot(x, component, "--")
pdf = self.pdf(x, instrument_gaussian_fwhm)
axis.plot(x, pdf, "k", lw=2, label=label)
axis.set_xlabel("Energy (eV)")
axis.set_ylabel(f"Counts per {float(x[1] - x[0]):.2} eV bin")
axis.set_xlim(x[0], x[-1])
if setylim:
axis.set_ylim(0, np.amax(pdf) * 1.05)
axis.set_title(f"{self.shortname} with resolution {instrument_gaussian_fwhm:.2f} eV FWHM")
return axis
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def plot_like_reference(self, axis=None):
if self.reference_plot_instrument_gaussian_fwhm is None:
fwhm = 0.001
else:
fwhm = self.reference_plot_instrument_gaussian_fwhm
axis = self.plot(
axis=axis, instrument_gaussian_fwhm=fwhm)
return axis
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def rvs(self, size, instrument_gaussian_fwhm, rng=None):
"""The CDF and PPF (cumulative distribution and percentile point functions) are hard to
compute. But it's easy enough to generate the random variates themselves, so we
override that method."""
if rng is None:
rng = _rng
gaussian_sigma = self._gaussian_sigma(instrument_gaussian_fwhm)
# Choose from among the N Lorentzian lines in proportion to the line amplitudes
iline = self.cumulative_amplitudes.searchsorted(
rng.uniform(0, self.cumulative_amplitudes[-1], size=size))
# Choose Lorentzian variates of the appropriate width (but centered on 0)
lor = rng.standard_cauchy(size=size) * self.lorentzian_fwhm[iline] * 0.5
# If necessary, add a Gaussian variate to mimic finite resolution
if gaussian_sigma > 0.0:
lor += rng.standard_normal(size=size) * gaussian_sigma
# Finally, add the line centers.
results = lor + self.energies[iline]
# We must check for non-positive results and replace them by recursive call
# to self.rvs().
not_positive = results <= 0.0
if np.any(not_positive):
Nbad = not_positive.sum()
results[not_positive] = self.rvs(
size=Nbad, instrument_gaussian_fwhm=instrument_gaussian_fwhm)
return results
@property
def shortname(self):
if self.is_default_material:
return f"{self.element}{self.linetype}"
else:
return f"{self.element}{self.linetype}_{self.material}"
@property
def reference(self):
return lineshape_references[self.reference_short]
def _gaussian_sigma(self, instrument_gaussian_fwhm):
"""combined intrinstic_sigma and insturment_gaussian_fwhm in quadrature and return the result
"""
assert instrument_gaussian_fwhm >= 0
return ((instrument_gaussian_fwhm / FWHM_OVER_SIGMA)**2 + self.intrinsic_sigma**2)**0.5
def __repr__(self):
return f"SpectralLine: {self.shortname}"
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def model(self, has_linear_background=True, has_tails=False, prefix="", qemodel=None):
"""Generate a LineModel instance from a SpectralLine"""
model_class = line_models.GenericLineModel
name = self.element + self.linetype
m = model_class(name=name, spect=self, has_linear_background=has_linear_background,
has_tails=has_tails, prefix=prefix, qemodel=qemodel)
return m
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def fitter(self):
return make_line_fitter(self)
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def minimum_fwhm(self, instrument_gaussian_fwhm):
"""for the narrowest lorentzian in the line model, calculate the combined fwhm including
the lorentzian, intrinstic_sigma, and instrument_gaussian_fwhm"""
fwhm2 = np.amin(self.lorentzian_fwhm)**2 + instrument_gaussian_fwhm**2 + \
(self.intrinsic_sigma * FWHM_OVER_SIGMA)**2
return np.sqrt(fwhm2)
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@classmethod
def quick_monochromatic_line(cls, name, energy, lorentzian_fwhm, intrinsic_sigma):
"""
Create a quick monochromatic line. Intended for use in calibration when we know a line energy, but not a lineshape model.
Returns and instrance of SpectralLine with most fields having contents like "unknown: quick_line". The line will have
a single lorentzian element with the given energy, fwhm, and intrinsic_sigma values.
"""
energy = float(energy)
element = name
material = "unknown: quick_line"
energies = np.array([energy])
if lorentzian_fwhm <= 0 and intrinsic_sigma <= 0:
intrinsic_sigma = 1e-4
lorentzian_fwhm = np.array([lorentzian_fwhm])
linetype = "quick_line"
reference_plot_instrument_gaussian_fwhm = "unkown: quick_line"
reference_short = "unkown: quick_line"
reference_amplitude = "unkown: quick_line"
reference_amplitude_type = "unkown: quick_line"
normalized_lorentzian_integral_intensity = np.array([1])
nominal_peak_energy = energy
fitter_type = line_models.GenericLineModel # dont float dph_de
position_uncertainty = "unknown: quick_line"
reference_measurement_type = "unkown: quick_line"
is_default_material = True
return cls(element, material, linetype, energies, lorentzian_fwhm, intrinsic_sigma,
reference_plot_instrument_gaussian_fwhm, reference_short, reference_amplitude, reference_amplitude_type,
normalized_lorentzian_integral_intensity, nominal_peak_energy, fitter_type, position_uncertainty,
reference_measurement_type, is_default_material)
lineshape_references = OrderedDict()
lineshape_references["Klauber 1993"] = """Data are from C. Klauber, Applied Surface Science 70/71 (1993) pages 35-39.
"Magnesium Kalpha X-ray line structure revisited". Also discussed in more
detail in C. Klauber, Surface & Interface Analysis 20 (1993), 703-715.
Klauber offers only an energy shift relative to some absolute standard. For
an absolute standard, we use the value 1253.687 as the Ka1 peak as found by
J. Schweppe, R. D. Deslattes, T. Mooney, and C. J. Powell in J. Electron
Spectroscopy and Related Phenomena 67 (1994) 463-478 titled "Accurate measurement
of Mg and Al Kalpha_{1,2} X-ray energy profiles". See Table 5 "Average" column.
"""
lineshape_references["Wollman 2000"] = """Data are from Wollman, Nam, Newbury, Hilton, Irwin, Berfren, Deiker, Rudman,
and Martinis, NIM A 444 (2000) page 145. They come from combining 8 earlier
references dated 1965 - 1993."""
lineshape_references["Chantler 2006"] = """Chantler, C., Kinnane, M., Su, C.-H., & Kimpton, J. (2006).
"Characterization of K spectral profiles for vanadium, component redetermination for
scandium, titanium, chromium, and manganese, and development of satellite structure
for Z=21 to Z=25." Physical Review A, 73(1), 012508. doi:10.1103/PhysRevA.73.012508
url: http://link.aps.org/doi/10.1103/PhysRevA.73.012508
Be sure to look at Table I, not the very similar Table II which lists parameters in different parameterization."""
lineshape_references["Chantler 2013"] = """C Chantler, L Smale, J Kimpton, et al., J Phys B 46, 145601 (2013).
http://iopscience.iop.org/0953-4075/46/14/145601"""
lineshape_references["Chantler 2013, Section 5"] = """C Chantler, L Smale, J Kimpton, et al., J Phys B 46, 145601 (2013).
http://iopscience.iop.org/0953-4075/46/14/145601
We were originally using L Smale, C Chantler, M Kinnane, J Kimpton, et al., Phys
Rev A 87 022512 (2013). http://pra.aps.org/abstract/PRA/v87/i2/e022512
BUT these were adjusted in C Chantler, L Smale, J Kimpton, et al., J Phys B
46, 145601 (2013). http://iopscience.iop.org/0953-4075/46/14/145601
(see Section 5 "Redefinition of vanadium K-beta standard") Both papers are
by the same group, of course.
"""
lineshape_references["Hoelzer 1997, NISTfits.ipf"] = """Data are from Hoelzer, Fritsch, Deutsch, Haertwig, Foerster in
Phys Rev A56 (#6) pages 4554ff (1997 December), ***as corrected***
by someone at LANL: see 11/30/2004 corrections in NISTfits.ipf (Igor code)."""
lineshape_references["Hoelzer 1997"] = """Data are from Hoelzer, Fritsch, Deutsch, Haertwig, Foerster in
Phys Rev A56 (#6) pages 4554ff (1997 December)."""
lineshape_references["Zn Hack"] = """This is a hack, a copy of the Hoelzer, Fritsch, Deutsch, Haertwig, Foerster
Phys Rev A56 (#6) pages 4554ff (1997 December) model, with the numbers
adjusted to get line energies of 8615.823, 8638.91 eV and widths 10% wider
than for Cu. Those widths are based on Zschornack's book.
The KBeta also appears to be a hack with scaled values."""
lineshape_references["Zschornack"] = """Zschornack, Günter H. (2007). Handbook of X-Ray Data. Springer-Verlag, Berlin."""
lineshape_references["Steve Smith"] = """This is what Steve Smith at NASA GSFC uses for Br K-alpha."""
lineshape_references["Joe Fowler"] = """This is what Joe Fowler measured for tungsten L-lines in 2018."""
lineshape_references["NIST ASD"] = """NIST Atomic Spectra Database
Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2018). NIST Atomic Spectra Database (ver. 5.6.1),
[Online]. Available: https://physics.nist.gov/asd [2018, December 12]. National Institute of Standards and
Technology, Gaithersburg, MD. DOI: https://doi.org/10.18434/T4W30F"""
lineshape_references["Clementson 2010"] = """J. Clementson, P. Beiersdorfer, G. V. Brown, and M. F. Gu,
"Spectroscopy of M-shell x-ray transitions in Zn-like through Co-like W,"
Physica Scripta 81, 015301 (2010). https://iopscience.iop.org/article/10.1088/0031-8949/81/01/015301/meta"""
lineshape_references["Nilsen 1995"] = """Elliott, S. R., Beiersdorfer, P., Macgowan, B. J., & Nilsen, J. (1995).
Measurements of line overlap for resonant spoiling of x-ray lasing transitions in nickel-like tungsten, 52(4),
2689–2692. https://doi.org/10.1103/PhysRevA.52.2689"""
lineshape_references["Deslattes Notebook Si"] = """Scanned pages from Deslattes/Mooney's notebook provided by Csilla Szabo-Foster.
Added by GCO Oct 7 2019. Used the postion and width values from the from the lowest listed fit, the one in energy units.
Used the intensities from the Second lowest fit, the one labeled PLUS-POSITION SCAN (best-fit Voight profile).
Also the notebook only included the Ka1 and Ka2, not the higher energy satellites, so I made up numbers for the
small feature at higher energy"""
lineshape_references["Schweppe 1992 Al"] = """J. Schweppe, R. D. Deslattes, T. Mooney, and C. J. Powell
in J. Electron Spectroscopy and Related Phenomena 67
(1994) 463-478 titled "Accurate measurement of Mg and Al Kalpha_{1,2} X-ray energy profiles". See Table 5
"Average" column. They do not provide a full lineshape, GCO interperpreted the paper as follows: Ka1 and Ka2
positions are taken from Table 6 "This work" column Ka1 and Ka2 widths were fixed as equal, and we taken the
value 0.43 eV from the 2nd to last paragraph The higher energy satellite features are not measured by
Schweppe, and instead taken from an email from Caroline Kilbourne to Joel Ullom dated 28 Sept 2010 We expect
these higher energy satellites do not affect the fitting of the peak location very much.
"""
lineshape_references["Mendenhall 2019"] = """Marcus H. Mendenhall et al., J. Phys B in press (2019).
https://doi.org/10.1088/1361-6455/ab45d6"""
lineshape_references["Deslattes Notebook S, Cl, K"] = """Scanned pages from Deslattes/Mooney's notebook
provided by Csilla Szabo-Foster. Added by GCO Oct 30 2019. Used
the postion and width values from the from the lowest listed fit, the one in energy units. Used the
intensities from the Second lowest fit, the one labeled PLUS-POSITION SCAN (best-fit Voight profile). The
detector resolution ("width of Gauss. res. func." in MINUS-POSITON scan) is less than the Gaussian Width
("Gaussian width" in PLUS-POSITON scan) I haven't accounted for that, so our models still don't match
Deslattes. We would need a gaussian_atomic_physics component added to our models. Also the notebook only
included the Ka1 and Ka2, not the higher energy satellites, so I made up numbers for the small feature at
higher energy or estimated them from data in Mauron, O., Dousse, J. C., Hoszowska, J., Marques, J. P.,
Parente, F., & Polasik, M. (2000). L-shell shake processes resulting from 1s photoionization in elements
11≤Z≤17. Physical Review A - Atomic, Molecular, and Optical Physics, 62(6), 062508–062501.
https://doi.org/10.1103/PhysRevA.62.062508"""
lineshape_references["Ravel 2018"] = """Bruce Ravel et al., Phys. Rev. B 97 (2018) 125139
https://doi.org/10.1103/PhysRevB.97.125139"""
lineshape_references["Ito 2020"] = """Ito, Y., Tochio, T., Yamashita, M., Fukushima, S., Vlaicu, A. M.,
Marques, J. P., ... Parente, F. (2020). Structure of Kα - and Kβ-emission x-ray spectra for Se, Y, and Zr.
Physical Review A, 102(5), 052820. https://doi.org/10.1103/PhysRevA.102.052820"""
lineshape_references["Menesguen 2022"] = """Ménesguen, Y., Lépy, M.-C., Ito, Y., Yamashita, M., Fukushima,
S., Tochio, T., ... Parente, F. (2022). Structure of single KL0–, double KL1–, and triple KL2 − ionization
in Mg, Al, and Si targets induced by photons, and their absorption spectra. Radiation Physics and Chemistry,
110048. https://doi.org/10.1016/j.radphyschem.2022.110048"""
lineshape_references["Dean 2019"] = """Dean, J. W., Melia, H. A., Chantler, C. T., Smale, L. F. (2019)
High accuracy characterisation for the absolute energy of scandium Kα. J. Phys. B: At. Mol. Opt. Phys. 52 165002
https://doi.org/10.1088/1361-6455/ab29b1"""
lineshape_references["Dean 2020"] = """Dean, J. W., Chantler, C. T., Smale, L. F., Melia, H. A. (2020)
An absolute energy characterisation of scandium Kβ to 2 parts per million. J. Phys. B: At. Mol. Opt. Phys. 53 205004.
https://doi.org/10.1088/1361-6455/abb1ff"""
lineshape_references["Rough Estimate"] = "Line energies from the stanard database, relative intensities and widths are guesses."
spectra = OrderedDict()
spectrum_classes = OrderedDict() # for backwards compatability
LORENTZIAN_PEAK_HEIGHT = 999
LORENTZIAN_INTEGRAL_INTENSITY = 9999
VOIGT_PEAK_HEIGHT = 99999
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def addline(element, linetype, material, reference_short, reference_plot_instrument_gaussian_fwhm, # noqa: PLR0917
nominal_peak_energy, energies, lorentzian_fwhm, reference_amplitude,
reference_amplitude_type, ka12_energy_diff=None, fitter_type=None,
position_uncertainty=np.nan, intrinsic_sigma=0, reference_measurement_type=None,
is_default_material=True, allow_replacement=False):
# require exactly one method of specifying the amplitude of each component
assert reference_amplitude_type in {LORENTZIAN_PEAK_HEIGHT,
LORENTZIAN_INTEGRAL_INTENSITY, VOIGT_PEAK_HEIGHT}
# require the reference exists in lineshape_references
assert reference_short in lineshape_references
# require kalpha lines to have ka12_energy_diff
if linetype.startswith("KAlpha"):
ka12_energy_diff = float(ka12_energy_diff)
# require reference_plot_instrument_gaussian_fwhm to be a float or None
assert reference_plot_instrument_gaussian_fwhm is None or isinstance(
reference_plot_instrument_gaussian_fwhm, float)
# calculate normalized lorentzian_integral_intensity
if reference_amplitude_type == VOIGT_PEAK_HEIGHT:
reference_instrument_gaussian_sigma = reference_plot_instrument_gaussian_fwhm / FWHM_OVER_SIGMA
lorentzian_integral_intensity = [ph / voigt(0, 0, lw / 2.0, reference_instrument_gaussian_sigma)
for ph, lw in zip(reference_amplitude, lorentzian_fwhm)]
elif reference_amplitude_type == LORENTZIAN_PEAK_HEIGHT:
lorentzian_integral_intensity = (
0.5 * np.pi * lorentzian_fwhm) * np.array(reference_amplitude)
elif reference_amplitude_type == LORENTZIAN_INTEGRAL_INTENSITY is not None:
lorentzian_integral_intensity = reference_amplitude
normalized_lorentzian_integral_intensity = np.array(lorentzian_integral_intensity) / \
float(np.sum(lorentzian_integral_intensity))
line = SpectralLine(
element=element,
material=material,
linetype=linetype,
energies=np.array(energies),
lorentzian_fwhm=np.array(lorentzian_fwhm),
intrinsic_sigma=intrinsic_sigma,
reference_plot_instrument_gaussian_fwhm=reference_plot_instrument_gaussian_fwhm,
reference_short=reference_short,
reference_amplitude=reference_amplitude,
reference_amplitude_type=reference_amplitude_type,
normalized_lorentzian_integral_intensity=np.array(normalized_lorentzian_integral_intensity),
nominal_peak_energy=float(nominal_peak_energy),
fitter_type=fitter_type,
position_uncertainty=float(position_uncertainty),
reference_measurement_type=reference_measurement_type,
is_default_material=is_default_material,
)
line.__doc__ = "Line auto-generated by calling addline(...) to create a SpectralLine"
if linetype.startswith("KAlpha"):
line.ka12_energy_diff = ka12_energy_diff
name = line.shortname
if name in spectra.keys() and (not allow_replacement):
raise ValueError(f"spectrum {name} already exists")
# Add this SpectralLine to spectra dict AND make it be a variable in the module
spectra[name] = line
spectrum_classes[name] = lambda: line
globals()[name] = line
def mlf():
f"Make a line fitter for {name}"
return make_line_fitter(line)
globals()[name + "Fitter"] = mlf
return line
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def make_line_fitter(line):
"""Generate a LineFitter instance from a SpectralLine (deprecated)"""
if line.fitter_type is not None:
fitter_class = line.fitter_type
else:
fitter_class = line_models.GenericLineModel
f = fitter_class(line)
f.name = line.element + line.linetype
return f
addline(
element="Fe",
material="metal",
linetype="LAlpha",
reference_short="Rough Estimate",
nominal_peak_energy=STANDARD_FEATURES["FeLAlpha"],
energies=np.array([STANDARD_FEATURES["FeLAlpha"], STANDARD_FEATURES["FeLBeta"]]),
lorentzian_fwhm=np.array(np.array([3, 3])),
reference_amplitude=np.array(np.array([2, 1])),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
ka12_energy_diff=np.abs(STANDARD_FEATURES["FeLAlpha"] - STANDARD_FEATURES["FeLBeta"]),
reference_plot_instrument_gaussian_fwhm=0.2, # a total guess
position_uncertainty=1.5
)
addline(
element="Mg",
material="metal",
linetype="KAlpha",
reference_short="Menesguen 2022",
nominal_peak_energy=1253.635,
energies=np.array((1253.666, 1253.401, 1253.422, 1258.457, 1261.887,
1262.156, 1263.758, 1271.034, 1272.601, 1274.187)),
lorentzian_fwhm=np.array((.380, .374, .859, 1.006, .485,
.585, .797, 1.213, .88, .852)),
reference_amplitude=np.array((100, 49.75, 19.7, 1.99, 8,
6, 8.32, 1.23, .23, .71)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=0.266,
reference_plot_instrument_gaussian_fwhm=0.2, # a total guess
position_uncertainty=0.016
)
addline(
element="Al",
material="metal",
linetype="KAlpha",
reference_short="Menesguen 2022",
nominal_peak_energy=1486.690,
energies=np.array((1486.709, 1486.305, 1486.314, 1492.305, 1496.227,
1496.635, 1498.397, 1506.719, 1510.212)),
lorentzian_fwhm=np.array((.392, .392, 1.12, 1.16, .647,
.685, .932, 1.49, 1.07)),
reference_amplitude=np.array((100, 49.4, 16.1, 1.21, 7.54,
3.7, 5.77, 0.70, 0.51)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=0.404,
reference_plot_instrument_gaussian_fwhm=0.2, # a total guess
position_uncertainty=0.005
)
addline(
element="Si",
material="Si wafer",
linetype="KAlpha",
reference_short="Menesguen 2022",
nominal_peak_energy=1739.961,
energies=np.array((1739.973, 1739.361, 1739.537, 1746.330, 1750.687,
1751.276, 1753.113, 1762.677, 1766.607)),
lorentzian_fwhm=np.array((.441, .458, 1.12, 1.18, .80, .74, .931, 1.83, 1.07)),
reference_amplitude=np.array((100, 50.35, 12.41, .78, 5.65, 2.03, 4.45, 0.29, 0.18)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=.612,
reference_plot_instrument_gaussian_fwhm=0.2, # a total guess
position_uncertainty=0.010
)
# With the publication of Ménesguen 2022, we want to keep our previous line shapes around for
# cross-checking. You can find them as, e.g., mass.MgKAlpha_v1
addline(
element="Mg",
material="metal_v1",
linetype="KAlpha",
reference_short="Klauber 1993",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=1253.687,
energies=np.array((-.265, 0, 4.740, 8.210, 8.487, 10.095, 17.404, 20.430)) + 1253.687,
lorentzian_fwhm=np.array((.541, .541, 1.1056, .6264, .7349, 1.0007, 1.4311, .8656)),
reference_amplitude=np.array((0.5, 1, .02099, .07868, .04712, .09071, .01129, .00538)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=2.2,
is_default_material=False
)
addline(
element="Al",
material="metal_v1992",
linetype="KAlpha",
reference_short="Schweppe 1992 Al",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=1486.88931733,
energies=np.array((1486.706, 1486.293, 1492.3, 1496.4, 1498.4)),
lorentzian_fwhm=np.array((0.43, 0.43, 1.34, 0.96, 1.255)),
reference_amplitude=np.array((1, .5, .02, .12, .06)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=3.0,
position_uncertainty=0.010,
is_default_material=False
)
addline(
element="Al",
material="AlO",
linetype="KAlpha",
reference_short="Wollman 2000",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=1486.930456,
energies=np.array((1486.94, 1486.52, 1492.94, 1496.85, 1498.70, 1507.4, 1510.9)),
lorentzian_fwhm=np.array((0.43, 0.43, 1.34, 0.96, 1.25, 1.5, 0.9)),
reference_amplitude=np.array((1.0, 0.5, 0.033, 0.12, 0.11, 0.07, 0.05)),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
ka12_energy_diff=3.,
is_default_material=False
)
addline(
element="Si",
material="Si crystal",
linetype="KAlpha",
reference_short="Deslattes Notebook Si",
reference_plot_instrument_gaussian_fwhm=0.245,
nominal_peak_energy=1739.986,
energies=np.array((1739.39, 1739.986, 1752.0)),
lorentzian_fwhm=np.array((0.539, 0.524, 5)),
reference_amplitude=np.array((3.134e2, 6.121e3, 8e2)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=.6,
position_uncertainty=0.040,
is_default_material=False
)
addline(
element="S",
material="MoS2 spray",
linetype="KAlpha",
reference_short="Deslattes Notebook S, Cl, K",
reference_plot_instrument_gaussian_fwhm=0.2414,
nominal_peak_energy=2307.89,
energies=np.array((2307.89, 2306.70)),
lorentzian_fwhm=np.array((0.769, 0.722)),
reference_amplitude=np.array((0.11951e5, 0.61114e4)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=1.19,
position_uncertainty=0.040
)
addline(
element="Cl",
material="KCl crystal",
linetype="KAlpha",
reference_short="Deslattes Notebook S, Cl, K",
reference_plot_instrument_gaussian_fwhm=0.266,
nominal_peak_energy=2622.44,
energies=np.array((2622.44, 2620.85)),
lorentzian_fwhm=np.array((0.925, 0.945)),
reference_amplitude=np.array((0.15153e5, 0.82429e4)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=1.6,
position_uncertainty=0.040
)
addline(
element="K",
material="KCl crystal",
linetype="KAlpha",
reference_short="Deslattes Notebook S, Cl, K",
reference_plot_instrument_gaussian_fwhm=0.0896,
nominal_peak_energy=3313.93,
energies=np.array((3313.93, 3311.17)),
lorentzian_fwhm=np.array((0.948, 0.939)),
reference_amplitude=np.array((0.15153e5, 0.82429e4)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=2.75,
position_uncertainty=0.020
)
addline(
element="Sc",
material="metal",
linetype="KAlpha",
reference_short="Dean 2019",
reference_plot_instrument_gaussian_fwhm=1.9,
nominal_peak_energy=4090.699,
energies=np.array((4090.709, 4089.418, 4087.752, 4093.508, 4085.918, 4083.926)), # Table 4 C_i
lorentzian_fwhm=np.array((1.15, 2.89, 1.02, 2.01, 1.40, 3.86)), # Table 4 W_i
reference_amplitude=np.array((501, 107, 15, 43, 321, 14)), # Table 4 Fraction
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=4.773,
position_uncertainty=0.010
)
# Keep Chantler 2006 version of scandium in MASS just in case. At resolution 1.9 eV, it differs
# by up to ±10% on either wing of the doublet (around 4082 and 4094 eV).
addline(
element="Sc",
material="metal_2006",
linetype="KAlpha",
is_default_material=False,
reference_short="Chantler 2006",
reference_plot_instrument_gaussian_fwhm=0.52,
nominal_peak_energy=4090.735,
energies=np.array((4090.745, 4089.452, 4087.782, 4093.547, 4085.941, 4083.976)), # Table I C_i
lorentzian_fwhm=np.array((1.17, 2.65, 1.41, 2.09, 1.53, 3.49)), # Table I W_i
reference_amplitude=np.array((8175, 878, 232, 287, 4290, 119)), # Table I A_i
reference_amplitude_type=VOIGT_PEAK_HEIGHT,
ka12_energy_diff=5.1,
position_uncertainty=0.019 # table 3
)
addline(
element="Sc",
material="metal",
linetype="KBeta",
reference_short="Dean 2020",
reference_plot_instrument_gaussian_fwhm=1.97,
nominal_peak_energy=4460.845,
energies=np.array((4460.972, 4459.841, 4458.467, 4455.979, 4463.544)), # Table 3 C_i
lorentzian_fwhm=np.array((1.22, 1.58, 2.51, 4.64, 2.10)), # Table 3 W_i
reference_amplitude=np.array((530, 234, 149, 43, 42)), # Table 3 Fraction
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
position_uncertainty=0.0092
)
addline(
# The paper has two sets of TiKAlpha data, I used the set Refit of [21] Kawai et al 1994
element="Ti",
material="metal",
linetype="KAlpha",
reference_short="Chantler 2006",
reference_plot_instrument_gaussian_fwhm=0.11,
nominal_peak_energy=4510.903,
energies=np.array((4510.918, 4509.954, 4507.763, 4514.002, 4504.910, 4503.088)), # Table I C_i
lorentzian_fwhm=np.array((1.37, 2.22, 3.75, 1.70, 1.88, 4.49)), # Table I W_i
reference_amplitude=np.array((4549, 626, 236, 143, 2034, 54)), # Table I A_i
reference_amplitude_type=VOIGT_PEAK_HEIGHT,
ka12_energy_diff=6.0,
position_uncertainty=0.003 # table 3, based on difference between two entries
)
addline(
element="Ti",
material="metal",
linetype="KBeta",
reference_short="Chantler 2013",
reference_plot_instrument_gaussian_fwhm=1.244 * 2.3548,
nominal_peak_energy=4931.966,
energies=np.array((25.37, 30.096, 31.967, 35.59)) + 4900,
lorentzian_fwhm=np.array((16.3, 4.25, 0.42, 0.47)),
reference_amplitude=np.array((199, 455, 326, 19.2)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
position_uncertainty=0.022 # figure 6 and seciton 3.1 text
)
addline(
element="V",
material="metal",
linetype="KAlpha",
reference_short="Chantler 2006",
reference_plot_instrument_gaussian_fwhm=1.99, # Table I, other parameters
nominal_peak_energy=4952.216,
energies=np.array((4952.237, 4950.656, 4948.266, 4955.269, 4944.672, 4943.014)), # Table I C_i
lorentzian_fwhm=np.array((1.45, 2.00, 1.81, 1.76, 2.94, 3.09)), # Table I W_i
reference_amplitude=np.array((25832, 5410, 1536, 956, 12971, 603)), # Table I A_i
reference_amplitude_type=VOIGT_PEAK_HEIGHT,
ka12_energy_diff=7.5,
position_uncertainty=0.059 # table 3
)
addline(
element="V",
material="metal",
linetype="KBeta",
reference_short="Chantler 2013, Section 5",
reference_plot_instrument_gaussian_fwhm=0.805 * 2.3548,
nominal_peak_energy=5426.956,
energies=np.array((18.19, 24.50, 26.992)) + 5400,
lorentzian_fwhm=np.array((18.86, 5.48, 2.499)),
reference_amplitude=np.array((258, 236, 507)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
)
addline(
element="Cr",
material="metal",
linetype="KAlpha",
reference_short="Hoelzer 1997, NISTfits.ipf",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=5414.81,
energies=5400 + np.array((14.874, 14.099, 12.745, 10.583, 18.304, 5.551, 3.986)),
lorentzian_fwhm=np.array((1.457, 1.760, 3.138, 5.149, 1.988, 2.224, 4.740)),
reference_amplitude=np.array((822, 237, 85, 45, 15, 386, 36)),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
ka12_energy_diff=9.2,
position_uncertainty=0.010 # table 4
)
addline(
element="Cr",
material="metal",
linetype="KBeta",
reference_short="Hoelzer 1997",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=5946.82,
energies=5900 + np.array((47.00, 35.31, 46.24, 42.04, 44.93)), # Table III E_i
lorentzian_fwhm=np.array((1.70, 15.98, 1.90, 6.69, 3.37)), # Table III W_i
reference_amplitude=np.array((670, 55, 337, 82, 151)), # Table III I_I
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
position_uncertainty=0.010 # table 4
)
addline(
element="Mn",
material="metal",
linetype="KAlpha",
reference_short="Hoelzer 1997, NISTfits.ipf",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=5898.802,
energies=5800 + np.array((98.853, 97.867, 94.829, 96.532, 99.417, 102.712, 87.743, 86.495)),
lorentzian_fwhm=np.array((1.715, 2.043, 4.499, 2.663, 0.969, 1.553, 2.361, 4.216)),
reference_amplitude=np.array((790, 264, 68, 96, 71, 10, 372, 100)),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
ka12_energy_diff=11.1,
position_uncertainty=0.010 # table 4
)
addline(
element="Mn",
material="metal",
linetype="KBeta",
reference_short="Hoelzer 1997",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=6490.18,
energies=6400 + np.array((90.89, 86.31, 77.73, 90.06, 88.83)), # Table III E_i
lorentzian_fwhm=np.array((1.83, 9.40, 13.22, 1.81, 2.81)), # Table III W_i
reference_amplitude=np.array((608, 109, 77, 397, 176)), # Table III I_I
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
position_uncertainty=0.010 # table 4
)
addline(
element="Fe",
material="metal",
linetype="KAlpha",
reference_short="Hoelzer 1997, NISTfits.ipf",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=6404.01,
energies=np.array((6404.148, 6403.295, 6400.653, 6402.077, 6391.190, 6389.106, 6390.275)),
lorentzian_fwhm=np.array((1.613, 1.965, 4.833, 2.803, 2.487, 4.339, 2.57)),
reference_amplitude=np.array((697, 376, 88, 136, 339, 60, 102)),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
ka12_energy_diff=13.0,
position_uncertainty=0.010 # table 4
)
# ERROR IN HOLZER PAPER:
# The FWHM in the Table II of Holzer have the Kalpha_22 and _23 widths as 2.339 and 4.433, but
# these disagree with their Figure 1c. Swapping the widths (as you see above) makes the curve
# match the figure, though the exact I_int values still don't match those in Table II.
# To get the I_int values close, we choose width 4.339 and 2.57. These are still just a guess,
# but that's where the above values come from. See conversation with Richard Gnewkow of the
# Technische Universität Berlin on April 23-24, 2020.
addline(
element="Fe",
material="metal",
linetype="KBeta",
reference_short="Hoelzer 1997",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=7058.18,
energies=np.array((7046.90, 7057.21, 7058.36, 7054.75)), # Table III E_i
lorentzian_fwhm=np.array((14.17, 3.12, 1.97, 6.38)), # Table III W_i
reference_amplitude=np.array((107, 448, 615, 141)), # Table III I_I
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
position_uncertainty=0.030 # table 4
)
addline(
element="Co",
material="metal",
linetype="KAlpha",
reference_short="Hoelzer 1997, NISTfits.ipf",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=6930.38,
energies=np.array((6930.425, 6929.388, 6927.676, 6930.941, 6915.713, 6914.659, 6913.078)),
lorentzian_fwhm=np.array((1.795, 2.695, 4.555, 0.808, 2.406, 2.773, 4.463)),
reference_amplitude=np.array((809, 205, 107, 41, 314, 131, 43)),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
ka12_energy_diff=15.0,
position_uncertainty=0.010 # table 4
)
# Notice that Co KAlpha in Holzer shows the 4th line as having integrated intensity of 0.088, but
# this is probably a typo (should read 0.008). No effect on the data above, though, because it's a
# derived quantity.
addline(
element="Co",
material="metal",
linetype="KBeta",
reference_short="Hoelzer 1997",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=7649.45,
energies=np.array((7649.60, 7647.83, 7639.87, 7645.49, 7636.21, 7654.13)), # Table III E_i
lorentzian_fwhm=np.array((3.05, 3.58, 9.78, 4.89, 13.59, 3.79)), # Table III W_i
reference_amplitude=np.array((798, 286, 85, 114, 33, 35)), # Table III I_I
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
position_uncertainty=0.010 # table 4
)
addline(
element="Ni",
material="metal",
linetype="KAlpha",
reference_short="Hoelzer 1997, NISTfits.ipf",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=7478.26,
energies=np.array((7478.281, 7476.529, 7461.131, 7459.874, 7458.029)),
lorentzian_fwhm=np.array((2.013, 4.711, 2.674, 3.039, 4.476)),
reference_amplitude=np.array((909, 136, 351, 79, 24)),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
ka12_energy_diff=17.2,
position_uncertainty=0.010 # table 4
)
addline(
element="Ni",
material="metal",
linetype="KBeta",
reference_short="Hoelzer 1997",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=8264.78,
energies=np.array((8265.01, 8263.01, 8256.67, 8268.70)), # Table III E_i
lorentzian_fwhm=np.array((3.76, 4.34, 13.70, 5.18)), # Table III W_i
reference_amplitude=np.array((722, 358, 89, 104)), # Table III I_I
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
position_uncertainty=0.010 # table 4
)
addline(
element="Cu",
material="metal",
linetype="KAlpha",
reference_short="Hoelzer 1997",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=8047.83,
energies=np.array((8047.8372, 8045.3672, 8027.9935, 8026.5041)),
lorentzian_fwhm=np.array((2.285, 3.358, 2.667, 3.571)),
reference_amplitude=np.array((957, 90, 334, 111)),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
ka12_energy_diff=20.0,
position_uncertainty=0.010 # table 4
)
addline(
element="Cu",
material="metal",
linetype="KBeta",
reference_short="Hoelzer 1997",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=8905.42,
energies=np.array((8905.532, 8903.109, 8908.462, 8897.387, 8911.393)), # Table III E_i
lorentzian_fwhm=np.array((3.52, 3.52, 3.55, 8.08, 5.31)), # Table III W_i
reference_amplitude=np.array((757, 388, 171, 68, 55)), # Table III I_I
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
position_uncertainty=0.030 # table 4
)
addline(
element="Zn",
material="metal",
linetype="KAlpha",
reference_short="Zn Hack",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=8638.91,
energies=[8638.8872, 8636.4172, 8615.9835, 8614.4941],
lorentzian_fwhm=np.array((2.285, 3.358, 2.667, 3.571)) * 1.1,
reference_amplitude=np.array((957, 90, 334, 111)),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
ka12_energy_diff=23.0,
)
addline(
element="Zn",
material="metal",
linetype="KBeta",
reference_short="Zn Hack",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=9572.03,
energies=np.array((8905.532, 8903.109, 8908.462, 8897.387, 8911.393)) * 1.06 + 133.85,
lorentzian_fwhm=np.array((3.52, 3.52, 3.55, 8.08, 5.31)) * 1.06,
reference_amplitude=np.array((757, 388, 171, 68, 55)), # Table III I_I
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
)
addline(
element="Se",
material="metal",
linetype="KAlpha",
reference_short="Ito 2020", # Table III
reference_plot_instrument_gaussian_fwhm=0.17,
nominal_peak_energy=11222.383,
energies=np.array((11222.380, 11217.573, 11181.48, 11178.55)),
lorentzian_fwhm=np.array((3.633, 3.53, 3.579, 3.02)),
reference_amplitude=np.array((100, 1.68, 50.83, 1.80)),
ka12_energy_diff=40.944,
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
)
addline(
element="Se",
material="metal",
linetype="KBeta",
reference_short="Ito 2020", # Table IV
reference_plot_instrument_gaussian_fwhm=0.17,
nominal_peak_energy=12495.911,
energies=np.array((12495.911, 12490.094, 12503.11, 12652.840)),
lorentzian_fwhm=np.array((4.285, 5.70, 6.25, 4.81)),
reference_amplitude=np.array((100, 63.3, 8.1, 5.24)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
)
addline(
element="Br",
material="metal",
linetype="KAlpha",
reference_short="Steve Smith",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=11924.36,
energies=np.array((11924.2, 11877.6)),
lorentzian_fwhm=np.array((3.60, 3.73)),
reference_amplitude=np.array((2, 1)),
ka12_energy_diff=46.6,
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
)
addline(
element="Y",
material="metal",
linetype="KAlpha",
reference_short="Ito 2020", # Table III
reference_plot_instrument_gaussian_fwhm=0.21,
nominal_peak_energy=14958.389,
energies=np.array((14958.389, 14883.403)),
lorentzian_fwhm=np.array((5.464, 5.393)),
reference_amplitude=np.array((100, 52.23)),
ka12_energy_diff=74.986,
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
)
addline(
element="Y",
material="metal",
linetype="KBeta",
reference_short="Ito 2020", # Table IV
reference_plot_instrument_gaussian_fwhm=0.21,
nominal_peak_energy=16737.89,
energies=np.array((16737.88, 16726.02, 16746.2, 17010.57)),
lorentzian_fwhm=np.array((5.60, 5.53, 17.0, 5.80)),
reference_amplitude=np.array((100, 52.6, 1.80, 1.68)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
)
addline(
element="Zr",
material="metal",
linetype="KAlpha",
reference_short="Ito 2020", # Table III
reference_plot_instrument_gaussian_fwhm=0.22,
nominal_peak_energy=15774.87,
energies=np.array((15774.87, 15690.77)),
lorentzian_fwhm=np.array((5.865, 5.845)),
reference_amplitude=np.array((100, 52.53)),
ka12_energy_diff=84.10,
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
)
addline(
element="Zr",
material="metal",
linetype="KBeta",
reference_short="Ito 2020", # Table IV
reference_plot_instrument_gaussian_fwhm=0.22,
nominal_peak_energy=17666.578,
energies=np.array((17667.78, 17654.31, 17680)),
# The last (Kb'') energy is reported as 15774.87(31), which is clearly a typo.
# We estimate 17680 by reading Figure 2.
lorentzian_fwhm=np.array((6.171, 5.89, 10.8)),
reference_amplitude=np.array((100, 50.49, 5.2)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
)
addline(
element="W",
material="metal",
linetype="LAlpha",
reference_short="Joe Fowler",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=8398.24,
energies=np.array((8335.34, 8398.24)),
lorentzian_fwhm=np.array((6.97, 7.01)),
reference_amplitude=np.array((.1020, .8980)),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
)
addline(
element="W",
material="metal",
linetype="LBeta1",
reference_short="Joe Fowler",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=9672.58,
energies=np.array((9672.58,)),
lorentzian_fwhm=np.array((7.71,)),
reference_amplitude=np.array((1,)),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
)
addline(
element="W",
material="metal",
linetype="LBeta2",
reference_short="Joe Fowler",
reference_plot_instrument_gaussian_fwhm=None,
nominal_peak_energy=9964.13,
energies=np.array((9950.82, 9962.93, 9967.53)) + 1,
lorentzian_fwhm=np.array((9.16, 9.82, 9.90)),
reference_amplitude=np.array((.0847, .7726, .1426)),
reference_amplitude_type=LORENTZIAN_PEAK_HEIGHT,
)
addline(
element="Ir",
linetype="LAlpha",
material="metal",
reference_short='Zschornack',
nominal_peak_energy=9175.2,
energies=np.array([9099.6, 9175.2]),
lorentzian_fwhm=np.array([7.34, 8.10]),
reference_amplitude=np.array([.123, 1.079]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Ir",
linetype="LBeta1",
material="metal",
reference_short='Zschornack',
nominal_peak_energy=10708.35,
energies=np.array([10708.35]),
lorentzian_fwhm=np.array((6.80,)),
reference_amplitude=np.array((1,)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Pt",
linetype="LAlpha",
material="metal",
reference_short='Zschornack',
nominal_peak_energy=9442.39,
energies=np.array([9361.96, 9442.39]),
lorentzian_fwhm=np.array([7.3, 7.4]),
reference_amplitude=np.array([.130, 1.145]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Pt",
linetype="LBeta1",
material="metal",
reference_short='Zschornack',
nominal_peak_energy=11070.84,
energies=np.array([11070.84]),
lorentzian_fwhm=np.array((7.43,)),
reference_amplitude=np.array((1,)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Au",
linetype="LAlpha",
material="metal",
reference_short='Zschornack',
nominal_peak_energy=9713.44,
energies=np.array([9628.05, 9713.44]),
lorentzian_fwhm=np.array([7.61, 8.60]),
reference_amplitude=np.array([.1377, 1.214]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Au",
linetype="LBeta1",
material="metal",
reference_short='Zschornack',
nominal_peak_energy=11442.5,
energies=np.array([11442.5]),
lorentzian_fwhm=np.array((8.5,)),
reference_amplitude=np.array((1,)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Pb",
linetype="LAlpha",
material="metal",
reference_short='Zschornack',
nominal_peak_energy=10551.7,
energies=np.array([10449.6, 10551.6]),
lorentzian_fwhm=np.array([9.35, 9.50]),
reference_amplitude=np.array([.1633, 1.438]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Pb",
linetype="LBeta1",
material="metal",
reference_short='Zschornack',
nominal_peak_energy=12613.80,
energies=np.array([12613.80]),
lorentzian_fwhm=np.array((8.40,)),
reference_amplitude=np.array((1,)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Bi",
linetype="LAlpha",
material="metal",
reference_short='Zschornack',
nominal_peak_energy=10838.94,
energies=np.array([10731.06, 10838.94]),
lorentzian_fwhm=np.array([8.67, 9.80]),
reference_amplitude=np.array([.1726, 1.519]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Bi",
linetype="LBeta1",
material="metal",
reference_short='Zschornack',
nominal_peak_energy=13023.65,
energies=np.array([13023.65]),
lorentzian_fwhm=np.array((9.603,)),
reference_amplitude=np.array((1,)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Nb",
linetype="KBeta",
material="Nb2O5",
reference_short="Ravel 2018",
reference_plot_instrument_gaussian_fwhm=1.2,
nominal_peak_energy=18625.4,
energies=np.array((18625.4, 18609.9)),
lorentzian_fwhm=np.array((6.7, 6.7)),
reference_amplitude=np.array((1, 0.5)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
)
addline(
element="Nb",
linetype="KBeta24",
material="Nb2O5",
reference_short="Ravel 2018",
reference_plot_instrument_gaussian_fwhm=1.2,
nominal_peak_energy=18952.79,
energies=np.array((18952.79, 18968.0, 18982.7)),
lorentzian_fwhm=np.array((8.67, 1.9, 5.2)),
reference_amplitude=np.array((14.07, 0.066, 0.359)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
)
addline(
element="Mo",
material="metal",
linetype="KAlpha",
reference_short="Mendenhall 2019",
reference_plot_instrument_gaussian_fwhm=0.02,
nominal_peak_energy=17479.389,
energies=np.array((17479.389, 17374.577)),
lorentzian_fwhm=np.array((6.389, 6.3876)),
reference_amplitude=np.array((3331.119, 1684.988)),
ka12_energy_diff=104.812,
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
)
addline(
element="Mo",
material="metal",
linetype="KBeta",
reference_short="Mendenhall 2019",
reference_plot_instrument_gaussian_fwhm=0.02,
nominal_peak_energy=19606.734,
energies=np.array((19606.733, 19589.251, 19623.217)),
lorentzian_fwhm=np.array((6.88, 6.88, 6.88)),
reference_amplitude=np.array((958.08, 488.67, 29.14)),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
)
addline(
element="Pr",
material="metal",
linetype="KAlpha",
reference_short="Zschornack",
nominal_peak_energy=36026.71,
energies=np.array([35550.59, 36026.71]),
lorentzian_fwhm=np.array([19.08, 1887]),
reference_amplitude=np.array([4.15, 7.57]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=36026.71 - 35550.59,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Pr",
material="metal",
linetype="KBeta",
reference_short="Zschornack",
nominal_peak_energy=40748.67,
energies=np.array([40653.27, 40748.67]),
lorentzian_fwhm=np.array([21.79, 22.73]),
reference_amplitude=np.array([0.742, 1.436]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Nd",
material="metal",
linetype="KAlpha",
reference_short="Zschornack",
nominal_peak_energy=37360.74,
energies=np.array([36847.50, 37360.74]),
lorentzian_fwhm=np.array([20.25, 20.05]),
reference_amplitude=np.array([4.51, 8.21]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=37360.74 - 36847.50,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Nd",
material="metal",
linetype="KBeta",
reference_short="Zschornack",
nominal_peak_energy=42271.2,
energies=np.array([42166.24, 42271.17]),
lorentzian_fwhm=np.array([23.22, 24.16]),
reference_amplitude=np.array([0.845, 1.636]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Sm",
material="metal",
linetype="KAlpha",
reference_short="Zschornack",
nominal_peak_energy=40118.48,
energies=np.array([39523.39, 40118.48]),
lorentzian_fwhm=np.array([22.8, 22.6]),
reference_amplitude=np.array([5.12, 9.27]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=40118.48 - 39523.39,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Sm",
material="metal",
linetype="KBeta",
reference_short="Zschornack",
nominal_peak_energy=45413.0,
energies=np.array([45288.6, 45413.0]),
lorentzian_fwhm=np.array([26.2, 26.6]),
reference_amplitude=np.array([0.927, 1.797]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Eu",
material="metal",
linetype="KAlpha",
reference_short="Zschornack",
nominal_peak_energy=41542.63,
energies=np.array([40902.33, 41542.63]),
lorentzian_fwhm=np.array([24.1, 23.93]),
reference_amplitude=np.array([5.54, 10.00]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=41542.63 - 40902.33,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Eu",
material="metal",
linetype="KBeta",
reference_short="Zschornack",
nominal_peak_energy=47038.4,
energies=np.array([46904.0, 47038.4]),
lorentzian_fwhm=np.array([27.86, 28.25]),
reference_amplitude=np.array([1.050, 2.031]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Gd",
material="metal",
linetype="KAlpha",
reference_short="Zschornack",
nominal_peak_energy=42996.72,
energies=np.array([42309.30, 42996.72]),
lorentzian_fwhm=np.array([25.5, 25.4]),
reference_amplitude=np.array([5.9, 10.6]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=42996.72 - 42309.30,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Gd",
material="metal",
linetype="KBeta",
reference_short="Zschornack",
nominal_peak_energy=48696.9,
energies=np.array([48555.8, 49696.9]),
lorentzian_fwhm=np.array([29.5, 30.0]),
reference_amplitude=np.array([1.10, 2.13]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Tb",
material="metal",
linetype="KAlpha",
reference_short="Zschornack",
nominal_peak_energy=44482.7,
energies=np.array([43744.6, 44482.7]),
lorentzian_fwhm=np.array([27.0, 26.9]),
reference_amplitude=np.array([6.3, 11.3]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=44482.7 - 43744.6,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Tb",
material="metal",
linetype="KBeta",
reference_short="Zschornack",
nominal_peak_energy=50382.9,
energies=np.array([50229.8, 50382.9]),
lorentzian_fwhm=np.array([31.7, 31.8]),
reference_amplitude=np.array([1.15, 2.33]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Dy",
material="metal",
linetype="KAlpha",
reference_short="Zschornack",
nominal_peak_energy=45998.94,
energies=np.array([45208.27, 45998.94]),
lorentzian_fwhm=np.array([28.54, 28.41]),
reference_amplitude=np.array([6.68, 11.94]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=45998.94 - 45208.27,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Dy",
material="metal",
linetype="KBeta",
reference_short="Zschornack",
nominal_peak_energy=52119.7,
energies=np.array([51958.1, 52119.7]),
lorentzian_fwhm=np.array([33.5, 33.66]),
reference_amplitude=np.array([1.23, 2.376]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Ho",
material="metal",
linetype="KAlpha",
reference_short="Zschornack",
nominal_peak_energy=47546.70,
energies=np.array([46699.70, 47546.70]),
lorentzian_fwhm=np.array([30.16, 30.04]),
reference_amplitude=np.array([7.13, 12.69]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
ka12_energy_diff=47546.70 - 46699.70,
reference_plot_instrument_gaussian_fwhm=None
)
addline(
element="Ho",
material="metal",
linetype="KBeta",
reference_short="Zschornack",
nominal_peak_energy=53877.0,
energies=np.array([53711.0, 53877.0]),
lorentzian_fwhm=np.array([35.4, 35.6]),
reference_amplitude=np.array([1.31, 2.54]),
reference_amplitude_type=LORENTZIAN_INTEGRAL_INTENSITY,
reference_plot_instrument_gaussian_fwhm=None
)
[docs]
def plot_all_spectra(maxplots=10):
"""Makes plots showing the line shape and component parts for some lines.
Intended to replicate plots in the literature giving spectral lineshapes."""
keys = list(spectra.keys())[:maxplots]
for name in keys:
spectrum = spectra[name]()
spectrum.plot_like_reference()