def check_if_eline_is_activated(elemental_line, incident_energy):
"""
Checks if emission line is activated at given incident beam energy
Parameters
----------
elemental_line : str
emission line in the format K_K or Fe_K
incident_energy : float
incident energy in keV
Returns
-------
bool value, indicating if the emission line is activated
"""
# Check if the emission line has correct format
if not re.search(r"^[A-Z][a-z]?_[KLM]([ab]\d?)?$", elemental_line):
raise RuntimeError(f"Elemental line {elemental_line} is improperly formatted")
# The validation of 'elemental_line' is strict enough to do the rest of the processing
# without further checks.
[element, line] = elemental_line.split('_')
line = line.lower()
if len(line) == 1:
line += 'a1'
elif len(line) == 1:
line += "1"
e = Element(element)
if e.cs(incident_energy)[line] == 0:
return False
else:
return True
def get_line(ax, name, incident_energy):
"""
Plot emission lines for a given element.
Parameters
----------
name : str or int
element name, or atomic number
incident_energy : float
xray incident energy for fluorescence emission
"""
e = XrfElement(name)
lines = e.emission_line.all
ratio = [val for val in e.cs(incident_energy).all if val[1] > 0]
i_min = 1e-6
for item in ratio:
for data in lines:
if item[0] == data[0]:
ax.plot([data[1], data[1]],
[i_min, item[1]], 'g-', linewidth=2.0)
ax.set_title('Emission lines for %s at %s eV' % (name, incident_energy))
ax.set_xlabel('Energy [KeV]')
ax.set_ylabel('Intensity')
def get_line(ax, name, incident_energy):
"""
Plot emission lines for a given element.
Parameters
----------
name : str or int
element name, or atomic number
incident_energy : float
xray incident energy for fluorescence emission
"""
e = XrfElement(name)
lines = e.emission_line.all
ratio = [val for val in e.cs(incident_energy).all if val[1] > 0]
i_min = 1e-6
for item in ratio:
for data in lines:
if item[0] == data[0]:
ax.plot([data[1], data[1]], [i_min, item[1]],
'g-',
linewidth=2.0)
ax.set_title('Emission lines for %s at %s eV' % (name, incident_energy))
ax.set_xlabel('Energy [KeV]')
ax.set_ylabel('Intensity')
def run_demo():
import matplotlib.pyplot as plt
e = XrfElement('Cu')
print('Cu ka1 = %s' % e.emission_line['ka1'])
print('all Cu emission lines\n{}'.format(e.emission_line.all))
print('fluorescence cross section of Cu at 12 eV = %s' % e.cs(12).all)
print('showing spectrum for Cu at 12 eV')
fig, ax = plt.subplots(nrows=2, ncols=2, sharex=True, sharey=True)
ax = ax.ravel()
get_line(ax[0], 'Cu', 12)
get_spectrum(ax[1], 'Cu', 12)
get_line(ax[2], 'Gd', 12)
get_spectrum(ax[3], 'Gd', 12)
plt.show()
def run_demo():
import matplotlib.pyplot as plt
e = XrfElement('Cu')
print('Cu ka1 = %s' % e.emission_line['ka1'])
print('all Cu emission lines\n{}'.format(e.emission_line.all))
print('fluorescence cross section of Cu at 12 eV = %s' % e.cs(12).all)
print('showing spectrum for Cu at 12 eV')
fig, ax = plt.subplots(nrows=2, ncols=2, sharex=True, sharey=True)
ax = ax.ravel()
get_line(ax[0], 'Cu', 12)
get_spectrum(ax[1], 'Cu', 12)
get_line(ax[2], 'Gd', 12)
get_spectrum(ax[3], 'Gd', 12)
plt.show()
def get_eline_parameters(elemental_line, incident_energy):
"""
Returns emission line parameters
Parameters
----------
elemental_line : str
emission line in the format K_K, Fe_K, Ca_k, Ca_ka, Ca_kb2 etc.
incident_energy : float
incident energy in keV
Returns
-------
dict
Computed parameters of the emission line. Keys: "energy" (central energy of the peak),
"cs" (crossection), "ratio" (normalized crossection, e.g. cs(Ca_kb2)/ cs(Ca_ka1)
"""
# Check if the emission line has correct format
# TODO: verify the correnct range for lines (a-z covers all the cases, but may be too broad)
if not re.search(r"^[A-Z][a-z]?_[KLMklm]([a-z]\d?)?$", elemental_line):
raise RuntimeError(
f"Elemental line {elemental_line} is improperly formatted")
# The validation of 'elemental_line' is strict enough to do the rest of the processing
# without further checks.
[element, line] = elemental_line.split("_")
line = line.lower()
if len(line) == 1:
line += "a1"
elif len(line) == 2:
line += "1"
# This is the name of line #1 (ka1, la1 etc.)
line_1 = line[0] + "a1"
try:
e = Element(element)
energy = e.emission_line[line]
cs = e.cs(incident_energy)[line]
cs_1 = e.cs(incident_energy)[line_1]
ratio = cs / cs_1 if cs_1 else 0
except Exception:
energy, cs, ratio = 0, 0, 0
return {"energy": energy, "cs": cs, "ratio": ratio}
def get_spectrum(ax, name, incident_energy, emax=15):
"""
Plot fluorescence spectrum for a given element.
Parameters
----------
name : str or int
element name, or atomic number
incident_energy : float
xray incident energy for fluorescence emission
emax : float
max value on spectrum
"""
e = XrfElement(name)
lines = e.emission_line.all
ratio = [val for val in e.cs(incident_energy).all if val[1] > 0]
x = np.arange(0, emax, 0.01)
spec = np.zeros(len(x))
i_min = 1e-6
for item in ratio:
for data in lines:
if item[0] == data[0]:
ax.plot([data[1], data[1]], [i_min, item[1]],
'g-',
linewidth=2.0)
std = 0.1
area = std * np.sqrt(2 * np.pi)
for item in ratio:
for data in lines:
if item[0] == data[0]:
spec += gaussian(x, area, data[1], std) * item[1]
#plt.semilogy(x, spec)
ax.set_title('Simulated spectrum for %s at %s eV' %
(name, incident_energy))
ax.set_xlabel('Energy [KeV]')
ax.set_ylabel('Intensity')
ax.plot(x, spec)
def get_spectrum(ax, name, incident_energy, emax=15):
"""
Plot fluorescence spectrum for a given element.
Parameters
----------
name : str or int
element name, or atomic number
incident_energy : float
xray incident energy for fluorescence emission
emax : float
max value on spectrum
"""
e = XrfElement(name)
lines = e.emission_line.all
ratio = [val for val in e.cs(incident_energy).all if val[1] > 0]
x = np.arange(0, emax, 0.01)
spec = np.zeros(len(x))
i_min = 1e-6
for item in ratio:
for data in lines:
if item[0] == data[0]:
ax.plot([data[1], data[1]],
[i_min, item[1]], 'g-', linewidth=2.0)
std = 0.1
area = std * np.sqrt(2 * np.pi)
for item in ratio:
for data in lines:
if item[0] == data[0]:
spec += gaussian(x, area, data[1], std) * item[1]
#plt.semilogy(x, spec)
ax.set_title('Simulated spectrum for %s at %s eV' % (name, incident_energy))
ax.set_xlabel('Energy [KeV]')
ax.set_ylabel('Intensity')
ax.plot(x, spec)
