def rayleigh(energy, compound):
'''
Compton scaterring crossection for a given compound in cm2g. Energy is given in KeV
'''
# xraylib might complain about types:
energy = numpy.double(energy)
if numpy.size(energy) == 1:
return xraylib.CS_Rayl_CP(compound, energy)
else:
return numpy.array([xraylib.CS_Rayl_CP(compound, e) for e in energy])
def mu(material='H2C'):
energy_range = np.arange(5., 800., 0.1, dtype=np.double)
density = GetDensity(material)
#print(f'density {material} = {density}')
mu_rho = [xrl.CS_Total_CP(material, E) * density for E in energy_range]
mu_rho_Photo = [
xrl.CS_Photo_CP(material, E) * density for E in energy_range
]
mu_rho_Compt = [
xrl.CS_Compt_CP(material, E) * density for E in energy_range
]
mu_rho_Rayl = [xrl.CS_Rayl_CP(material, E) * density for E in energy_range]
plt.close(1)
fig = plt.figure(num=1, dpi=150, clear=True)
mpl.rcParams.update({'font.size': 6})
axMW = plt.subplot(111)
axMW.plot(energy_range,
mu_rho,
color="black",
linewidth=2.,
linestyle="-",
label='Total')
axMW.plot(energy_range,
mu_rho_Photo,
color="red",
linewidth=2.,
linestyle="-",
label='Photoelectric')
axMW.plot(energy_range,
mu_rho_Compt,
color="blue",
linewidth=2.,
linestyle="-",
label='Compton')
axMW.plot(energy_range,
mu_rho_Rayl,
color="green",
linewidth=2.,
linestyle="-",
label='Rayleigh')
axMW.set_xscale('log')
axMW.set_yscale('log')
axMW.set_xlim(np.min(energy_range), np.max(energy_range))
axMW.set_ylim(1e-2, 1e4)
plt.legend(loc='center right', frameon=True)
plt.xlabel('Énergie (keV)')
plt.ylabel("Coefficient d'atténuation linéique (cm$^{-1}$)")
axMW.grid(which='major',
axis='x',
linewidth=0.5,
linestyle='-',
color='0.75')
axMW.grid(which='minor',
axis='x',
linewidth=0.3,
linestyle='-',
color='0.75')
axMW.grid(which='major',
axis='y',
linewidth=0.5,
linestyle='-',
color='0.75')
axMW.grid(which='minor',
axis='y',
linewidth=0.3,
linestyle='-',
color='0.75')
axMW.xaxis.set_major_formatter(mpl.ticker.FormatStrFormatter("%d"))
#axMW.xaxis.set_minor_formatter(mpl.ticker.FormatStrFormatter("%d"))
axMW.grid(True)
#symbol=xrl.AtomicNumberToSymbol(material)
axMW.set_title("%s" % material, va='bottom')
#plt.savefig('mu_over_rho_W.pdf', format='PDF')
text = axMW.text(np.min(energy_range), 1e4, "", va="top", ha="left")
def onclick(event):
energy = np.round(event.xdata * 10) * 0.1
energyidx = int(
np.where(
np.min(np.abs(energy_range - energy)) == np.abs(energy_range -
energy))[0])
tx = 'Le coefficient d\'atténuation linéique de ' + material + ' à %.1f keV est %1.4e cm$^{-1}$\n(Rayleigh %1.4e cm$^{-1}$, Photoelectric %1.4e cm$^{-1}$, Compton %1.4e cm$^{-1}$)' % (
energy, mu_rho[energyidx], mu_rho_Rayl[energyidx],
mu_rho_Photo[energyidx], mu_rho_Compt[energyidx])
text.set_text(tx)
text.set_x(axMW.get_xlim()[0])
text.set_y(axMW.get_ylim()[1])
cid = fig.canvas.mpl_connect('button_press_event', onclick)
plt.show()
def get_xray_categories(self,
xray_beam,
measurement,
output,
return_aux=False):
energy = xray_beam.energy
# Abbe criterion applied
wavelen = xray_beam.wavelength
num_aperture = measurement.get_numerical_aperture(xray_beam)
(eta_el_f,
eta_inel_f) = scat_efficiencies(energy, self.sample.feature_mw,
self.sample.feature_elements,
self.sample.feature_stoic)
(eta_el_b, eta_inel_b) = scat_efficiencies(energy,
self.sample.matrix_mw,
self.sample.matrix_elements,
self.sample.matrix_stoic)
# frac1 is the fraction in forward scattered (detectable) photons that finally enter the aperture
frac1 = inna_frac(wavelen, num_aperture)
# frac2 is the fraction of forward scattered inelastic scattered or plural scattered photons that enter the
# aperture and contribute to PCI background
frac2 = num_aperture**2 / 2
cs_inel_b = xraylib.CS_Compt_CP(self.sample.matrix, energy)
cs_el_b = xraylib.CS_Rayl_CP(self.sample.matrix, energy)
cs_pi_b = xraylib.CS_Photo_CP(self.sample.matrix, energy)
cs_tot_b = xraylib.CS_Total_CP(self.sample.matrix, energy)
cs_inel_f = xraylib.CS_Compt_CP(self.sample.feature, energy)
cs_el_f = xraylib.CS_Rayl_CP(self.sample.feature, energy)
cs_pi_f = xraylib.CS_Photo_CP(self.sample.feature, energy)
cs_tot_f = xraylib.CS_Total_CP(self.sample.feature, energy)
# probability per length in um-1
k_el_b = cs_el_b * self.sample.matrix_den * 1e-4
k_inel_b = cs_inel_b * self.sample.matrix_den * 1e-4
k_elin_b = cs_el_b * (1 - eta_el_b) * self.sample.matrix_den * 1e-4
k_inelin_b = cs_inel_b * (1 -
eta_inel_b) * self.sample.matrix_den * 1e-4
k_out_b = (cs_el_b * eta_el_b * self.sample.matrix_den +
cs_inel_b * eta_inel_b * self.sample.matrix_den) * 1e-4
k_pi_b = cs_pi_b * self.sample.matrix_den * 1e-4
k_tot_b = k_inel_b + k_el_b + k_pi_b
# probability per length in um-1
k_el_f = cs_el_f * self.sample.feature_den * 1e-4
k_inel_f = cs_inel_f * self.sample.feature_den * 1e-4
k_elin_f = cs_el_f * (1 - eta_el_f) * self.sample.feature_den * 1e-4
k_inelin_f = cs_inel_f * (1 -
eta_inel_f) * self.sample.feature_den * 1e-4
k_out_f = (cs_el_f * eta_el_f * self.sample.feature_den +
cs_inel_f * eta_inel_f * self.sample.feature_den) * 1e-4
k_pi_f = cs_pi_f * self.sample.feature_den * 1e-4
k_tot_f = k_inel_f + k_el_f + k_pi_f
t_b = output.t_b
t_f = output.t_f
t = output.t
# intensity fractions for matrix relative to primary beam
i_noscat_b_func = lambda t: np.exp(-k_tot_b * t)
i_1el_b_func = lambda t: k_elin_b * t * i_noscat_b_func(t)
i_1elpc_b_func = lambda t: frac1 * i_1el_b_func(t)
i_pc_b_func = lambda t: i_noscat_b_func(t) + i_1elpc_b_func(t)
i_innoinel_b_func = lambda t: np.exp(-(k_inelin_b + k_out_b + k_pi_b) *
t)
i_elpl_b_func = lambda t: i_innoinel_b_func(t) - i_noscat_b_func(
t) - i_1el_b_func(t)
i_elplpc_b_func = lambda t: i_elpl_b_func(t) * frac2
i_out_b_func = lambda t: (k_out_b / (k_out_b + k_pi_b)) * (1 - np.exp(
-(k_out_b + k_pi_b) * t))
i_pi_b_func = lambda t: (k_pi_b / (k_out_b + k_pi_b)) * (1 - np.exp(-(
k_out_b + k_pi_b) * t))
i_inel_b_func = lambda t: np.exp(-(k_out_b + k_pi_b) * t_b
) - i_innoinel_b_func(t)
i_inelpc_b_func = lambda t: i_inel_b_func(t) * frac2
i_noscat_b = np.exp(-k_tot_b * t)
i_1el_b = k_elin_b * t * i_noscat_b
i_1elpc_b = frac1 * i_1el_b
i_pc_b = i_noscat_b + i_1elpc_b
i_innoinel_b = np.exp(-(k_inelin_b + k_out_b + k_pi_b) * t)
i_elpl_b = i_innoinel_b - i_noscat_b - i_1el_b
i_elplpc_b = i_elpl_b * frac2
i_out_b = (k_out_b /
(k_out_b + k_pi_b)) * (1 - np.exp(-(k_out_b + k_pi_b) * t))
i_pi_b = (k_pi_b /
(k_out_b + k_pi_b)) * (1 - np.exp(-(k_out_b + k_pi_b) * t))
i_inel_b = np.exp(-(k_out_b + k_pi_b) * t_b) - i_innoinel_b
i_inelpc_b = i_inel_b * frac2
i_noscat_ftf = np.exp(-k_tot_f * t_f)
i_1el_ftf = k_elin_f * t_f * i_noscat_ftf
i_1elpc_ftf = frac1 * i_1el_ftf
i_pc_ftf = i_noscat_ftf + i_1elpc_ftf
i_innoinel_ftf = np.exp(-(k_inelin_f + k_out_f + k_pi_f) * t_f)
i_elpl_ftf = i_innoinel_ftf - i_noscat_ftf - i_1el_ftf
i_elplpc_ftf = i_elpl_ftf * frac2
i_out_ftf = (k_out_f /
(k_out_f + k_pi_f)) * (1 -
np.exp(-(k_out_f + k_pi_f) * t_f))
i_pi_ftf = (k_pi_f /
(k_out_f + k_pi_f)) * (1 -
np.exp(-(k_out_f + k_pi_f) * t_f))
i_inel_ftf = np.exp(-(k_out_f + k_pi_f) * t_f) - i_innoinel_ftf
i_inelpc_ftf = i_inel_ftf * frac2
i_noscat_btf = np.exp(-k_tot_b * t_f)
i_1el_btf = k_elin_b * t_f * i_noscat_btf
i_innoinel_btf = np.exp(-(k_inelin_b + k_out_b + k_pi_b) * t_f)
i_elpl_btf = i_innoinel_btf - i_noscat_btf - i_1el_btf
i_out_btf = (k_out_b /
(k_out_b + k_pi_b)) * (1 -
np.exp(-(k_out_b + k_pi_b) * t_f))
i_pi_btf = (k_pi_b /
(k_out_b + k_pi_b)) * (1 -
np.exp(-(k_out_b + k_pi_b) * t_f))
i_inel_btf = np.exp(-(k_out_b + k_pi_b) * t_f) - i_innoinel_btf
i_noscat_btb = np.exp(-k_tot_b * t_b)
i_1el_btb = k_elin_b * t_b * i_noscat_btb
i_innoinel_btb = np.exp(-(k_inelin_b + k_out_b + k_pi_b) * t_b)
i_elpl_btb = i_innoinel_btb - i_noscat_btb - i_1el_btb
i_out_btb = (k_out_b /
(k_out_b + k_pi_b)) * (1 -
np.exp(-(k_out_b + k_pi_b) * t_b))
i_pi_btb = (k_pi_b /
(k_out_b + k_pi_b)) * (1 -
np.exp(-(k_out_b + k_pi_b) * t_b))
i_inel_btb = np.exp(-(k_out_b + k_pi_b) * t_b) - i_innoinel_btb
i_noscat_f = np.exp(-k_tot_b * t_b) * np.exp(-k_tot_f * t_f)
i_1el_f = (k_elin_b * t_b + k_elin_f * t_f) * i_noscat_f
i_innoinel_f = np.exp(-(k_out_b + k_inelin_b + k_pi_b) * t_b) * np.exp(
-(k_out_f + k_inelin_f + k_pi_f) * t_f)
i_elpl_f = i_innoinel_f - i_noscat_f - i_1el_f
i_out_ff = (1 - i_out_b_func(t_b / 2) - i_pi_b_func(t_b / 2)) * (
k_out_f /
(k_out_f + k_pi_f)) * (1 - np.exp(-(k_out_f + k_pi_f) * t_f))
i_pi_ff = (1 - i_out_b_func(t_b / 2) - i_pi_b_func(t_b / 2)) * (
k_pi_f /
(k_out_f + k_pi_f)) * (1 - np.exp(-(k_out_f + k_pi_f) * t_f))
i_out_f = i_out_b_func(
t_b / 2) + i_out_ff + (1 - i_out_b_func(t_b / 2) - i_pi_b_func(
t_b / 2) - i_out_ff - i_pi_ff) * i_out_b_func(t_b / 2)
# i_out_f = (1 - i_out_b_func(t_b / 2) - i_pi_b_func(t_b / 2)) * (k_out_f / (k_out_f + k_pi_f)) * (1 - np.exp(-(k_out_f + k_pi_f) * t_f)) + i_out_b_func(t_b)
i_pi_f = i_pi_b_func(
t_b / 2) + i_pi_ff + (1 - i_out_b_func(t_b / 2) - i_pi_b_func(
t_b / 2) - i_out_ff - i_pi_ff) * i_pi_b_func(t_b / 2)
# i_pi_f = (1 - i_out_b_func(t_b / 2) - i_pi_b_func(t_b / 2)) * (k_out_f / (k_out_f + k_pi_f)) * (1 - np.exp(-(k_out_f + k_pi_f) * t_f)) + i_pi_b_func(t_b)
# i_inel_f = np.exp(-(k_out_f + k_pi_f) * t_f) - i_innoinel_f
i_inel_f = 1 - i_out_f - i_pi_f - i_innoinel_f
# print('inside i_inel', i_inel_f[0], i_inel_b[0])
# print('inside i_innoinel', i_innoinel_f[0], i_innoinel_b[0])
# print('inside i_out', i_out_f[0], i_out_b[0])
# print('inside i_pi', i_pi_f[0], i_pi_b[0])
print('i_out_ff', i_out_ff)
print('i_pi_ff', i_pi_ff)
print('i_out_f', i_out_f)
print('i_pi_f', i_pi_f)
print('i_out_b', i_out_f)
print('i_pi_b', i_pi_b)
x_matrix = result_holder(xray_beam,
output,
measurement,
constants={
'k_tot_b': k_tot_b,
'k_pi_f': k_pi_f,
'k_pi_b': k_pi_b,
'k_el_b': k_el_b
},
i_noscat=i_noscat_b,
i_1el=i_1el_b,
i_innoinel=i_innoinel_b,
i_elpl=i_elpl_b,
i_out=i_out_b,
i_pi=i_pi_b,
i_inel=i_inel_b)
x_feature = result_holder(xray_beam,
output,
measurement,
constants={
'k_tot_f': k_tot_f,
'k_pi_f': k_pi_f,
'k_pi_b': k_pi_b,
'k_el_f': k_el_f
},
i_noscat=i_noscat_f,
i_1el=i_1el_f,
i_innoinel=i_innoinel_f,
i_elpl=i_elpl_f,
i_out=i_out_f,
i_pi=i_pi_f,
i_inel=i_inel_f)
x_ftf = result_holder(xray_beam,
output,
measurement,
constants={
'k_tot_b': k_tot_b,
'k_pi_f': k_pi_f,
'k_pi_b': k_pi_b,
'k_el_b': k_el_b
},
i_noscat=i_noscat_ftf,
i_1el=i_1el_ftf,
i_1elpc=i_1elpc_ftf,
i_pc=i_pc_ftf,
i_innoinel=i_innoinel_ftf,
i_elpl=i_elpl_ftf,
i_elplpc=i_elplpc_ftf,
i_out=i_out_ftf,
i_pi=i_pi_ftf,
i_inel=i_inel_ftf,
i_inelpc=i_inelpc_ftf,
i_pi_ff=i_pi_ff)
x_btf = result_holder(xray_beam,
output,
measurement,
constants={
'k_tot_b': k_tot_b,
'k_pi_f': k_pi_f,
'k_pi_b': k_pi_b,
'k_el_b': k_el_b
},
i_noscat=i_noscat_btf,
i_1el=i_1el_btf,
i_innoinel=i_innoinel_btf,
i_elpl=i_elpl_btf,
i_out=i_out_btf,
i_pi=i_pi_btf,
i_inel=i_inel_btf)
x_btb = result_holder(xray_beam,
output,
measurement,
constants={
'k_tot_b': k_tot_b,
'k_pi_f': k_pi_f,
'k_pi_b': k_pi_b,
'k_el_b': k_el_b
},
i_noscat=i_noscat_btb,
i_1el=i_1el_btb,
i_innoinel=i_innoinel_btb,
i_elpl=i_elpl_btb,
i_out=i_out_btb,
i_pi=i_pi_btb,
i_inel=i_inel_btb)
if return_aux:
return x_matrix, x_feature, x_ftf, x_btb, x_btf
else:
return x_matrix, x_feature
print("Density of pure Al : {} g/cm3".format(xraylib.ElementDensity(13)))
print("Ca K-alpha Fluorescence Line Energy: {}".format(
xraylib.LineEnergy(20, xraylib.KA_LINE)))
print("Fe partial photoionization cs of L3 at 6.0 keV: {}".format(
xraylib.CS_Photo_Partial(26, xraylib.L3_SHELL, 6.0)))
print("Zr L1 edge energy: {}".format(xraylib.EdgeEnergy(40, xraylib.L1_SHELL)))
print("Pb Lalpha XRF production cs at 20.0 keV (jump approx): {}".format(
xraylib.CS_FluorLine(82, xraylib.LA_LINE, 20.0)))
print("Pb Lalpha XRF production cs at 20.0 keV (Kissel): {}".format(
xraylib.CS_FluorLine_Kissel(82, xraylib.LA_LINE, 20.0)))
print("Bi M1N2 radiative rate: {}".format(
xraylib.RadRate(83, xraylib.M1N2_LINE)))
print("U M3O3 Fluorescence Line Energy: {}".format(
xraylib.LineEnergy(92, xraylib.M3O3_LINE)))
print("Ca(HCO3)2 Rayleigh cs at 10.0 keV: {}".format(
xraylib.CS_Rayl_CP("Ca(HCO3)2", 10.0)))
cdtest = xraylib.CompoundParser("Ca(HCO3)2")
print(
"Ca(HCO3)2 contains {} atoms, {} elements and has a molar mass of {} g/mol"
.format(cdtest['nAtomsAll'], cdtest['nElements'], cdtest['molarMass']))
for i in range(cdtest['nElements']):
print("Element {}: %lf %% and {} atoms".format(
cdtest['Elements'][i], cdtest['massFractions'][i] * 100.0,
cdtest['nAtoms'][i]))
cdtest = xraylib.CompoundParser("SiO2")
print("SiO2 contains {} atoms, {} elements and has a molar mass of {} g/mol".
format(cdtest['nAtomsAll'], cdtest['nElements'], cdtest['molarMass']))
for i in range(cdtest['nElements']):
print("Element {}: %lf %% and {} atoms".format(
import math
if __name__ == '__main__' :
xraylib.XRayInit()
xraylib.SetErrorMessages(0)
print ("Example of python program using xraylib")
print ("Density of pure Al : %f g/cm3" % xraylib.ElementDensity(13))
print ("Ca K-alpha Fluorescence Line Energy: %f" % xraylib.LineEnergy(20,xraylib.KA_LINE))
print ("Fe partial photoionization cs of L3 at 6.0 keV: %f" % xraylib.CS_Photo_Partial(26,xraylib.L3_SHELL,6.0))
print ("Zr L1 edge energy: %f" % xraylib.EdgeEnergy(40,xraylib.L1_SHELL))
print ("Pb Lalpha XRF production cs at 20.0 keV (jump approx): %f" % xraylib.CS_FluorLine(82,xraylib.LA_LINE,20.0))
print ("Pb Lalpha XRF production cs at 20.0 keV (Kissel): %f" % xraylib.CS_FluorLine_Kissel(82,xraylib.LA_LINE,20.0))
print ("Bi M1N2 radiative rate: %f" % xraylib.RadRate(83,xraylib.M1N2_LINE))
print ("U M3O3 Fluorescence Line Energy: %f" % xraylib.LineEnergy(92,xraylib.M3O3_LINE))
print ("Ca(HCO3)2 Rayleigh cs at 10.0 keV: %f" % xraylib.CS_Rayl_CP("Ca(HCO3)2",10.0))
cdtest = xraylib.CompoundParser("Ca(HCO3)2")
print ("Ca(HCO3)2 contains %g atoms and %i elements"% (cdtest['nAtomsAll'], cdtest['nElements']))
for i in range(cdtest['nElements']):
print ("Element %i: %lf %%" % (cdtest['Elements'][i],cdtest['massFractions'][i]*100.0))
cdtest = xraylib.CompoundParser("SiO2")
print ("SiO2 contains %g atoms and %i elements"% (cdtest['nAtomsAll'], cdtest['nElements']))
for i in range(cdtest['nElements']):
print ("Element %i: %lf %%" % (cdtest['Elements'][i],cdtest['massFractions'][i]*100.0))
print ("CS2 Refractive Index at 10.0 keV : %g - %g i" % (xraylib.Refractive_Index_Re("CS2",10.0,1.261),xraylib.Refractive_Index_Im("CS2",10.0,1.261)))
print ("C16H14O3 Refractive Index at 1 keV : %g - %g i" % (xraylib.Refractive_Index_Re("C16H14O3",1.0,1.2),xraylib.Refractive_Index_Im("C16H14O3",1.0,1.2)))
print ("SiO2 Refractive Index at 5 keV : %g - %g i" % (xraylib.Refractive_Index_Re("SiO2",5.0,2.65),xraylib.Refractive_Index_Im("SiO2",5.0,2.65)))
import numpy as np
xraylib.XRayInit()
print("Example of python program using xraylib")
print("xraylib version: {}".format(xraylib.__version__))
print("Density of pure Al : {} g/cm3".format(xraylib.ElementDensity(13)))
print("Ca K-alpha Fluorescence Line Energy: {}".format(xraylib.LineEnergy(20, xraylib.KA_LINE)))
print("Fe partial photoionization cs of L3 at 6.0 keV: {}".format(xraylib.CS_Photo_Partial(26, xraylib.L3_SHELL,6.0)))
print("Zr L1 edge energy: {}".format(xraylib.EdgeEnergy(40, xraylib.L1_SHELL)))
print("Pb Lalpha XRF production cs at 20.0 keV (jump approx): {}".format(xraylib.CS_FluorLine(82, xraylib.LA_LINE,20.0)))
print("Pb Lalpha XRF production cs at 20.0 keV (Kissel): {}".format(xraylib.CS_FluorLine_Kissel(82, xraylib.LA_LINE,20.0)))
print("Bi M1N2 radiative rate: {}".format(xraylib.RadRate(83, xraylib.M1N2_LINE)))
print("U M3O3 Fluorescence Line Energy: {}".format(xraylib.LineEnergy(92, xraylib.M3O3_LINE)))
print("Ca(HCO3)2 Rayleigh cs at 10.0 keV: {}".format(xraylib.CS_Rayl_CP("Ca(HCO3)2",10.0)))
cdtest = xraylib.CompoundParser("Ca(HCO3)2")
print("Ca(HCO3)2 contains {} atoms, {} elements and has a molar mass of {} g/mol".format(cdtest['nAtomsAll'], cdtest['nElements'], cdtest['molarMass']))
for i in range(cdtest['nElements']):
print("Element {}: {} % and {} atoms".format(cdtest['Elements'][i], cdtest['massFractions'][i]*100.0, cdtest['nAtoms'][i]))
cdtest = xraylib.CompoundParser("SiO2")
print("SiO2 contains {} atoms, {} elements and has a molar mass of {} g/mol".format(cdtest['nAtomsAll'], cdtest['nElements'], cdtest['molarMass']))
for i in range(cdtest['nElements']):
print("Element {}: {} % and {} atoms".format(cdtest['Elements'][i], cdtest['massFractions'][i]*100.0, cdtest['nAtoms'][i]))
print("CS2 Refractive Index at 10.0 keV : {} - {} i".format(xraylib.Refractive_Index_Re("CS2",10.0,1.261), xraylib.Refractive_Index_Im("CS2",10.0,1.261)))
print("C16H14O3 Refractive Index at 1 keV : {} - {} i".format(xraylib.Refractive_Index_Re("C16H14O3",1.0,1.2), xraylib.Refractive_Index_Im("C16H14O3",1.0,1.2)))
print("SiO2 Refractive Index at 5 keV : {} - {} i".format(xraylib.Refractive_Index_Re("SiO2",5.0,2.65), xraylib.Refractive_Index_Im("SiO2",5.0,2.65)))
print("Compton profile for Fe at pz = 1.1 : {}".format(xraylib.ComptonProfile(26,1.1)))
def xoppy_calc_xraylib_widget(FUNCTION=0,ELEMENT=26,ELEMENTORCOMPOUND="FeSO4",COMPOUND="Ca5(PO4)3",TRANSITION_IUPAC_OR_SIEGBAHN=1,\
TRANSITION_IUPAC_TO=0,TRANSITION_IUPAC_FROM=0,TRANSITION_SIEGBAHN=0,SHELL=0,ENERGY=10.0):
functions = [
'0 Fluorescence line energy', '1 Absorption edge energy',
'2 Atomic weight', '3 Elemental density',
'4 Total absorption cross section', '5 Photoionization cross section',
'6 Partial photoionization cross section',
'7 Rayleigh scattering cross section',
'8 Compton scattering cross section', '9 Klein-Nishina cross section',
'10 Mass energy-absorption cross section',
'11 Differential unpolarized Klein-Nishina cross section',
'12 Differential unpolarized Thomson cross section',
'13 Differential unpolarized Rayleigh cross section',
'14 Differential unpolarized Compton cross section',
'15 Differential polarized Klein-Nishina cross section',
'16 Differential polarized Thomson cross section',
'17 Differential polarized Rayleigh cross section',
'18 Differential polarized Compton cross section',
'19 Atomic form factor', '20 Incoherent scattering function',
'21 Momentum transfer function',
'22 Coster-Kronig transition probability', '23 Fluorescence yield',
'24 Jump factor', '25 Radiative transition probability',
'26 Energy after Compton scattering',
'27 Anomalous scattering factor φ′',
'28 Anomalous scattering factor φ″',
'29 Electronic configuration',
'30 X-ray fluorescence production cross section (with full cascade)',
'31 X-ray fluorescence production cross section (with radiative cascade)',
'32 X-ray fluorescence production cross section (with non-radiative cascade)',
'33 X-ray fluorescence production cross section (without cascade)',
'34 Atomic level width', '35 Auger yield', '36 Auger rate',
'37 Refractive index', '38 Compton broadening profile',
'39 Partial Compton broadening profile',
'40 List of NIST catalog compounds',
'41 Get composition of NIST catalog compound',
'42 List of X-ray emitting radionuclides',
'43 Get excitation profile of X-ray emitting radionuclide',
'44 Compoundparser'
]
print("\nInside xoppy_calc_xraylib with FUNCTION = %s. " %
(functions[FUNCTION]))
if FUNCTION == 0:
if TRANSITION_IUPAC_OR_SIEGBAHN == 0:
lines = [
'K', 'L1', 'L2', 'L3', 'M1', 'M2', 'M3', 'M4', 'M5', 'N1',
'N2', 'N3', 'N4', 'N5', 'N6', 'N7', 'O1', 'O2', 'O3', 'O4',
'O5', 'O6', 'O7', 'P1', 'P2', 'P3', 'P4', 'P5', 'Q1', 'Q2',
'Q3'
]
line = lines[TRANSITION_IUPAC_TO] + lines[
TRANSITION_IUPAC_FROM] + "_LINE"
command = "result = xraylib.LineEnergy(%d,xraylib.%s)" % (ELEMENT,
line)
print("executing command: ", command)
line = getattr(xraylib, line)
result = xraylib.LineEnergy(ELEMENT, line)
print("result: %f keV" % (result))
if TRANSITION_IUPAC_OR_SIEGBAHN == 1:
lines = [
'KA1_LINE', 'KA2_LINE', 'KB1_LINE', 'KB2_LINE', 'KB3_LINE',
'KB4_LINE', 'KB5_LINE', 'LA1_LINE', 'LA2_LINE', 'LB1_LINE',
'LB2_LINE', 'LB3_LINE', 'LB4_LINE', 'LB5_LINE', 'LB6_LINE',
'LB7_LINE', 'LB9_LINE', 'LB10_LINE', 'LB15_LINE', 'LB17_LINE',
'LG1_LINE', 'LG2_LINE', 'LG3_LINE', 'LG4_LINE', 'LG5_LINE',
'LG6_LINE', 'LG8_LINE', 'LE_LINE', 'LL_LINE', 'LS_LINE',
'LT_LINE', 'LU_LINE', 'LV_LINE'
]
line = lines[TRANSITION_SIEGBAHN]
command = "result = xraylib.LineEnergy(%d,xraylib.%s)" % (ELEMENT,
line)
print("executing command: ", command)
line = getattr(xraylib, line)
result = xraylib.LineEnergy(ELEMENT, line)
print("result: %f keV" % (result))
if TRANSITION_IUPAC_OR_SIEGBAHN == 2:
lines = [
'K', 'L1', 'L2', 'L3', 'M1', 'M2', 'M3', 'M4', 'M5', 'N1',
'N2', 'N3', 'N4', 'N5', 'N6', 'N7', 'O1', 'O2', 'O3', 'O4',
'O5', 'O6', 'O7', 'P1', 'P2', 'P3', 'P4', 'P5', 'Q1', 'Q2',
'Q3'
]
for i1, l1 in enumerate(lines):
for i2, l2 in enumerate(lines):
if i1 != i2:
line = l1 + l2 + "_LINE"
try:
line = getattr(xraylib, line)
result = xraylib.LineEnergy(ELEMENT, line)
except:
pass
else:
if result != 0.0:
print("%s%s %f keV" % (l1, l2, result))
elif FUNCTION == 1:
shells = [
'All shells', 'K_SHELL', 'L1_SHELL', 'L2_SHELL', 'L3_SHELL',
'M1_SHELL', 'M2_SHELL', 'M3_SHELL', 'M4_SHELL', 'M5_SHELL',
'N1_SHELL', 'N2_SHELL', 'N3_SHELL', 'N4_SHELL', 'N5_SHELL',
'N6_SHELL', 'N7_SHELL', 'O1_SHELL', 'O2_SHELL', 'O3_SHELL',
'O4_SHELL', 'O5_SHELL', 'O6_SHELL', 'O7_SHELL', 'P1_SHELL',
'P2_SHELL', 'P3_SHELL', 'P4_SHELL', 'P5_SHELL', 'Q1_SHELL',
'Q2_SHELL', 'Q3_SHELL'
]
if SHELL == 0: #"all"
for i, myshell in enumerate(shells):
if i >= 1:
# command = "result = xraylib.EdgeEnergy(%d,xraylib.%s)"%(ELEMENT,myshell)
# print("executing command: ",command)
shell_index = getattr(xraylib, myshell)
try:
result = xraylib.EdgeEnergy(ELEMENT, shell_index)
except:
pass
else:
if result != 0.0:
print("%s %f keV" % (myshell, result))
else:
print("No result")
else:
shell_index = getattr(xraylib, shells[SHELL])
try:
command = "result = xraylib.EdgeEnergy(%d,xraylib.%s)" % (
ELEMENT, shells[SHELL])
print("executing command: ", command)
result = xraylib.EdgeEnergy(ELEMENT, shell_index)
except:
pass
else:
if result != 0.0:
print("Z=%d %s : %f keV" %
(ELEMENT, shells[SHELL], result))
else:
print("No result")
elif FUNCTION == 2:
result = xraylib.AtomicWeight(ELEMENT)
if result != 0.0:
print("Atomic weight for Z=%d : %f g/mol" % (ELEMENT, result))
elif FUNCTION == 3:
result = xraylib.ElementDensity(ELEMENT)
if result != 0.0:
print("Element density for Z=%d : %f g/cm3" % (ELEMENT, result))
else:
print("No result")
elif FUNCTION == 4:
command = "result = xraylib.CS_Total_CP('%s',%f)" % (ELEMENTORCOMPOUND,
ENERGY)
print("executing command: ", command)
result = xraylib.CS_Total_CP(ELEMENTORCOMPOUND, ENERGY)
if result != 0.0:
print("Total absorption cross section: %f g/cm3" % (result))
else:
print("No result")
elif FUNCTION == 5:
command = "result = xraylib.CS_Photo_CP('%s',%f)" % (ELEMENTORCOMPOUND,
ENERGY)
print("executing command: ", command)
result = xraylib.CS_Photo_CP(ELEMENTORCOMPOUND, ENERGY)
if result != 0.0:
print("Photoionization cross section: %f g/cm3" % (result))
else:
print("No result")
elif FUNCTION == 6:
shells = [
'All shells', 'K_SHELL', 'L1_SHELL', 'L2_SHELL', 'L3_SHELL',
'M1_SHELL', 'M2_SHELL', 'M3_SHELL', 'M4_SHELL', 'M5_SHELL',
'N1_SHELL', 'N2_SHELL', 'N3_SHELL', 'N4_SHELL', 'N5_SHELL',
'N6_SHELL', 'N7_SHELL', 'O1_SHELL', 'O2_SHELL', 'O3_SHELL',
'O4_SHELL', 'O5_SHELL', 'O6_SHELL', 'O7_SHELL', 'P1_SHELL',
'P2_SHELL', 'P3_SHELL', 'P4_SHELL', 'P5_SHELL', 'Q1_SHELL',
'Q2_SHELL', 'Q3_SHELL'
]
if SHELL == 0: #"all"
for index in range(1, len(shells)):
shell_index = getattr(xraylib, shells[index])
try:
command = "result = xraylib.xraylib.CS_Photo_Partial('%d',xraylib.%s,%f)" % (
ELEMENT, shells[index], ENERGY)
print("executing command: ", command)
result = xraylib.CS_Photo_Partial(ELEMENT, shell_index,
ENERGY)
except:
pass
else:
if result != 0.0:
print("Z=%d, %s at E=%f keV: %f cm2/g" %
(ELEMENT, shells[index], ENERGY, result))
else:
print("No result")
else:
shell_index = getattr(xraylib, shells[SHELL])
try:
command = "result = xraylib.xraylib.CS_Photo_Partial('%d',xraylib.%s,%f)" % (
ELEMENT, shells[SHELL], ENERGY)
print("executing command: ", command)
result = xraylib.CS_Photo_Partial(ELEMENT, shell_index, ENERGY)
except:
pass
else:
if result != 0.0:
print("Z=%d, %s at E=%f keV: %f cm2/g" %
(ELEMENT, shells[SHELL], ENERGY, result))
else:
print("No result")
elif FUNCTION == 7:
command = "result = xraylib.CS_Rayl_CP('%s',%f)" % (ELEMENTORCOMPOUND,
ENERGY)
print("executing command: ", command)
result = xraylib.CS_Rayl_CP(ELEMENTORCOMPOUND, ENERGY)
if result != 0.0: print("Rayleigh cross section: %f cm2/g" % (result))
else: print("No result")
elif FUNCTION == 8:
command = "result = xraylib.CS_Compt_CP('%s',%f)" % (ELEMENTORCOMPOUND,
ENERGY)
print("executing command: ", command)
result = xraylib.CS_Compt_CP(ELEMENTORCOMPOUND, ENERGY)
if result != 0.0: print("Compton cross section: %f cm2/g" % (result))
else: print("No result")
elif FUNCTION == 9:
command = "result = xraylib.CS_KN(%f)" % (ENERGY)
print("executing command: ", command)
result = xraylib.CS_KN(ENERGY)
if result != 0.0:
print("Klein Nishina cross section: %f cm2/g" % (result))
else:
print("No result")
elif FUNCTION == 10:
command = "result = xraylib.CS_Energy_CP('%s',%f)" % (
ELEMENTORCOMPOUND, ENERGY)
print("executing command: ", command)
result = xraylib.CS_Energy_CP(ELEMENTORCOMPOUND, ENERGY)
if result != 0.0:
print("Mass-energy absorption cross section: %f cm2/g" % (result))
else:
print("No result")
else:
print("\n#### NOT YET IMPLEMENTED ####")
def rayleigh(energy, compound):
'''
Compton scaterring crossection for a given compound in cm2g. Energy is given in KeV
'''
return xraylib.CS_Rayl_CP(compound, energy)
def get_xray_categories(self, xray_beam, measurement, output, new_sample=None):
"""
:param energy: beam energy in keV
:param thickness: sample thickness in cm
:param step: step length in cm
:return:
"""
if new_sample is not None:
self.sample = sample
thickness = self.sample.thickness
step = output.step
energy = xray_beam.energy
print("-----------------------------------------------")
print("Energy: %.2f keV" % energy)
print("Thickness limit: %.2f um" % thickness)
print("Thickness resolution: %.2f um" % (step))
# Abbe criterion applied
wavelen = xray_beam.wavelength
num_aperture = measurement.get_numerical_aperture(xray_beam)
(eta_el, eta_inel) = scat_efficiencies(energy, self.sample.mw, self.sample.elements, self.sample.stoic)
# frac1 is the fraction in forward scattered (detectable) photons that finally enter the aperture
frac1 = inna_frac(wavelen, num_aperture)
# frac2 is the fraction of forward scattered inelastic scattered or plural scattered photons that enter the
# aperture and contribute to PCI background
frac2 = num_aperture ** 2 / 2
# retrieve cross sections in cm2/g
cs_inel = xraylib.CS_Compt_CP(self.sample.compound, energy)
cs_el = xraylib.CS_Rayl_CP(self.sample.compound, energy)
cs_pi = xraylib.CS_Photo_CP(self.sample.compound, energy)
cs_tot = xraylib.CS_Total_CP(self.sample.compound, energy)
# probability per thickness
k_el = cs_el * self.sample.density * 1e-4
k_inel = cs_inel * self.sample.density * 1e-4
k_elin = cs_el * (1 - eta_el) * self.sample.density * 1e-4
k_inelin = cs_inel * (1 - eta_inel) * self.sample.density * 1e-4
k_out = (cs_el * eta_el * self.sample.density + cs_inel * eta_inel * self.sample.density) * 1e-4
k_pi = cs_pi * self.sample.density * 1e-4
k_tot = k_inel + k_el + k_pi
# intensity fractions relative to primary beam
t = output.t
i_noscat = np.exp(-k_tot * t)
i_1el = k_elin * t * i_noscat
i_1elpc = frac1 * i_1el
i_pc = i_noscat + i_1elpc
i_elpl = np.exp(-(k_inelin + k_out + k_pi) * t) - i_noscat - i_1el
i_elplpc = i_elpl * frac2
i_out = (k_out / (k_out + k_pi)) * (1 - np.exp(-(k_out + k_pi) * t))
i_pi = (k_pi / (k_out + k_pi)) * (1 - np.exp(-(k_out + k_pi) * t))
i_inel = np.exp(-(k_out + k_pi) * t) - np.exp(-(k_inelin + k_out + k_pi) * t)
i_inelpc = i_inel * frac2
# res = result_holder(xray_beam, output, measurement, i_noscat=i_noscat, i_1el=i_1el, i_1elpc=None, i_pc=i_pc,
# i_elpl=i_elpl, i_elplpc=i_elplpc, i_out=i_out, i_pi=i_pi, i_inel=i_inel, i_inelpc=i_inelpc,
# i_df=i_1elpc)
res = result_holder(xray_beam, output, measurement, i_noscat=i_noscat, i_1el=i_1el,
i_elpl=i_elpl, i_out=i_out, i_pi=i_pi, i_inel=i_inel)
self.results.append(res)
return