def _xrf_intensity(self,z,line):
if "name" not in [*self.tgt.keys()]:
sys.stderr.write('Error: _xrf_intensity, tgt has no name\n')
return 0.
beamene=self.bem['beamene']
thickness=self.tgt['thickness']
density=self.tgt['density']
nel=self.tgt['nElements']
els=[*self.tgt['Elements']]# Z
massfr=[*self.tgt['massFractions']]
el_ind=np.where(np.array(els)==z)[0][0]
A_corr = self._selfabs_corr(z,int(line))
try:
Q = xrl.CS_FluorLine_Kissel(z,int(line),beamene)
except:
Q=0.
return Q * massfr[el_ind] * density * thickness * A_corr
def _calculate_fpm_intensity(input, theta):
alpha = math.radians(90.0 - theta)
beta = math.radians(theta)
discrete = input.excitation.get_energy_discrete(0)
I0 = discrete.horizontal_intensity + discrete.vertical_intensity
E0 = discrete.energy
layer = input.composition.get_layer(0)
_theta = math.atan(math.sqrt(input.geometry.area_detector / math.pi) / math.fabs(input.geometry.p_detector_window[1]))
Omega_DET = 2 * math.pi * (1.0 - math.cos(_theta))
G = Omega_DET / 4.0 / math.pi / math.sin(alpha)
rv = []
for i in zip(layer.Z, layer.weight):
(Z, weight) = i
chi = TestBatchSingle._chi(E0, xrl.LineEnergy(Z, xrl.KL3_LINE), layer, alpha, beta)
tmp = I0 * G * weight * xrl.CS_FluorLine_Kissel(Z, xrl.KL3_LINE, E0) * \
(1.0 - math.exp(-1.0 * chi * layer.density * layer.thickness)) / chi
rv.append(tmp)
return rv
def phantom_assign_concentration(ph_or, data_type=np.float32):
"""Builds the phantom used in:
- N. Viganò and V. A. Solé, “Physically corrected forward operators for
induced emission tomography: a simulation study,” Meas. Sci. Technol., no.
Advanced X-Ray Tomography, pp. 1–26, Nov. 2017.
:param ph_or: DESCRIPTION
:type ph_or: TYPE
:param data_type: DESCRIPTION, defaults to np.float32
:type data_type: TYPE, optional
:return: DESCRIPTION
:rtype: TYPE
"""
# ph_air = ph_or < 0.1
ph_FeO = 0.5 < ph_or
ph_CaO = np.logical_and(0.25 < ph_or, ph_or < 0.5)
ph_CaC = np.logical_and(0.1 < ph_or, ph_or < 0.25)
conv_mm_to_cm = 1e-1
conv_um_to_mm = 1e-3
voxel_size_um = 0.5
voxel_size_cm = voxel_size_um * conv_um_to_mm * conv_mm_to_cm # cm to micron
print("Sample size: [%g %g] um" %
(ph_or.shape[0] * voxel_size_um, ph_or.shape[1] * voxel_size_um))
import xraylib
xraylib.XRayInit()
cp_fo = xraylib.GetCompoundDataNISTByName("Ferric Oxide")
cp_co = xraylib.GetCompoundDataNISTByName("Calcium Oxide")
cp_cc = xraylib.GetCompoundDataNISTByName("Calcium Carbonate")
ca_an = xraylib.SymbolToAtomicNumber("Ca")
ca_kal = xraylib.LineEnergy(ca_an, xraylib.KA_LINE)
in_energy_keV = 20
out_energy_keV = ca_kal
ph_lin_att_in = (
ph_FeO * xraylib.CS_Total_CP("Ferric Oxide", in_energy_keV) *
cp_fo["density"] +
ph_CaC * xraylib.CS_Total_CP("Calcium Carbonate", in_energy_keV) *
cp_cc["density"] + ph_CaO *
xraylib.CS_Total_CP("Calcium Oxide", in_energy_keV) * cp_co["density"])
ph_lin_att_out = (
ph_FeO * xraylib.CS_Total_CP("Ferric Oxide", out_energy_keV) *
cp_fo["density"] +
ph_CaC * xraylib.CS_Total_CP("Calcium Carbonate", out_energy_keV) *
cp_cc["density"] +
ph_CaO * xraylib.CS_Total_CP("Calcium Oxide", out_energy_keV) *
cp_co["density"])
vol_att_in = ph_lin_att_in * voxel_size_cm
vol_att_out = ph_lin_att_out * voxel_size_cm
ca_cs = xraylib.CS_FluorLine_Kissel(
ca_an, xraylib.KA_LINE, in_energy_keV) # fluo production for cm2/g
ph_CaC_mass_fract = cp_cc["massFractions"][np.where(
np.array(cp_cc["Elements"]) == ca_an)[0][0]]
ph_CaO_mass_fract = cp_co["massFractions"][np.where(
np.array(cp_co["Elements"]) == ca_an)[0][0]]
ph = ph_CaC * ph_CaC_mass_fract * cp_cc[
"density"] + ph_CaO * ph_CaO_mass_fract * cp_co["density"]
ph = ph * ca_cs * voxel_size_cm
return (ph, vol_att_in, vol_att_out)
def get_element_xrf_lines(Z,
lines='all',
incident_energy=100.0,
lowE=0.0,
highE=100.0,
norm_to_one=False,
include_escape=True,
detector_element='Si'):
"""
Generate a list of lines that a given element will generate for energy range listed
"""
result = {}
xrf_list = []
escape_list = []
#
# This isn't very elegant...
#
if lines.upper() == 'K':
linelist = siegbahn_k_list
namelist = siegbahn_k_name_list
elif lines.upper() == 'KA':
linelist = siegbahn_ka_list
namelist = siegbahn_ka_name_list
if lines.upper() == 'KB':
linelist = siegbahn_kb_list
namelist = siegbahn_kb_name_list
elif lines.upper() == 'L':
linelist = siegbahn_l_list
namelist = siegbahn_l_name_list
elif lines.upper() == 'LA' or lines.upper() == 'L1':
linelist = siegbahn_l1_list
namelist = siegbahn_l1_name_list
elif lines.upper() == 'LB' or lines.upper() == 'L2':
linelist = siegbahn_l2_list
namelist = siegbahn_l2_name_list
elif lines.upper() == 'LG' or lines.upper() == 'L3':
linelist = siegbahn_l3_list
namelist = siegbahn_l3_name_list
elif lines.upper() == 'M':
linelist = siegbahn_m_list
namelist = siegbahn_m_name_list
elif lines.upper() == 'MA':
linelist = siegbahn_ma_list
namelist = siegbahn_ma_name_list
elif lines.upper() == 'MB':
linelist = siegbahn_mb_list
namelist = siegbahn_mb_name_list
elif lines.upper() == 'MG':
linelist = siegbahn_mg_list
namelist = siegbahn_mg_name_list
else:
linelist = siegbahn_all_list
namelist = siegbahn_all_name_list
for label, line in zip(namelist, linelist):
lineE = xraylib.LineEnergy(Z, line)
if lineE > 2.0 and lineE <= highE:
cs = xraylib.CS_FluorLine_Kissel(Z, line, incident_energy)
if cs > 0.0:
# xrf_list.append(XrayLine(label,lineE,cs))
xrf_list.append([label, lineE, cs])
if (include_escape):
ratio = calc_escape_peak_ratios(lineE)
escape_energy = calc_escape_peak_energy(
lineE, detector_element)
# escape_list.append(EscapeLine(label,lineE,escape_energy,cs*ratio))
escape_list.append(
[label, lineE, escape_energy, cs * ratio])
# if norm_to_one:
# for line in xrf_list:
# line1[2] = line[2]/nsum
# for line in escape_list:
# line1[3] = line[3]/nsum
result["lines"] = xrf_list
result["escape"] = escape_list
return result
import numpy as np
xraylib.XRayInit()
xraylib.SetErrorMessages(0)
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 {}: %lf %% and {} atoms".format(
cdtest['Elements'][i], cdtest['massFractions'][i] * 100.0,
cdtest['nAtoms'][i]))
#from xraylib import *
import sys, string
import xraylib
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))
def cs_fluorline_kissel(element, line,excitation_energy):
z = elementDB[element]["Z"]
if not isinstance(line,LinePair):
line = _lookupxlsubline(line)
return xraylib.CS_FluorLine_Kissel(z,line.subline,excitation_energy)
