def line_energy(element,line):
"""
Get the emission energy for a given element and line
using the xraylib backend
Parameters:
Element : Name, Symbol or Atomic Number (Z) as input
Line : Accepts Siegbahn and line notations
: line can be one of the following
For line averages:
'ka','lb','l1','l2','l3','la','lb','lg',
or for the exact lines
'ka1', 'ka2', 'ka3','kb1', 'kb2', 'kb3','kb4','kb5',
'la1', 'la2', 'lb1', 'lb2', 'lb3', 'lb4', 'lb5',
'lg1', 'lg2', 'lg3', 'lg4', 'll', 'ln',
'ma1','ma2','mb','mg'
Returns:
line energy: energy at which this fluorescence line appears
"""
z = elementDB[element]["Z"]
if not isinstance(line,LinePair):
line = _lookupxlsubline(line)
return xraylib.LineEnergy(z,line.subline)
def parse_raw_fluoro(fn, edge, trans, acqTime):
rv = []
with open(fn) as f:
total_count = 0
background_count = 0
for i, l in enumerate(f):
if i > 2:
e, cts = l.strip().split()
total_count += float(cts)
background_count += min(float(cts), 2)
# crude but works I guess...
if float(e) > (float(edge) - 1250.0):
break
if (total_count - background_count) > 100:
FilePrefix = os.path.splitext(os.path.basename(fn))[0]
pure_path = PurePath(fn).parts
VisitDir = pure_path[:6]
RestOfFilename = os.path.join(*pure_path[6:])
RestOfDirs = os.path.dirname(RestOfFilename)
OutputDir = os.path.join(*VisitDir, 'processed/pymca', RestOfDirs)
elf = os.path.join(OutputDir, FilePrefix) + '.results.dat'
els = []
# contains lines like
# Cu-K 7929.020000 90.714300
with open(elf) as f:
rv.append("Element\tCounts\t%age\tExpected Emission Energies")
for i, l in enumerate(f):
el, pk, conf = l.strip().split()
symbol, edge = el.split('-')
Z = xrl.SymbolToAtomicNumber(symbol)
edgesEnergies = "<b>{:g}</b>,{:g}".format(
xrl.LineEnergy(Z, LINE_MAPPER[edge]) * 1000.0,
xrl.EdgeEnergy(Z, EDGE_MAPPER[edge]) * 1000.0)
if float(pk) >= 100000:
counts = int(float(pk))
else:
counts = round(float(pk), 1)
rv.append("{}\t{:g}\t{:g}\t{}".format(
el, counts, round(100 * float(pk) / total_count, 1),
edgesEnergies))
if i == 5:
break
else:
rv.append("No fluorescence peaks detected, try a higher transmission")
rv.append("\nCounts (total): {:g} (background): {:g}".format(
total_count, background_count))
return rv
def eleXRF_energy(ele, energy):
Z = xl.SymbolToAtomicNumber(ele); F = xl.LineEnergy(Z, xl.KA1_LINE)
if xl.EdgeEnergy(Z, xl.K_SHELL) > energy: F = xl.LineEnergy(Z, xl.LA1_LINE)
elif xl.EdgeEnergy(Z, xl.L1_SHELL) > energy: F = xl.LineEnergy(Z, xl.LB1_LINE)
elif xl.EdgeEnergy(Z, xl.L2_SHELL) > energy: F = xl.LineEnergy(Z, xl.LB1_LINE)
elif xl.EdgeEnergy(Z, xl.L3_SHELL) > energy: F = xl.LineEnergy(Z, xl.LG1_LINE)
elif xl.EdgeEnergy(Z, xl.M1_SHELL) > energy: F = xl.LineEnergy(Z, xl.MA1_LINE)
return F
def fluoro_emission_map(p, n_map, angle, el):
"""Compute the maia-detector-shaped map of K-edge
fluorescence from the element map for an incident irradiance map n_map.
Parameters
----------
p : Phantom2d object
p.energy - incident beam photon energy (keV).
p.um_per_px - length of one pixel of the map (um).
n_map : 2d ndarray of float
Map of incident irradiance.
angle : float
Stage rotation angle (degrees).
el : string
Name of fluorescing element (e.g. 'Fe').
Returns
-------
2d ndarray of float
The fluorescence emission map for the requested edge.
"""
# edge_map = zero_outside_circle(p.el_maps[el])
edge_map = p.el_maps[el]
edge_map_r = rotate(edge_map, angle)
del edge_map
# Get Z for the fluorescing element
el_z = xrl.SymbolToAtomicNumber(el)
line = xrl.KA_LINE
# Sanity check that el K_alpha is below the incident energy.
k_alpha_energy = xrl.LineEnergy(el_z, line)
# assert k_alpha_energy < p.energy
if k_alpha_energy >= p.energy:
Q = 0.0
else:
# Simulate fluorescence event:
# CS_FluorLine_Kissel_Cascade is the XRF cross section Q_{i,YX} in Eq. (12)
# of Schoonjans et al.
Q = xrl.CS_FluorLine_Kissel_Cascade(el_z, line, p.energy)
# print(el, end=' ')
# 2d array for results
emission_map = n_map * Q * edge_map_r * p.um_per_px / UM_PER_CM
return emission_map
def get_roi_from_XRF_line(self, XRFline):
"""This function determines the region of interest that
should be used to represent an XRF line"""
# first thing to do is determine which element and line we are dealing with
# split the string along the dash
try:
(element, line) = XRFline.split('-')
#print('element: ' + element)
#print('line: ' + line)
atomic_number = xraylib.SymbolToAtomicNumber(element)
if (atomic_number == 0):
raise ValueError(
element +
' could not be parsed by xraylib.SymbolToAtomicNumber')
#print('atomic_number:' + str(atomic_number))
# I can probably also get the same result with 'vars'
line_macro = xraylib.__dict__[line.upper() + '_LINE']
#print('line_macro:' + str(line_macro))
line_energy = xraylib.LineEnergy(atomic_number, line_macro)
#print('line_energy: ' + str(line_energy))
if (line_energy == 0.0):
raise ValueError('XRF line ' + XRFline +
' does not exist in the xraylib database')
if (self.PixelType != 2):
raise ValueError(
'get_roi_from_XRF_line requires that the object has PixelType 2'
)
channel = int(self.NBins * (line_energy - self.Emin) /
(self.Emax - self.Emin))
#print('channel:' + str(channel))
if (channel < 0 or channel >= self.NBins):
raise ValueError('requested XRF line not covered by spectrum')
return slice(max(0, channel - 10), min(self.NBins - 1,
channel + 10))
except Exception as e:
raise Exception(str(e))
def XRF_line(Element, Beam_Energy):
Z = xl.SymbolToAtomicNumber(str(Element))
F = xl.LineEnergy(Z, xl.KA1_LINE)
if xl.EdgeEnergy(Z, xl.K_SHELL) > Beam_Energy:
F = xl.LineEnergy(Z, xl.LA1_LINE)
if xl.EdgeEnergy(Z, xl.L1_SHELL) > Beam_Energy:
F = xl.LineEnergy(Z, xl.LB1_LINE)
if xl.EdgeEnergy(Z, xl.L2_SHELL) > Beam_Energy:
F = xl.LineEnergy(Z, xl.LB1_LINE)
if xl.EdgeEnergy(Z, xl.L3_SHELL) > Beam_Energy:
F = xl.LineEnergy(Z, xl.LG1_LINE)
if xl.EdgeEnergy(Z, xl.M1_SHELL) > Beam_Energy:
F = xl.LineEnergy(Z, xl.MA1_LINE)
return F
def get_Ele_XRF_Energy(ele, energy):
Z = xl.SymbolToAtomicNumber(ele)
#will it abosrb? if so, it will fluoresce
F = xl.LineEnergy(Z, xl.KA1_LINE)
if xl.EdgeEnergy(Z, xl.K_SHELL) > energy:
F = xl.LineEnergy(Z, xl.LA1_LINE)
if xl.EdgeEnergy(Z, xl.L1_SHELL) > energy:
F = xl.LineEnergy(Z, xl.LB1_LINE)
if xl.EdgeEnergy(Z, xl.L2_SHELL) > energy:
F = xl.LineEnergy(Z, xl.LB1_LINE)
if xl.EdgeEnergy(Z, xl.L3_SHELL) > energy:
F = xl.LineEnergy(Z, xl.LG1_LINE)
if xl.EdgeEnergy(Z, xl.M1_SHELL) > energy:
F = xl.LineEnergy(Z, xl.MA1_LINE)
return F
def GetFluorescenceEnergy(Element,Beam): # send in the element and the beam energy to get the Excited Fluorescence Energy
#this will return the highest energy fluorescence photon capable of being excited by the beam
Z = xraylib.SymbolToAtomicNumber(Element)
F = xraylib.LineEnergy(Z,xraylib.KA1_LINE)
if xraylib.EdgeEnergy(Z,xraylib.K_SHELL) > Beam:
F = xraylib.LineEnergy(Z,xraylib.LA1_LINE)
if xraylib.EdgeEnergy(Z,xraylib.L1_SHELL) > Beam:
F = xraylib.LineEnergy(Z,xraylib.LB1_LINE)
if xraylib.EdgeEnergy(Z,xraylib.L2_SHELL) > Beam:
F = xraylib.LineEnergy(Z,xraylib.LB1_LINE)
if xraylib.EdgeEnergy(Z,xraylib.L3_SHELL) > Beam:
F = xraylib.LineEnergy(Z,xraylib.LG1_LINE)
if xraylib.EdgeEnergy(Z,xraylib.M1_SHELL) > Beam:
F = xraylib.LineEnergy(Z,xraylib.MA1_LINE)
return F
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 XRF_line(Element, Beam_Energy):
Z = xl.SymbolToAtomicNumber(
str(Element)) #converts element string to element atomic number
F = xl.LineEnergy(
Z, xl.KA1_LINE
) #initialize energy of fluorescence photon as highest energy K-line transition for the element
if xl.EdgeEnergy(
Z, xl.K_SHELL
) > Beam_Energy: #if beam energy is less than K ABSORPTION energy,
F = xl.LineEnergy(
Z, xl.LA1_LINE
) #energy of fluorescence photon equals highest energy L-line transition for the element
if xl.EdgeEnergy(
Z, xl.L1_SHELL
) > Beam_Energy: #if beam energy is less than L1 ABSORPTION energy, and so on...
F = xl.LineEnergy(Z, xl.LB1_LINE)
if xl.EdgeEnergy(Z, xl.L2_SHELL) > Beam_Energy:
F = xl.LineEnergy(Z, xl.LB1_LINE)
if xl.EdgeEnergy(Z, xl.L3_SHELL) > Beam_Energy:
F = xl.LineEnergy(Z, xl.LG1_LINE)
if xl.EdgeEnergy(Z, xl.M1_SHELL) > Beam_Energy:
F = xl.LineEnergy(Z, xl.MA1_LINE)
return F
#THIS SOFTWARE IS PROVIDED BY Tom Schoonjans ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL Tom Schoonjans BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#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']))
def get_lineenergy(z, line):
try:
ene = xrl.LineEnergy(z, int(line))
except:
ene = 0.
return ene
def findLines(self, paramdict=XRFDataset().paramdict):
"""
Calculates the line energies to fit
"""
# Incident Energy used in the experiment
# Energy range to use for fitting
pileup_cut_off = paramdict["FitParams"]["pileup_cutoff_keV"]
include_pileup = paramdict["FitParams"]["include_pileup"]
include_escape = paramdict["FitParams"]["include_escape"]
fitting_range = paramdict["FitParams"]["fitted_energy_range_keV"]
# x = paramdict["FitParams"]["mca_energies_used"]
energy = paramdict["Experiment"]["incident_energy_keV"]
detectortype = 'Vortex_SDD_Xspress'
fitelements = paramdict["Experiment"]["elements"]
peakpos = []
escape_peaks = []
for _j, el in enumerate(fitelements):
z = xl.SymbolToAtomicNumber(str(el))
for i, shell in enumerate(shells):
if (xl.EdgeEnergy(z, shell) < energy - 0.5):
linepos = 0.0
count = 0.0
for line in transitions[i]:
en = xl.LineEnergy(z, line)
if (en > 0.0):
linepos += en
count += 1.0
if (count == 0.0):
break
linepos = linepos / count
if (linepos > fitting_range[0]
and linepos < fitting_range[1]):
peakpos.append(linepos)
peakpos = np.array(peakpos)
too_low = set(list(peakpos[peakpos > fitting_range[0]]))
too_high = set(list(peakpos[peakpos < fitting_range[1]]))
bar = list(too_low and too_high)
bar = np.unique(bar)
peakpos = list(bar)
peaks = []
peaks.extend(peakpos)
if (include_escape):
for i in range(len(peakpos)):
escape_energy = calc_escape_energy(peakpos[i], detectortype)[0]
if (escape_energy > fitting_range[0]):
if (escape_energy < fitting_range[1]):
escape_peaks.extend([escape_energy])
# print escape_peaks
peaks.extend(escape_peaks)
if (include_pileup): # applies just to the fluorescence lines
pileup_peaks = []
peakpos1 = np.array(peakpos)
peakpos_high = peakpos1[peakpos1 > pileup_cut_off]
peakpos_high = list(peakpos_high)
for i in range(len(peakpos_high)):
foo = [peakpos_high[i] + x for x in peakpos_high[i:]]
foo = np.array(foo)
pileup_peaks.extend(foo)
pileup_peaks = np.unique(sorted(pileup_peaks))
peaks.extend(pileup_peaks)
peakpos = peaks
peakpos = np.array(peakpos)
too_low = set(list(peakpos[peakpos > fitting_range[0]]))
too_high = set(list(peakpos[peakpos < fitting_range[1] - 0.5]))
bar = list(too_low and too_high)
bar = np.unique(bar)
peakpos = list(bar)
peakpos = np.unique(peakpos)
# print peakpos
return peakpos
def index():
form = Xraylib_Request()
version = xraylib.__version__
# Populates select fields
form.function.choices = form.function.choices + cs_tup + dcs_tup
form.transition.siegbahn.choices = trans_S_tup
form.shell.choices = shell_tup
form.nistcomp.choices = nist_tup
form.rad_nuc.choices = rad_name_tup
if request.method == 'POST':
# Get user input
select_input = request.form.get('function')
examples = request.form.get('examples')
notation = request.form.get('transition-notation')
siegbahn = request.form.get('transition-siegbahn')
iupac1 = request.form.get('transition-iupac1')
iupac2 = request.form.get('transition-iupac2')
ex_shell = request.form.get('augtrans-ex_shell')
trans_shell = request.form.get('augtrans-trans_shell')
aug_shell = request.form.get('augtrans-aug_shell')
cktrans = request.form.get('cktrans')
nistcomp = request.form.get('nistcomp')
rad_nuc = request.form.get('rad_nuc')
shell = request.form.get('shell')
int_z = request.form['int_z']
float_q = request.form['float_q']
comp = request.form['comp']
int_z_or_comp = request.form['int_z_or_comp']
energy = request.form['energy']
theta = request.form['theta']
phi = request.form['phi']
density = request.form['density']
pz = request.form['pz']
# Turns user input => valid args for calc_output
trans = iupac1 + iupac2 + '_LINE'
augtrans = ex_shell + '_' + trans_shell + aug_shell + '_AUGER'
if select_input == 'AtomicWeight' or select_input == 'ElementDensity':
if validate_int(int_z) or validate_str(int_z):
examples = code_example(form.examples.choices, select_input,
int_z)
output = calc_output(select_input, int_z)
return render_template('index.html',
form=form,
version=version,
output=output,
units=getattr(Request_Units,
select_input + '_u'),
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'FF_Rayl' or select_input == 'SF_Compt':
if validate_int(
int_z) or validate_str(int_z) and validate_float(float_q):
examples = code_example(form.examples.choices, select_input,
int_z, float_q)
output = calc_output(select_input, int_z, float_q)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'AugerRate':
if validate_int(int_z) or validate_str(int_z):
examples = code_example(form.examples.choices, select_input,
int_z, augtrans)
output = calc_output(select_input, int_z, augtrans)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'LineEnergy' or select_input == 'RadRate':
if notation == 'IUPAC':
if validate_int(int_z) or validate_str(int_z):
examples = code_example(form.examples.choices,
select_input, int_z, trans)
output = calc_output(select_input, int_z, trans)
if select_input == 'LineEnergy':
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.Energy_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif notation == 'Siegbahn':
if validate_int(int_z) or validate_str(int_z):
examples = code_example(form.examples.choices,
select_input, int_z, siegbahn)
output = calc_output(select_input, int_z, siegbahn)
print(output)
if select_input == 'LineEnergy':
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.Energy_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif notation == 'All':
if validate_int(int_z) or validate_str(int_z):
output = all_trans(trans_I_tup, select_input, int_z)
if select_input == 'LineEnergy':
#needs units
#output = dict(out, Line = 'Energies')
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.Energy_u)
else:
return render_template('index.html',
form=form,
version=version,
output=output)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
else:
return render_template('index.html', error=Request_Error.error)
elif (select_input == 'EdgeEnergy' or select_input == 'JumpFactor'
or select_input == 'FluorYield' or select_input == 'AugerYield'
or select_input == 'AtomicLevelWidth'
or select_input == 'ElectronConfig'):
if validate_int(int_z) or validate_str(int_z):
examples = code_example(form.examples.choices, select_input,
int_z, shell)
output = calc_output(select_input, int_z, shell)
if select_input == 'EdgeEnergy' or select_input == 'AtomicLevelWidth':
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.Energy_u,
code_examples=examples)
elif select_input == 'ElectronConfig':
return render_template(
'index.html',
form=form,
version=version,
output=output,
units=Request_Units.ElectronConfig_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'CS_Photo_Partial':
if validate_int(
int_z) or validate_str(int_z) and validate_float(energy):
output = calc_output(select_input, int_z, shell, energy)
examples = code_example(form.examples.choices, select_input,
int_z, shell, energy)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.CS_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'CS_KN':
if validate_float(energy) and energy != '0':
output = calc_output(select_input, energy)
examples = code_example(form.examples.choices, select_input,
energy)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.CS_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input.startswith('CS_FluorLine'):
if validate_float(energy):
if notation == 'IUPAC':
if validate_int(int_z) or validate_str(int_z):
examples = code_example(form.examples.choices,
select_input, int_z, trans,
energy)
output = calc_output(select_input, int_z, trans,
energy)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.CS_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif notation == 'Siegbahn':
if validate_int(int_z) or validate_str(int_z):
examples = code_example(form.examples.choices,
select_input, int_z, siegbahn,
energy)
output = calc_output(select_input, int_z, siegbahn,
energy)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.CS_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif notation == 'All':
if validate_int(int_z) or validate_str(int_z):
output = all_trans_xrf(form.transition.iupac.choices,
select_input, int_z, energy)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.CS_u)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input.startswith('CS_'):
if validate_float(energy) and validate_int(
int_z_or_comp) or validate_str(int_z_or_comp):
examples = code_example(form.examples.choices, select_input,
int_z_or_comp, energy)
output = calc_output(select_input, int_z_or_comp, energy)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.CS_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'DCS_Thoms':
if validate_float(theta):
output = calc_output(select_input, theta)
examples = code_example(form.examples.choices, select_input,
theta)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.DCS_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'DCS_KN' or select_input == 'ComptonEnergy':
if validate_float(energy, theta):
output = calc_output(select_input, energy, theta)
examples = code_example(form.examples.choices, select_input,
energy, theta)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.DCS_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input.startswith('DCS_'):
if validate_float(energy, theta) and validate_int(
int_z_or_comp) or validate_str(int_z_or_comp):
output = calc_output(select_input, int_z_or_comp, energy,
theta)
examples = code_example(form.examples.choices, select_input,
int_z_or_comp, energy, theta)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.DCS_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'DCSP_KN':
if validate_float(energy, theta, phi):
output = calc_output(select_input, energy, theta, phi)
examples = code_example(form.examples.choices, select_input,
energy, theta, phi)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.DCS_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'DCSP_Thoms':
if validate_float(theta, phi):
output = calc_output(select_input, theta, phi)
examples = code_example(form.examples.choices, select_input,
theta, phi)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.DCS_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input.startswith('DCSP_'):
if validate_float(energy, theta, phi) and validate_int(
int_z_or_comp) or validate_str(int_z_or_comp):
output = calc_output(select_input, int_z_or_comp, energy,
theta, phi)
examples = code_example(form.examples.choices, select_input,
int_z_or_comp, energy, theta, phi)
return render_template('index.html',
form=form,
version=version,
output=output,
units=Request_Units.DCS_u,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input.startswith('Fi'):
if validate_int(
int_z) or validate_str(int_z) and validate_float(energy):
output = calc_output(select_input, int_z, energy)
examples = code_example(form.examples.choices, select_input,
int_z, energy)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'CosKronTransProb':
if validate_int(int_z) or validate_str(int_z):
output = calc_output(select_input, int_z, cktrans)
examples = code_example(form.examples.choices, select_input,
int_z, cktrans)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'ComptonProfile':
if validate_float(pz) and validate_int(int_z) or validate_str(
int_z):
output = calc_output(select_input, int_z, pz)
examples = code_example(form.examples.choices, select_input,
int_z, pz)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'ComptonProfile_Partial':
if validate_float(pz) and validate_int(int_z) or validate_str(
int_z):
output = calc_output(select_input, int_z, shell, pz)
examples = code_example(form.examples.choices, select_input,
int_z, shell, pz)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'MomentTransf':
if validate_float(energy, theta) == True:
output = calc_output(select_input, energy, theta)
examples = code_example(form.examples.choices, select_input,
energy, theta)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'Refractive_Index':
# Special Case: Refractive_Index input needs to be const char compound
if validate_float(energy, density) and validate_int(
int_z_or_comp) or validate_str(int_z_or_comp):
try:
output = xraylib.Refractive_Index(
xraylib.AtomicNumberToSymbol(int(int_z_or_comp),
float(energy),
float(density)))
examples = code_example(form.examples.choices,
select_input, int_z_or_comp,
energy, density)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
except:
output = xraylib.Refractive_Index(int_z_or_comp,
float(energy),
float(density))
examples = code_example(form.examples.choices,
select_input, int_z_or_comp,
energy, density)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'CompoundParser':
# Special Case: CompoundParser input needs to be const char compound
if validate_str(comp):
try:
out = xraylib.CompoundParser(str(comp))
# Format output
w_fracts = out['massFractions']
w_pers = [str(round(i * 100, 2)) + ' %' for i in w_fracts]
z = out['Elements']
sym = [
'<sub>' + str(i) + '</sub>' +
str(xraylib.AtomicNumberToSymbol(i)) for i in z
]
mmass = str(out['molarMass']) + ' g mol<sup>-1</sup>'
output = {
'Elements': sym,
'Weight Fraction': w_pers,
'Number of Atoms': out['nAtoms'],
' Molar Mass': mmass
}
examples = code_example(form.examples.choices,
select_input, comp)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples,
units=Request_Units.per_u)
except:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
else:
return render_template('index.html',
form=form,
version=version,
error=Request_Error.error)
elif select_input == 'GetRadioNuclideDataList':
output = xraylib.GetRadioNuclideDataList()
output.insert(0, '<b> Radionuclides: </b>')
output = '<br/>'.join(output)
examples = code_example(form.examples.choices, select_input)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
elif select_input == 'GetRadioNuclideDataByIndex':
out = calc_output(select_input, rad_nuc)
print(out)
# Format output
line_nos = out['XrayLines']
x_energy = [xraylib.LineEnergy(out['Z_xray'], i) for i in line_nos]
output = {
'X-ray Energies': x_energy,
'Disintegrations s<sup>-1</sup>': out['XrayIntensities'],
'Gamma-ray Energy': out['GammaEnergies'],
'Disintegrations s<sup>-1</sup> ': out['GammaIntensities']
}
examples = code_example(form.examples.choices,
'GetRadioNuclideDataByName', rad_nuc)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
elif select_input == 'GetCompoundDataNISTList':
output = xraylib.GetCompoundDataNISTList()
output.insert(0, '<b> NIST Compounds: </b>')
output = '<br/>'.join(output)
examples = code_example(form.examples.choices, select_input)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
elif select_input == 'GetCompoundDataNISTByIndex':
out = calc_output(select_input, nistcomp)
# Format output
w_fracts = out['massFractions']
w_pers = [str(round(i * 100, 2)) + ' %' for i in w_fracts]
z = out['Elements']
sym = [
'<sub>' + str(i) + '</sub>' +
str(xraylib.AtomicNumberToSymbol(i)) for i in z
]
density = str(out['density']) + ' g cm<sup>-3</sup>'
output = {
'Elements': sym,
'Weight Fraction': w_pers,
' Density': density
}
examples = code_example(form.examples.choices,
'GetCompoundDataNISTByName', nistcomp)
return render_template('index.html',
form=form,
version=version,
output=output,
code_examples=examples)
return render_template('index.html', form=form, version=version)
def channel_rayleigh_map(p, q, maia_d, n_map, angle):
"""Compute the maia-detector-shaped map of Rayleigh scattering
from the element map for an incident irradiance map n_map.
Parameters
----------
p : Phantom2d object
p.energy - incident beam photon energy (keV).
p.um_per_px - length of one pixel of the map (um).
q : int
Maia detector channel id
maia_d : Maia() instance
n_map : 2d ndarray of float
Map of incident irradiance.
angle : float
Stage rotation angle (degrees).
Returns
-------
2d ndarray of float
The fluorescence emission map for the requested edge.
"""
solid_angle = maia_d.pads[q].omega
# Get spherical angles (polar theta & azimuthal phi) to detector element
theta = maia_d.pads[q].theta
phi = maia_d.pads[q].phi
energy = outgoing_photon_energy('rayleigh', p)
# get a list of all elements el and their weights w_el
# The absorption map mu = ma_M * mu_M + sum_k ( ma_k * mu_k )
mu = p.matrix.ma(energy) * p.el_maps['matrix']
for el in p.el_maps:
if el == 'matrix':
continue
Z = xrl.SymbolToAtomicNumber(el)
mu += p.matrix.cp[el] * xrl.DCSP_Rayl(Z, energy, theta, phi) * \
p.el_maps[el]
ma += xrl.DCSP_Rayl(Z, energy, theta, phi)
# edge_map = zero_outside_circle(p.el_maps[el])
edge_map_r = rotate(edge_map, angle)
del edge_map
# Get Z for the fluorescing element
el_z = xrl.SymbolToAtomicNumber(el)
line = xrl.KA_LINE
# Sanity check that el K_alpha is below the incident energy.
k_alpha_energy = xrl.LineEnergy(el_z, line)
assert k_alpha_energy < p.energy
# Simulate fluorescence event:
# CS_FluorLine_Kissel_Cascade is the XRF cross section Q_{i,YX} in Eq. (12)
# of Schoonjans et al.
Q = xrl.CS_FluorLine_Kissel_Cascade(el_z, line, p.energy)
# 2d array for results
emission_map = n_map * Q * edge_map_r * p.um_per_px / UM_PER_CM
return emission_map
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 k_alpha_energy(el):
el_z = xrl.SymbolToAtomicNumber(el)
line = xrl.KA_LINE
energy = xrl.LineEnergy(el_z, line)
# assert energy < p.energy
return energy
def GenerateSpectrum(i, u, z, num_points=100, spec_type='XRAYTUBE'):
"""
Intensity of Characteristic Lines by formula R=BIA(UA-UK)1,5
:param i: (float): Current in [a]
:param u: (float): Voltage [keV]
:param z: (int): The sequence number of the item
:param num_points: number of points
:param spec_type: type of XRay spevtrum can be one of 'XRAYTUBE', 'BRELUNG' or 'CHARLINES'
Returns:
objec Spectrum
"""
widht = {
24: (1.97, 2.39, 70, 30), #Cr
29: (2.4, 2.98, 100, 50), # Cu
42: (6.42, 6.66, 500, 150), # Mo
47: (8.6, 8.9, 150, 50), # Ag
74: (8.6, 8.9, 500, 200)
} # W
energies = np.linspace(u * 1e-3, u, num_points)
spectrum = np.zeros_like(energies)
if spec_type == 'BRELUNG' or spec_type == 'XRAYTUBE':
c = 3.0
lambda_0 = 12.398 / u # Critical wavelength [A]
lambdas = 12.398 / energies
spectrum += c * c / lambda_0 * i * 0.001 * z * (lambdas -
lambda_0) / lambdas**3
if spec_type == 'CHARLINES' or spec_type == 'XRAYTUBE':
w1, w2, k1, k2 = widht[z]
w1 *= 2e-1
w2 *= 2e-1
spec = np.zeros_like(energies)
energy = xraylib.LineEnergy(z, xraylib.KA1_LINE)
intensity = k1 * i * 0.001 * np.power(u - energy, 1.5)
indexes = np.where((energies < energy + w1) & (energies > energy - w1))
int1 = np.linspace(0.0, intensity, len(indexes[0]) / 2)
int2 = np.linspace(intensity, 0.0,
len(indexes[0]) - len(indexes[0]) / 2)
spec[indexes] = np.concatenate((int1, int2), axis=0)
energy = xraylib.LineEnergy(z, xraylib.KA2_LINE)
intensity = k1 * i * 0.001 * np.power(u - energy, 1.5)
indexes = np.where((energies < energy + w2) & (energies > energy - w2))
int1 = np.linspace(0.0, intensity, len(indexes[0]) / 2)
int2 = np.linspace(intensity, 0.0,
len(indexes[0]) - len(indexes[0]) / 2)
spec[indexes] = np.concatenate((int1, int2), axis=0)
energy = xraylib.LineEnergy(z, xraylib.KB1_LINE)
intensity = k2 * i * 0.001 * np.power(u - energy, 1.5)
indexes = np.where((energies < energy + w1) & (energies > energy - w1))
int1 = np.linspace(0.0, intensity, len(indexes[0]) / 2)
int2 = np.linspace(intensity, 0.0,
len(indexes[0]) - len(indexes[0]) / 2)
spec[indexes] = np.concatenate((int1, int2), axis=0)
#energy = xraylib.LineEnergy(z, xraylib.KB2_LINE)
#intensity = k2 * i * 0.001 * np.power(u - energy, 1.5)
#indexes = np.where((energies < energy + w2) & (energies > energy - w2))
#int1 = np.linspace(0.0, intensity, len(indexes[0]) / 2)
#int2 = np.linspace(intensity, 0.0, len(indexes[0]) - len(indexes[0]) / 2)
#spec[indexes] = np.concatenate((int1, int2), axis=0)
spectrum += spec
return Spectrum(energy=energies,
intensity=spectrum,
label='I={} mA, U={} kV, Z={}'.format(i, u, z))
def calc_escape_peak_ratios(lineE, detectorelement='Si'):
"""
Calculate ratio of escape peak to main peak based on emperical calculation
from Alves et. al.
Parameters
----------
detectorelement : string
"Si" or "Ge"
Returns
-------
ratio of a single Si K escape peak to a single input peak
or
ratio of Ge Ka, Kb escape peaks to a single input peak
References
----------
[1]
"Experimental X-Ray peak-shape determination for a Si(Li) detector",
L.C. Alves et al., Nucl. Instr. and Meth. in Phys. Res. B 109|110
(1996) 129-133.
"""
if (detectorelement == 'Si'):
#
# For Si the K peak is 95% of the transition
# and the photoionization to total cross section is ~ 95%
# Si escape peak is typically only 0.2-1% (bigger at lower energies)
#
jump = xl.JumpFactor(14, xl.K_SHELL)
fluy = xl.FluorYield(14, xl.K_SHELL)
corr = fluy * (jump - 1.0) / jump
corr_photo = xl.CS_Photo(14, lineE) / xl.CS_Total(14, lineE)
corr_trans = xl.RadRate(14, xl.KA_LINE) + xl.RadRate(14, xl.KB_LINE)
mu_si = xl.CS_Total(14, lineE)
mu_internal = xl.CS_Total(14, 1.73998)
r = mu_internal / mu_si
eta = corr_trans * corr_photo * corr * 0.5 * (1.0 -
r * log(1.0 + 1.0 / r))
ratio = eta / (1.0 - eta)
#
# escape peak sigma should be narrower than the main peak.
#
return ratio
else:
#
# Ge detector...
# Ge has a large escape peak ratio ~ 5-15% and a Ka and kb component
#
if (lineE < 11.5):
return 0.0, 0.0
jump = xl.JumpFactor(32, xl.K_SHELL)
fluy = xl.FluorYield(32, xl.K_SHELL)
corr = fluy * (jump - 1.0) / jump
corr_photo = xl.CS_Photo(32, lineE) / xl.CS_Total(32, lineE)
corr_trans_ka = xl.RadRate(32, xl.KA_LINE)
corr_trans_kb = xl.RadRate(32, xl.KB_LINE)
mu_ge = xl.CS_Total(32, lineE) #
# one for the Ka and one for the Kb peak...
mu_internal_ka = xl.CS_Total(32, xl.LineEnergy(32, xl.KA_LINE))
r_ka = mu_internal_ka / mu_ge
eta_ka = corr_trans_ka * corr_photo * corr * 0.5 * (
1.0 - r_ka * log(1.0 + 1.0 / r_ka))
ratio_ka = eta_ka / (1.0 - eta_ka)
mu_internal_kb = xl.CS_Total(32, xl.LineEnergy(32, xl.KB_LINE))
r_kb = mu_internal_kb / mu_ge
eta_kb = corr_trans_kb * corr_photo * corr * 0.5 * (
1.0 - r_kb * log(1.0 + 1.0 / r_kb))
ratio_kb = eta_kb / (1.0 - eta_kb)
return ratio_ka, ratio_kb
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
# * The names of the contributors may not be used to endorse or promote products derived from this software without specific prior written permission.
#THIS SOFTWARE IS PROVIDED BY Tom Schoonjans ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL Tom Schoonjans BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""Example of using various xraylib functionality in python."""
import xraylib
import math
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")
def setroi(element=None, line='Ka', roisize=200, roi=1):
'''
setting rois for Xspress3 by providing elements
input:
element (string): element of interest, e.g. 'Se'
line (string): default 'Ka', options:'Ka', 'Kb', 'La', 'Lb', 'M', Ka1', 'Ka2', 'Kb1', 'Kb2', 'Lb2', 'Ma1'
roisize (int): roi window size in the unit of eV, default = 200
roi (int): 1, 2, or 3: the roi number to set, default = 1
'''
atomic_num = xraylib.SymbolToAtomicNumber(element)
multilineroi_flag = False
print('element:', element)
print('roi window size (eV):', roisize)
#calculate the roi low and high bound, based on the line
if line is 'Ka': #using average of Ka1 and Ka2 as the center of the energy/roi
line_h = xraylib.LineEnergy(atomic_num, xraylib.KL3_LINE) * 1000 #Ka1
line_l = xraylib.LineEnergy(atomic_num, xraylib.KL2_LINE) * 1000 #Ka2
print('Ka1 line (eV):', line_h)
print('Ka2 line (eV):', line_l)
energy_cen = (line_l + line_h) / 2
multilineroi_flag = True
elif line is 'Kb': #using Kb1 line only as the center of the energy/roi
energy_cen = xraylib.LineEnergy(atomic_num, xraylib.KM3_LINE) * 1000
print('Kb1 line (eV):', energy_cen)
elif line is 'La': #using average of La1 and La2 as the center of the energy/roi
line_h = xraylib.LineEnergy(atomic_num, xraylib.L3M5_LINE) * 1000 #La1
line_l = xraylib.LineEnergy(atomic_num, xraylib.L3M4_LINE) * 1000 #La2
print('La1 line (eV):', line_h)
print('La2 line (eV):', line_l)
energy_cen = (line_l + line_h) / 2
multilineroi_flag = True
elif line is 'Lb': #using average of Lb1 and Lb2 as the center of the energy/roi
line_l = xraylib.LineEnergy(atomic_num, xraylib.L2M4_LINE) * 1000 #Lb1
line_h = xraylib.LineEnergy(atomic_num, xraylib.L3N5_LINE) * 1000 #Lb2
print('Lb2 line (eV):', line_h)
print('Lb1 line (eV):', line_l)
energy_cen = (line_l + line_h) / 2
multilineroi_flag = True
elif line is 'M': #using Ma1 line only as the center of the energy/roi
energy_cen = xraylib.LineEnergy(atomic_num, xraylib.M5N7_LINE) * 1000
print('Ma1 line (eV):', energy_cen)
elif line is 'Ka1':
energy_cen = xraylib.LineEnergy(atomic_num, xraylib.KL3_LINE) * 1000
print('Ka1 line (eV):', energy_cen)
elif line is 'Ka2':
energy_cen = xraylib.LineEnergy(atomic_num, xraylib.KL2_LINE) * 1000
print('Ka2 line (eV):', energy_cen)
elif line is 'Kb1':
energy_cen = xraylib.LineEnergy(atomic_num, xraylib.KM3_LINE) * 1000
print('Kb1 line (eV):', energy_cen)
elif line is 'Lb1':
energy_cen = xraylib.LineEnergy(atomic_num, xraylib.L2M4_LINE) * 1000
print('Kb2 line (eV):', energy_cen)
elif line is 'Lb2':
energy_cen = xraylib.LineEnergy(atomic_num, xraylib.L3N5_LINE) * 1000
print('Lb2 line (eV):', energy_cen)
elif line is 'Ma1':
energy_cen = xraylib.LineEnergy(atomic_num, xraylib.M5N7_LINE) * 1000
print('Ma1 line (eV):', energy_cen)
print('energy center (eV):', energy_cen)
roi_cen = energy_cen / 10. #converting energy center position from keV to eV, then to channel number
roi_l = round(roi_cen - roisize / 10 / 2)
roi_h = round(roi_cen + roisize / 10 / 2)
print('roi center:', roi_cen)
print('roi lower bound:', roi_l, ' (', roi_l * 10, ' eV )')
print('roi higher bound:', roi_h, ' (', roi_h * 10, ' eV )')
if roi_l <= 0:
raise Exception('Lower roi bound is at or less than zero.')
if roi_h >= 2048:
raise Exception('Higher roi bound is at or larger than 2048.')
if multilineroi_flag is True:
print('lowest emission line to roi lower bound:', line_l - roi_l * 10,
'eV')
print('highest emission line to roi higher bound:',
line_h - roi_h * 10, 'eV')
if roi_l * 10 - line_l > 0:
print(
'Warning: window does not cover the lower emission line. Consider making roisize larger.\n',
'currently the window lower bound is higher than lower emission line by ',
roi_l * 10 - line_l, 'eV')
if line_h - roi_h * 10 > 0:
print(
'Warning: window does not cover the higher emission line. Consider making roisize larger.\n',
'currently the window higher bound is less than higher emission line by ',
line_h - roi_h * 10, 'eV')
#set up roi values
if roi is 1:
xs.channel1.rois.roi01.bin_low.set(roi_l)
xs.channel1.rois.roi01.bin_high.set(roi_h)
xs.channel2.rois.roi01.bin_low.set(roi_l)
xs.channel2.rois.roi01.bin_high.set(roi_h)
xs.channel3.rois.roi01.bin_low.set(roi_l)
xs.channel3.rois.roi01.bin_high.set(roi_h)
elif roi is 2:
xs.channel1.rois.roi02.bin_low.set(roi_l)
xs.channel1.rois.roi02.bin_high.set(roi_h)
xs.channel2.rois.roi02.bin_low.set(roi_l)
xs.channel2.rois.roi02.bin_high.set(roi_h)
xs.channel3.rois.roi02.bin_low.set(roi_l)
xs.channel3.rois.roi02.bin_high.set(roi_h)
elif roi is 3:
xs.channel1.rois.roi03.bin_low.set(roi_l)
xs.channel1.rois.roi03.bin_high.set(roi_h)
xs.channel2.rois.roi03.bin_low.set(roi_l)
xs.channel2.rois.roi03.bin_high.set(roi_h)
xs.channel3.rois.roi03.bin_low.set(roi_l)
xs.channel3.rois.roi03.bin_high.set(roi_h)
else:
print('cannot set roi values; roi = 1, 2, or 3')
"""Example of using various xraylib functionality in python."""
import xraylib
import math
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 node in xray_nodes:
xray_intensity = node.xpath("td[2]/text()")[0]
line = node.xpath("td[3]/text()")[0]
line = line.replace(Z_xray, "")
line_major = line.upper()
line_minor = node.xpath("td[3]/sub/*/text()")[0].upper()
try:
line_micro = node.xpath("td[3]/sub/text()")[0].upper()
except IndexError:
line_micro = ""
line = line_major + line_minor + line_micro + "_LINE"
line = line.strip()
print("line: {}".format(line))
try:
xray_intensity = float(xray_intensity)
xray_energy = xrl.LineEnergy(nuclideDataSingle['Z_xray'],
getattr(xrl, line))
if xray_energy == 0.0:
raise Exception("LineEnergy not found for {} {}",
nuclideDataSingle['Z_xray'], line)
print("Energies: {} {}".format(
node.xpath("td[1]/text()")[0], xray_energy))
xray_intensities.append("{:g}".format(xray_intensity /
100.0))
xray_lines.append(line)
except Exception as e:
print("Exception: " + str(e))
nuclideDataSingle['nXrays'] = len(xray_intensities)
print("nXrays: {}".format(nuclideDataSingle['nXrays']))
nuclideDataSingle['xrayIntensities'] = xray_intensities
nuclideDataSingle['xrayLines'] = xray_lines
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 ####")
