def _getFisxDetector(fitConfiguration, attenuatorsDetector=None):
distance = fitConfiguration["concentrations"]["distance"]
area = fitConfiguration["concentrations"]["area"]
detectorMaterial = fitConfiguration["detector"]["detele"]
if attenuatorsDetector is None:
# user is not interested on accounting for detection efficiency
if fitConfiguration["fit"]["escapeflag"]:
# but wants to account for escape peaks
# we can forget about efficiency but not about detector composition
# assign "infinite" efficiency
density = 0.0
thickness = 0.0
fisxDetector = Detector(detectorMaterial,
density=density,
thickness=thickness)
else:
# user is not interested on considering the escape peaks
fisxDetector = None
else:
# make sure information is consistent
if attenuatorsDetector[0] not in [
detectorMaterial, detectorMaterial + "1"
]:
print("%s not equal to %s" %
(attenuatorsDetector[0], detectorMaterial))
msg = "Inconsistent detector material between DETECTOR and ATTENUATORS tab"
msg += "\n%s not equal to %s" % (attenuatorsDetector[0],
detectorMaterial)
raise ValueError(msg)
if len(attenuatorsDetector) == 3:
fisxDetector = Detector(detectorMaterial,
density=attenuatorsDetector[1],
thickness=attenuatorsDetector[2])
else:
fisxDetector = Detector(detectorMaterial,
density=attenuatorsDetector[1],
thickness=attenuatorsDetector[2],
funny=attenuatorsDetector[3])
fisxDetector.setActiveArea(area)
fisxDetector.setDistance(distance)
if fisxDetector is not None:
nThreshold = fitConfiguration["detector"]["nthreshold"]
fisxDetector.setMaximumNumberOfEscapePeaks(nThreshold)
return fisxDetector
def _getFisxDetector(fitConfiguration, attenuatorsDetector=None):
distance = fitConfiguration["concentrations"]["distance"]
area = fitConfiguration["concentrations"]["area"]
detectorMaterial = fitConfiguration["detector"]["detele"]
if attenuatorsDetector is None:
# user is not interested on accounting for detection efficiency
if fitConfiguration["fit"]["escapeflag"]:
# but wants to account for escape peaks
# we can forget about efficiency but not about detector composition
# assign "infinite" efficiency
density = 0.0
thickness = 0.0
fisxDetector = Detector(detectorMaterial,
density=density,
thickness=thickness)
else:
# user is not interested on considering the escape peaks
fisxDetector = None
else:
# make sure information is consistent
if attenuatorsDetector[0] not in [detectorMaterial, detectorMaterial+"1"]:
_logger.warning("%s not equal to %s",
attenuatorsDetector[0], detectorMaterial)
msg = "Inconsistent detector material between DETECTOR and ATTENUATORS tab"
msg += "\n%s not equal to %s" % (attenuatorsDetector[0], detectorMaterial)
raise ValueError(msg)
if len(attenuatorsDetector) == 3:
fisxDetector = Detector(detectorMaterial,
density=attenuatorsDetector[1],
thickness=attenuatorsDetector[2])
else:
fisxDetector = Detector(detectorMaterial,
density=attenuatorsDetector[1],
thickness=attenuatorsDetector[2],
funny=attenuatorsDetector[3])
fisxDetector.setActiveArea(area)
fisxDetector.setDistance(distance)
if fisxDetector is not None:
nThreshold = fitConfiguration["detector"]["nthreshold"]
fisxDetector.setMaximumNumberOfEscapePeaks(nThreshold)
return fisxDetector
def _getDetector(webConfiguration):
# Detector is described as a list [material, density, thickness]
# Translation dictionnary
Thickness = "thickness"
Density = "density"
Material = "material"
Area = "area"
Distance = "distance"
material = webConfiguration["detector"].get(Material, None)
if material is None:
# No detector
return None
else:
density = float(webConfiguration["detector"][Density])
thickness = float(webConfiguration["detector"][Thickness])
area = float(webConfiguration["detector"][Area])
distance = float(webConfiguration["detector"][Distance])
detectorInstance = Detector(material, density, thickness)
detectorInstance.setActiveArea(area)
detectorInstance.setDistance(distance)
return detectorInstance
def testXRFResults(self):
from fisx import Elements
from fisx import Material
from fisx import Detector
from fisx import XRF
elementsInstance = Elements()
elementsInstance.initializeAsPyMca()
# After the slow initialization (to be made once), the rest is fairly fast.
xrf = XRF()
xrf.setBeam(
16.0) # set incident beam as a single photon energy of 16 keV
xrf.setBeamFilters([["Al1", 2.72, 0.11, 1.0]]) # Incident beam filters
# Steel composition of Schoonjans et al, 2012 used to generate table I
steel = {
"C": 0.0445,
"N": 0.04,
"Si": 0.5093,
"P": 0.02,
"S": 0.0175,
"V": 0.05,
"Cr": 18.37,
"Mn": 1.619,
"Fe":
64.314, # calculated by subtracting the sum of all other elements
"Co": 0.109,
"Ni": 12.35,
"Cu": 0.175,
"As": 0.010670,
"Mo": 2.26,
"W": 0.11,
"Pb": 0.001
}
SRM_1155 = Material("SRM_1155", 1.0, 1.0)
SRM_1155.setComposition(steel)
elementsInstance.addMaterial(SRM_1155)
xrf.setSample([["SRM_1155", 1.0,
1.0]]) # Sample, density and thickness
xrf.setGeometry(45., 45.) # Incident and fluorescent beam angles
detector = Detector("Si1", 2.33,
0.035) # Detector Material, density, thickness
detector.setActiveArea(0.50) # Area and distance in consistent units
detector.setDistance(2.1) # expected cm2 and cm.
xrf.setDetector(detector)
Air = Material("Air", 0.0012048, 1.0)
Air.setCompositionFromLists(
["C1", "N1", "O1", "Ar1", "Kr1"],
[0.0012048, 0.75527, 0.23178, 0.012827, 3.2e-06])
elementsInstance.addMaterial(Air)
xrf.setAttenuators([["Air", 0.0012048, 5.0, 1.0],
["Be1", 1.848, 0.002, 1.0]]) # Attenuators
fluo = xrf.getMultilayerFluorescence(["Cr K", "Fe K", "Ni K"],
elementsInstance,
secondary=2,
useMassFractions=1)
print(
"\nElement Peak Energy Rate Secondary Tertiary"
)
for key in fluo:
for layer in fluo[key]:
peakList = list(fluo[key][layer].keys())
peakList.sort()
for peak in peakList:
# energy of the peak
energy = fluo[key][layer][peak]["energy"]
# expected measured rate
rate = fluo[key][layer][peak]["rate"]
# primary photons (no attenuation and no detector considered)
primary = fluo[key][layer][peak]["primary"]
# secondary photons (no attenuation and no detector considered)
secondary = fluo[key][layer][peak]["secondary"]
# tertiary photons (no attenuation and no detector considered)
tertiary = fluo[key][layer][peak].get("tertiary", 0.0)
# correction due to secondary excitation
enhancement2 = (primary + secondary) / primary
enhancement3 = (primary + secondary + tertiary) / primary
print("%s %s %.4f %.3g %.5g %.5g" % \
(key, peak + (13 - len(peak)) * " ", energy,
rate, enhancement2, enhancement3))
# compare against expected values from Schoonjans et al.
testXMI = True
if (key == "Cr K") and peak.startswith("KL3"):
second = 1.626
third = 1.671
elif (key == "Cr K") and peak.startswith("KM3"):
second = 1.646
third = 1.694
elif (key == "Fe K") and peak.startswith("KL3"):
second = 1.063
third = 1.064
elif (key == "Fe K") and peak.startswith("KL3"):
second = 1.065
third = 1.066
else:
testXMI = False
if testXMI:
discrepancy = 100 * (abs(second - enhancement2) /
second)
self.assertTrue(discrepancy < 1.5,
"%s %s secondary discrepancy = %.1f %%" % \
(key, peak, discrepancy))
discrepancy = 100 * (abs(third - enhancement3) / third)
self.assertTrue(discrepancy < 1.5,
"%s %s tertiary discrepancy = %.1f %%" % \
(key, peak, discrepancy))
def testXRFResults(self):
from fisx import Elements
from fisx import Material
from fisx import Detector
from fisx import XRF
elementsInstance = Elements()
elementsInstance.initializeAsPyMca()
# After the slow initialization (to be made once), the rest is fairly fast.
xrf = XRF()
xrf.setBeam(16.0) # set incident beam as a single photon energy of 16 keV
xrf.setBeamFilters([["Al1", 2.72, 0.11, 1.0]]) # Incident beam filters
# Steel composition of Schoonjans et al, 2012 used to generate table I
steel = {"C": 0.0445,
"N": 0.04,
"Si": 0.5093,
"P": 0.02,
"S": 0.0175,
"V": 0.05,
"Cr":18.37,
"Mn": 1.619,
"Fe":64.314, # calculated by subtracting the sum of all other elements
"Co": 0.109,
"Ni":12.35,
"Cu": 0.175,
"As": 0.010670,
"Mo": 2.26,
"W": 0.11,
"Pb": 0.001}
SRM_1155 = Material("SRM_1155", 1.0, 1.0)
SRM_1155.setComposition(steel)
elementsInstance.addMaterial(SRM_1155)
xrf.setSample([["SRM_1155", 1.0, 1.0]]) # Sample, density and thickness
xrf.setGeometry(45., 45.) # Incident and fluorescent beam angles
detector = Detector("Si1", 2.33, 0.035) # Detector Material, density, thickness
detector.setActiveArea(0.50) # Area and distance in consistent units
detector.setDistance(2.1) # expected cm2 and cm.
xrf.setDetector(detector)
Air = Material("Air", 0.0012048, 1.0)
Air.setCompositionFromLists(["C1", "N1", "O1", "Ar1", "Kr1"],
[0.0012048, 0.75527, 0.23178, 0.012827, 3.2e-06])
elementsInstance.addMaterial(Air)
xrf.setAttenuators([["Air", 0.0012048, 5.0, 1.0],
["Be1", 1.848, 0.002, 1.0]]) # Attenuators
fluo = xrf.getMultilayerFluorescence(["Cr K", "Fe K", "Ni K"],
elementsInstance,
secondary=2,
useMassFractions=1)
print("\nElement Peak Energy Rate Secondary Tertiary")
for key in fluo:
for layer in fluo[key]:
peakList = list(fluo[key][layer].keys())
peakList.sort()
for peak in peakList:
# energy of the peak
energy = fluo[key][layer][peak]["energy"]
# expected measured rate
rate = fluo[key][layer][peak]["rate"]
# primary photons (no attenuation and no detector considered)
primary = fluo[key][layer][peak]["primary"]
# secondary photons (no attenuation and no detector considered)
secondary = fluo[key][layer][peak]["secondary"]
# tertiary photons (no attenuation and no detector considered)
tertiary = fluo[key][layer][peak].get("tertiary", 0.0)
# correction due to secondary excitation
enhancement2 = (primary + secondary) / primary
enhancement3 = (primary + secondary + tertiary) / primary
print("%s %s %.4f %.3g %.5g %.5g" % \
(key, peak + (13 - len(peak)) * " ", energy,
rate, enhancement2, enhancement3))
# compare against expected values from Schoonjans et al.
testXMI = True
if (key == "Cr K") and peak.startswith("KL3"):
second = 1.626
third = 1.671
elif (key == "Cr K") and peak.startswith("KM3"):
second = 1.646
third = 1.694
elif (key == "Fe K") and peak.startswith("KL3"):
second = 1.063
third = 1.064
elif (key == "Fe K") and peak.startswith("KL3"):
second = 1.065
third = 1.066
else:
testXMI = False
if testXMI:
discrepancy = 100 * (abs(second-enhancement2)/second)
self.assertTrue(discrepancy < 1.5,
"%s %s secondary discrepancy = %.1f %%" % \
(key, peak, discrepancy))
discrepancy = 100 * (abs(third-enhancement3)/third)
self.assertTrue(discrepancy < 1.5,
"%s %s tertiary discrepancy = %.1f %%" % \
(key, peak, discrepancy))