def getElementsInstance(dataDir=None, bindingEnergies=None, xcomFile=None):
if dataDir is None:
dataDir = DataDir.FISX_DATA_DIR
try:
from PyMca5.PyMcaDataDir import PYMCA_DATA_DIR as pymcaDataDir
from PyMca5 import getDataFile
except:
_logger.info("Using fisx shell constants and ratios")
pymcaDataDir = None
if bindingEnergies is None:
if pymcaDataDir is None:
bindingEnergies = os.path.join(dataDir, "BindingEnergies.dat")
else:
bindingEnergies = getDataFile("BindingEnergies.dat")
if xcomFile is None:
if pymcaDataDir is None:
xcomFile = os.path.join(dataDir, "XCOM_CrossSections.dat")
else:
xcomFile = getDataFile("XCOM_CrossSections.dat")
t0 = time.time()
instance = FisxElements(dataDir, bindingEnergies, xcomFile)
_logger.debug("Shell constants")
# the files should be taken from PyMca to make sure the same data are used
for key in ["K", "L", "M"]:
fname = instance.getShellConstantsFile(key)
if sys.version > '3.0':
# we have to make sure we have got a string
if hasattr(fname, "decode"):
fname = fname.decode("latin-1")
_logger.debug("Before %s", fname)
if pymcaDataDir is not None:
fname = getDataFile(key + "ShellConstants.dat")
else:
fname = os.path.join(os.path.dirname(fname),
key + "ShellConstants.dat")
instance.setShellConstantsFile(key, fname)
_logger.debug("After %s", instance.getShellConstantsFile(key))
_logger.debug("Radiative transitions")
for key in ["K", "L", "M"]:
fname = instance.getShellRadiativeTransitionsFile(key)
if sys.version > '3.0':
# we have to make sure we have got a string ...
if hasattr(fname, "decode"):
fname = fname.decode("latin-1")
_logger.debug("Before %s", fname)
if pymcaDataDir is not None:
fname = getDataFile(key + "ShellRates.dat")
else:
fname = os.path.join(os.path.dirname(fname),
key + "ShellRates.dat")
instance.setShellRadiativeTransitionsFile(key, fname)
_logger.debug("After %s ",
instance.getShellRadiativeTransitionsFile(key))
_logger.debug("Reading Elapsed = %s", time.time() - t0)
return instance
def getElementsInstance(dataDir=None, bindingEnergies=None, xcomFile=None):
if dataDir is None:
dataDir = DataDir.FISX_DATA_DIR
try:
from PyMca5.PyMcaDataDir import PYMCA_DATA_DIR as pymcaDataDir
from PyMca5 import getDataFile
except:
_logger.info("Using fisx shell constants and ratios")
pymcaDataDir = None
if bindingEnergies is None:
if pymcaDataDir is None:
bindingEnergies = os.path.join(dataDir, "BindingEnergies.dat")
else:
bindingEnergies = getDataFile("BindingEnergies.dat")
if xcomFile is None:
if pymcaDataDir is None:
xcomFile = os.path.join(dataDir, "XCOM_CrossSections.dat")
else:
xcomFile = getDataFile("XCOM_CrossSections.dat")
t0 = time.time()
instance = FisxElements(dataDir, bindingEnergies, xcomFile)
_logger.debug("Shell constants")
# the files should be taken from PyMca to make sure the same data are used
for key in ["K", "L", "M"]:
fname = instance.getShellConstantsFile(key)
if sys.version > '3.0':
# we have to make sure we have got a string
if hasattr(fname, "decode"):
fname = fname.decode("latin-1")
_logger.debug("Before %s", fname)
if pymcaDataDir is not None:
fname = getDataFile(key + "ShellConstants.dat")
else:
fname = os.path.join(os.path.dirname(fname),
key + "ShellConstants.dat")
instance.setShellConstantsFile(key, fname)
_logger.debug("After %s", instance.getShellConstantsFile(key))
_logger.debug("Radiative transitions")
for key in ["K", "L", "M"]:
fname = instance.getShellRadiativeTransitionsFile(key)
if sys.version > '3.0':
# we have to make sure we have got a string ...
if hasattr(fname, "decode"):
fname = fname.decode("latin-1")
_logger.debug("Before %s", fname)
if pymcaDataDir is not None:
fname = getDataFile(key + "ShellRates.dat")
else:
fname = os.path.join(os.path.dirname(fname), key + "ShellRates.dat")
instance.setShellRadiativeTransitionsFile(key, fname)
_logger.debug("After %s ", instance.getShellRadiativeTransitionsFile(key))
_logger.debug("Reading Elapsed = %s", time.time() - t0)
return instance
def testDetectorResults(self):
from fisx import Elements
from fisx import Detector
elementsInstance = Elements()
elementsInstance.initializeAsPyMca()
# Make a detector from a formula
detectorName = "NaI"
detectorDensity = 4.0
detectorThickness = 0.00350
detectorInstance = Detector(detectorName,
detectorDensity,
detectorThickness)
# Check the composition is returned as string and not bytes under
# Python 3
composition = detectorInstance.getComposition(elementsInstance)
if sys.version_info >= (3, ):
for key in composition:
self.assertTrue(isinstance(key, str),
"Expected string, received %s" % type(key))
# check the returned keys are correct
self.assertTrue(len(list(composition.keys())) == 2,
"Incorrect number of keys returned")
for key in ["Na", "I"]:
self.assertTrue(key in composition,
"key %s not found" % key)
thickness = detectorInstance.getThickness()
self.assertTrue(abs( thickness - detectorThickness) < 1.0e-7,
"Wrong detector thickness!")
density = detectorInstance.getDensity()
self.assertTrue(abs(density - detectorDensity) < 1.0e-7,
"Wrong detector density!")
# check the return of the getEscape method
escape = detectorInstance.getEscape(100.0, elementsInstance)
if sys.version_info >= (3, ):
for key in escape:
self.assertTrue(isinstance(key, str),
"Expected string, received %s" % type(key))
def testDetectorResults(self):
from fisx import Elements
from fisx import Detector
elementsInstance = Elements()
elementsInstance.initializeAsPyMca()
# Make a detector from a formula
detectorName = "NaI"
detectorDensity = 4.0
detectorThickness = 0.00350
detectorInstance = Detector(detectorName, detectorDensity,
detectorThickness)
# Check the composition is returned as string and not bytes under
# Python 3
composition = detectorInstance.getComposition(elementsInstance)
if sys.version_info >= (3, ):
for key in composition:
self.assertTrue(isinstance(key, str),
"Expected string, received %s" % type(key))
# check the returned keys are correct
self.assertTrue(
len(list(composition.keys())) == 2,
"Incorrect number of keys returned")
for key in ["Na", "I"]:
self.assertTrue(key in composition, "key %s not found" % key)
thickness = detectorInstance.getThickness()
self.assertTrue(
abs(thickness - detectorThickness) < 1.0e-7,
"Wrong detector thickness!")
density = detectorInstance.getDensity()
self.assertTrue(
abs(density - detectorDensity) < 1.0e-7, "Wrong detector density!")
# check the return of the getEscape method
escape = detectorInstance.getEscape(100.0, elementsInstance)
if sys.version_info >= (3, ):
for key in escape:
self.assertTrue(isinstance(key, str),
"Expected string, received %s" % type(key))
def getElementsInstance(dataDir=None, bindingEnergies=None, xcomFile=None):
if dataDir is None:
dataDir = DataDir.DATA_DIR
if bindingEnergies is None:
bindingEnergies = os.path.join(dataDir, "BindingEnergies.dat")
if xcomFile is None:
xcomFile = os.path.join(dataDir, "XCOM_CrossSections.dat")
if DEBUG:
t0 = time.time()
instance = FisxElements(dataDir, bindingEnergies, xcomFile)
if DEBUG:
print("Shell constants")
for key in ["K", "L", "M"]:
fname = instance.getShellConstantsFile(key)
if sys.version > '3.0':
# we have to make sure we have got a string
if hasattr(fname, "decode"):
fname = fname.decode("latin-1")
if DEBUG:
print("Before %s" % fname)
fname = os.path.join(os.path.dirname(fname), key + "ShellConstants.dat")
instance.setShellConstantsFile(key, fname)
if DEBUG:
print("After %s" % instance.getShellConstantsFile(key))
if DEBUG:
print("Radiative transitions")
for key in ["K", "L", "M"]:
fname = instance.getShellRadiativeTransitionsFile(key)
if sys.version > '3.0':
# we have to make sure we have got a string ...
if hasattr(fname, "decode"):
fname = fname.decode("latin-1")
if DEBUG:
print("Before %s" % fname)
fname = os.path.join(os.path.dirname(fname), key + "ShellRates.dat")
instance.setShellRadiativeTransitionsFile(key, fname)
if DEBUG:
print("After %s " % instance.getShellRadiativeTransitionsFile(key))
if DEBUG:
print("Reading Elapsed = ", time.time() - t0)
return instance
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))
for i, element_attrs in enumerate(ptable):
_draw_box(ax, element_attrs, facecolor=colors[i])
ax.set_xlim(0, 19)
ax.set_ylim(8, 0)
ax.axis('off');
if figname is not None:
fig.savefig(figname)
# fisx instantiation is needed before continuing
elementsInstance = Elements()
elementsInstance.initializeAsPyMca()
class XFluo:
def __init__(self, element, tube_keV, weight_list='equal', std=0.01, min_prom=0.001):
'''Create an annotated x-ray fluorescence spectrum object.
Args:
element (str): Chemical symbol e.g 'Fe'
tube_keV (float or list of floats): X-ray tube energies in keV.
For a poly chromatic X-ray tube multiple energies can be provided.
weight_list (list of numbers): X-ray energy weights.
Corresponding to energy_list
std (number): Peak width used for plotting
min_prom (number): Minimal peak prominance.
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 getElementsInstance():
elementsInstance = Elements()
elementsInstance.initializeAsPyMca()
return elementsInstance