#/*########################################################################## # # The fisx library for X-Ray Fluorescence # # Copyright (c) 2014-2020 European Synchrotron Radiation Facility # # This file is part of the fisx X-ray developed by V.A. Sole # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # #############################################################################*/ __author__ = "V.A. Sole - ESRF Data Analysis" import unittest import sys import os ElementList= ['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt'] def getSymbol(z): return ElementList[z-1] def getZ(ele): return ElementList.index(ele) + 1 class testXRF(unittest.TestCase): def setUp(self): """ import the module """ try: from fisx import XRF self._module = XRF except: self._module = None def tearDown(self): self._module = None def testXRFImport(self): self.assertTrue(self._module is not None, 'Unsuccessful fisx.XRF import') def testXRFInstantiation(self): try: instance = self._module() except: instance = None print("Instantiation error: ", sys.exc_info()[0], sys.exc_info()[1], sys.exc_info()[2]) self.assertTrue(instance is not None, 'Unsuccesful XRF() instantiation') 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)) # check user beamfilters xrf.setUserBeamFilters([[[0.0, 100.], [0.5, 0.5], "half", "half intensity expected"]]) fluo2 = xrf.getMultilayerFluorescence(["Cr K", "Fe K", "Ni K"], elementsInstance, secondary=2, useMassFractions=1) for key in ["rate", "primary", "secondary"]: before = fluo["Cr K"][0]["KL3"][key] after = fluo2["Cr K"][0]["KL3"][key] self.assertTrue(abs( before - 2.0 * after) < 1.0e-8, "Expected to measure half %s and not %f" % \ (key, after / before)) # check removal of user beam filters xrf.setUserBeamFilters([]) fluo2 = xrf.getMultilayerFluorescence(["Cr K", "Fe K", "Ni K"], elementsInstance, secondary=2, useMassFractions=1) for key in ["rate", "primary", "secondary"]: before = fluo["Cr K"][0]["KL3"][key] after = fluo2["Cr K"][0]["KL3"][key] self.assertTrue(abs( before - after) < 1.0e-8, "Expected to measure a 1 ratio and not %f" % \ (after / before)) # check user attenuators xrf.setUserAttenuators([[{0.0:0.25, 100.:0.25}, "quarter", "quarter intensity expected"]]) fluo2 = xrf.getMultilayerFluorescence(["Cr K", "Fe K", "Ni K"], elementsInstance, secondary=2, useMassFractions=1) for key in ["rate"]: before = fluo["Cr K"][0]["KL3"][key] after = fluo2["Cr K"][0]["KL3"][key] self.assertTrue(abs( before - 4.0 * after) < 1.0e-8, "Expected to measure 1/4 intensity and not %f" % \ (after / before)) # check removal of user attenuators xrf.setUserAttenuators([]) fluo2 = xrf.getMultilayerFluorescence(["Cr K", "Fe K", "Ni K"], elementsInstance, secondary=2, useMassFractions=1) for key in ["rate"]: before = fluo["Cr K"][0]["KL3"][key] after = fluo2["Cr K"][0]["KL3"][key] self.assertTrue(abs( before - after) < 1.0e-8, "Expected to measure a 1 ratio and not %f" % \ (after / before)) def getSuite(auto=True): testSuite = unittest.TestSuite() if auto: testSuite.addTest(\ unittest.TestLoader().loadTestsFromTestCase(testXRF)) else: # use a predefined order testSuite.addTest(testXRF("testXRFImport")) testSuite.addTest(testXRF("testXRFInstantiation")) testSuite.addTest(testXRF("testXRFResults")) return testSuite def test(auto=False): unittest.TextTestRunner(verbosity=2).run(getSuite(auto=auto)) if __name__ == '__main__': test()