#/*########################################################################## # # The PyMca X-Ray Fluorescence Toolkit # # Copyright (c) 2004-2018 European Synchrotron Radiation Facility # # This file is part of the PyMca X-ray Fluorescence Toolkit developed at # the ESRF by the Software group. # # 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. Armando Sole - ESRF Data Analysis" __contact__ = "sole@esrf.fr" __license__ = "MIT" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import unittest import os import numpy DEBUG = 0 class testElements(unittest.TestCase): ELEMENTS = ['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 setUp(self): """ Get the data directory """ try: from PyMca5 import PyMcaDataDir self.dataDir = PyMcaDataDir.PYMCA_DATA_DIR except: self.dataDir = None from PyMca5.PyMcaPhysics import Elements self._elements = Elements def testDataDirectoryPresence(self): # Testing directory presence try: self.assertTrue(self.dataDir is not None) self.assertTrue(os.path.exists(self.dataDir)) self.assertTrue(os.path.isdir(self.dataDir)) except: print("\n Cannot find PyMcaData directory: %s" % self.dataDir) raise def testPeakIdentification(self): # energy in keV energy = 5.9 # 10 eV threshold threshold = 0.010 lines = self._elements.getcandidates(energy, threshold=threshold, targetrays=['K']) self.assertTrue(len(lines[0]['elements']) == 1) self.assertTrue(lines[0]['energy'] == energy) self.assertTrue(lines[0]['elements'][0] == 'Mn') energy = 10.550 threshold = 0.030 lines = self._elements.getcandidates(energy, threshold=threshold, targetrays=['K']) self.assertTrue(len(lines[0]['elements']) == 1) self.assertTrue(lines[0]['energy'] == energy) self.assertTrue('As' in lines[0]['elements']) self.assertTrue('Pb' not in lines[0]['elements']) # Test K and L lines lines = self._elements.getcandidates(energy, threshold=threshold, targetrays=['K', 'L']) self.assertTrue(len(lines[0]['elements']) > 1) self.assertTrue('As' in lines[0]['elements']) self.assertTrue('Pb' in lines[0]['elements']) # Test all energy = 2.280 threshold = 0.030 lines = self._elements.getcandidates(energy, threshold=threshold) self.assertTrue(len(lines[0]['elements']) > 1) self.assertTrue('As' not in lines[0]['elements']) self.assertTrue('Pb' not in lines[0]['elements']) self.assertTrue('S' in lines[0]['elements']) self.assertTrue('Hg' in lines[0]['elements']) def testElementCrossSectionsReadout(self): if DEBUG: print() print("Test XCOM Cross Sections Readout") from PyMca5 import getDataFile from PyMca5.PyMcaIO import specfile xcomFile = getDataFile('XCOM_CrossSections.dat') sf = specfile.Specfile(xcomFile) for ele in ['Si', 'Fe', 'Pb', 'U']: if DEBUG: print("Testing element %s" % ele) z = self._elements.getz(ele) scan = sf[z-1] xcomLabels = scan.alllabels() self.assertTrue('ENERGY' in xcomLabels[0].upper()) self.assertTrue('COHERENT' in xcomLabels[1].upper()) self.assertTrue('COMPTON' in xcomLabels[2].upper()) self.assertTrue('PHOTO' in xcomLabels[-3].upper()) self.assertTrue('PAIR' in xcomLabels[-2].upper()) self.assertTrue('TOTAL' in xcomLabels[-1].upper()) xcomData = scan.data() # WARNING: This call is to read XCOM data # only in case energy is None the data are the same as # those found later on in the 'xcom' key of the element. data = self._elements.getelementmassattcoef(ele, energy=None) # The original data are in the xcom key data = self._elements.Element[ele]['xcom'] # Energy grid self.assertTrue(numpy.allclose(data['energy'], xcomData[0, :])) # Test the different cross sections self.assertTrue(numpy.allclose(data['coherent'], xcomData[1, :])) self.assertTrue(numpy.allclose(data['compton'], xcomData[2, :])) self.assertTrue(numpy.allclose(data['photo'], xcomData[-3, :])) self.assertTrue(numpy.allclose(data['pair'], xcomData[-2, :])) self.assertTrue(numpy.allclose(data['total'], xcomData[-1, :])) total = xcomData[1, :] + xcomData[2, :] +\ xcomData[-3, :] + xcomData[-2, :] # Check the total is self-consistent self.assertTrue(numpy.allclose(total, xcomData[-1, :])) def getCrossSections(self, element, energy): # perform log-log interpolation in the read data # to see if we get the same results # now perform a log-log interpolation when needed # lin-lin interpolation: # # y0 (x1-x) + y1 (x-x0) # y = ------------------------- # x1 - x0 # # log-log interpolation: # # log(y0) * log(x1/x) + log(y1) * log(x/x0) # log(y) = ------------------------------------------ # log (x1/x0) # log = numpy.log10 # make sure data for the element are loaded # the test for proper loading is made somewhere else self._elements.getelementmassattcoef(element) # and work with them xcomData = self._elements.Element[element]['xcom'] i0 = numpy.nonzero(xcomData['energy'] <= energy)[0].max() i1 = numpy.nonzero(xcomData['energy'] >= energy)[0].min() x = numpy.array(energy) x0 = xcomData['energy'][i0] x1 = xcomData['energy'][i1] ddict = {} total = 0.0 for key in ['coherent', 'compton', 'photo']: y0 = xcomData[key][i0] y1 = xcomData[key][i1] if x1 != x0: logy = (log(y0) * log(x1/x) + log(y1) * log(x/x0))\ /log(x1/x0) y = pow(10.0, logy) else: y = y1 ddict[key] = y total += y ddict['total'] = total return ddict def testElementCrossSectionsCalculation(self): if DEBUG: print() print("Testing Element Mass Attenuation Cross Sections Calculation") for ele in ['Ge', 'Mn', 'Au', 'U']: if DEBUG: print("Testing element = %s" % ele) # take a set of energies not present in the grid energyList = [1.0533, 2.03166, 5.82353, 10.3123, 24.7431] data = self._elements.getelementmassattcoef(ele, energy=energyList) energyIndex = 0 for x in energyList: if DEBUG: print("Testing energy %f" % x) refData = self.getCrossSections(ele, x) for key in ['coherent', 'compton', 'photo', 'total']: if DEBUG: print("Testing key = %s" % key) yRef = refData[key] yTest = data[key][energyIndex] self.assertTrue((100.0 * abs(yTest-yRef)/yRef) < 0.01) energyIndex += 1 def testMaterialCrossSectionsCalculation(self): if DEBUG: print() print("Testing Material Mass Attenuation Cross Sections Calculation") formulae = ['H2O1', 'Hg1S1', 'Ca1C1O3'] unpackedFormulae = [(('H', 2), ('O', 1)), (('Hg', 1), ('S', 1)), (('Ca', 1), ('C', 1.0), ('O', 3.0))] for i in range(len(unpackedFormulae)): if DEBUG: print("Testing formula %s" % formulae[i]) # calculate mass fractions totalMass = 0.0 massFractions = numpy.zeros((len(unpackedFormulae[i]),), numpy.float64) j = 0 for ele, amount in unpackedFormulae[i]: tmpValue = amount * self._elements.Element[ele]['mass'] totalMass += tmpValue massFractions[j] = tmpValue j += 1 massFractions /= totalMass # the list of energies energyList = [1.5, 3.33, 10., 20.4, 30.6, 90.33] # get the data to be checked data = self._elements.getmassattcoef(formulae[i], energyList) energyIndex = 0 for energy in energyList: if DEBUG: print("Testing energy %f" % energy) # initialize reference data refData = {} for key in ['coherent', 'compton', 'photo', 'total']: refData[key] = 0.0 # calculate reference data for j in range(len(unpackedFormulae[i])): ele = unpackedFormulae[i][j][0] tmpData = self.getCrossSections(ele, energy) for key in ['coherent', 'compton', 'photo', 'total']: refData[key] += tmpData[key] * massFractions[j] # test for key in ['coherent', 'compton', 'photo', 'total']: if DEBUG: print("Testing key %s" % key) yRef = refData[key] yTest = data[key][energyIndex] self.assertTrue((100.0 * abs(yTest-yRef)/yRef) < 0.01) energyIndex += 1 def testMaterialCompositionCalculation(self): if DEBUG: print() print("Testing Material Composition Calculation (issue #298)") mat1 = "Kapton" mat2 = "Mylar" c1 = self._elements.getMaterialMassFractions([mat1, mat2], [0.5, 0.5]) c2 = self._elements.getMaterialMassFractions([mat2, mat1], [0.5, 0.5]) for key in c1: self.assertTrue(abs(c1[key] - c2[key]) < 1.0e-7, "Inconsistent calculation for element %s" % key) def getSuite(auto=True): testSuite = unittest.TestSuite() if auto: testSuite.addTest(\ unittest.TestLoader().loadTestsFromTestCase(testElements)) else: testSuite.addTest(testElements("testDataDirectoryPresence")) testSuite.addTest(testElements("testPeakIdentification")) testSuite.addTest(testElements("testElementCrossSectionsReadout")) testSuite.addTest(testElements("testElementCrossSectionsCalculation")) testSuite.addTest(testElements("testMaterialCrossSectionsCalculation")) testSuite.addTest(testElements("testMaterialCompositionCalculation")) return testSuite def test(auto=False): unittest.TextTestRunner(verbosity=2).run(getSuite(auto=auto)) if __name__ == '__main__': DEBUG = 1 test()